Daily Papers

The growing sophistication of drug discovery calls for new advances in artificial intelligence (AI). Transformers have underpinned recent breakthroughs in AI, yet their conventional source-target attention mechanism can become a bottleneck for modeling complex interactions. Here, we introduce TopoLIA, a topology-inspired latent interaction attention mechanism that learns not only how much information should be exchanged between interaction partners, but also how that information should be transformed. Source-target-dependent attention is mediated through a compact latent interaction space, providing a structured representation of complex interactions. We further incorporate topological spectral representations to capture multiscale data geometry and extract algebraic relationships. TopoLIA thus incorporates topological principles into both data representation and neural network architecture. We demonstrate TopoLIA on protein-ligand binding, where persistent spectra encode multiscale topological and geometric patterns in 3D protein-ligand complexes, while latent interaction attention (LIA) enables structured, source-target-dependent information exchange. We pretrain TopoLIA by reconstructing masked multiscale spectral tokens from unlabeled molecular structures, yielding transferable structural representations without task-specific annotations. Across multiple scoring and docking benchmarks, TopoLIA achieves state-of-the-art performance and consistently outperforms its standard-attention counterpart. Rank analyses show that compact latent dimensions yield the best performance, supporting compact interaction spaces as an effective inductive bias for biomolecular learning. More broadly, LIA provides a general framework for structured, source-target-dependent information exchange that is applicable to diverse scientific and AI problems involving complex heterogeneous interactions.

AlphaFold has transformed protein structure prediction, but emerging applications such as virtual ligand screening, proteome-wide folding, and de novo binder design demand predictions at a massive scale, where runtime and memory costs become prohibitive. A major bottleneck lies in the Pairformer backbone of AlphaFold3-style models, which relies on computationally expensive triangular primitives-especially triangle attention-for pairwise reasoning. We introduce Pairmixer, a streamlined alternative that eliminates triangle attention while preserving higher-order geometric reasoning capabilities that are critical for structure prediction. Pairmixer substantially improves computational efficiency, matching state-of-the-art structure predictors across folding and docking benchmarks, delivering up to 4x faster inference on long sequences while reducing training cost by 34%. Its efficiency alleviates the computational burden of downstream applications such as modeling large protein complexes, high-throughput ligand and binder screening, and hallucination-based design. Within BoltzDesign, for example, Pairmixer delivers over 2x faster sampling and scales to sequences ~30% longer than the memory limits of Pairformer.

Accurate blind docking has the potential to lead to new biological breakthroughs, but for this promise to be realized, docking methods must generalize well across the proteome. Existing benchmarks, however, fail to rigorously assess generalizability. Therefore, we develop DockGen, a new benchmark based on the ligand-binding domains of proteins, and we show that existing machine learning-based docking models have very weak generalization abilities. We carefully analyze the scaling laws of ML-based docking and show that, by scaling data and model size, as well as integrating synthetic data strategies, we are able to significantly increase the generalization capacity and set new state-of-the-art performance across benchmarks. Further, we propose Confidence Bootstrapping, a new training paradigm that solely relies on the interaction between diffusion and confidence models and exploits the multi-resolution generation process of diffusion models. We demonstrate that Confidence Bootstrapping significantly improves the ability of ML-based docking methods to dock to unseen protein classes, edging closer to accurate and generalizable blind docking methods.

The effects of ligand binding on protein structures and their in vivo functions carry numerous implications for modern biomedical research and biotechnology development efforts such as drug discovery. Although several deep learning (DL) methods and benchmarks designed for protein-ligand docking have recently been introduced, to date no prior works have systematically studied the behavior of the latest docking and structure prediction methods within the broadly applicable context of (1) using predicted (apo) protein structures for docking (e.g., for applicability to new proteins); (2) binding multiple (cofactor) ligands concurrently to a given target protein (e.g., for enzyme design); and (3) having no prior knowledge of binding pockets (e.g., for generalization to unknown pockets). To enable a deeper understanding of docking methods' real-world utility, we introduce PoseBench, the first comprehensive benchmark for broadly applicable protein-ligand docking. PoseBench enables researchers to rigorously and systematically evaluate DL methods for apo-to-holo protein-ligand docking and protein-ligand structure prediction using both primary ligand and multi-ligand benchmark datasets, the latter of which we introduce for the first time to the DL community. Empirically, using PoseBench, we find that (1) DL co-folding methods generally outperform comparable conventional and DL docking baselines, yet popular methods such as AlphaFold 3 are still challenged by prediction targets with novel protein sequences; (2) certain DL co-folding methods are highly sensitive to their input multiple sequence alignments, while others are not; and (3) DL methods struggle to strike a balance between structural accuracy and chemical specificity when predicting novel or multi-ligand protein targets. Code, data, tutorials, and benchmark results are available at https://github.com/BioinfoMachineLearning/PoseBench.

Recently, significant progress has been made in protein-ligand docking, especially in modern deep learning methods, and some benchmarks were proposed, e.g., PoseBench, Plinder. However, these benchmarks suffer from less practical evaluation setups (e.g., blind docking, self docking), or heavy framework that involves training, raising challenges to assess docking methods efficiently. To fill this gap, we proposed PoseX, an open-source benchmark focusing on self-docking and cross-docking, to evaluate the algorithmic advances practically and comprehensively. Specifically, first, we curate a new evaluation dataset with 718 entries for self docking and 1,312 for cross docking; second, we incorporate 22 docking methods across three methodological categories, including (1) traditional physics-based methods (e.g., Schr\"odinger Glide), (2) AI docking methods (e.g., DiffDock), (3) AI co-folding methods (e.g., AlphaFold3); third, we design a relaxation method as post-processing to minimize conformation energy and refine binding pose; fourth, we released a leaderboard to rank submitted models in real time. We draw some key insights via extensive experiments: (1) AI-based approaches have already surpassed traditional physics-based approaches in overall docking accuracy (RMSD). The longstanding generalization issues that have plagued AI molecular docking have been significantly alleviated in the latest models. (2) The stereochemical deficiencies of AI-based approaches can be greatly alleviated with post-processing relaxation. Combining AI docking methods with the enhanced relaxation method achieves the best performance to date. (3) AI co-folding methods commonly face ligand chirality issues, which cannot be resolved by relaxation. The code, curated dataset and leaderboard are released at https://github.com/CataAI/PoseX.

GUI web agents require realistic and interactive environments that remain stable during both evaluation and training. Live website evaluation suffers from changing content, access restrictions, and limited coverage of authenticated workflows, while existing synthetic environments for training often lack functional depth and visual fidelity. We propose WebHarbor, a suite of 153 executable and dockerized website environments that faithfully reconstruct the visual interfaces, content, and functional workflows of real-world web services under deterministic control. We build WebHarbor through task-driven human-agent collaboration, where environments evolve as new tasks expand their functional scope, coding agents implement the required changes, and human contributors audit visual fidelity, functional correctness, and task validity. The resulting suite comprises 3,518 tasks spanning multi-step and post-authentication workflows, where existing works often fail to cover. Beyond reliable evaluation, WebHarbor provides high-fidelity synthetic web environments for cost-efficient reinforcement learning (RL). We demonstrate that a Qwen 4B-level GUI agent trained with RL in WebHarbor generalizes to unseen tasks and performs competitively with leading open-source GUI web agents across four benchmarks. The code and data are publicly available at https://github.com/aiming-lab/WebHarbor.

Powerful generative AI models of protein-ligand structure have recently been proposed, but few of these methods support both flexible protein-ligand docking and affinity estimation. Of those that do, none can directly model multiple binding ligands concurrently or have been rigorously benchmarked on pharmacologically relevant drug targets, hindering their widespread adoption in drug discovery efforts. In this work, we propose FlowDock, the first deep geometric generative model based on conditional flow matching that learns to directly map unbound (apo) structures to their bound (holo) counterparts for an arbitrary number of binding ligands. Furthermore, FlowDock provides predicted structural confidence scores and binding affinity values with each of its generated protein-ligand complex structures, enabling fast virtual screening of new (multi-ligand) drug targets. For the well-known PoseBusters Benchmark dataset, FlowDock outperforms single-sequence AlphaFold 3 with a 51% blind docking success rate using unbound (apo) protein input structures and without any information derived from multiple sequence alignments, and for the challenging new DockGen-E dataset, FlowDock outperforms single-sequence AlphaFold 3 and matches single-sequence Chai-1 for binding pocket generalization. Additionally, in the ligand category of the 16th community-wide Critical Assessment of Techniques for Structure Prediction (CASP16), FlowDock ranked among the top-5 methods for pharmacological binding affinity estimation across 140 protein-ligand complexes, demonstrating the efficacy of its learned representations in virtual screening. Source code, data, and pre-trained models are available at https://github.com/BioinfoMachineLearning/FlowDock.

Docking is a crucial component in drug discovery aimed at predicting the binding conformation and affinity between small molecules and target proteins. ML-based docking has recently emerged as a prominent approach, outpacing traditional methods like DOCK and AutoDock Vina in handling the growing scale and complexity of molecular libraries. However, the availability of comprehensive and user-friendly datasets for training and benchmarking ML-based docking algorithms remains limited. We introduce Smiles2Dock, an open large-scale multi-task dataset for molecular docking. We created a framework combining P2Rank and AutoDock Vina to dock 1.7 million ligands from the ChEMBL database against 15 AlphaFold proteins, giving us more than 25 million protein-ligand binding scores. The dataset leverages a wide range of high-accuracy AlphaFold protein models, encompasses a diverse set of biologically relevant compounds and enables researchers to benchmark all major approaches for ML-based docking such as Graph, Transformer and CNN-based methods. We also introduce a novel Transformer-based architecture for docking scores prediction and set it as an initial benchmark for our dataset. Our dataset and code are publicly available to support the development of novel ML-based methods for molecular docking to advance scientific research in this field.

Motivation: Ab initio protein docking represents a major challenge for optimizing a noisy and costly "black box"-like function in a high-dimensional space. Despite progress in this field, there is no docking method available for rigorous uncertainty quantification (UQ) of its solution quality (e.g. interface RMSD or iRMSD). Results: We introduce a novel algorithm, Bayesian Active Learning (BAL), for optimization and UQ of such black-box functions and flexible protein docking. BAL directly models the posterior distribution of the global optimum (or native structures for protein docking) with active sampling and posterior estimation iteratively feeding each other. Furthermore, we use complex normal modes to represent a homogeneous Euclidean conformation space suitable for high-dimension optimization and construct funnel-like energy models for encounter complexes. Over a protein docking benchmark set and a CAPRI set including homology docking, we establish that BAL significantly improve against both starting points by rigid docking and refinements by particle swarm optimization, providing for one third targets a top-3 near-native prediction. BAL also generates tight confidence intervals with half range around 25% of iRMSD and confidence level at 85%. Its estimated probability of a prediction being native or not achieves binary classification AUROC at 0.93 and AUPRC over 0.60 (compared to 0.14 by chance); and also found to help ranking predictions. To the best of our knowledge, this study represents the first uncertainty quantification solution for protein docking, with theoretical rigor and comprehensive assessment. Source codes are available at https://github.com/Shen-Lab/BAL.

The last few years have seen the development of numerous deep learning-based protein-ligand docking methods. They offer huge promise in terms of speed and accuracy. However, despite claims of state-of-the-art performance in terms of crystallographic root-mean-square deviation (RMSD), upon closer inspection, it has become apparent that they often produce physically implausible molecular structures. It is therefore not sufficient to evaluate these methods solely by RMSD to a native binding mode. It is vital, particularly for deep learning-based methods, that they are also evaluated on steric and energetic criteria. We present PoseBusters, a Python package that performs a series of standard quality checks using the well-established cheminformatics toolkit RDKit. Only methods that both pass these checks and predict native-like binding modes should be classed as having "state-of-the-art" performance. We use PoseBusters to compare five deep learning-based docking methods (DeepDock, DiffDock, EquiBind, TankBind, and Uni-Mol) and two well-established standard docking methods (AutoDock Vina and CCDC Gold) with and without an additional post-prediction energy minimisation step using a molecular mechanics force field. We show that both in terms of physical plausibility and the ability to generalise to examples that are distinct from the training data, no deep learning-based method yet outperforms classical docking tools. In addition, we find that molecular mechanics force fields contain docking-relevant physics missing from deep-learning methods. PoseBusters allows practitioners to assess docking and molecular generation methods and may inspire new inductive biases still required to improve deep learning-based methods, which will help drive the development of more accurate and more realistic predictions.

The regulation of various cellular processes heavily relies on the protein complexes within a living cell, necessitating a comprehensive understanding of their three-dimensional structures to elucidate the underlying mechanisms. While neural docking techniques have exhibited promising outcomes in binary protein docking, the application of advanced neural architectures to multimeric protein docking remains uncertain. This study introduces SyNDock, an automated framework that swiftly assembles precise multimeric complexes within seconds, showcasing performance that can potentially surpass or be on par with recent advanced approaches. SyNDock possesses several appealing advantages not present in previous approaches. Firstly, SyNDock formulates multimeric protein docking as a problem of learning global transformations to holistically depict the placement of chain units of a complex, enabling a learning-centric solution. Secondly, SyNDock proposes a trainable two-step SE(3) algorithm, involving initial pairwise transformation and confidence estimation, followed by global transformation synchronization. This enables effective learning for assembling the complex in a globally consistent manner. Lastly, extensive experiments conducted on our proposed benchmark dataset demonstrate that SyNDock outperforms existing docking software in crucial performance metrics, including accuracy and runtime. For instance, it achieves a 4.5% improvement in performance and a remarkable millionfold acceleration in speed.

Molecular docking is critical to structure-based virtual screening, yet the throughput of such workflows is limited by the expensive optimization of scoring functions involved in most docking algorithms. We explore how machine learning can accelerate this process by learning a scoring function with a functional form that allows for more rapid optimization. Specifically, we define the scoring function to be the cross-correlation of multi-channel ligand and protein scalar fields parameterized by equivariant graph neural networks, enabling rapid optimization over rigid-body degrees of freedom with fast Fourier transforms. The runtime of our approach can be amortized at several levels of abstraction, and is particularly favorable for virtual screening settings with a common binding pocket. We benchmark our scoring functions on two simplified docking-related tasks: decoy pose scoring and rigid conformer docking. Our method attains similar but faster performance on crystal structures compared to the widely-used Vina and Gnina scoring functions, and is more robust on computationally predicted structures. Code is available at https://github.com/bjing2016/scalar-fields.

Predicting the binding structure of a small molecule ligand to a protein -- a task known as molecular docking -- is critical to drug design. Recent deep learning methods that treat docking as a regression problem have decreased runtime compared to traditional search-based methods but have yet to offer substantial improvements in accuracy. We instead frame molecular docking as a generative modeling problem and develop DiffDock, a diffusion generative model over the non-Euclidean manifold of ligand poses. To do so, we map this manifold to the product space of the degrees of freedom (translational, rotational, and torsional) involved in docking and develop an efficient diffusion process on this space. Empirically, DiffDock obtains a 38% top-1 success rate (RMSD<2A) on PDBBind, significantly outperforming the previous state-of-the-art of traditional docking (23%) and deep learning (20%) methods. Moreover, while previous methods are not able to dock on computationally folded structures (maximum accuracy 10.4%), DiffDock maintains significantly higher precision (21.7%). Finally, DiffDock has fast inference times and provides confidence estimates with high selective accuracy.

Molecular docking is an important tool for structure-based drug design, accelerating the efficiency of drug development. Complex and dynamic binding processes between proteins and small molecules require searching and sampling over a wide spatial range. Traditional docking by searching for possible binding sites and conformations is computationally complex and results poorly under blind docking. Quantum-inspired algorithms combining quantum properties and annealing show great advantages in solving combinatorial optimization problems. Inspired by this, we achieve an improved in blind docking by using quantum-inspired combined with gradients learned by deep learning in the encoded molecular space. Numerical simulation shows that our method outperforms traditional docking algorithms and deep learning-based algorithms over 10\%. Compared to the current state-of-the-art deep learning-based docking algorithm DiffDock, the success rate of Top-1 (RMSD<2) achieves an improvement from 33\% to 35\% in our same setup. In particular, a 6\% improvement is realized in the high-precision region(RMSD<1) on molecules data unseen in DiffDock, which demonstrates the well-generalized of our method.

Accurate prediction of protein-ligand binding poses is crucial for structure-based drug design, yet existing methods struggle to balance speed, accuracy, and physical plausibility. We introduce Matcha, a novel molecular docking pipeline that combines multi-stage flow matching with learned scoring and physical validity filtering. Our approach consists of three sequential stages applied consecutively to refine docking predictions, each implemented as a flow matching model operating on appropriate geometric spaces (R^3, SO(3), and SO(2)). We enhance the prediction quality through a dedicated scoring model and apply unsupervised physical validity filters to eliminate unrealistic poses. Compared to various approaches, Matcha demonstrates superior performance on Astex and PDBbind test sets in terms of docking success rate and physical plausibility. Moreover, our method works approximately 25 times faster than modern large-scale co-folding models. The model weights and inference code to reproduce our results are available at https://github.com/LigandPro/Matcha.

