Daily Papers

Deep-learning survival models for electronic health record (EHR) data are hard to compare across papers because the upstream preprocessing step, which includes cohort definition, time discretisation, missingness handling, and censoring rules, is typically undocumented and inconsistent. A reported difference in concordance between two mortality models can therefore reflect any of these choices rather than a modelling contribution. We present SurvBench, an open-source preprocessing pipeline that converts raw PhysioNet exports into model-ready tensors for survival analysis. SurvBench covers four critical-care databases (MIMIC-IV, eICU, MC-MED, HiRID) and four input modalities: time-series vitals and laboratory values, static demographics, International Classification of Diseases (ICD) codes, and radiology report embeddings. Every preprocessing decision is controlled through YAML configuration. Imputation, scaling, and feature filtering are fit on the training fold only. Missingness is recorded as a binary mask alongside each feature tensor. The pipeline handles single-risk endpoints (in-hospital and in-ICU mortality) and competing-risks endpoints (a three-way emergency-department admission pathway, with home discharge treated as administrative censoring). We also provide support for harmonised cross-dataset external validation between eICU and MIMIC-IV. SurvBench is publicly available at https://github.com/munibmesinovic/SurvBench, providing a robust platform that future deep-learning EHR survival work, especially nascent multi-modal approaches, can be measured against under matched preprocessing.

Peptide therapeutics are widely regarded as the "third generation" of drugs, yet progress in peptide Machine Learning (ML) are hindered by the absence of standardized benchmarks. Here we present PepBenchmark, which unifies datasets, preprocessing, and evaluation protocols for peptide drug discovery. PepBenchmark comprises three components: (1) PepBenchData, a well-curated collection comprising 29 canonical-peptide and 6 non-canonical-peptide datasets across 7 groups, systematically covering key aspects of peptide drug development, representing, to the best of our knowledge, the most comprehensive AI-ready dataset resource to date; (2) PepBenchPipeline, a standardized preprocessing pipeline that ensures consistent dataset cleaning, construction, splitting, and feature transformation, mitigating quality issues common in ad hoc pipelines; and (3) PepBenchLeaderboard, a unified evaluation protocol and leaderboard with strong baselines across 4 major methodological families: Fingerprint-based, GNN-based, PLM-based, and SMILES-based models. Together, PepBenchmark provides the first standardized and comparable foundation for peptide drug discovery, facilitating methodological advances and translation into real-world applications. The data and code are publicly available at https://github.com/ZGCI-AI4S-Pep/PepBenchmark/.

Research in self-supervised learning (SSL) with natural images has progressed rapidly in recent years and is now increasingly being applied to and benchmarked with datasets containing remotely sensed imagery. A common benchmark case is to evaluate SSL pre-trained model embeddings on datasets of remotely sensed imagery with small patch sizes, e.g., 32x32 pixels, whereas standard SSL pre-training takes place with larger patch sizes, e.g., 224x224. Furthermore, pre-training methods tend to use different image normalization preprocessing steps depending on the dataset. In this paper, we show, across seven satellite and aerial imagery datasets of varying resolution, that by simply following the preprocessing steps used in pre-training (precisely, image sizing and normalization methods), one can achieve significant performance improvements when evaluating the extracted features on downstream tasks -- an important detail overlooked in previous work in this space. We show that by following these steps, ImageNet pre-training remains a competitive baseline for satellite imagery based transfer learning tasks -- for example we find that these steps give +32.28 to overall accuracy on the So2Sat random split dataset and +11.16 on the EuroSAT dataset. Finally, we report comprehensive benchmark results with a variety of simple baseline methods for each of the seven datasets, forming an initial benchmark suite for remote sensing imagery.

Multimodal misinformation detection methods often rely on different preprocessing pipelines and auxiliary resources, making experimental comparisons difficult to interpret. We present MMFact, a collection of shared resources and tools that simplifies this research workflow. It brings together 47 detector implementations and baselines, three multimodal datasets, and prepared materials ranging from semantic features to OCR, image descriptions, and external evidence. Compatible methods can use the same materials, reducing variation introduced by preprocessing and supporting fairer comparisons. A modular training and evaluation framework preserves method-specific designs while providing common experimental procedures. By treating prepared materials as a shared research resource, MMFact helps researchers focus on developing and evaluating detection methods.

Hand-drawn sketches are a natural and efficient medium for capturing and conveying ideas. Despite significant advancements in controllable natural image generation, translating freehand sketches into structured, machine-readable diagrams remains a labor-intensive and predominantly manual task. The primary challenge stems from the inherent ambiguity of sketches, which lack the structural constraints and semantic precision required for automated diagram generation. To address this challenge, we introduce SketchAgent, a multi-agent system designed to automate the transformation of hand-drawn sketches into structured diagrams. SketchAgent integrates sketch recognition, symbolic reasoning, and iterative validation to produce semantically coherent and structurally accurate diagrams, significantly reducing the need for manual effort. To evaluate the effectiveness of our approach, we propose the Sketch2Diagram Benchmark, a comprehensive dataset and evaluation framework encompassing eight diverse diagram categories, such as flowcharts, directed graphs, and model architectures. The dataset comprises over 6,000 high-quality examples with token-level annotations, standardized preprocessing, and rigorous quality control. By streamlining the diagram generation process, SketchAgent holds great promise for applications in design, education, and engineering, while offering a significant step toward bridging the gap between intuitive sketching and machine-readable diagram generation. The benchmark is released at https://huggingface.co/datasets/DiagramAgent/Sketch2Diagram-Benchmark.

Recent provenance-based intrusion detection systems (PIDSs) have demonstrated strong potential for detecting advanced persistent threats (APTs) by applying machine learning to system provenance graphs. However, evaluating and comparing PIDSs remains difficult: prior work uses inconsistent preprocessing pipelines, non-standard dataset splits, and incompatible ground-truth labeling and metrics. These discrepancies undermine reproducibility, impede fair comparison, and impose substantial re-implementation overhead on researchers. We present PIDSMaker, an open-source framework for developing and evaluating PIDSs under consistent protocols. PIDSMaker consolidates eight state-of-the-art systems into a modular, extensible architecture with standardized preprocessing and ground-truth labels, enabling consistent experiments and apples-to-apples comparisons. A YAML-based configuration interface supports rapid prototyping by composing components across systems without code changes. PIDSMaker also includes utilities for ablation studies, hyperparameter tuning, multi-run instability measurement, and visualization, addressing methodological gaps identified in prior work. We demonstrate PIDSMaker through concrete use cases and release it with preprocessed datasets and labels to support shared evaluation for the PIDS community.

The HuggingFace Datasets Hub hosts thousands of datasets. This provides exciting opportunities for language model training and evaluation. However, the datasets for a given type of task are stored with different schemas, and harmonization is harder than it seems (https://xkcd.com/927/). Multi-task training or evaluation requires manual work to fit data into task templates. Various initiatives independently address this problem by releasing the harmonized datasets or harmonization codes to preprocess datasets to the same format. We identify patterns across previous preprocessings, e.g. mapping of column names, and extraction of a specific sub-field from structured data in a column, and propose a structured annotation framework that makes our annotations fully exposed and not buried in unstructured code. We release a dataset annotation framework and dataset annotations for more than 400 English tasks (https://github.com/sileod/tasksource). These annotations provide metadata, like the name of the columns that should be used as input or labels for all datasets, and can save time for future dataset preprocessings, even if they do not use our framework. We fine-tune a multi-task text encoder on all tasksource tasks, outperforming every publicly available text encoder of comparable size on an external evaluation https://hf.co/sileod/deberta-v3-base-tasksource-nli.