We introduce AInsteinBench, a large-scale benchmark for evaluating whether large language model (LLM) agents can operate as scientific computing development agents within real research software ecosystems. Unlike existing scientific reasoning benchmarks which focus on conceptual knowledge, or software engineering benchmarks that emphasize generic feature implementation and issue resolving, AInsteinBench evaluates models in end-to-end scientific development settings grounded in production-grade scientific repositories. The benchmark consists of tasks derived from maintainer-authored pull requests across six widely used scientific codebases, spanning quantum chemistry, quantum computing, molecular dynamics, numerical relativity, fluid dynamics, and cheminformatics. All benchmark tasks are carefully curated through multi-stage filtering and expert review to ensure scientific challenge, adequate test coverage, and well-calibrated difficulty. By leveraging evaluation in executable environments, scientifically meaningful failure modes, and test-driven verification, AInsteinBench measures a model's ability to move beyond surface-level code generation toward the core competencies required for computational scientific research.

Determining the binding pose of a ligand to a protein, known as molecular docking, is a fundamental task in drug discovery. Generative approaches promise faster, improved, and more diverse pose sampling than physics-based methods, but are often hindered by chemically implausible outputs, poor generalisability, and high computational cost. To address these challenges, we introduce a novel fragmentation scheme, leveraging inductive biases from structural chemistry, to decompose ligands into rigid-body fragments. Building on this decomposition, we present SigmaDock, an SE(3) Riemannian diffusion model that generates poses by learning to reassemble these rigid bodies within the binding pocket. By operating at the level of fragments in SE(3), SigmaDock exploits well-established geometric priors while avoiding overly complex diffusion processes and unstable training dynamics. Experimentally, we show SigmaDock achieves state-of-the-art performance, reaching Top-1 success rates (RMSD<2 & PB-valid) above 79.9% on the PoseBusters set, compared to 12.7-30.8% reported by recent deep learning approaches, whilst demonstrating consistent generalisation to unseen proteins. SigmaDock is the first deep learning approach to surpass classical physics-based docking under the PB train-test split, marking a significant leap forward in the reliability and feasibility of deep learning for molecular modelling.

Benchmarking multi-object tracking and object detection model performance is an essential step in machine learning model development, as it allows researchers to evaluate model detection and tracker performance on human-generated 'test' data, facilitating consistent comparisons between models and trackers and aiding performance optimization. In this study, a novel benchmark video dataset was developed and used to assess the performance of several Monterey Bay Aquarium Research Institute object detection models and a FathomNet single-class object detection model together with several trackers. The dataset consists of four video sequences representing midwater and benthic deep-sea habitats. Performance was evaluated using Higher Order Tracking Accuracy, a metric that balances detection, localization, and association accuracy. To the best of our knowledge, this is the first publicly available benchmark for multi-object tracking in deep-sea video footage. We provide the benchmark data, a clearly documented workflow for generating additional benchmark videos, as well as example Python notebooks for computing metrics.

Protein-ligand modeling underpins computational drug discovery and molecular design. Existing protein-ligand benchmarks typically evaluate whether a protein and ligand interact and how strongly they bind, through tasks such as binary binding prediction and affinity regression. However, these evaluations provide limited evidence of whether models can localize binding sites or identify the non-covalent interactions underlying molecular recognition. To address this gap, we introduce InteractBind, a large-scale protein-ligand dataset comprising approximately 100k protein-ligand pairs, together with a benchmark for fine-grained evaluation. The core fine-grained task is that of binding-site localization, which uses protein-residue and ligand-atom interaction maps spanning six major types of non-covalent interactions to assess whether model-derived interaction maps localize binding sites. InteractBind further includes binding affinity and protein similarity-controlled splits to support realistic generalization assessment. Using InteractBind, we evaluate eight existing sequence-based and interaction-aware models, assessing binary binding prediction and binding-site localization. Results reveal limited binding-site localization despite strong binary binding prediction, with marked variation across non-covalent interaction types. Overall, InteractBind establishes a benchmark paradigm that encourages the development of more interpretable and physically grounded protein-ligand models.

Molecular docking is a key computational tool utilized to predict the binding conformations of small molecules to protein targets, which is fundamental in the design of novel drugs. Despite recent advancements in geometric deep learning-based approaches leading to improvements in blind docking efficiency, these methods have encountered notable challenges, such as limited generalization performance on unseen proteins, the inability to concurrently address the settings of blind docking and site-specific docking, and the frequent occurrence of physical implausibilities such as inter-molecular steric clash. In this study, we introduce DeltaDock, a robust and versatile framework designed for efficient molecular docking to overcome these challenges. DeltaDock operates in a two-step process: rapid initial complex structures sampling followed by multi-scale iterative refinement of the initial structures. In the initial stage, to sample accurate structures with high efficiency, we develop a ligand-dependent binding site prediction model founded on large protein models and graph neural networks. This model is then paired with GPU-accelerated sampling algorithms. The sampled structures are updated using a multi-scale iterative refinement module that captures both protein-ligand atom-atom interactions and residue-atom interactions in the following stage. Distinct from previous geometric deep learning methods that are conditioned on the blind docking setting, DeltaDock demonstrates superior performance in both blind docking and site-specific docking settings. Comprehensive experimental results reveal that DeltaDock consistently surpasses baseline methods in terms of docking accuracy. Furthermore, it displays remarkable generalization capabilities and proficiency for predicting physically valid structures, thereby attesting to its robustness and reliability in various scenarios.

Deep learning promises to dramatically improve scoring functions for molecular docking, leading to substantial advances in binding pose prediction and virtual screening. To train scoring functions-and to perform molecular docking-one must generate a set of candidate ligand binding poses. Unfortunately, the sampling protocols currently used to generate candidate poses frequently fail to produce any poses close to the correct, experimentally determined pose, unless information about the correct pose is provided. This limits the accuracy of learned scoring functions and molecular docking. Here, we describe two improved protocols for pose sampling: GLOW (auGmented sampLing with sOftened vdW potential) and a novel technique named IVES (IteratiVe Ensemble Sampling). Our benchmarking results demonstrate the effectiveness of our methods in improving the likelihood of sampling accurate poses, especially for binding pockets whose shape changes substantially when different ligands bind. This improvement is observed across both experimentally determined and AlphaFold-generated protein structures. Additionally, we present datasets of candidate ligand poses generated using our methods for each of around 5,000 protein-ligand cross-docking pairs, for training and testing scoring functions. To benefit the research community, we provide these cross-docking datasets and an open-source Python implementation of GLOW and IVES at https://github.com/drorlab/GLOW_IVES .

This benchmark suite provides a comprehensive evaluation framework for assessing both individual LLMs and multi-agent systems in Real-world planning and scheduling scenarios. The suite encompasses 14 designed planning and scheduling problems that progress from basic to highly complex, incorporating key aspects such as multi-agent coordination, inter-agent dependencies, and dynamic environmental disruptions. Each problem can be scaled along three dimensions: the number of parallel planning threads, the complexity of inter-dependencies, and the frequency of unexpected disruptions requiring Real-time adaptation. The benchmark includes 14 detailed problem specifications, 15 comparison methods including Random, LPT, SPT, STPT, MPSR, DRL-Liu, GP, GEP, LSO, SPT/TWKR, DRL-Chen, DRL-Zhang, 2+ evaluation metrics, and baseline implementations using 3+ LLMs including GPT-4o, Claude-3.7, DeepSeek-R1, and 4 contemporary frameworks including LangGraph, AutoGen, CrewAI, and Swarm, enabling rigorous testing of both single-agent and multi-agent planning capabilities. Through standardized evaluation criteria and scalable complexity, this benchmark aims to be opened to public, and drive progress in developing more adaptable, robust, and scalable AI planning systems for Real-world applications.

Structure-based drug design (SBDD) leverages the 3D structure of biomolecular targets to guide the creation of new therapeutic agents. Recent advances in generative models, including diffusion models and geometric deep learning, have demonstrated promise in optimizing ligand generation. However, the scarcity of high-quality protein-ligand complex data and the inherent challenges in aligning generated ligands with target proteins limit the effectiveness of these methods. We propose BoKDiff, a novel framework that enhances ligand generation by combining multi-objective optimization and Best-of-K alignment methodologies. Built upon the DecompDiff model, BoKDiff generates diverse candidates and ranks them using a weighted evaluation of molecular properties such as QED, SA, and docking scores. To address alignment challenges, we introduce a method that relocates the center of mass of generated ligands to their docking poses, enabling accurate sub-component extraction. Additionally, we integrate a Best-of-N (BoN) sampling approach, which selects the optimal ligand from multiple generated candidates without requiring fine-tuning. BoN achieves exceptional results, with QED values exceeding 0.6, SA scores above 0.75, and a success rate surpassing 35%, demonstrating its efficiency and practicality. BoKDiff achieves state-of-the-art results on the CrossDocked2020 dataset, including a -8.58 average Vina docking score and a 26% success rate in molecule generation. This study is the first to apply Best-of-K alignment and Best-of-N sampling to SBDD, highlighting their potential to bridge generative modeling with practical drug discovery requirements. The code is provided at https://github.com/khodabandeh-ali/BoKDiff.git.

Benchmarks increasingly guide deployment, procurement and scientific screening, yet a score supports only the response it records, not necessarily the deployment action. We introduce deployment-complete benchmarking, which tests whether benchmark evidence determines a deployment action. A benchmark is complete for a claim exactly when the action is constant on each evidence fiber; mixed fibers expose missing deployment information, and completion curves quantify the evidence required to resolve ambiguity. In controlled response spaces, benchmark-channel conformal coverage of 94.98% transferred poorly to an unmeasured deployment channel (10.07%), whereas response-rank intervals achieved 94.91% coverage; even zero benchmark error certified only 45.4% of candidates at the largest residual size. Public audits revealed incompleteness, including 97.9% mixed Tox21 fibers and zero median certifiable fraction in main Matbench and JARVIS audits. In held-out replays, certify-then-acquire reduced false decisions from 1.19% to 0.027% in Tox21 and from 20.3% to 0.128% in JARVIS, while changing model choice and identifying deployment-relevant probes. Deployment-ready benchmarks should report evidence, supported actions, ambiguity and completion cost rather than scores alone.

Spacecraft deployed in outer space are routinely subjected to various forms of damage due to exposure to hazardous environments. In addition, there are significant risks to the subsequent process of in-space repairs through human extravehicular activity or robotic manipulation, incurring substantial operational costs. Recent developments in image segmentation could enable the development of reliable and cost-effective autonomous inspection systems. While these models often require large amounts of training data to achieve satisfactory results, publicly available annotated spacecraft segmentation data are very scarce. Here, we present a new dataset of nearly 64k annotated spacecraft images that was created using real spacecraft models, superimposed on a mixture of real and synthetic backgrounds generated using NASA's TTALOS pipeline. To mimic camera distortions and noise in real-world image acquisition, we also added different types of noise and distortion to the images. Finally, we finetuned YOLOv8 and YOLOv11 segmentation models to generate performance benchmarks for the dataset under well-defined hardware and inference time constraints to mimic real-world image segmentation challenges for real-time onboard applications in space on NASA's inspector spacecraft. The resulting models, when tested under these constraints, achieved a Dice score of 0.92, Hausdorff distance of 0.69, and an inference time of about 0.5 second. The dataset and models for performance benchmark are available at https://github.com/RiceD2KLab/SWiM.

Modeling protein-protein interactions requires accurate scoring functions that can rank potential poses (conformations) of a protein-protein complex to differentiate near-native poses from incorrect ones. Here, we propose a general framework for improving protein-protein pose ranking and other biomolecular interaction models using the LambdaLoss loss function from the Learning-to-Rank field. We test this framework by fine-tuning the energy prediction head of DFMDock with the LambdaLoss on an augmented dataset of 2.9M decoy poses derived from the DIPS dataset. On targets from the CAPRI score set benchmark, our fine-tuned ranking model LambdaDockScore is better at identifying correct poses in its top-1 and top-5 predictions compared to EuDockScore, a state-of-the-art method. LambdaDockScore also improves upon baseline DFMDock ranking performance for scoring antibody-antigen complexes and protein-protein complexes with very large or small binding interfaces.

Open-ended language-model benchmarks usually inherit a judge: a human preference panel, another model, or a brittle exact-match key. We introduce FlavourBench, an automated benchmark in which a versioned culinary system supplies dense, executable ground truth. Each task presents eight ingredients and asks for a three-ingredient portfolio; before model execution, Epicure scores all 56 possible portfolios. We evaluate 27 frontier endpoints on an identical 534-task core spanning substitution, pairing, and constrained composition. Every ranked model has exactly 89 valid responses per panel and family (14,418 model-task cells total), eliminating differential missingness from the leaderboard. The FlavourBench Score is the equal-family mean of the frozen task scores. We use 50,000 anchor-cluster bootstrap replicates for simultaneous 95% score bands and 100,000 sign-flip draws for all 351 paired model contrasts, with Holm control. The two independently compiled panels correlate at r = 0.89 (rank rho = 0.80). Grok 4.6 has the largest point estimate at 65.1 (simultaneous 95% CI 61.0-69.2); 101 of 351 model pairs are resolved. The release includes the prompts, all portfolio score maps, raw responses, exact routes, content hashes, and an offline verifier that reconstructs every result.

The rapid development of large language models and multimodal large language models has accelerated the emergence of proactive agents capable of operating everyday tools and assisting users in real-world environments. However, existing benchmarks struggle to evaluate such agents effectively, as they often rely on sandboxed environments and single-turn evaluation paradigms. Moreover, their scenario-based task taxonomies mix multiple model capabilities within the same task category, making it difficult to identify the root causes of agent failures. To address these limitations, we introduce UniClawBench, the first capability-driven benchmark designed to evaluate proactive agents in dynamic, real-world settings. UniClawBench is built around five foundational model capabilities: Skill Usage, Exploration, Long-Context Reasoning, Multimodal Understanding, and Cross-Platform Coordination. Based on these capabilities, we design 400 bilingual real-world tasks. Unlike previous benchmarks that rely on static, pre-recorded answers, our benchmark evaluates agents in live Docker containers using fine-grained, step-by-step completion checkpoints. Furthermore, we design a closed-loop evaluation strategy comprising an executor agent, a hidden supervisor agent, and a user agent to simulate realistic multi-turn human feedback without leaking grading criteria. To disentangle base model capabilities from framework-level design choices, we evaluate state-of-the-art models under multiple agent frameworks. Through comprehensive comparisons across both models and frameworks, we show how base model capabilities and agent framework designs jointly shape performance in real-world environments. To facilitate future research, we make our benchmark and code publicly available at https://github.com/HKU-MMLab/UniClawBench.

The ``LLM-as-a-judge'' paradigm has become a standard method for evaluating open-ended generation. To address the quadratic scalability costs of pairwise comparisons, popular benchmarks like Arena-Hard and AlpacaEval compare all models against a single anchor. However, despite its widespread use, the impact of anchor selection on the reliability of the results remains largely unexplored. In this work, we systematically investigate the effect of anchor selection by evaluating 22 different anchors on the Arena-Hard-v2.0 dataset. We find that the choice of anchor is critical: a poor anchor can dramatically reduce correlation with human rankings. We identify that common anchor choices (best-performing and worst-performing models) make poor anchors. Because these extreme anchors are consistently better or worse than all other models, they are seldom indicative of the relative ranking of the models. We further quantify the effect size of anchor selection, showing it is comparable to the selection of a judge model. We conclude with actionable recommendations. First, we conduct a power analysis, and compute sufficient benchmark sizes for anchor-based evaluation, finding that standard benchmark sizes are insufficient for pairwise evaluation and fail to distinguish between competitive models reliably. Second, we provide guidelines for selecting informative anchors to ensure reliable and efficient evaluation practices.

AI agents may soon become capable of autonomously completing valuable, long-horizon tasks in diverse domains. Current benchmarks either do not measure real-world tasks, or are not sufficiently difficult to meaningfully measure frontier models. To this end, we present Terminal-Bench 2.0: a carefully curated hard benchmark composed of 89 tasks in computer terminal environments inspired by problems from real workflows. Each task features a unique environment, human-written solution, and comprehensive tests for verification. We show that frontier models and agents score less than 65\% on the benchmark and conduct an error analysis to identify areas for model and agent improvement. We publish the dataset and evaluation harness to assist developers and researchers in future work at https://www.tbench.ai/ .