Knowledge tracing (KT) is the task of using students' historical learning interaction data to model their knowledge mastery over time so as to make predictions on their future interaction performance. Recently, remarkable progress has been made of using various deep learning techniques to solve the KT problem. However, the success behind deep learning based knowledge tracing (DLKT) approaches is still left somewhat unknown and proper measurement and analysis of these DLKT approaches remain a challenge. First, data preprocessing procedures in existing works are often private and custom, which limits experimental standardization. Furthermore, existing DLKT studies often differ in terms of the evaluation protocol and are far away real-world educational contexts. To address these problems, we introduce a comprehensive python based benchmark platform, pyKT, to guarantee valid comparisons across DLKT methods via thorough evaluations. The pyKT library consists of a standardized set of integrated data preprocessing procedures on 7 popular datasets across different domains, and 10 frequently compared DLKT model implementations for transparent experiments. Results from our fine-grained and rigorous empirical KT studies yield a set of observations and suggestions for effective DLKT, e.g., wrong evaluation setting may cause label leakage that generally leads to performance inflation; and the improvement of many DLKT approaches is minimal compared to the very first DLKT model proposed by Piech et al. piech2015deep. We have open sourced pyKT and our experimental results at https://pykt.org/. We welcome contributions from other research groups and practitioners.

Action models are essential for enabling autonomous agents to perform complex tasks. However, training large action models remains challenging due to the diversity of agent environments and the complexity of agentic data. Despite growing interest, existing infrastructure provides limited support for scalable, agent-specific fine-tuning. We present ActionStudio, a lightweight and extensible data and training framework designed for large action models. ActionStudio unifies heterogeneous agent trajectories through a standardized format, supports diverse training paradigms including LoRA, full fine-tuning, and distributed setups, and integrates robust preprocessing and verification tools. We validate its effectiveness across both public and realistic industry benchmarks, demonstrating strong performance and practical scalability. We open-sourced code and data at https://github.com/SalesforceAIResearch/xLAM to facilitate research in the community.

We introduce a novel Longitudinal Focused Attention Meditation Electroencephalography (L-FAME) dataset and an accompanying benchmark, designed to foster research into the neural effects of various meditation practices and the evolution of these effects over a six-week training period. The dataset contains EEG recordings and psychological assessments from 74 healthy college participants, collected at two distinct time points: pre-intervention and post-intervention. Participants were randomly assigned to one of three distinct meditation groups: two mantra-based techniques (SA-TA-NA-MA and Hare Krishna) and one Breath Focus practice. Leveraging this unique longitudinal and comparative dataset, we propose a benchmark suite comprising three distinct classification tasks: (1) cognitive state decoding to distinguish between resting and meditation states, (2) fine-grained classification of the specific meditation techniques, and (3) cross-session adaptation to evaluate model generalization across the longitudinal time gap. We provide comprehensive baseline results for these tasks utilizing a range of classical machine learning algorithms and deep learning architectures. The complete dataset, preprocessing pipelines, and benchmark evaluation code will be publicly released, offering a valuable resource and a standardized framework for the development and comparison of new analytical methods in computational meditation research and EEG-based machine learning. The dataset is available at https://huggingface.co/datasets/L-FAME-Dataset-Benchmark/L-FAME

This paper introduces MCTrack, a new 3D multi-object tracking method that achieves state-of-the-art (SOTA) performance across KITTI, nuScenes, and Waymo datasets. Addressing the gap in existing tracking paradigms, which often perform well on specific datasets but lack generalizability, MCTrack offers a unified solution. Additionally, we have standardized the format of perceptual results across various datasets, termed BaseVersion, facilitating researchers in the field of multi-object tracking (MOT) to concentrate on the core algorithmic development without the undue burden of data preprocessing. Finally, recognizing the limitations of current evaluation metrics, we propose a novel set that assesses motion information output, such as velocity and acceleration, crucial for downstream tasks. The source codes of the proposed method are available at this link: https://github.com/megvii-research/MCTrack}{https://github.com/megvii-research/MCTrack

We introduce ArtBench-10, the first class-balanced, high-quality, cleanly annotated, and standardized dataset for benchmarking artwork generation. It comprises 60,000 images of artwork from 10 distinctive artistic styles, with 5,000 training images and 1,000 testing images per style. ArtBench-10 has several advantages over previous artwork datasets. Firstly, it is class-balanced while most previous artwork datasets suffer from the long tail class distributions. Secondly, the images are of high quality with clean annotations. Thirdly, ArtBench-10 is created with standardized data collection, annotation, filtering, and preprocessing procedures. We provide three versions of the dataset with different resolutions (32times32, 256times256, and original image size), formatted in a way that is easy to be incorporated by popular machine learning frameworks. We also conduct extensive benchmarking experiments using representative image synthesis models with ArtBench-10 and present in-depth analysis. The dataset is available at https://github.com/liaopeiyuan/artbench under a Fair Use license.

Respiratory viral infections pose a global health burden, yet the cellular immune responses driving protection or pathology remain unclear. Natural infection cohorts often lack pre-exposure baseline data and structured temporal sampling. In contrast, inoculation and vaccination trials generate insightful longitudinal transcriptomic data. However, the scattering of these datasets across platforms, along with inconsistent metadata and preprocessing procedure, hinders AI-driven discovery. To address these challenges, we developed the Human Respiratory Viral Immunization LongitudinAl Gene Expression (HR-VILAGE-3K3M) repository: an AI-ready, rigorously curated dataset that integrates 14,136 RNA-seq profiles from 3,178 subjects across 66 studies encompassing over 2.56 million cells. Spanning vaccination, inoculation, and mixed exposures, the dataset includes microarray, bulk RNA-seq, and single-cell RNA-seq from whole blood, PBMCs, and nasal swabs, sourced from GEO, ImmPort, and ArrayExpress. We harmonized subject-level metadata, standardized outcome measures, applied unified preprocessing pipelines with rigorous quality control, and aligned all data to official gene symbols. To demonstrate the utility of HR-VILAGE-3K3M, we performed predictive modeling of vaccine responders and evaluated batch-effect correction methods. Beyond these initial demonstrations, it supports diverse systems immunology applications and benchmarking of feature selection and transfer learning algorithms. Its scale and heterogeneity also make it ideal for pretraining foundation models of the human immune response and for advancing multimodal learning frameworks. As the largest longitudinal transcriptomic resource for human respiratory viral immunization, it provides an accessible platform for reproducible AI-driven research, accelerating systems immunology and vaccine development against emerging viral threats.

Tabular foundation models represent a growing paradigm in structured data learning, extending the benefits of large-scale pretraining to tabular domains. However, their adoption remains limited due to heterogeneous preprocessing pipelines, fragmented APIs, inconsistent fine-tuning procedures, and the absence of standardized evaluation for deployment-oriented metrics such as calibration and fairness. We present TabTune, a unified library that standardizes the complete workflow for tabular foundation models through a single interface. TabTune provides consistent access to seven state-of-the-art models supporting multiple adaptation strategies, including zero-shot inference, meta-learning, supervised fine-tuning (SFT), and parameter-efficient fine-tuning (PEFT). The framework automates model-aware preprocessing, manages architectural heterogeneity internally, and integrates evaluation modules for performance, calibration, and fairness. Designed for extensibility and reproducibility, TabTune enables consistent benchmarking of adaptation strategies of tabular foundation models. The library is open source and available at https://github.com/Lexsi-Labs/TabTune .

Imitation learning for robotic manipulation relies on large sets of human demonstration trajectories, which are often noisy and temporally irregular due to variable operator speed, intermittent pauses, and inconsistent action density. A common preprocessing strategy is time-uniform downsampling to shorten sequences, but it cannot effectively remove speed-induced non-uniformity or redundant pauses. This mismatch degrades data quality and hinders policy learning. To address this issue, we propose Information-Standardized Trajectory Resampling (ISR), an offline preprocessing method for effective imitation learning. ISR resamples each trajectory by enforcing approximately equal information distance between adjacent points. Specifically, we map trajectories onto an information-modulated Riemannian manifold and perform geodesic-equidistant parameterization. We construct an information-intensity field from velocity and acceleration norms: the velocity term removes small-motion redundancy, while the acceleration term preserves high-curvature and fine-manipulation phases. We evaluate ISR on three real-world manipulation tasks with mainstream imitation learning policies. Compared with the baseline time-uniform 3x downsampling, ISR improves task success rates by about 25%, remains robust across datasets collected from different operators, and reduces both dataset size and training cost. The code and videos are publicly available at https://d-robotics-ai-lab.github.io/isr.page.