Rigorous performance evaluation is essential for developing robust algorithms for high-throughput computational chemistry. Traditional benchmarking, however, often struggles to account for system-specific variability, making it difficult to form actionable conclusions. We present a Bayesian hierarchical modeling framework that rigorously quantifies performance metrics and their uncertainty, enabling a nuanced comparison of algorithmic strategies. We apply this framework to analyze the Dimer method, comparing Conjugate Gradient (CG) and L-BFGS rotation optimizers, with and without the removal of external rotations, across a benchmark of 500 molecular systems. Our analysis confirms that CG offers higher overall robustness than L-BFGS in this context. While the theoretically-motivated removal of external rotations led to higher computational cost (>40% more energy and force calls) for most systems in this set, our models also reveal a subtle interplay, hinting that this feature may improve the reliability of the L-BFGS optimizer. Rather than identifying a single superior method, our findings support the design of adaptive "chain of methods" workflows. This work showcases how a robust statistical paradigm can move beyond simple performance rankings to inform the intelligent, context-dependent application of computational chemistry methods.

Can the rapid advances in code generation, function calling, and data analysis using large language models (LLMs) help automate the search and verification of hypotheses purely from a set of provided datasets? To evaluate this question, we present DiscoveryBench, the first comprehensive benchmark that formalizes the multi-step process of data-driven discovery. The benchmark is designed to systematically assess current model capabilities in discovery tasks and provide a useful resource for improving them. Our benchmark contains 264 tasks collected across 6 diverse domains, such as sociology and engineering, by manually deriving discovery workflows from published papers to approximate the real-world challenges faced by researchers, where each task is defined by a dataset, its metadata, and a discovery goal in natural language. We additionally provide 903 synthetic tasks to conduct controlled evaluations across task complexity. Furthermore, our structured formalism of data-driven discovery enables a facet-based evaluation that provides useful insights into different failure modes. We evaluate several popular LLM-based reasoning frameworks using both open and closed LLMs as baselines on DiscoveryBench and find that even the best system scores only 25%. Our benchmark, thus, illustrates the challenges in autonomous data-driven discovery and serves as a valuable resource for the community to make progress.

Evaluation of foundation models often rely on aggregate scores from benchmarks that lack comprehensive coverage and metadata for a fine-grained evaluation. We introduce a framework for automated benchmark generation. Our framework generates evaluation problems grounded in reference material, such as textbooks, producing benchmarks with broad coverage, rich metadata, and robustness to contamination. The pipeline employs a multi-agent architecture for problem generation and a solution-graph-driven strategy that significantly improves the reliability of ground truth solutions. Using the framework, we generate three benchmarks in Machine Learning, Corporate Finance, and Personal Finance. Expert review finds a significantly lower ground-truth error rate than previous benchmarks such as MMLU and GSM8K. Evaluation of 12 commercial and open-source models shows that our benchmarks achieve near-uniform competency coverage and surface performance differences across models that existing benchmarks fail to capture. We will open-source the framework and our curated benchmarks soon.

Modeling the interaction between proteins and ligands and accurately predicting their binding structures is a critical yet challenging task in drug discovery. Recent advancements in deep learning have shown promise in addressing this challenge, with sampling-based and regression-based methods emerging as two prominent approaches. However, these methods have notable limitations. Sampling-based methods often suffer from low efficiency due to the need for generating multiple candidate structures for selection. On the other hand, regression-based methods offer fast predictions but may experience decreased accuracy. Additionally, the variation in protein sizes often requires external modules for selecting suitable binding pockets, further impacting efficiency. In this work, we propose FABind, an end-to-end model that combines pocket prediction and docking to achieve accurate and fast protein-ligand binding. FABind incorporates a unique ligand-informed pocket prediction module, which is also leveraged for docking pose estimation. The model further enhances the docking process by incrementally integrating the predicted pocket to optimize protein-ligand binding, reducing discrepancies between training and inference. Through extensive experiments on benchmark datasets, our proposed FABind demonstrates strong advantages in terms of effectiveness and efficiency compared to existing methods. Our code is available at https://github.com/QizhiPei/FABind

Structure-Based molecule optimization (SBMO) aims to optimize molecules with both continuous coordinates and discrete types against protein targets. A promising direction is to exert gradient guidance on generative models given its remarkable success in images, but it is challenging to guide discrete data and risks inconsistencies between modalities. To this end, we leverage a continuous and differentiable space derived through Bayesian inference, presenting Molecule Joint Optimization (MolJO), the gradient-based SBMO framework that facilitates joint guidance signals across different modalities while preserving SE(3)-equivariance. We introduce a novel backward correction strategy that optimizes within a sliding window of the past histories, allowing for a seamless trade-off between explore-and-exploit during optimization. MolJO achieves state-of-the-art performance on CrossDocked2020 benchmark (Success Rate 51.3%, Vina Dock -9.05 and SA 0.78), more than 4x improvement in Success Rate compared to the gradient-based counterpart, and 2x "Me-Better" Ratio as much as 3D baselines. Furthermore, we extend MolJO to a wide range of optimization settings, including multi-objective optimization and challenging tasks in drug design such as R-group optimization and scaffold hopping, further underscoring its versatility. Code is available at https://github.com/AlgoMole/MolCRAFT.

Tool-calling benchmarks are increasingly used to rank language-model agents, yet their scores are often treated as ground truth without validating the evaluators themselves. We present a systematic validity and reproducibility audit of four major tool-calling benchmark families: BFCL v4, τ2-Bench, LiveMCPBench, and MCP-Atlas. Across 496 expert-reviewed benchmark tasks, we find 92 evaluator-human disagreements, corresponding to an 18.5% misalignment rate. The failures are not isolated annotation mistakes: deterministic benchmarks exhibit brittle state matching, trajectory lock-in, incorrect ground truths, substring-based communication failures, and reward-basis misalignment, while LLM-judge benchmarks exhibit rubric drift, hallucinated completion, answer-only scoring, and substantial run-to-run variance. In LiveMCPBench, 23 repeated evaluations of the same setup produce scores ranging from 57.9% to 76.8%, a spread of 18.9 percentage points, large enough to change leaderboard conclusions. These results show that current tool-calling scores can reflect evaluator artifacts rather than agent capability. We introduce a unified taxonomy of tool-calling evaluation failures, release trace-level audit artifacts and corrected evaluation components, and argue for decomposed metrics that separately measure tool invocation, task completion, and outcome verification. Our findings suggest that progress in tool-using agents requires benchmarks whose evaluators are themselves reproducible, auditable, and aligned with human judgments of task success. We further introduce Tool-Veritas, a configurable benchmark that combines deterministic state verification with optional qualitative judging, and Harness Lab, an open-source system for benchmark execution, trace inspection, repeated-run comparison, and evaluator debugging.

Benchmark quality is critical for meaningful evaluation and sustained progress in time series forecasting, particularly given the recent rise of pretrained models. Existing benchmarks often have narrow domain coverage or overlook important real-world settings, such as tasks with covariates. Additionally, their aggregation procedures often lack statistical rigor, making it unclear whether observed performance differences reflect true improvements or random variation. Many benchmarks also fail to provide infrastructure for consistent evaluation or are too rigid to integrate into existing pipelines. To address these gaps, we propose fev-bench, a benchmark comprising 100 forecasting tasks across seven domains, including 46 tasks with covariates. Supporting the benchmark, we introduce fev, a lightweight Python library for benchmarking forecasting models that emphasizes reproducibility and seamless integration with existing workflows. Usingfev, fev-bench employs principled aggregation methods with bootstrapped confidence intervals to report model performance along two complementary dimensions: win rates and skill scores. We report results on fev-bench for various pretrained, statistical and baseline models, and identify promising directions for future research.

The issue-resolving task, where a model generates patches to fix real-world bugs, has emerged as a critical benchmark for evaluating the capabilities of large language models (LLMs). While SWE-bench and its variants have become standard in this domain, they suffer from key limitations: they have not been updated since their initial releases, cover a narrow set of repositories, and depend heavily on manual effort for instance construction and environment setup. These factors hinder scalability and introduce risks of overfitting and data contamination. In this work, we present SWE-bench-Live, a live-updatable benchmark designed to overcome these challenges. Our initial release consists of 1,319 tasks derived from real GitHub issues created since 2024, spanning 93 repositories. Each task is accompanied by a dedicated Docker image to ensure reproducible execution. Central to our benchmark is \method, an automated curation pipeline that streamlines the entire process from instance creation to environment setup, removing manual bottlenecks and enabling scalability and continuous updates. We evaluate a range of state-of-the-art agent frameworks and LLMs on SWE-bench-Live, revealing a substantial performance gap compared to static benchmarks like SWE-bench, even under controlled evaluation conditions. To better understand this discrepancy, we perform detailed analyses across repository origin, issue recency, and task difficulty. By providing a fresh, diverse, and executable benchmark grounded in live repository activity, SWE-bench-Live facilitates rigorous, contamination-resistant evaluation of LLMs and agents in dynamic, real-world software development settings.

Large language models (LLMs) are powerful tools capable of handling diverse tasks. Comparing and selecting appropriate LLMs for specific tasks requires systematic evaluation methods, as models exhibit varying capabilities across different domains. However, finding suitable benchmarks is difficult given the many available options. This complexity not only increases the risk of benchmark misuse and misinterpretation but also demands substantial effort from LLM users, seeking the most suitable benchmarks for their specific needs. To address these issues, we introduce BenchmarkCards, an intuitive and validated documentation framework that standardizes critical benchmark attributes such as objectives, methodologies, data sources, and limitations. Through user studies involving benchmark creators and users, we show that BenchmarkCards can simplify benchmark selection and enhance transparency, facilitating informed decision-making in evaluating LLMs. Data & Code: https://github.com/SokolAnn/BenchmarkCards

We introduce the first version of KWBench (Knowledge Work Bench), a benchmark for unprompted problem recognition in large language models: can an LLM identify a professional scenario before attempting to solve it. Existing frontier benchmarks have saturated, and most knowledge-work evaluations to date reduce to extraction or task completion against a specification. KWBench targets the step before that: recognizing the governing structure of the situation from raw inputs alone. The benchmark contains 223 tasks sourced from practitioners across acquisitions, contract negotiations, clinical pharmacy, organizational politics, fraud analysis, and incentive design. Each task encodes a formal game-theoretic pattern (principal-agent conflict, signaling, mechanism design failure, strategic omission, coalitional dynamics, strategic interdependence) and carries structured ground truth recording the expert reading of the situation and the anticipated failure modes. Models receive raw data and a task prompt with no indication of problem type. Scoring is a three-tier rubric gated by a mandatory conjunctive check. Mandatory criteria encode the predicted wrong paths. We evaluate 16 models. The best model passes on 27.9% of tasks. The top two models agree on only 31.7% of their passes. Among the top 8, 44 tasks are solved by exactly one model; routing across the top 8 covers 50.7% of the benchmark, nearly double the best single model. Conditional on passing, quality scores converge (approx 83% across models); unconditional scores do not. Same models articulate the relevant game-theoretic concept correctly when asked, then fail to apply it unprompted. We release KWBench to shift how frontier models are evaluated on knowledge work, scoring them on whether they recognize the right problem from the situation alone, not only on how well they execute once the problem has been framed for them.

Development and operation of commercially viable fusion energy reactors such as tokamaks require accurate predictions of plasma dynamics from sparse, noisy, and incomplete sensors readings. The complexity of the underlying physics and the heterogeneity of experimental data pose formidable challenges for conventional numerical methods, while simultaneously highlight the promise of modern data-native AI approaches. A major obstacle in realizing this potential is, however, the lack of curated, openly available datasets and standardized benchmarks. Existing fusion datasets are scarce, fragmented across institutions, facility-specific, and inconsistently annotated, which limits reproducibility and prevents a fair and scalable comparison of AI approaches. In this paper, we introduce TokaMark, a structured benchmark to evaluate AI models on real experimental data collected from the Mega Ampere Spherical Tokamak (MAST). TokaMark provides a comprehensive suite of tools designed to (i) unify access to multi-modal heterogeneous fusion data, and (ii) harmonize formats, metadata, temporal alignment and evaluation protocols to enable consistent cross-model and cross-task comparisons. The benchmark includes a curated list of 14 tasks spanning a range of physical mechanisms, exploiting a variety of diagnostics and covering multiple operational use cases. A baseline model is provided to facilitate transparent comparison and validation within a unified framework. By establishing a unified benchmark for both the fusion and AI-for-science communities, TokaMark aims to accelerate progress in data-driven AI-based plasma modeling, contributing to the broader goal of achieving sustainable and stable fusion energy. The benchmark, documentation, and tooling will be fully open sourced upon acceptance to encourage community adoption and contribution.

Benchmarks are essential for consistent evaluation and reproducibility. The integration of Artificial Intelligence into Software Engineering (AI4SE) has given rise to numerous benchmarks for tasks such as code generation and bug fixing. However, this surge presents challenges: (1) scattered benchmark knowledge across tasks, (2) difficulty in selecting relevant benchmarks, (3) the absence of a uniform standard for benchmark development, and (4) limitations of existing benchmarks. In this paper, we review 173 studies and identify 204 AI4SE benchmarks. We classify these benchmarks, analyze their limitations, and expose gaps in practices. Based on our review, we created BenchScout, a semantic search tool to find relevant benchmarks, using automated clustering of the contexts from associated studies. We conducted a user study with 22 participants to evaluate BenchScout's usability, effectiveness, and intuitiveness which resulted in average scores of 4.5, 4.0, and 4.1 out of 5. To advance benchmarking standards, we propose BenchFrame, a unified method to enhance benchmark quality. As a case study, we applied BenchFrame to the HumanEval benchmark and addressed its main limitations. This led to HumanEvalNext, featuring (1) corrected errors, (2) improved language conversion, (3) expanded test coverage, and (4) increased difficulty. We then evaluated ten state-of-the-art code language models on HumanEval, HumanEvalPlus, and HumanEvalNext. On HumanEvalNext, models showed a pass@1 score reduction of 31.22% and 19.94% compared to HumanEval and HumanEvalPlus, respectively.

We introduce Telco-GAIA, a bilingual, multi-modal benchmark for evaluating tool-using agents on the data of a real-world telecommunications operator. Telco-GAIA comprises 100 human-verified question-answering tasks, in English and Arabic, that each demand multi-hop reasoning (4.2 hops on average) over three heterogeneous sources: a static website snapshot (HTML, images, and linked PDFs), a synthetic relational SQL database, and external web archives, spanning text, image, and tabular modalities. The benchmark is delivered as a sandboxed Docker environment and scored by normalized exact string matching, making evaluation objective, deterministic, and reproducible over time without any LLM-as-a-Judge. Evaluating a purpose-built reference agent across twelve commercial and open LLMs, we find Telco-GAIA challenging: even the strongest model solves only 71% of tasks; under a moderate cost budget, this falls to about 40%, and the visually grounded categories remain the weakest, where the average backend scores below 30%, leaving substantial headroom in document and image understanding. Telco-GAIA offers a rigorous, reproducible testbed for enterprise agents and a template for constructing closed-domain benchmarks.

The ability to generate proteins with desired functions is a central goal of computational biology. Although natural language can express diverse design objectives, existing protein generation methods often support only narrow tasks or make limited use of biological constraints. We develop InstructPro2 to translate natural-language design objectives into protein sequences while incorporating task-specific biological context. A text encoder captures the design instructions, while dedicated ligand and antigen encoders provide biological context to the sequence-generating decoder. For pretraining, we assemble InstructPro2Bench, comprising 205.7 million <function description, protein> pairs from UniProtKB. We subsequently adapt the model to ligand-binding protein and antibody design. On functional protein generation benchmarks, InstructPro2 outperforms Pinal, the strongest baseline, achieving a functional recovery F1 of 74.8 versus 62.2 and lowering global RMSD from 5.33A to 3.04A. For antibody design, the model obtains a DockQ score of 0.39, while ligand-binding protein design reaches a docking success rate of 72.6%. These findings highlight how integrating language-based instructions with biological conditioning can extend protein generation to distinct design settings.

Protein motif scaffolding benchmarks assess whether generative models can build scaffolds around functionally important residues. Their conclusions depend on which motifs are tested and which criteria define success. Existing benchmarks typically use small hand-curated motif sets and static refolding criteria, but protein function often depends on conformational ensembles and transitions. Here, we address both benchmark scope and success criteria. We introduce BILBY-PRO, a systematically derived benchmark of structurally conserved functional motifs from PROSITE-linked experimental structures, comprising 220 cases from 174 PROSITE motif-pattern entries. Evaluating six recent scaffold-generation models reveals distinct patterns in target coverage and unique-solution yield: RFDiffusion and Proteina solve more targets, whereas ESM3 produces more unique successful scaffolds on the targets it solves. We further introduce BILBY-MD, a reference-based all-atom molecular dynamics evaluation framework. Applied to statically solved designs from the original MotifBench benchmark, it compares motif drift, scaffold drift, motif-contact preservation, and motif-dihedral free-energy landscapes against reference simulations. Of 55 statically solved model-problem pairs, 31 satisfy our MD-supported criterion and only 8 pass all checks. Compact, self-contained motifs are often MD-supported, whereas interface-like or context-dependent motifs fail more frequently. Static refolding success therefore provides useful evidence of local motif recovery but does not establish dynamical fidelity of the full scaffold. BILBY highlights three complementary axes of motif-scaffolding evaluation: target coverage, unique-solution yield, and MD-supported dynamical fidelity.