Visual Simultaneous Localization and Mapping (VSLAM) research faces significant challenges due to fragmented toolchains, complex system configurations, and inconsistent evaluation methodologies. To address these issues, we present VSLAM-LAB, a unified framework designed to streamline the development, evaluation, and deployment of VSLAM systems. VSLAM-LAB simplifies the entire workflow by enabling seamless compilation and configuration of VSLAM algorithms, automated dataset downloading and preprocessing, and standardized experiment design, execution, and evaluation--all accessible through a single command-line interface. The framework supports a wide range of VSLAM systems and datasets, offering broad compatibility and extendability while promoting reproducibility through consistent evaluation metrics and analysis tools. By reducing implementation complexity and minimizing configuration overhead, VSLAM-LAB empowers researchers to focus on advancing VSLAM methodologies and accelerates progress toward scalable, real-world solutions. We demonstrate the ease with which user-relevant benchmarks can be created: here, we introduce difficulty-level-based categories, but one could envision environment-specific or condition-specific categories.

While deep learning has revolutionized computer-aided drug discovery, the AI community has predominantly focused on model innovation and placed less emphasis on establishing best benchmarking practices. We posit that without a sound model evaluation framework, the AI community's efforts cannot reach their full potential, thereby slowing the progress and transfer of innovation into real-world drug discovery. Thus, in this paper, we seek to establish a new gold standard for small molecule drug discovery benchmarking, WelQrate. Specifically, our contributions are threefold: WelQrate Dataset Collection - we introduce a meticulously curated collection of 9 datasets spanning 5 therapeutic target classes. Our hierarchical curation pipelines, designed by drug discovery experts, go beyond the primary high-throughput screen by leveraging additional confirmatory and counter screens along with rigorous domain-driven preprocessing, such as Pan-Assay Interference Compounds (PAINS) filtering, to ensure the high-quality data in the datasets; WelQrate Evaluation Framework - we propose a standardized model evaluation framework considering high-quality datasets, featurization, 3D conformation generation, evaluation metrics, and data splits, which provides a reliable benchmarking for drug discovery experts conducting real-world virtual screening; Benchmarking - we evaluate model performance through various research questions using the WelQrate dataset collection, exploring the effects of different models, dataset quality, featurization methods, and data splitting strategies on the results. In summary, we recommend adopting our proposed WelQrate as the gold standard in small molecule drug discovery benchmarking. The WelQrate dataset collection, along with the curation codes, and experimental scripts are all publicly available at WelQrate.org.

CCTV safety monitoring demands anomaly detectors combine reliable clip-level accuracy with predictable per-clip latency despite weak supervision. This work investigates compact vision-language models (VLMs) as practical detectors for this regime. A unified evaluation protocol standardizes preprocessing, prompting, dataset splits, metrics, and runtime settings to compare parameter-efficiently adapted compact VLMs against training-free VLM pipelines and weakly supervised baselines. Evaluation spans accuracy, precision, recall, F1, ROC-AUC, and average per-clip latency to jointly quantify detection quality and efficiency. With parameter-efficient adaptation, compact VLMs achieve performance on par with, and in several cases exceeding, established approaches while retaining competitive per-clip latency. Adaptation further reduces prompt sensitivity, producing more consistent behavior across prompt regimes under the shared protocol. These results show that parameter-efficient fine-tuning enables compact VLMs to serve as dependable clip-level anomaly detectors, yielding a favorable accuracy-efficiency trade-off within a transparent and consistent experimental setup.

We present PharmaShip, a real-world Chinese dataset of scanned pharmaceutical shipping documents designed to stress-test pre-trained text-layout models under noisy OCR and heterogeneous templates. PharmaShip covers three complementary tasks-sequence entity recognition (SER), relation extraction (RE), and reading order prediction (ROP)-and adopts an entity-centric evaluation protocol to minimize confounds across architectures. We benchmark five representative baselines spanning pixel-aware and geometry-aware families (LiLT, LayoutLMv3-base, GeoLayoutLM and their available RORE-enhanced variants), and standardize preprocessing, splits, and optimization. Experiments show that pixels and explicit geometry provide complementary inductive biases, yet neither alone is sufficient: injecting reading-order-oriented regularization consistently improves SER and EL and yields the most robust configuration, while longer positional coverage stabilizes late-page predictions and reduces truncation artifacts. ROP is accurate at the word level but challenging at the segment level, reflecting boundary ambiguity and long-range crossings. PharmaShip thus establishes a controlled, reproducible benchmark for safety-critical document understanding in the pharmaceutical domain and highlights sequence-aware constraints as a transferable bias for structure modeling. We release the dataset at https://github.com/KevinYuLei/PharmaShip.

Data standardization is a crucial part of the data science life cycle. While tools like Pandas offer robust functionalities, their complexity and the manual effort required for customizing code to diverse column types pose significant challenges. Although large language models (LLMs) like ChatGPT have shown promise in automating this process through natural language understanding and code generation, it still demands expert-level programming knowledge and continuous interaction for prompt refinement. To solve these challenges, our key idea is to propose a Python library with declarative, unified APIs for standardizing different column types, simplifying the LLM's code generation with concise API calls. We first propose Dataprep.Clean, a component of the Dataprep Python Library, significantly reduces the coding complexity by enabling the standardization of specific column types with a single line of code. Then, we introduce the CleanAgent framework integrating Dataprep.Clean and LLM-based agents to automate the data standardization process. With CleanAgent, data scientists only need to provide their requirements once, allowing for a hands-free process. To demonstrate the practical utility of CleanAgent, we developed a user-friendly web application, allowing attendees to interact with it using real-world datasets.

Clinical notes are assigned ICD codes - sets of codes for diagnoses and procedures. In the recent years, predictive machine learning models have been built for automatic ICD coding. However, there is a lack of widely accepted benchmarks for automated ICD coding models based on large-scale public EHR data. This paper proposes a public benchmark suite for ICD-10 coding using a large EHR dataset derived from MIMIC-IV, the most recent public EHR dataset. We implement and compare several popular methods for ICD coding prediction tasks to standardize data preprocessing and establish a comprehensive ICD coding benchmark dataset. This approach fosters reproducibility and model comparison, accelerating progress toward employing automated ICD coding in future studies. Furthermore, we create a new ICD-9 benchmark using MIMIC-IV data, providing more data points and a higher number of ICD codes than MIMIC-III. Our open-source code offers easy access to data processing steps, benchmark creation, and experiment replication for those with MIMIC-IV access, providing insights, guidance, and protocols to efficiently develop ICD coding models.

Medical Vision-Language Pretraining (MedVLP) shows promise in learning generalizable and transferable visual representations from paired and unpaired medical images and reports. MedVLP can provide useful features to downstream tasks and facilitate adapting task-specific models to new setups using fewer examples. However, existing MedVLP methods often differ in terms of datasets, preprocessing, and finetuning implementations. This pose great challenges in evaluating how well a MedVLP method generalizes to various clinically-relevant tasks due to the lack of unified, standardized, and comprehensive benchmark. To fill this gap, we propose BenchX, a unified benchmark framework that enables head-to-head comparison and systematical analysis between MedVLP methods using public chest X-ray datasets. Specifically, BenchX is composed of three components: 1) Comprehensive datasets covering nine datasets and four medical tasks; 2) Benchmark suites to standardize data preprocessing, train-test splits, and parameter selection; 3) Unified finetuning protocols that accommodate heterogeneous MedVLP methods for consistent task adaptation in classification, segmentation, and report generation, respectively. Utilizing BenchX, we establish baselines for nine state-of-the-art MedVLP methods and found that the performance of some early MedVLP methods can be enhanced to surpass more recent ones, prompting a revisiting of the developments and conclusions from prior works in MedVLP. Our code are available at https://github.com/yangzhou12/BenchX.

Cross-validation is the de facto standard for predictive model evaluation and selection. In proper use, it provides an unbiased estimate of a model's predictive performance. However, data sets often undergo various forms of data-dependent preprocessing, such as mean-centering, rescaling, dimensionality reduction, and outlier removal. It is often believed that such preprocessing stages, if done in an unsupervised manner (that does not incorporate the class labels or response values) are generally safe to do prior to cross-validation. In this paper, we study three commonly-practiced preprocessing procedures prior to a regression analysis: (i) variance-based feature selection; (ii) grouping of rare categorical features; and (iii) feature rescaling. We demonstrate that unsupervised preprocessing can, in fact, introduce a substantial bias into cross-validation estimates and potentially hurt model selection. This bias may be either positive or negative and its exact magnitude depends on all the parameters of the problem in an intricate manner. Further research is needed to understand the real-world impact of this bias across different application domains, particularly when dealing with small sample sizes and high-dimensional data.