The efficient exploration of chemical space to design molecules with intended properties enables the accelerated discovery of drugs, materials, and catalysts, and is one of the most important outstanding challenges in chemistry. Encouraged by the recent surge in computer power and artificial intelligence development, many algorithms have been developed to tackle this problem. However, despite the emergence of many new approaches in recent years, comparatively little progress has been made in developing realistic benchmarks that reflect the complexity of molecular design for real-world applications. In this work, we develop a set of practical benchmark tasks relying on physical simulation of molecular systems mimicking real-life molecular design problems for materials, drugs, and chemical reactions. Additionally, we demonstrate the utility and ease of use of our new benchmark set by demonstrating how to compare the performance of several well-established families of algorithms. Surprisingly, we find that model performance can strongly depend on the benchmark domain. We believe that our benchmark suite will help move the field towards more realistic molecular design benchmarks, and move the development of inverse molecular design algorithms closer to designing molecules that solve existing problems in both academia and industry alike.

This paper introduces the human-curated PandasPlotBench dataset, designed to evaluate language models' effectiveness as assistants in visual data exploration. Our benchmark focuses on generating code for visualizing tabular data - such as a Pandas DataFrame - based on natural language instructions, complementing current evaluation tools and expanding their scope. The dataset includes 175 unique tasks. Our experiments assess several leading Large Language Models (LLMs) across three visualization libraries: Matplotlib, Seaborn, and Plotly. We show that the shortening of tasks has a minimal effect on plotting capabilities, allowing for the user interface that accommodates concise user input without sacrificing functionality or accuracy. Another of our findings reveals that while LLMs perform well with popular libraries like Matplotlib and Seaborn, challenges persist with Plotly, highlighting areas for improvement. We hope that the modular design of our benchmark will broaden the current studies on generating visualizations. Our benchmark is available online: https://huggingface.co/datasets/JetBrains-Research/plot_bench. The code for running the benchmark is also available: https://github.com/JetBrains-Research/PandasPlotBench.

The study of rigid protein-protein docking plays an essential role in a variety of tasks such as drug design and protein engineering. Recently, several learning-based methods have been proposed for the task, exhibiting much faster docking speed than those computational methods. In this paper, we propose a novel learning-based method called ElliDock, which predicts an elliptic paraboloid to represent the protein-protein docking interface. To be specific, our model estimates elliptic paraboloid interfaces for the two input proteins respectively, and obtains the roto-translation transformation for docking by making two interfaces coincide. By its design, ElliDock is independently equivariant with respect to arbitrary rotations/translations of the proteins, which is an indispensable property to ensure the generalization of the docking process. Experimental evaluations show that ElliDock achieves the fastest inference time among all compared methods and is strongly competitive with current state-of-the-art learning-based models such as DiffDock-PP and Multimer particularly for antibody-antigen docking.

Physical AI models are evaluated on suites of benchmarks that differ across model reports, leaving the model-by-benchmark matrix sparse and the relationship between benchmarks unmeasured. We construct a matrix of 51 models on 12 physical AI benchmarks, selected from a registry of 51 benchmarks and 152 models by reporting density, combining scores from model cards and benchmark papers with our own evaluation runs under each benchmark's official protocol. We measure how much information the benchmarks share and show quantitative evidence of Redundancy. Redundancy affects reported rankings: collapsing the two substitute pairs into single columns moves 22 of 51 models by three or more places under an equally weighted average. We then select benchmarks greedily under a utility combining score dispersion with variance not explained by the already-selected set, and obtain a four-benchmark subset retaining 78.5\% of the utility of all 12, on which we fit a Bradley--Terry ranking. The procedure requires only benchmark-level scores with sufficient overlap and is not specific to physical AI.

We present a new reproducible benchmark for evaluating robot manipulation in the real world, specifically focusing on pick-and-place. Our benchmark uses the YCB objects, a commonly used dataset in the robotics community, to ensure that our results are comparable to other studies. Additionally, the benchmark is designed to be easily reproducible in the real world, making it accessible to researchers and practitioners. We also provide our experimental results and analyzes for model-based and model-free 6D robotic grasping on the benchmark, where representative algorithms are evaluated for object perception, grasping planning, and motion planning. We believe that our benchmark will be a valuable tool for advancing the field of robot manipulation. By providing a standardized evaluation framework, researchers can more easily compare different techniques and algorithms, leading to faster progress in developing robot manipulation methods.

Mobile robots are increasingly deployed in unstructured environments where obstacles and objects are movable. Navigation in such environments is known as interactive navigation, where task completion requires not only avoiding obstacles but also strategic interactions with movable objects. Non-prehensile interactive navigation focuses on non-grasping interaction strategies, such as pushing, rather than relying on prehensile manipulation. Despite a growing body of research in this field, most solutions are evaluated using case-specific setups, limiting reproducibility and cross-comparison. In this paper, we present Bench-NPIN, the first comprehensive benchmark for non-prehensile interactive navigation. Bench-NPIN includes multiple components: 1) a comprehensive range of simulated environments for non-prehensile interactive navigation tasks, including navigating a maze with movable obstacles, autonomous ship navigation in icy waters, box delivery, and area clearing, each with varying levels of complexity; 2) a set of evaluation metrics that capture unique aspects of interactive navigation, such as efficiency, interaction effort, and partial task completion; and 3) demonstrations using Bench-NPIN to evaluate example implementations of established baselines across environments. Bench-NPIN is an open-source Python library with a modular design. The code, documentation, and trained models can be found at https://github.com/IvanIZ/BenchNPIN.

Scientific method figures often provide researchers with a clear visual entry point into a paper's methodology and core contributions, yet their dense layouts and complex information flows are difficult for Vision Language Models (VLMs) to interpret. Existing benchmarks predominantly focus on coarse-grained tasks, such as context-based retrieval or holistic comprehension, overlooking the fine-grained content and inter-module relations within complex methodological diagrams. To address these overlooked aspects, we introduce Scientific Figure Benchmark (SciFigBench), a benchmark for evaluating core capabilities required for scientific method figure understanding. Specifically, it targets three capabilities: dense content perception, visual relation comprehension, and information-flow tracing. For this purpose, we curate 4,352 scientific method figures from real-world research papers and construct 40,670 QA pairs to operationalize these capabilities as measurable question-answering tasks. All annotations are generated by dedicated pipelines and then manually verified. We further propose SciFigCue, a training-free visual prompting module that externalizes arrow-induced dependencies as visual relational evidence for method-figure reasoning. Experiments across open-source and proprietary VLMs show that even strong models remain substantially limited in visual relation comprehension, while SciFigCue improves performance across several tasks without parameter updates. The code and related resources are available at https://github.com/LeNcyer/SciFigBench.

De novo design seeks to generate molecules with required property profiles by virtual design-make-test cycles. With the emergence of deep learning and neural generative models in many application areas, models for molecular design based on neural networks appeared recently and show promising results. However, the new models have not been profiled on consistent tasks, and comparative studies to well-established algorithms have only seldom been performed. To standardize the assessment of both classical and neural models for de novo molecular design, we propose an evaluation framework, GuacaMol, based on a suite of standardized benchmarks. The benchmark tasks encompass measuring the fidelity of the models to reproduce the property distribution of the training sets, the ability to generate novel molecules, the exploration and exploitation of chemical space, and a variety of single and multi-objective optimization tasks. The benchmarking open-source Python code, and a leaderboard can be found on https://benevolent.ai/guacamol

Language model benchmarks are pervasive and computationally-efficient proxies for real-world downstream performance. However, many recent works find that benchmarks often fail to predict downstream utility. While some works have begun diagnosing sources of misalignment, there remain no ways to systematically update benchmarks to align their scores with downstream usage. Towards bridging this gap, we introduce and study benchmark alignment, where we use information about downstream model performance to automatically update benchmarks, specifically aiming to update static benchmarks so they generalizably rank models according to new pairwise preferences. Our experiments involving 4576 language models and 6 benchmarks show that reweighting benchmark items can successfully rank unseen models, even generalizing across model scales in most cases. And while naive alignment unsurprisingly requires large numbers of models and benchmark questions, an oracle experiment suggests this could be reduced to as few as 20 well-chosen models. Overall, our work takes a step towards efficiently aligning benchmark development with downstream tasks.\footnote{All of our code, models, and data are publicly-available.

This paper introduces Amazon Robotic Manipulation Benchmark (ARMBench), a large-scale, object-centric benchmark dataset for robotic manipulation in the context of a warehouse. Automation of operations in modern warehouses requires a robotic manipulator to deal with a wide variety of objects, unstructured storage, and dynamically changing inventory. Such settings pose challenges in perceiving the identity, physical characteristics, and state of objects during manipulation. Existing datasets for robotic manipulation consider a limited set of objects or utilize 3D models to generate synthetic scenes with limitation in capturing the variety of object properties, clutter, and interactions. We present a large-scale dataset collected in an Amazon warehouse using a robotic manipulator performing object singulation from containers with heterogeneous contents. ARMBench contains images, videos, and metadata that corresponds to 235K+ pick-and-place activities on 190K+ unique objects. The data is captured at different stages of manipulation, i.e., pre-pick, during transfer, and after placement. Benchmark tasks are proposed by virtue of high-quality annotations and baseline performance evaluation are presented on three visual perception challenges, namely 1) object segmentation in clutter, 2) object identification, and 3) defect detection. ARMBench can be accessed at http://armbench.com

Hyperparameter Optimization (HPO) is crucial to develop well-performing machine learning models. In order to ease prototyping and benchmarking of HPO methods, we propose carps, a benchmark framework for Comprehensive Automated Research Performance Studies allowing to evaluate N optimizers on M benchmark tasks. In this first release of carps, we focus on the four most important types of HPO task types: blackbox, multi-fidelity, multi-objective and multi-fidelity-multi-objective. With 3 336 tasks from 5 community benchmark collections and 28 variants of 9 optimizer families, we offer the biggest go-to library to date to evaluate and compare HPO methods. The carps framework relies on a purpose-built, lightweight interface, gluing together optimizers and benchmark tasks. It also features an analysis pipeline, facilitating the evaluation of optimizers on benchmarks. However, navigating a huge number of tasks while developing and comparing methods can be computationally infeasible. To address this, we obtain a subset of representative tasks by minimizing the star discrepancy of the subset, in the space spanned by the full set. As a result, we propose an initial subset of 10 to 30 diverse tasks for each task type, and include functionality to re-compute subsets as more benchmarks become available, enabling efficient evaluations. We also establish a first set of baseline results on these tasks as a measure for future comparisons. With carps (https://www.github.com/automl/CARP-S), we make an important step in the standardization of HPO evaluation.

High-quality benchmarks are the foundation for embodied AI research, enabling significant advancements in long-horizon navigation, manipulation and rearrangement tasks. However, as frontier tasks in robotics get more advanced, they require faster simulation speed, more intricate test environments, and larger demonstration datasets. To this end, we present MS-HAB, a holistic benchmark for low-level manipulation and in-home object rearrangement. First, we provide a GPU-accelerated implementation of the Home Assistant Benchmark (HAB). We support realistic low-level control and achieve over 3x the speed of previous magical grasp implementations at similar GPU memory usage. Second, we train extensive reinforcement learning (RL) and imitation learning (IL) baselines for future work to compare against. Finally, we develop a rule-based trajectory filtering system to sample specific demonstrations from our RL policies which match predefined criteria for robot behavior and safety. Combining demonstration filtering with our fast environments enables efficient, controlled data generation at scale.

Training web agents to navigate complex, real-world websites requires them to master subtasks - short-horizon interactions on multiple UI components (e.g., choosing the correct date in a date picker, or scrolling in a container to extract information). We introduce WARC-Bench (Web Archive Benchmark), a novel web navigation benchmark featuring 438 tasks designed to evaluate multimodal AI agents on subtasks. WARC-Bench enables sandboxed interactions with dynamic and realistic webpages using Web ARChive files. We show that WARC-Bench is challenging for leading computer-use models, with the highest observed success rate being 64.8%. To improve open source models on subtask, we explore two common training techniques: supervised fine-tuning (SFT) and reinforcement learning with verifiable rewards (RLVR). Experiments show that SFT models obtain a 48.8% success rate on the benchmark. Training with RLVR over SFT checkpoints, even in data-scarce settings, improves the score to 52.8% on WARC-Bench, outperforming many frontier models. Our analysis concludes that mastering these subtasks is essential for robust web planning and navigation, and is a capability not extensively evaluated by existing benchmarks.

Mobile GUI agents powered by large language models have progressed rapidly, creating urgent needs for realistic and comprehensive evaluation. Existing benchmarks prioritize reproducibility but are often limited to open-source apps or file-operation tasks for the difficulty of constructing rewards on real applications, leaving a gap between benchmark settings and real-world usage. Moreover, most benchmarks focus on basic grounding and navigation, with limited coverage of complex, long-horizon interactions. To address these limitations, we introduce SimuWoB, a fully synthetic benchmark for mobile GUI agents with 120 challenging tasks spanning diverse types and difficulty levels. We build a robust virtual environment generation framework that synthesizes high-fidelity tasks and environments, and automatically provides valid rewards for each task. Each environment is deployed as a backend-free webpage accessible via URL, enabling efficient and reproducible evaluation. We conduct comprehensive experiments on several state-of-the-art mobile GUI agents. The average success rate is only 27.92%, dropping to 17.82% on long-horizon tasks, which reveals substantial weaknesses in current agents under complex scenarios. Evaluation result comparison with real-world sample tasks demonstrate that agent assessments based on our synthetic environment generalize well. We further provide diagnostic insights across key capability dimensions and discuss implications for future mobile GUI agent development.

Motivation: The development of novel compounds targeting proteins of interest is one of the most important tasks in the pharmaceutical industry. Deep generative models have been applied to targeted molecular design and have shown promising results. Recently, target-specific molecule generation has been viewed as a translation between the protein language and the chemical language. However, such a model is limited by the availability of interacting protein-ligand pairs. On the other hand, large amounts of unlabeled protein sequences and chemical compounds are available and have been used to train language models that learn useful representations. In this study, we propose exploiting pretrained biochemical language models to initialize (i.e. warm start) targeted molecule generation models. We investigate two warm start strategies: (i) a one-stage strategy where the initialized model is trained on targeted molecule generation (ii) a two-stage strategy containing a pre-finetuning on molecular generation followed by target specific training. We also compare two decoding strategies to generate compounds: beam search and sampling. Results: The results show that the warm-started models perform better than a baseline model trained from scratch. The two proposed warm-start strategies achieve similar results to each other with respect to widely used metrics from benchmarks. However, docking evaluation of the generated compounds for a number of novel proteins suggests that the one-stage strategy generalizes better than the two-stage strategy. Additionally, we observe that beam search outperforms sampling in both docking evaluation and benchmark metrics for assessing compound quality. Availability and implementation: The source code is available at https://github.com/boun-tabi/biochemical-lms-for-drug-design and the materials are archived in Zenodo at https://doi.org/10.5281/zenodo.6832145

Existing benchmarks for hardware design primarily evaluate Large Language Models (LLMs) on isolated, component-level tasks such as generating HDL modules from specifications, leaving repository-scale evaluation unaddressed. We introduce HWE-Bench, the first large-scale, repository-level benchmark for evaluating LLM agents on real-world hardware bug repair tasks. HWE-Bench comprises 417 task instances derived from real historical bug-fix pull requests across six major open-source projects spanning both Verilog/SystemVerilog and Chisel, covering RISC-V cores, SoCs, and security roots-of-trust. Each task is grounded in a fully containerized environment where the agent must resolve a real bug report, with correctness validated through the project's native simulation and regression flows. The benchmark is built through a largely automated pipeline that enables efficient expansion to new repositories. We evaluate seven LLMs with four agent frameworks and find that the best agent resolves 70.7% of tasks overall, with performance exceeding 90% on smaller cores but dropping below 65% on complex SoC-level projects. We observe larger performance gaps across models than commonly reported on software benchmarks, and difficulty is driven by project scope and bug-type distribution rather than code size alone. Our failure analysis traces agent failures to three stages of the debugging process: fault localization, hardware-semantic reasoning, and cross-artifact coordination across RTL, configuration, and verification components, providing concrete directions for developing more capable hardware-aware agents.