Pretraining data processing is critical to the downstream performance of Large Language Models (LLMs). However, many existing approaches define a fixed processing strategy at the corpus or domain level and apply it uniformly to many examples, without adapting to the needs of each example. We propose DataOrchestra, a framework that unifies different processing operations and orchestrates an example-specific pipeline for each example. Given a chunk of pretraining data, an orchestrator decides whether to drop, untouch, or clean it. For a chunk to be cleaned, it selects one or more downstream operations, ranging from programmatic editing to different forms of LLM-based rewriting. For each rewriting step, it further generates a concrete instruction, which is executed by the corresponding downstream tool model. We pretrain models from 0.5B to 7B from scratch on web data processed by DataOrchestra and observe stable average gains over individual data-processing methods across 11 benchmarks. DataOrchestra is also effective for math continued pretraining and outperforms stronger processing baselines, while reducing processing compute by skipping unnecessary downstream operations.

Data preparation is the first and a very important step towards any Large Language Model (LLM) development. This paper introduces an easy-to-use, extensible, and scale-flexible open-source data preparation toolkit called Data Prep Kit (DPK). DPK is architected and designed to enable users to scale their data preparation to their needs. With DPK they can prepare data on a local machine or effortlessly scale to run on a cluster with thousands of CPU Cores. DPK comes with a highly scalable, yet extensible set of modules that transform natural language and code data. If the user needs additional transforms, they can be easily developed using extensive DPK support for transform creation. These modules can be used independently or pipelined to perform a series of operations. In this paper, we describe DPK architecture and show its performance from a small scale to a very large number of CPUs. The modules from DPK have been used for the preparation of Granite Models [1] [2]. We believe DPK is a valuable contribution to the AI community to easily prepare data to enhance the performance of their LLM models or to fine-tune models with Retrieval-Augmented Generation (RAG).

Domain experts across engineering, healthcare, and education follow strict standards for producing quality content such as technical manuals, medication instructions, and children's reading materials. However, current works in controllable text generation have yet to explore using these standards as references for control. Towards this end, we introduce Standardize, a retrieval-style in-context learning-based framework to guide large language models to align with expert-defined standards. Focusing on English language standards in the education domain as a use case, we consider the Common European Framework of Reference for Languages (CEFR) and Common Core Standards (CCS) for the task of open-ended content generation. Our findings show that models can gain 40% to 100% increase in precise accuracy for Llama2 and GPT-4, respectively, demonstrating that the use of knowledge artifacts extracted from standards and integrating them in the generation process can effectively guide models to produce better standard-aligned content.

This paper proposes a method for the automatic creation of variables (in the case of regression) that complement the information contained in the initial input vector. The method works as a pre-processing step in which the continuous values of the variable to be regressed are discretized into a set of intervals which are then used to define value thresholds. Then classifiers are trained to predict whether the value to be regressed is less than or equal to each of these thresholds. The different outputs of the classifiers are then concatenated in the form of an additional vector of variables that enriches the initial vector of the regression problem. The implemented system can thus be considered as a generic pre-processing tool. We tested the proposed enrichment method with 5 types of regressors and evaluated it in 33 regression datasets. Our experimental results confirm the interest of the approach.

There is renewed interest in modeling and understanding the nervous system of the nematode Caenorhabditis elegans (C. elegans), as this small model system provides a path to bridge the gap between nervous system structure (connectivity) and function (physiology). However, existing physiology datasets, whether involving passive recording or stimulation, are in distinct formats, and connectome datasets require preprocessing before analysis can commence. Here we compile and homogenize datasets of neural activity and connectivity. Our neural activity dataset is derived from 11 C. elegans neuroimaging experiments, while our connectivity dataset is compiled from 9 connectome annotations based on 3 primary electron microscopy studies and 1 signal propagation study. Physiology datasets, collected under varying protocols, measure calcium fluorescence in labeled subsets of the worm's 300 neurons. Our preprocessing pipeline standardizes these datasets by consistently ordering labeled neurons and resampling traces to a common sampling rate, yielding recordings from approximately 900 worms and 250 uniquely labeled neurons. The connectome datasets, collected from electron microscopy reconstructions, represent the entire nervous system as a graph of connections. Our collection is accessible on HuggingFace, facilitating analysis of the structure-function relationship in biology using modern neural network architectures and enabling cross-lab and cross-animal comparisons.