As on-device LLM agents evolve into personal copilots, the mobile operating system has become a key testbed for this paradigm, making rigorous capability evaluation essential. Yet existing benchmarks fall into two camps, each with a critical blind spot: GUI-centric benchmarks test surface-level screen manipulation while overlooking background tool use and long-horizon planning, whereas static function-calling benchmarks rely on offline API matching that is detached from real runtime constraints. To close this gap, we present MobilePA-Bench, an interactive, stateful, and tool-centric benchmark for evaluating the tool-calling and planning abilities of mobile planning agents. MobilePA-Bench runs on an executable sandbox that maintains live application databases and returns structured feedback, spanning 13 functional domains and 212 realistic mobile tools. Beyond basic tool use, it evaluates a central planning agent along three advanced dimensions: (1)~Sub-agent Collaboration---decomposing a complex task and delegating specialized work to capable sub-agents; (2)~Memory Usage---recalling stored memories, user profiles, and past preferences to resolve implicit requests; and (3)~Skill Usage---invoking pre-packaged composite skills instead of planning every step from scratch. Extensive experiments show that current frontier LLMs remain unreliable in mobile settings: performance drops sharply under strict tool ordering, permission limits, and unexpected runtime errors. By pairing an interactive function-calling sandbox with evidence-based verification, MobilePA-Bench serves as both a practical diagnostic benchmark and an interactive foundation for agentic reinforcement learning---accelerating the development of dependable mobile agents.

Deep research requires models to retrieve, connect, and synthesize evidence from large-scale heterogeneous sources to answer complex queries and produce analytical reports. Existing benchmarks mainly evaluate final outcomes, such as answer correctness, report quality, or citation alignment, while providing limited visibility into whether evidence is correctly selected, linked, and aggregated into supported claims and conclusions. To address this gap, we introduce HiEviDR-Bench, a benchmark for evaluating Hierarchical Evidence Aggregation in Deep Research. HiEviDR-Bench covers open-domain and academic-domain settings under both text-only and multimodal conditions, and represents each instance with an explicit evidence graph that captures evidence selection, cross-source linking, and aggregation from evidence to intermediate claims and final conclusions. Based on this formulation, we develop a traceability-oriented evaluation framework with five dimensions: report quality, evidence traceability, citation accuracy, claim verification, and answer correctness, together with a progressive gating mechanism for fine-grained error localization. HiEviDR-Bench contains 2,000 human-validated questions with evidence graphs across multiple difficulty levels. Experiments on 16 representative multimodal large language models show that, although many systems achieve strong report quality, their performance drops markedly on citation accuracy, claim construction, and answer correctness. Further analysis shows that the main bottlenecks lie in evidence identification and intermediate claim construction, revealing that strong surface-level report quality does not necessarily imply grounded multi-stage reasoning on our benchmark.

We introduce a comprehensive framework for modeling single cell transcriptomic responses to perturbations, aimed at standardizing benchmarking in this rapidly evolving field. Our approach includes a modular and user-friendly model development and evaluation platform, a collection of diverse perturbational datasets, and a set of metrics designed to fairly compare models and dissect their performance. Through extensive evaluation of both published and baseline models across diverse datasets, we highlight the limitations of widely used models, such as mode collapse. We also demonstrate the importance of rank metrics which complement traditional model fit measures, such as RMSE, for validating model effectiveness. Notably, our results show that while no single model architecture clearly outperforms others, simpler architectures are generally competitive and scale well with larger datasets. Overall, this benchmarking exercise sets new standards for model evaluation, supports robust model development, and furthers the use of these models to simulate genetic and chemical screens for therapeutic discovery.

In Machine Learning, a benchmark refers to an ensemble of datasets associated with one or multiple metrics together with a way to aggregate different systems performances. They are instrumental in (i) assessing the progress of new methods along different axes and (ii) selecting the best systems for practical use. This is particularly the case for NLP with the development of large pre-trained models (e.g. GPT, BERT) that are expected to generalize well on a variety of tasks. While the community mainly focused on developing new datasets and metrics, there has been little interest in the aggregation procedure, which is often reduced to a simple average over various performance measures. However, this procedure can be problematic when the metrics are on a different scale, which may lead to spurious conclusions. This paper proposes a new procedure to rank systems based on their performance across different tasks. Motivated by the social choice theory, the final system ordering is obtained through aggregating the rankings induced by each task and is theoretically grounded. We conduct extensive numerical experiments (on over 270k scores) to assess the soundness of our approach both on synthetic and real scores (e.g. GLUE, EXTREM, SEVAL, TAC, FLICKR). In particular, we show that our method yields different conclusions on state-of-the-art systems than the mean-aggregation procedure while being both more reliable and robust.

Large pre-trained language models have shown promise for few-shot learning, completing text-based tasks given only a few task-specific examples. Will models soon solve classification tasks that have so far been reserved for human research assistants? Existing benchmarks are not designed to measure progress in applied settings, and so don't directly answer this question. The RAFT benchmark (Real-world Annotated Few-shot Tasks) focuses on naturally occurring tasks and uses an evaluation setup that mirrors deployment. Baseline evaluations on RAFT reveal areas current techniques struggle with: reasoning over long texts and tasks with many classes. Human baselines show that some classification tasks are difficult for non-expert humans, reflecting that real-world value sometimes depends on domain expertise. Yet even non-expert human baseline F1 scores exceed GPT-3 by an average of 0.11. The RAFT datasets and leaderboard will track which model improvements translate into real-world benefits at https://raft.elicit.org .

Artificial intelligence holds immense promise for transforming biology, yet a lack of standardized, cross domain, benchmarks undermines our ability to build robust, trustworthy models. Here, we present insights from a recent workshop that convened machine learning and computational biology experts across imaging, transcriptomics, proteomics, and genomics to tackle this gap. We identify major technical and systemic bottlenecks such as data heterogeneity and noise, reproducibility challenges, biases, and the fragmented ecosystem of publicly available resources and propose a set of recommendations for building benchmarking frameworks that can efficiently compare ML models of biological systems across tasks and data modalities. By promoting high quality data curation, standardized tooling, comprehensive evaluation metrics, and open, collaborative platforms, we aim to accelerate the development of robust benchmarks for AI driven Virtual Cells. These benchmarks are crucial for ensuring rigor, reproducibility, and biological relevance, and will ultimately advance the field toward integrated models that drive new discoveries, therapeutic insights, and a deeper understanding of cellular systems.

Computer-use agents ground natural-language instructions in screenshots to locate interface elements, yet existing benchmarks do not isolate whether models bind relational language to the correct element. We introduce GUI-Primitives, a 994-item benchmark of contrastive instruction pairs over seven spatial relations in graphical user interfaces (left/right, above/below, containment, alignment, proximity, list ordinal, occlusion). Each pair holds the screenshot and anchor fixed while changing the relation expression, so the correct target moves between two designated candidates. Five annotators validate a 196-item subset (κ= 0.94 well-formedness; κ= 0.79 target selection). Nineteen vision-language models reach at most 32% strict point-in-box accuracy. Because models emit unconstrained coordinates, we classify each prediction by the candidate region it falls within. Predictions fall outside both candidates on 60-92% of items. Conditional on falling within a candidate region, target selection reaches 0.82-0.90 for horizontal position, vertical position, proximity, and list ordinal, but does not differ significantly from 0.50 for containment and occlusion: most failures reflect candidate localization rather than relation understanding. Across ten models, benchmark accuracy correlates with ScreenSpot-Pro accuracy (Spearman ρ= +0.74), an exploratory association at this sample size. Marking the two designated candidates raises selection accuracy by 35--57 percentage points, an oracle diagnostic that supplies the candidate set rather than a deployable method. We release the benchmark, predictions, and code.

Patent retrieval underpins critical decisions in innovation, examination, and IP strategy, yet progress has been hampered by the absence of benchmarks that reflect the diversity of real world search scenarios. We address this gap with two contributions. First, we introduce Sophiabench, a large-scale patent retrieval benchmark comprising 10,000 queries and 75,000 corpus documents stratified across ten years, eight IPC technology sections, and twelve filing jurisdictions. Unlike prior benchmarks, Sophia-bench tests retrieval using 12 different query types-from structured patent fields to AI-generated summaries-and evaluates results against citation-based ground truth enhanced with a novel domain-relevance metric (InScope). Together, these enable systematic measurement of how well models perform across query types, technology domains, and jurisdictions. Second, we introduce QaECTER, a 344M-parameter embedding model trained on patent citation graphs and multi-view self-alignment. Despite its compact size, QaECTER establishes a new state of the art for patent retrieval. It outperforms the \#1 model on the English retrieval text embedding benchmark (RTEB), a model 23x larger, as well as all existing patent specific models across every query type, IPC section, and jurisdiction on Sophia-bench, with gains of up to 7.2% average NDCG@10 over the next-best model. These results are confirmed on an independent external benchmark, where QaECTER surpasses all prior models without requiring task-specific instruction prompts. Both the benchmark and the model are designed for practical deployment in large-scale patent search systems.

With the rapid spread of retrieval-augmented generation and semantic search, choosing the right embedding and retrieval configuration is increasingly hard. Large retrieval benchmarks are comprehensive but too heavy to rerun during development, and there is little infrastructure for comparing production settings--dimensionality reduction, quantization, reranking--across many models under identical conditions. We present HAKARI-Bench, a lightweight benchmark that reconstructs existing retrieval suites into small datasets (Nano-sets): 35 benchmarks and 551 tasks across 43 languages in a unified format, enabling same-condition, model-agnostic comparison of five retrieval families (BM25, dense, sparse, late interaction, rerankers) and their efficiency variants. Across 55 models, its overall ranking reproduces the official MTEB retrieval v2, MMTEB v2 retrieval, and English BEIR (full) at Spearman >0.97. HAKARI-Bench does not replace full evaluation; it enables rapid model selection, regression detection, and reading the quality-efficiency Pareto frontier. Code, data, and leaderboard are released under the MIT license.

Spreadsheets are widely used for business analysis, financial modeling, reporting, and decision-making. However, most existing spreadsheet benchmarks evaluate isolated operations such as single-formula generation or local cell edits, and therefore fail to capture end-to-end workflows in realistic business settings. We introduce SpreadsheetBench 2, a workflow-level benchmark for spreadsheet agents that covers three task categories: generation, debugging, and visualization. The benchmark is constructed from authentic business data, including financial reports and corporate filings, and is annotated and validated by domain experts. The benchmark contains 321 tasks; each instance averages 11.8 worksheets and requires 593.5 cell modifications, reflecting large multi-sheet workbooks with cross-sheet dependencies. We evaluate eight frontier large language models under a unified multi-turn agent scaffold, and additionally include several LLM-based spreadsheet products as complementary baselines. Results show that current systems remain far from reliable on real-world workflows: the best model achieves 34.89\% overall task accuracy, and debugging accuracy is as low as 12.00\%. Trajectory analysis and a failure taxonomy further indicate that insufficient spreadsheet inspection and incorrect target-cell selection are the dominant bottlenecks. Together, these findings position SpreadsheetBench 2 as a challenging testbed for advancing reliable spreadsheet automation. Project page: https://spreadsheetbench.github.io/

Large language model (LLM) assistants are being deployed to clinicians across health systems, and judgments about their readiness rest largely on benchmark scores, most of them derived from examination questions or curated cases. A benchmark predicts performance in deployment only to the extent that its items resemble real use, yet whether benchmarks reflect the work these systems receive has rarely been measured. Here we analyze 127,833 queries sent by 6,342 physicians, advanced practice providers and nurses in 35 specialties to an institutional assistant during an eight-month roll-out. We characterize each query with RCQ-Map, a clinician-validated framework grounded in taxonomies of clinical questions and of LLM evaluation, which records its task, intent, answerability, missing information and potential harm. Documentation and administration (36.2%) and knowledge retrieval (28.9%) made up nearly two-thirds of use, and diagnosis 3.7%; more than a third of queries could not be answered well as posed. Applying RCQ-Map to 58 public benchmarks drawn from major evaluation suites and frontier model reports, which we assemble into the Clinical AI Benchmark Atlas, showed that the median benchmark contained no documentation requests and shared 31% of the task mix of real use, less than an even spread across task categories would. Benchmarks in suites designed to resemble clinical practice were individually no closer to real use than those used in frontier model reports. Benchmark scores therefore say little about how clinical AI performs on most of the work it is actually given, and evaluation should be matched to real clinical use.

Vericoding refers to the generation of formally verified code from rigorous specifications. Recent AI models show promise in vericoding, but a unified methodology for cross-paradigm evaluation is lacking. Existing benchmarks test only individual languages/tools (e.g., Dafny, Verus, and Lean) and each covers very different tasks, so the performance numbers are not directly comparable. We address this gap with AlgoVeri, a benchmark that evaluates vericoding of 77 classical algorithms in Dafny, Verus, and Lean. By enforcing identical functional contracts, AlgoVeri reveals critical capability gaps in verification systems. While frontier models achieve tractable success in Dafny (40.3% for Gemini-3 Flash), where high-level abstractions and SMT automation simplify the workflow, performance collapses under the systems-level memory constraints of Verus (24.7%) and the explicit proof construction required by Lean (7.8%). Beyond aggregate metrics, we uncover a sharp divergence in test-time compute dynamics: Gemini-3 effectively utilizes iterative repair to boost performance (e.g., tripling pass rates in Dafny), whereas GPT-OSS saturates early. Finally, our error analysis shows that language design affects the refinement trajectory: while Dafny allows models to focus on logical correctness, Verus and Lean trap models in persistent syntactic and semantic barriers. All data and evaluation code can be found at https://github.com/haoyuzhao123/algoveri.

Open-source benchmark datasets have been a critical component for advancing machine learning for robot perception in terrestrial applications. Benchmark datasets enable the widespread development of state-of-the-art machine learning methods, which require large datasets for training, validation, and thorough comparison to competing approaches. Underwater environments impose several operational challenges that hinder efforts to collect large benchmark datasets for marine robot perception. Furthermore, a low abundance of targets of interest relative to the size of the search space leads to increased time and cost required to collect useful datasets for a specific task. As a result, there is limited availability of labeled benchmark datasets for underwater applications. We present the AI4Shipwrecks dataset, which consists of 24 distinct shipwreck sites totaling 286 high-resolution labeled side scan sonar images to advance the state-of-the-art in autonomous sonar image understanding. We leverage the unique abundance of targets in Thunder Bay National Marine Sanctuary in Lake Huron, MI, to collect and compile a sonar imagery benchmark dataset through surveys with an autonomous underwater vehicle (AUV). We consulted with expert marine archaeologists for the labeling of robotically gathered data. We then leverage this dataset to perform benchmark experiments for comparison of state-of-the-art supervised segmentation methods, and we present insights on opportunities and open challenges for the field. The dataset and benchmarking tools will be released as an open-source benchmark dataset to spur innovation in machine learning for Great Lakes and ocean exploration. The dataset and accompanying software are available at https://umfieldrobotics.github.io/ai4shipwrecks/.

We introduce a benchmark to evaluate the capability of AI to solve problems in theoretical physics, focusing on high-energy theory and cosmology. The first iteration of our benchmark consists of 57 problems of varying difficulty, from undergraduate to research level. These problems are novel in the sense that they do not come from public problem collections. We evaluate our data set on various open and closed language models, including o3-mini, o1, DeepSeek-R1, GPT-4o and versions of Llama and Qwen. While we find impressive progress in model performance with the most recent models, our research-level difficulty problems are mostly unsolved. We address challenges of auto-verifiability and grading, and discuss common failure modes. While currently state-of-the art models are still of limited use for researchers, our results show that AI assisted theoretical physics research may become possible in the near future. We discuss the main obstacles towards this goal and possible strategies to overcome them. The public problems and solutions, results for various models, and updates to the data set and score distribution, are available on the website of the dataset tpbench.org.

Scientific discovery begins where known problems end. There, AI systems must engage in exploration: framing hypotheses, designing experiments, and iterating on the results. However, evaluating this ability is difficult: (1) how to verify whether a genuinely new hypothesis holds, and (2) how to determine whether a system has discovered it through exploration or merely recalled related knowledge from pre-training data. To this end, we introduce ExplorationBench, which turns the wicked problem of evaluating scientific exploration into a concrete and tractable framework built on verifiable Alien Worlds: their rules are executable, so every answer can be checked exactly, and they conflict with familiar knowledge, so recall alone cannot solve the tasks. The benchmark contains two sandboxes, AlienCode (31 discovery targets, 70 tasks) and AlienLogic (24 discovery targets, 70 tasks). Each sandbox provides a flawed manual, task-specific environmental feedback, and a dedicated tool-call schema. Systems use these resources to explore the sandbox, then solve held-out tasks. We evaluate 10 AI systems and find that the strongest systems can acquire and apply unfamiliar rules, while performance varies substantially across trajectories and continued exploration can stall or reverse earlier gains. ExplorationBench represents a step towards AI systems that can acquire and apply genuinely new knowledge through exploration in unknown environments.

Lack of rigorous reproducibility and validation are major hurdles for scientific development across many fields. Materials science in particular encompasses a variety of experimental and theoretical approaches that require careful benchmarking. Leaderboard efforts have been developed previously to mitigate these issues. However, a comprehensive comparison and benchmarking on an integrated platform with multiple data modalities with both perfect and defect materials data is still lacking. This work introduces JARVIS-Leaderboard, an open-source and community-driven platform that facilitates benchmarking and enhances reproducibility. The platform allows users to set up benchmarks with custom tasks and enables contributions in the form of dataset, code, and meta-data submissions. We cover the following materials design categories: Artificial Intelligence (AI), Electronic Structure (ES), Force-fields (FF), Quantum Computation (QC) and Experiments (EXP). For AI, we cover several types of input data, including atomic structures, atomistic images, spectra, and text. For ES, we consider multiple ES approaches, software packages, pseudopotentials, materials, and properties, comparing results to experiment. For FF, we compare multiple approaches for material property predictions. For QC, we benchmark Hamiltonian simulations using various quantum algorithms and circuits. Finally, for experiments, we use the inter-laboratory approach to establish benchmarks. There are 1281 contributions to 274 benchmarks using 152 methods with more than 8 million data-points, and the leaderboard is continuously expanding. The JARVIS-Leaderboard is available at the website: https://pages.nist.gov/jarvis_leaderboard

A benchmark score means nothing without knowing what a trivial method achieves and what the best possible method could achieve. We construct both bounds for a task with a rare kind of ground truth: predicting which sentences a crowd of readers -- highlighting for their own purposes, unpaid, uninstructed, and blind to each other -- marked in 120 web documents. The floor is naive truncation (lead); the ceiling is a split-half oracle: half the crowd predicting the other half. The gap between them is +0.2028 AP [+0.1698, +0.2342, domain-clustered], and three findings structure it. First, the gap is semantic: position and length features recover 5% of it. Second, frontier language models reach 35-53% of it zero-shot -- far above classical baselines, far below the crowd; a state-of-the-art prompt compressor (LLMLingua-2) lands below the floor, indistinguishable from random selection. Third, an unweighted cross-vendor fusion of five frontier rankings plus a position prior reaches 60%, beating the best single model by +0.0159 [+0.0044, +0.0269; Holm p=0.019] -- a gain that survives ablation of its best member, split-half arm selection, prompt paraphrase, and label, gate, and seed perturbations, and was CONFIRMED by a pre-registered replication on 217 independent documents (+0.0179, Holm p=0.042). Finally, the bracket compresses: distilling the fusion into one open-weight 8B student that reads the whole document retains 90% of the fusion's edge and reaches statistical parity with the strongest single frontier model (+0.0070 [-0.0068, +0.0200]), where a local-context student retains only 63% -- the crowd's signal lives in document-level structure, and the cheapest known improvement is to ask several different models and average.

As AI coding agents take on increasingly complex, long-horizon software engineering tasks, existing benchmarks are rapidly saturating and their evaluation quality has come under serious scrutiny: a recent audit found that nearly 60% of unsolved SWE-bench Verified instances contain flawed tests -- either overly narrow tests that reject correct solutions or overly broad tests that check unstated requirements -- and that frontier models can verbatim reproduce gold patches from training data. Code refactoring, which requires coordinated, behavior-preserving changes across many files, offers a substantially harder and more realistic test of agent capability, yet remains underserved by current benchmarks. We introduce SWE-Bench ProMax, an expert-curated, multilingual code refactoring benchmark of 170 instances drawn from real commits across seven programming languages (Python, Java, TypeScript, Go, C, C++, and Rust). Every instance undergoes rigorous, multi-stage curation that directly addresses the quality problems identified in prior benchmarks: issue descriptions are rewritten from scratch to provide precise, unambiguous specifications, and test suites are manually reviewed to remove overly narrow and overly broad tests. Tasks with insufficient complexity or limited cross-file scope are filtered out, yielding a benchmark of challenging, large-scale refactoring tasks that average 11.4 modified files and 261.6 lines of code per instance, substantially exceeding the scale of existing benchmarks. Experiments with frontier models under two agent scaffolds show that the best model achieves only 41.2% resolve rate, confirming that SWE-Bench ProMax presents a meaningful and unsaturated challenge for current AI coding agents. Our benchmark is available at https://huggingface.co/datasets/swe-bench-promax/SWE-Bench-ProMax.

AI models are increasingly prevalent in high-stakes environments, necessitating thorough assessment of their capabilities and risks. Benchmarks are popular for measuring these attributes and for comparing model performance, tracking progress, and identifying weaknesses in foundation and non-foundation models. They can inform model selection for downstream tasks and influence policy initiatives. However, not all benchmarks are the same: their quality depends on their design and usability. In this paper, we develop an assessment framework considering 46 best practices across an AI benchmark's lifecycle and evaluate 24 AI benchmarks against it. We find that there exist large quality differences and that commonly used benchmarks suffer from significant issues. We further find that most benchmarks do not report statistical significance of their results nor allow for their results to be easily replicated. To support benchmark developers in aligning with best practices, we provide a checklist for minimum quality assurance based on our assessment. We also develop a living repository of benchmark assessments to support benchmark comparability, accessible at betterbench.stanford.edu.

This study presents a novel benchmark for evaluating Large Language Models (LLMs) using challenges derived from the Financial Modeling World Cup (FMWC) Excel competitions. We introduce a methodology for converting 113 existing FMWC challenges into programmatically evaluable JSON formats and use this dataset to compare the performance of several leading LLMs. Our findings demonstrate significant variations in performance across different challenge categories, with models showing specific strengths in pattern recognition tasks but struggling with complex numerical reasoning. The benchmark provides a standardized framework for assessing LLM capabilities in realistic business-oriented tasks rather than abstract academic problems. This research contributes to the growing field of AI benchmarking by establishing proficiency among the 1.5 billion people who daily use Microsoft Excel as a meaningful evaluation metric that bridges the gap between academic AI benchmarks and practical business applications.

With the deep integration of artificial intelligence and interactive technology, Graphical User Interface (GUI) Agent, as the carrier connecting goal-oriented natural language and real-world devices, has received widespread attention from the community. Contemporary benchmarks aim to evaluate the comprehensive capabilities of GUI agents in GUI operation tasks, generally determining task completion solely by inspecting the final screen state. However, GUI operation tasks consist of multiple chained steps while not all critical information is presented in the final few pages. Although a few research has begun to incorporate intermediate steps into evaluation, accurately and automatically capturing this process information still remains an open challenge. To address this weakness, we introduce ProBench, a comprehensive mobile benchmark with over 200 challenging GUI tasks covering widely-used scenarios. Remaining the traditional State-related Task evaluation, we extend our dataset to include Process-related Task and design a specialized evaluation method. A newly introduced Process Provider automatically supplies accurate process information, enabling presice assessment of agent's performance. Our evaluation of advanced GUI agents reveals significant limitations for real-world GUI scenarios. These shortcomings are prevalent across diverse models, including both large-scale generalist models and smaller, GUI-specific models. A detailed error analysis further exposes several universal problems, outlining concrete directions for future improvements.

Identifying drug-target interactions is essential for developing effective therapeutics. Binding affinity quantifies these interactions, and traditional approaches rely on computationally intensive 3D structural data. In contrast, language models can efficiently process sequential data, offering an alternative approach to molecular representation. In the current study, we introduce BAPULM, an innovative sequence-based framework that leverages the chemical latent representations of proteins via ProtT5-XL-U50 and ligands through MolFormer, eliminating reliance on complex 3D configurations. Our approach was validated extensively on benchmark datasets, achieving scoring power (R) values of 0.925 pm 0.043, 0.914 pm 0.004, and 0.8132 pm 0.001 on benchmark1k2101, Test2016_290, and CSAR-HiQ_36, respectively. These findings indicate the robustness and accuracy of BAPULM across diverse datasets and underscore the potential of sequence-based models in-silico drug discovery, offering a scalable alternative to 3D-centric methods for screening potential ligands.

Deep-Research agents, which integrate large language models (LLMs) with search tools, have shown success in improving the effectiveness of handling complex queries that require iterative search planning and reasoning over search results. Evaluations on current benchmarks like BrowseComp relies on black-box live web search APIs, have notable limitations in (1) fairness: dynamic and opaque web APIs hinder fair comparisons and reproducibility of deep research methods; (2) transparency: lack of control over the document corpus makes it difficult to isolate retriever contributions. In other words, the current evaluations may compare a complete deep research system at a given time, but they do not foster well-controlled experiments to provide insights into the capability of underlying deep research LLMs. To address these challenges, we introduce BrowseComp-Plus, a benchmark derived from BrowseComp, employing a fixed, carefully curated corpus. Each query in BrowseComp-Plus includes human-verified supporting documents and mined challenging negatives, enabling controlled experimentation. The benchmark is shown to be effective in distinguishing the performance of deep research systems. For instance, the open-source model Search-R1, when paired with the BM25 retriever, achieves 3.86% accuracy, whereas the GPT-5 achieves 55.9%. Integrating the GPT-5 with the Qwen3-Embedding-8B retriever further enhances its accuracy to 70.1% with fewer search calls. This benchmark allows comprehensive evaluation and disentangled analysis of deep research agents and retrieval methods, fostering insights into retrieval effectiveness, citation accuracy, and context engineering in Deep-Research system.

Deep research benchmarks require expert-level tasks and reliable evaluation grounded in task-specific knowledge. Existing benchmarks rely heavily on expert authoring or pre-existing human-authored materials, while fully automatic construction struggles to ensure consistent and traceable verification. To address this gap, we introduce a verifiable benchmark of 500 deep research tasks spanning 31 topics and 10 major categories, with three query forms designed to probe complementary capabilities required for deep research. The benchmark is constructed automatically using an iterative Explorer-Formalizer-Challenger pipeline that progressively transforms simple questions into deep research tasks. Each task is represented as a directed acyclic graph (DAG) of atomic steps and associated checkpoints, enabling the query, DAG, and rubrics to evolve together in a controlled manner. Experiments demonstrate that the benchmark clearly discriminates among models and query types, while its fact-grounded pointwise rubrics enable fine-grained, human-aligned, and stable evaluation. Our data, implementation, and results are publicly available.

Agent benchmarks often evaluate only final answers even when agents run on stateful runtimes. We argue this under-specifies what is being evaluated: the proper unit is a declared model-plus-runtime configuration whose failures can occur in evidence acquisition, runtime routing, safety boundaries, or repeated execution. We present ClawProBench, a trace-aware benchmark for runtime-native agent evaluation instantiated on OpenClaw, a live agent runtime with workspace tools and native surfaces for browsing, memory, messaging, scheduling, skills, and subagents. ClawProBench defines two tracks: a 102-scenario full profile with live workspace and native-runtime routing tasks, and a frozen 68-scenario holdout with closed-world JSON output contracts for robust ranking. Trials are scored from execution traces via a safety-gated formula combining correctness, process quality, and efficiency, preserving failure evidence for audit. Our anonymous artifact includes benchmark definitions, scoring code, manifests and sanitized traces. We evaluate 68 configurations on the full profile and 37 on holdout. The top safety-gated average trace score is 0.7671. Native-runtime tasks underperform workspace-live tasks (0.5238 vs. 0.6415). On holdout, pass@k-any outperforms strict three-trial pass (0.6638 vs. 0.2890), while full-profile and holdout rankings show weak alignment (Spearman 0.1300). Rankings based purely on correctness differ substantially from process-aware, safety-gated and strict-pass views. Final-answer leaderboards may hide native-surface weaknesses, one-off successes and trace-local agent failure modes.

Time series captioning, the task of describing numeric time series in natural language, requires numerical reasoning, trend interpretation, and contextual understanding. Existing benchmarks, however, often rely on synthetic data or overly simplistic captions, and typically neglect metadata and visual representations. To close this gap, we introduce CaTS-Bench, the first large-scale, real-world benchmark for Context-aware Time Series captioning. CaTS-Bench is derived from 11 diverse datasets reframed as captioning and Q&A tasks, comprising roughly 465k training and 105k test timestamps. Each sample includes a numeric series segment, contextual metadata, a line-chart image, and a caption. A key contribution of this work is the scalable pipeline used to generate reference captions: while most references are produced by an oracle LLM and verified through factual checks, human indistinguishability studies, and diversity analyses, we also provide a human-revisited subset of 579 test captions, refined from LLM outputs to ensure accuracy and human-like style. Beyond captioning, CaTS-Bench offers 460 multiple-choice questions targeting deeper aspects of time series reasoning. We further propose new tailored evaluation metrics and benchmark leading VLMs, highlighting both their strengths and persistent limitations. Together, these contributions establish CaTS-Bench and its captioning pipeline as a reliable and extensible foundation for future research at the intersection of time series analysis and foundation models.

The needle-in-a-haystack (NIAH) benchmark was introduced as a test for measuring a model's ability to find small relevant facts within a very large body of input text. However, existing NIAH benchmarks each suffer from one or more of the following limitations: (1) reliance on synthetic data, so their evaluations may not generalize to real-world settings; (2) reuse of previously published datasets, leading to the risk of benchmark contamination; (3) dependence on manual annotation, which requires human effort to create and update data and is prone to future benchmark contamination; and (4) unrealistic simplification of long-context multi-hop reasoning where each next step is trivial given previous steps, while real-world reasoning often requires planning over multiple possible proof paths. To address these limitations, we introduce \Benchmark, a dynamic benchmark built from real citation relationships among scientific papers published after the evaluated models' knowledge cutoff date, which utilizes real-world information while ensuring no benchmark contamination. The fully automated benchmark construction pipeline samples representative subgraphs of the citation graph formed by these papers and converts each subgraph into a long-context QA example with a verifiable answer. We use GraphNIAH to evaluate eight LLMs from the GPT-5.6, Gemini-3, and Qwen3.5 families. We find that accuracy falls as questions require longer reasoning paths: at question depths of 16 and 32, the GPT-5.6 and Qwen3.5 models answer YES/NO questions no better than random guessing, mostly by answering NO; four of the eight models answer no counting example correctly, and the others model get worse as the subgraph size increases. These findings suggest that current LLMs often stop searching the citation relationships in their context before they reach the answer, even though every fact they need is in the context.

Capturing a loose object inside a spacecraft requires a robot to approach a target that can translate and rotate, and whose motion changes when contact is made. These conditions motivate evaluation beyond manipulation of supported objects. We introduce AstroBench, an open benchmark for free-floating capture and space robotic manipulation with a fixed-base arm. The task suite combines four initial-motion tracks with sample-storage operations based on MELFI hardware and cap and captive-screw servicing based on the Robotic Refueling Mission. The two workcells provide nine task definitions and 29 task-target combinations. A metadata-filtered Objaverse inventory supplies 8,414 object instances for asset expansion, alongside five cabin visual contexts and versioned task instructions. We report two acquisition-focused experiments using existing checkpoints. A frozen π_{0.5} DROID joint-position policy captures 2 of 200 static targets and 4 of 200 moving targets across twenty object identities. A cube-specific ACT policy captures 8 of 10 static targets and 6 of 10 moving targets in a separate experiment. Each experiment retains its recorded observation, action and capture configuration. The results document difficult direct transfer for the tested generalist checkpoint and successful task-specific capture behavior, while identifying concrete settings for studying motion-aware perception and contact-sensitive control. Code, task definitions and editable workcell assets are available at https://github.com/AstroUpLab/AstroBench.

Computer use agents (CUAs) have advanced rapidly in desktop automation, and a growing number of users deploy CUAs such as OpenClaw on Mac Mini for always-on automation. However, existing benchmarks, including those for macOS, evaluate agents without framework augmentation and rely on binary evaluation. As a result, they fail to capture both the framework capabilities leveraged by modern CUAs and the partial progress on long-horizon, multi-application tasks. We present MacAgentBench, a comprehensive macOS agent benchmark comprising 676 tasks across 25 applications, with nearly 60% involving both GUI and CLI interaction. The benchmark adopts deterministic rule-based evaluation and introduces fine-grained multi-checkpoint scoring with capability annotations for multi-application tasks. Experiments across three frameworks and 16 models show that the best configuration, Claude Opus 4.6 on OpenClaw, attains 73.7% Pass@1, while this advantage is primarily driven by the skill library rather than by framework design. Fine-grained metrics further reveal that models with similar Pass@1 can differ substantially in sub-goal completion. Our code and data are publicly available at https://github.com/JetAstra/MacAgentBench.

A modern model release reports scores on 40+ benchmarks and the same evaluations were run many more times before it: to track training progress, compare design choices, and select the checkpoint for the release. But do we need to run every eval? We compile a public score matrix of 84 frontier models on 133 benchmarks (2,604 cells, 23.3% filled) and find it is approximately rank-2: a model's scores across all 133 benchmarks are largely determined by just two numbers. We confirm this in two ways: scores hidden from the matrix are best recovered using two factors, and two factors already explain over 90% of the variation among models on the benchmarks they share. Building on this, we design BenchPress: a logit-space rank-2 matrix completion method that recovers held-out scores to within 4.6 points, and a confidence layer that says when each prediction can be trusted. Using BenchPress, we find a subset of five benchmarks {GPQA-D, HLE, Codeforces, MMLU-Pro, ARC-AGI-1} that can recover the rest of a model's public scorecard to within 3.93 points. For a tighter inference budget, a cheaper set {GPQA-D, MMLU-Pro, Aider Polyglot, MATH-500, AIME 2026} can predict a model's evals to within 4.55. We release the score matrix, the BenchPress code, and an interactive tool that predicts any model's score on any benchmark.

Benchmark researchers and developers of large language models (LLMs) and other AI systems need to find relevant evaluations, locate their benchmark datasets and code, and understand the settings behind reported scores. We present Benchmark Radar, a living database and search engine for retrieval and discovery of AI benchmarks, covering LLM evaluation, agentic and tool-use benchmarks, coding, reasoning, safety, and domain-specific evaluations. The system combines daily discovery of benchmark papers, repositories, datasets, and releases with a searchable benchmark catalog, mentions in model cards and technical reports, and score histories. It retains source identities and citations so readers can inspect candidate benchmarks and their evaluation evidence. Daily discovery draws on 37 sources: 13 direct connectors and 24 first-party research and engineering feeds. The catalog contains 1,283 source records drawn from 4 benchmark catalogs and 12,916 numeric observations on 790 records. We describe collection and retrieval, audit the full catalog, and examine benchmark saturation, adoption trends, and the limits of score comparisons. A worked example walks through a complete prior-art search, showing how to query the catalog and inspect benchmark evidence when designing a new evaluation. We release the web dashboard with a benchmark leaderboard, a Pareto frontier view of score against measured use, saturation and trend views, daily feeds, downloadable evidence, a command-line interface (CLI) for offline queries, and reproducible analysis.

Data-driven molecular discovery leverages artificial intelligence/machine learning (AI/ML) and generative modeling to filter and design novel molecules. Discovering novel molecules requires accurate out-of-distribution (OOD) predictions, but ML models struggle to generalize OOD. Currently, no systematic benchmarks exist for molecular OOD prediction tasks. We present BOOM, benchmarks for out-of-distribution molecular property predictions: a chemically-informed benchmark for OOD performance on common molecular property prediction tasks. We evaluate over 150 model-task combinations to benchmark deep learning models on OOD performance. Overall, we find that no existing model achieves strong generalization across all tasks: even the top-performing model exhibited an average OOD error 3x higher than in-distribution. Current chemical foundation models do not show strong OOD extrapolation, while models with high inductive bias can perform well on OOD tasks with simple, specific properties. We perform extensive ablation experiments, highlighting how data generation, pre-training, hyperparameter optimization, model architecture, and molecular representation impact OOD performance. Developing models with strong OOD generalization is a new frontier challenge in chemical ML. This open-source benchmark is available at https://github.com/FLASK-LLNL/BOOM

Supervised machine learning approaches have been increasingly used in accelerating electronic structure prediction as surrogates of first-principle computational methods, such as density functional theory (DFT). While numerous quantum chemistry datasets focus on chemical properties and atomic forces, the ability to achieve accurate and efficient prediction of the Hamiltonian matrix is highly desired, as it is the most important and fundamental physical quantity that determines the quantum states of physical systems and chemical properties. In this work, we generate a new Quantum Hamiltonian dataset, named as QH9, to provide precise Hamiltonian matrices for 999 or 2998 molecular dynamics trajectories and 130,831 stable molecular geometries, based on the QM9 dataset. By designing benchmark tasks with various molecules, we show that current machine learning models have the capacity to predict Hamiltonian matrices for arbitrary molecules. Both the QH9 dataset and the baseline models are provided to the community through an open-source benchmark, which can be highly valuable for developing machine learning methods and accelerating molecular and materials design for scientific and technological applications. Our benchmark is publicly available at https://github.com/divelab/AIRS/tree/main/OpenDFT/QHBench.

Language-model agents are increasingly used as persistent coworkers that assist users across multiple working days. During such workflows, the surrounding environment may change independently of the agent: new emails arrive, calendar entries shift, knowledge-base records are updated, and evidence appears across images, scanned PDFs, audio, video, and spreadsheets. Existing benchmarks do not adequately evaluate this setting because they typically run within a single static episode and remain largely text-centric. We introduce , a benchmark for coworker agents built around multi-turn multi-day tasks, a stateful sandboxed service environment whose state evolves between turns, and rule-based verification. The current release contains 100 tasks across 13 professional scenarios, executed against five stateful sandboxed services (filesystem, email, calendar, knowledge base, spreadsheet) and scored by 1537 deterministic Python checkers over post-execution service state; no LLM-as-judge is invoked during scoring. We benchmark seven frontier agent systems. The strongest model reaches 75.8 weighted score, but the best strict Task Success is only 20.0\%, indicating that partial progress is common while complete end-to-end workflow completion remains rare. Turn-level analysis shows that performance drops after the first exogenous environment update, highlighting adaptation to changing state as a key open challenge. We release the benchmark, evaluation harness, and construction pipeline to support reproducible coworker-agent evaluation.

We present OPENHARMONY BENCH, an app-level coding benchmark for evaluating LLM-based coding agents on OpenHarmony ArkTS applications. Unlike function-level benchmarks, it evaluates complete app-level changes: each task requires an agent to modify a buildable ArkTS project so that a requested behavior works end to end, involving UI state, data persistence, build configuration, and platform APIs. The benchmark installs and drives the delivered application on a device to check whether the behavior is observable. It covers three input sources: natural-language feature requests (new-feature), structured scenario specifications (spec-driven), and bug descriptions (bug-fix). The benchmark contains 153 top-level tasks and 242 Feature points (F-points), where an F-point is one executable behavior check. The snapshot includes 32 new-feature tasks, 50 spec-driven tasks with 139 F-points, and 71 bug-fix tasks. The main leaderboard is scored over top-level tasks rather than independently weighted F-points. We describe the benchmark construction, statistics, and build-and-test evaluation pipeline, and evaluate DevEco Code with eight LLMs across three independent full-suite runs per configuration. Three findings emerge. First, newer generations complete more tasks than their predecessors within evaluated model-family pairs. Second, buildability is close to saturated while behavioral correctness is not: mean Final Build Success Rate is 94.77% to 100.00%, whereas mean Task Completion is 48.36% to 58.39%. Third, spec-driven tasks have the lowest Task Completion under all-checks task scoring, with no configuration exceeding 35%. The code, data, tasks, reference solutions, tests, evaluation scripts, and leaderboard are released through the official OPENHARMONY BENCH website at https://bench.matrix.openharmony.cn/.

With the rapid advancement of generative artificial intelligence technology, Graphical User Interface (GUI) agents have demonstrated tremendous potential for autonomously managing daily tasks through natural language instructions. However, current evaluation frameworks for GUI agents suffer from fundamental flaws: existing benchmarks overly focus on coarse-grained task completion while neglecting fine-grained control capabilities crucial for real-world applications. To address this, we introduce FineState-Bench, the first evaluation and diagnostic standard for fine-grained GUI proxy operations, designed to quantify fine-grained control. This multi-platform (desktop, Web, mobile) framework includes 2257 task benchmarks in four components and uses a four-phase indicator for comprehensive perception-to-control assessment. To analyze perception and positioning for refined operations, we developed the plug-and-play Visual Diagnostic Assistant (VDA), enabling the first quantitative decoupling analysis of these capabilities. Experimental results on our benchmark show that the most advanced models achieve only 32.8% fine-grained interaction accuracy. Using our VDA in controlled experiments, quantifying the impact of visual capabilities, we showed that ideal visual localization boosts Gemini-2.5-Flash's success rate by 14.9\%. Our diagnostic framework confirms for the first time that the primary bottleneck for current GUI proxies is basic visual positioning capability.All resources are fully open-source. github: https://github.com/AnonymousThewarehouse/FineState-Bench huggingface: https://huggingface.co/datasets/Willtime2006/Static-FineBench

Recent advances in machine learning and large-scale biological data collections have revived the prospect of building a virtual cell, a computational model of cellular behavior that could accelerate biological discovery. One of the most compelling promises of this vision is the ability to perform in silico phenotypic screens, in which a model predicts the effects of cellular perturbations in unseen biological contexts. This task combines heterogeneous textual inputs with diverse phenotypic outputs, making it particularly well-suited to LLMs and agentic systems. Yet, no standard benchmark currently exists for this task, as existing efforts focus on narrower molecular readouts that are only indirectly aligned with the phenotypic endpoints driving many real-world drug discovery workflows. In this work, we present AssayBench, a benchmark for phenotypic screen prediction, built from 1,920 publicly available CRISPR screens spanning five broad classes of cellular phenotypes. We formulate the screen prediction task as a gene rank prediction for each screen and introduce the adjusted nDCG, a continuous metric for comparing performance across heterogeneous assays. Our extensive evaluation shows that existing methods remain far from empirically estimated performance ceilings and zero-shot generalist LLMs outperform biology-specific LLMs and trainable baselines. Optimization techniques such as fine-tuning, ensembling, and prompt optimization can further improve LLM performance on this task. Overall, AssayBench offers a practical testbed for measuring progress toward in silico phenotypic screening and, more broadly, virtual cell models.

Users across enterprises increasingly rely on AI agents to query their data through natural language. However, building reliable data agents remains difficult because real-world data is often fragmented across multiple heterogeneous database systems, with inconsistent references and information buried in unstructured text. Existing benchmarks only tackle individual pieces of this problem -- e.g., translating natural-language questions into SQL queries, answering questions over small tables provided in context -- but do not evaluate the full pipeline of integrating, transforming, and analyzing data across multiple database systems. To fill this gap, we present the Data Agent Benchmark (DAB), grounded in a formative study of enterprise data agent workloads across six industries. DAB comprises 54 queries across 12 datasets, 9 domains, and 4 database management systems. On DAB, the best frontier model (Gemini-3-Pro) achieves only 38% pass@1 accuracy. We benchmark five frontier LLMs, analyze their failure modes, and distill takeaways for future data agent development. Our benchmark and experiment code are published at github.com/ucbepic/DataAgentBench.

As web agents increasingly demonstrate capabilities in automated task execution, the development of robust evaluation frameworks for assessing their navigation and task completion performance has emerged as a critical research priority. However, existing benchmarks exhibit fundamental limitations. First, they suffer from insufficient scale and limited domain diversity, constraining comprehensive evaluation of cross-domain generalization. Second, prevailing LLM-as-Judge evaluation methodologies inadequately capture fine-grained interaction semantics, particularly regarding precise query formulation and filtering operations. Third, current benchmarks predominantly emphasize navigation success metrics while neglecting critical requirements for real-world deployment scenarios. To address these limitations, we introduce WebRetriever, a large-scale benchmark encompassing 800 websites and 1,550 tasks across diverse domains, including consumer, professional, and enterprise sectors, with comprehensive coverage of user intent patterns. We propose NavEval (Navigation Evaluation), a novel LLM-as-Judge framework that leverages rich interaction context beyond visual screenshots, achieving state-of-the-art alignment with human judgment across multiple evaluation datasets. Furthermore, we establish three complementary evaluation protocols that collectively provide holistic assessment of web agent capabilities: navigation proficiency, knowledge-assisted interaction, and end-to-end task completion with information extraction. Extensive experimental analysis reveals substantial performance disparities across evaluation protocols, demonstrating that navigation success alone is an insufficient predictor of real-world application effectiveness. WebRetriever delivers fine-grained diagnostic insights into agent capabilities and establishes a rigorous foundation for advancing web agent research and development.

Reliable benchmarking is critical for developing machine learning models for tandem mass spectrometry (MS/MS) based molecule discovery. Subtle issues in experimental design and model evaluation procedures can degrade the trustworthiness of such benchmarks and lead to erroneous conclusions. We conduct a thorough review of model evaluation issues in the recent MS/MS machine learning literature, using the standard MassSpecGym benchmark suite as a case study to illustrate the impact of these issues. We find evaluation issues in at least 17 of 26 papers reporting MassSpecGym benchmark results in the first year of its adoption. We isolate three classes of failures: (i) data leakage, (ii) shortcut learning, and (iii) implementation bugs and metric divergence. Through extensive experimentation and code replication, we quantify the impact of these issues and show how they corrupt the evaluation standards MassSpecGym was designed to enforce. We distill our findings into recommendations generalizable to MS/MS challenges, benchmarks, and custom evaluation setups. We also release MassSpecGym v1.5, an implementation of our recommendations in the MassSpecGym benchmarking suite which addresses the failure modes identified in this audit. MassSpecGym v1.5 is publicly available at https://github.com/pluskal-lab/MassSpecGym.

Deep learning models have driven significant progress in predicting protein function and interactions at the protein level. While these advancements have been invaluable for many biological applications such as enzyme engineering and function annotation, a more detailed perspective is essential for understanding protein functional mechanisms and evaluating the biological knowledge captured by models. To address this demand, we introduce VenusX, the first large-scale benchmark for fine-grained functional annotation and function-based protein pairing at the residue, fragment, and domain levels. VenusX comprises three major task categories across six types of annotations, including residue-level binary classification, fragment-level multi-class classification, and pairwise functional similarity scoring for identifying critical active sites, binding sites, conserved sites, motifs, domains, and epitopes. The benchmark features over 878,000 samples curated from major open-source databases such as InterPro, BioLiP, and SAbDab. By providing mixed-family and cross-family splits at three sequence identity thresholds, our benchmark enables a comprehensive assessment of model performance on both in-distribution and out-of-distribution scenarios. For baseline evaluation, we assess a diverse set of popular and open-source models, including pre-trained protein language models, sequence-structure hybrids, structure-based methods, and alignment-based techniques. Their performance is reported across all benchmark datasets and evaluation settings using multiple metrics, offering a thorough comparison and a strong foundation for future research. Code and data are publicly available at https://github.com/ai4protein/VenusX.

Polymer property prediction lacks open, standardized benchmarks that enable rigorous comparison of machine-learning methods, with existing resources covering only a narrow fraction of polymer architectures, such as homopolymers. We introduce Polymer Benchmark 2026 (PolyBench26), an open dataset comprising nearly 250,000 polymer-property datapoints across eight physical properties, including data from experimental measurements, density functional theory, and molecular dynamics. The benchmark supports four evaluation tasks across homopolymers and alternating, random, and block copolymers: in-distribution property prediction, dataset-size scaling, repeat-unit complexity, and transfer to held-out polymer architectures. We compare language model, graph-based, and descriptor-based approaches and find graph-based models provide the lowest errors in property prediction, retain their advantage across the evaluated training-set sizes, and remain robust to increasing repeat-unit complexity. PolyBench26 provides a reproducible foundation for developing models for the increasingly complex polymer design space. The PolyBench26 benchmark is available open-source at https://github.com/rlearsch/PolymerBenchmark2026.

Large language models (LLMs) are increasingly integrated into legal drafting and research workflows, where incorrect citations or fabricated precedents can cause serious professional harm. Existing legal benchmarks largely emphasize statutory reasoning, contract understanding, or general legal question answering, but they do not directly study a central common-law failure mode: when asked to provide case authorities without external grounding, models may return plausible-looking but incorrect citations or cases. We introduce LegalCiteBench, a benchmark for studying closed-book citation recovery, citation verification, and case matching in legal language models. LegalCiteBench contains approximately 24K evaluation instances constructed from 1,000 real U.S. judicial opinions from the Case Law Access Project. The benchmark covers five citation-centric tasks: citation retrieval, citation completion, citation error detection, case matching, and case verification and correction. Across 21 LLMs, exact citation recovery remains highly challenging in this closed-book setting: even the strongest models score below 7/100 on citation retrieval and completion. Within the evaluated models, scale and legal-domain pretraining provide limited gains and do not resolve this difficulty. Models also frequently provide concrete but incorrect or low-overlap authorities under our evaluation protocol, with Misleading Answer Rates (MAR) exceeding 94% for 20 of 21 evaluated models on retrieval-heavy tasks. A prompt-only abstention experiment shows that explicit uncertainty instructions reduce some confident fabrication but do not improve citation correctness. LegalCiteBench is intended as a diagnostic framework for studying authority generation failures, verification behavior, and abstention when external grounding is absent, incomplete, or bypassed.

A benchmark score compares a system output against a reference, and methodological attention falls almost entirely on the first term. We measure the second. The retained annotation record of a six-language benchmark for personally identifiable information contains two independent annotator labellings, the aggregate shipped as gold, and a reviewer gold from independent expert re-annotation of a sample. Using it, we hold the scored output fixed and exchange the reference. The score moves by 4.95 F1 points for one output and 2.00 for the other (95% CIs [3.23, 6.27] and [0.26, 3.37]), and by 7.55 in the worst language. The comparison between two outputs moves as well: the paired interaction between reference and system is +2.95 points (CI [+1.97, +3.87]), survives correction for multiple testing, and changes one language's margin outright. The cause is an undocumented aggregation default that usually kept one annotator when adjudication did not fire, making the shipped reference a partial copy of an output being scored. We report the resulting reference-sensitivity band, show how to compute one from any retained annotation record, and argue that the quantity belongs beside the score.

The widespread application of Artificial Intelligence (AI) techniques has significantly influenced the development of new therapeutic agents. These computational methods can be used to design and predict the properties of generated molecules. Multi-target Drug Discovery (MTDD) is an emerging paradigm for discovering drugs against complex disorders that do not respond well to more traditional target-specific treatments, such as central nervous system, immune system, and cardiovascular diseases. Still, there is yet to be an established benchmark suite for assessing the effectiveness of AI tools for designing multi-target compounds. Standardized benchmarks allow for comparing existing techniques and promote rapid research progress. Hence, this work proposes an evaluation framework for molecule generation techniques in MTDD scenarios, considering brain diseases as a case study. Our methodology involves using large language models to select the appropriate molecular targets, gathering and preprocessing the bioassay datasets, training quantitative structure-activity relationship models to predict target modulation, and assessing other essential drug-likeness properties for implementing the benchmarks. Additionally, this work will assess the performance of four deep generative models and evolutionary algorithms over our benchmark suite. In our findings, both evolutionary algorithms and generative models can achieve competitive results across the proposed benchmarks.

Large language models are increasingly applied to various development scenarios. However, in on-chain transaction scenarios, even a minor error can cause irreversible loss for users. Existing evaluations often overlook execution accuracy and safety. We introduce EVM-QuestBench, an execution-grounded benchmark for natural-language transaction-script generation on EVM-compatible chains. The benchmark employs dynamic evaluation: instructions are sampled from template pools, numeric parameters are drawn from predefined intervals, and validators verify outcomes against these instantiated values. EVM-QuestBench contains 107 tasks (62 atomic, 45 composite). Its modular architecture enables rapid task development. The runner executes scripts on a forked EVM chain with snapshot isolation; composite tasks apply step-efficiency decay. We evaluate 20 models and find large performance gaps, with split scores revealing persistent asymmetry between single-action precision and multi-step workflow completion. Code: https://anonymous.4open.science/r/bsc_quest_bench-A9CF/.

Recent advancements in Language Models (LMs) have catalyzed the creation of multiple benchmarks, designed to assess these models' general capabilities. A crucial task, however, is assessing the validity of the benchmarks themselves. This is most commonly done via Benchmark Agreement Testing (BAT), where new benchmarks are validated against established ones using some agreement metric (e.g., rank correlation). Despite the crucial role of BAT for benchmark builders and consumers, there are no standardized procedures for such agreement testing. This deficiency can lead to invalid conclusions, fostering mistrust in benchmarks and upending the ability to properly choose the appropriate benchmark to use. By analyzing over 40 prominent benchmarks, we demonstrate how some overlooked methodological choices can significantly influence BAT results, potentially undermining the validity of conclusions. To address these inconsistencies, we propose a set of best practices for BAT and demonstrate how utilizing these methodologies greatly improves BAT robustness and validity. To foster adoption and facilitate future research,, we introduce BenchBench, a python package for BAT, and release the BenchBench-leaderboard, a meta-benchmark designed to evaluate benchmarks using their peers. Our findings underscore the necessity for standardized BAT, ensuring the robustness and validity of benchmark evaluations in the evolving landscape of language model research. BenchBench Package: https://github.com/IBM/BenchBench Leaderboard: https://huggingface.co/spaces/per/BenchBench

Extensive research has been conducted to explore the capabilities of large language models (LLMs) in table reasoning. However, the essential task of transforming tables information into reports remains a significant challenge for industrial applications. This task is plagued by two critical issues: 1) the complexity and diversity of tables lead to suboptimal reasoning outcomes; and 2) existing table benchmarks lack the capacity to adequately assess the practical application of this task. To fill this gap, we propose the table-to-report task and construct a bilingual benchmark named T2R-bench, where the key information flow from the tables to the reports for this task. The benchmark comprises 457 industrial tables, all derived from real-world scenarios and encompassing 19 industry domains as well as 4 types of industrial tables. Furthermore, we propose an evaluation criteria to fairly measure the quality of report generation. The experiments on 25 widely-used LLMs reveal that even state-of-the-art models like Deepseek-R1 only achieves performance with 62.71 overall score, indicating that LLMs still have room for improvement on T2R-bench. Source code and data will be available after acceptance.

Can AI agents organize scientific investigations that lead to well-supported conclusions? To evaluate this capability, we introduce PhysClosureBench, a benchmark of 50 expert-verified, goal-specified research tasks spanning strong-field, attosecond, and neighboring physics areas. Each task specifies the research objective and essential scientific constraints, while leaving the agent to organize the investigation and determine how to generate and validate the evidence needed to answer the question. A 20-criterion Atomic Score measures local scientific accomplishment, while Research Closure (RC0--RC4) assesses how fully the investigation resolves the specified research question based on whether its indispensable evidence requirements and applicable scope conditions are satisfied. We evaluate seven frontier LLMs, where Claude-Opus-5 achieves the highest mean Atomic Score (6.29/10) but reaches RC4 in only 32.7% of attempts. Across the benchmark, 36.2% of attempts scoring at least 8/10 still fall short of RC4, while all seven models reach RC4 on substantially fewer tasks in all three runs than in at least one. Case-level analysis further illustrates how misinterpretation of generated results and unresolved physical applicability limits can lead to incomplete closure. Together, these results reveal a persistent gap between AI agents' local scientific accomplishments and their ability to achieve complete research closure.

When can an agent failure be caught? An audit is usually limited by the record rather than by the method. CatchBench therefore puts one auditor's question to three information states: the declared configuration before a run (PRE), a growing prefix of its trace (LIVE), and the finished trace (POST). Prior benchmarks fix one of these states or vary the telemetry; to our knowledge none scores all three under one task-method interface. Each state admits different questions, so seven task contracts carry their own labels and metrics rather than one leaderboard. Four are evidential; three are Gold-derived mechanism diagnostics. The release scores 72 entrants, from rule scanners and structural models to eleven LLM judges across nine model families (GPT, Claude, Gemini, Gemma, Llama, Qwen, DeepSeek, Mistral, Nova), over 1187 declared configurations and 1162 recorded runs. Most of the arena does not order: 56 of 138 registered contrasts separate, and the rest are published unresolved rather than ranked. The two sharpest results cut against our own data. One rule ignores every name and permission; it flags each capability declared after the first. On one of six configuration sources it reaches a perfect F1, so a score there measures how the corpus was built rather than how well a method reasons. Our admissibility bar then rejected one injected substrate and withheld evidential status from the other. A benchmark number is therefore not interpretable until the process behind its labels is published and tested for the shortcut it may leave. We report both, and regenerate every ordering from released predictions with no model call.

Approximate nearest neighbor (ANN) search is a performance-critical component of many machine learning pipelines, and rigorous benchmarking is essential for assessing the performance of vector indexes for ANN search. However, the datasets of existing benchmarks no longer represent modern ANN applications, creating a need for an up-to-date benchmark. To address this gap, we introduce Vector Index Benchmark for Embeddings (VIBE), an open-source framework for benchmarking ANN algorithms. VIBE provides a pipeline for generating benchmark datasets with dense embedding models representative of modern applications, including retrieval-augmented generation (RAG). To represent real-world workloads, we also include out-of-distribution (OOD) datasets where the queries and the corpus are drawn from different distributions. These include multimodal retrieval datasets and maximum inner product search (MIPS) datasets covering two recent use cases: approximate attention computation and reductions of multi-vector retrieval to single-vector MIPS. We use VIBE to conduct a comprehensive evaluation of 22 open-source vector-index implementations across 11 in-distribution and 8 out-of-distribution datasets. The benchmark is available at https://github.com/vector-index-bench/vibe

Evaluating agents on the growing number of agentic benchmarks is challenging because they often require complex environments and agent integrations. We introduce Harbor Adapters, a unified evaluation infrastructure for agentic benchmarks. Our work makes three contributions. First, we develop benchmark adapters that port more than 80 benchmarks to evaluate arbitrary agents, and validate them through rigorous code review and parity experiments. Second, we conduct a large-scale evaluation of 8 models spanning capability tiers across 54 benchmarks; every model is run with Terminus-2 and with one of 3 native harnesses. This enables a broader analysis of agent capabilities and failure modes than was previously possible. Third, we introduce Harbor-Index, a curated set of 82 difficult, diverse, and high-quality tasks spanning 29 benchmarks, refined from the adapted suite through difficulty filtering, AI and human audit, and an audit-and-fix loop. Harbor-Index preserves the challenge and breadth of large-scale agentic evaluations while being affordable to run; no evaluated model-harness configuration exceeds 30% pass rate, and the strongest (GPT-5.5 with Codex) reaches 28.0%. We release the adapters, evaluation results, in-depth analysis, and Harbor-Index as open-source artifacts to support more reliable and comprehensive evaluation of language-model agents.

Legal AI systems are increasingly used to answer legal questions, yet existing benchmarks assume queries arrive fully specified. In practice, users omit facts that materially determine the legal outcome. We introduce InsufficiencyBench, the first legal benchmark targeting query-side insufficiency: whether a model recognizes when a query lacks legally material information, identifies what is missing, and refrains from premature conclusions. We formalize a taxonomy of eight canonical missing-element categories across three structural failure modes---switch, gating, and fatal prerequisite--- and construct 202 benchmark items (58 base queries, 144 deficient variants) spanning six legal domains and 24 US jurisdictions and annotated by practising attorneys. Evaluating ten frontier models, we find that no model exceeds F2 = 0.46 on missing-element identification and that the median recall is 0.44. Models either hedge indiscriminately or answer silently under fabricated presumptions. No model both identifies and qualifies responses to deficient queries while directly addressing complete ones.

The motif-scaffolding problem is a central task in computational protein design: Given the coordinates of atoms in a geometry chosen to confer a desired biochemical function (a motif), the task is to identify diverse protein structures (scaffolds) that include the motif and maintain its geometry. Significant recent progress on motif-scaffolding has been made due to computational evaluation with reliable protein structure prediction and fixed-backbone sequence design methods. However, significant variability in evaluation strategies across publications has hindered comparability of results, challenged reproducibility, and impeded robust progress. In response we introduce MotifBench, comprising (1) a precisely specified pipeline and evaluation metrics, (2) a collection of 30 benchmark problems, and (3) an implementation of this benchmark and leaderboard at github.com/blt2114/MotifBench. The MotifBench test cases are more difficult compared to earlier benchmarks, and include protein design problems for which solutions are known but on which, to the best of our knowledge, state-of-the-art methods fail to identify any solution.

LLM-based agents process external content, exposing them to prompt injection and multi-turn manipulation. Most safety benchmarks evaluate defenders against fixed attack pools collected before evaluation, single-turn or multi-turn. We present a 21-scenario benchmark for adaptive multi-round attacks against memoryless LLM defenders: an autonomous LLM attacker observes prior defender responses and pivots across rounds, while each defender response is evaluated as a fresh interaction. Holding the 21 scenarios, attackers, defenders, and structured-output scoring fixed, restricting scoring to the first attacker turn yields 0-1% attack success rate (ASR); allowing 15 rounds of adaptive attack yields 5.4-14.0%. Pooling three frontier attacker LLMs uncovers 1.4-2.2times as many unique successful attacks as the best single attacker, and the generated attacks have low cosine similarity (0.02-0.14) to attacks in existing benchmarks. Claude Opus 4.6 and GPT-5.4 are tied in aggregate (5.4% each; overlapping 95% CIs), but their weaknesses differ sharply: on one scenario Opus reaches 60% ASR (95% CI 36--80%) while GPT-5.4 and Gemini each stay at 7% (CI 1-30%; the gap is preserved in a higher-N replication). 13 of 21 scenarios distinguish at least one defender pair, yet rankings disagree across scenarios (Kendall's W = 0.19). We release the benchmark -- 21 evaluation scenarios, 10 public development scenarios, the orchestrator, baseline harnesses, and a multi-attacker CLI -- plus 945 transcripts from the 3times3 frontier matrix, an attack-replay dataset, and 18{,}422 gpt-oss-20b battles from an open competition's final scoring rounds.

Time series forecasting is critical across finance, healthcare, and cloud computing, yet progress is constrained by a fundamental bottleneck: the scarcity of large-scale, high-quality benchmarks. To address this gap, we introduce QuitoBench, a regime-balanced benchmark for time series forecasting with coverage across eight trendtimesseasonalitytimesforecastability (TSF) regimes, designed to capture forecasting-relevant properties rather than application-defined domain labels. The benchmark is built upon Quito, a billion-scale time series corpus of application traffic from Alipay spanning nine business domains. Benchmarking 10 models from deep learning, foundation models, and statistical baselines across 232,200 evaluation instances, we report four key findings: (i) a context-length crossover where deep learning models lead at short context (L=96) but foundation models dominate at long context (L ge 576); (ii) forecastability is the dominant difficulty driver, producing a 3.64 times MAE gap across regimes; (iii) deep learning models match or surpass foundation models at 59 times fewer parameters; and (iv) scaling the amount of training data provides substantially greater benefit than scaling model size for both model families. These findings are validated by strong cross-benchmark and cross-metric consistency. Our open-source release enables reproducible, regime-aware evaluation for time series forecasting research.

Because large language models are expensive to pretrain on different datasets, using smaller-scale experiments to decide on data is crucial for reducing costs. Which benchmarks and methods of making decisions from observed performance at small scale most accurately predict the datasets that yield the best large models? To empower open exploration of this question, we release models, data, and evaluations in DataDecide -- the most extensive open suite of models over differences in data and scale. We conduct controlled pretraining experiments across 25 corpora with differing sources, deduplication, and filtering up to 100B tokens, model sizes up to 1B parameters, and 3 random seeds. We find that the ranking of models at a single, small size (e.g., 150M parameters) is a strong baseline for predicting best models at our larger target scale (1B) (~80% of com parisons correct). No scaling law methods among 8 baselines exceed the compute-decision frontier of single-scale predictions, but DataDecide can measure improvement in future scaling laws. We also identify that using continuous likelihood metrics as proxies in small experiments makes benchmarks including MMLU, ARC, HellaSwag, MBPP, and HumanEval >80% predictable at the target 1B scale with just 0.01% of the compute.

We introduce MSC-Bench, a large-scale benchmark for evaluating multi-hop, end-to-end tool orchestration by LLM agents in a hierarchical Model-Context Protocol (MCP) ecosystem. Existing benchmarks often evaluate tools in isolation, ignoring challenges such as functional overlap and cross-server orchestration, leading to overly optimistic assessments. MSC-Bench addresses these gaps by constructing ground truth through 'equal function sets', allowing objective metrics such as F1 score and reducing the dependency on LLM-as-a-judge evaluation. Organized as a five-level curriculum, it systematically tests agent capabilities from single-tool orchestration to complex cross-server planning, and robustness to out-of-scope requests. Experiments reveal that rigid hierarchies can hinder performance without co-designed strategies, and even state-of-the-art agents exhibit systemic weaknesses in robustness. MSC-Bench provides a diagnostic framework to expose these limitations and guide the development of more capable and efficient tool-using agents. The benchmark and resources are publicly available at https://github.com/snooow1029/MSC_Bench.

Benchmarks play a central role in the development and governance of models, yet it is often unclear whether they actually measure the concepts they purport to measure (e.g., reasoning, refusal). We adapt convergent and discriminant validity from the social sciences into an approach for interrogating AI benchmarks, applying it to 56 capability and safety benchmarks across 53 models. We label benchmarks with substantively similar purported concepts to a shared assigned concept, and ask whether model rankings on benchmarks with the same assigned concept correlate more strongly than rankings on benchmarks with different assigned concepts. We ask analogous questions at the item level using item response theory (IRT) models. We find that correlations between model rankings on benchmarks with the same assigned safety concepts are often weak, suggesting these concepts may be conceptualized inconsistently across benchmarks. For assigned capability concepts (e.g., reasoning, knowledge), model rankings are often as strongly correlated among benchmarks with the same assigned concept as between benchmarks with different assigned concepts, suggesting these capability concepts may not discriminate well from one another. In some cases, benchmarks that share design elements (e.g., score format) correlate more strongly than benchmarks with the same assigned concept. Finally, some individual benchmarks correlate more strongly with benchmarks assigned a different concept than with benchmarks sharing their own assigned concept, suggesting they may measure a different concept than they purport to. For example, BBQ-accuracy correlates more strongly with benchmarks labeled reasoning than with benchmarks that share its assigned concept, bias. To support future empirical work on benchmark validity, we release our extensive dataset of model outputs and scores at the item- and benchmark-level.