TorchXRayVision is an open source software library for working with chest X-ray datasets and deep learning models. It provides a common interface and common pre-processing chain for a wide set of publicly available chest X-ray datasets. In addition, a number of classification and representation learning models with different architectures, trained on different data combinations, are available through the library to serve as baselines or feature extractors.

Data preprocessing pipelines, which includes data decoding, cleaning, and transforming, are a crucial component of Machine Learning (ML) training. Thy are computationally intensive and often become a major bottleneck, due to the increasing performance gap between the CPUs used for preprocessing and the GPUs used for model training. Recent studies show that a significant number of CPUs across several machines are required to achieve sufficient throughput to saturate the GPUs, leading to increased resource and energy consumption. When the pipeline involves vocabulary generation, the preprocessing performance scales poorly due to significant row-wise synchronization overhead between different CPU cores and servers. To address this limitation, in this paper we present the design of Piper, a hardware accelerator for tabular data preprocessing, prototype it on FPGAs, and demonstrate its potential for training pipelines of commercial recommender systems. Piper achieves 4.7 sim 71.3times speedup in latency over a 128-core CPU server and outperforms a data-center GPU by 4.8sim 20.3times when using binary input. The impressive performance showcases Piper's potential to increase the efficiency of data preprocessing pipelines and significantly reduce their resource consumption.

Continued pre-training of small language models offers a promising path for domain adaptation with limited computational resources. I've investigated this approach within educational domains, evaluating it as a resource-efficient alternative to training models from scratch. Using a 125M parameter model, I demonstrate significant performance improvements through incremental training on 400 million tokens, followed by further training to reach 1 billion tokens. My approach includes comprehensive data preprocessing, memory-optimized training configurations, and benchmark-based evaluation. Results show notable gains in knowledge-intensive tasks (MMLU +8.1%) and contextual understanding (HellaSwag +7.6%), while revealing educational domain specialization trade-offs. I analyze token efficiency, catastrophic forgetting mitigation strategies, and scaling patterns. My findings suggest that thoughtful preprocessing and training methodologies enable meaningful improvements in language model capabilities even with constrained computational resources, opening pathways for domain-specific adaptation of smaller language models.

We present a novel approach to data preparation for developing multilingual Indic large language model. Our meticulous data acquisition spans open-source and proprietary sources, including Common Crawl, Indic books, news articles, and Wikipedia, ensuring a diverse and rich linguistic representation. For each Indic language, we design a custom preprocessing pipeline to effectively eliminate redundant and low-quality text content. Additionally, we perform deduplication on Common Crawl data to address the redundancy present in 70% of the crawled web pages. This study focuses on developing high-quality data, optimizing tokenization for our multilingual dataset for Indic large language models with 3B and 7B parameters, engineered for superior performance in Indic languages. We introduce a novel multilingual tokenizer training strategy, demonstrating our custom-trained Indic tokenizer outperforms the state-of-the-art OpenAI Tiktoken tokenizer, achieving a superior token-to-word ratio for Indic languages.

Recent parameter-efficient finetuning (PEFT) techniques aim to improve over the considerable cost of fully finetuning large pretrained language models (PLM). As different PEFT techniques proliferate, it is becoming difficult to compare them, in particular in terms of (i) the structure and functionality they add to the PLM, (ii) the different types and degrees of efficiency improvements achieved, (iii) performance at different downstream tasks, and (iv) how differences in structure and functionality relate to efficiency and task performance. To facilitate such comparisons, this paper presents a reference architecture which standardises aspects shared by different PEFT techniques, while isolating differences to specific locations and interactions with the standard components. Through this process of standardising and isolating differences, a modular view of PEFT techniques emerges, supporting not only direct comparison of different techniques and their efficiency and task performance, but also systematic exploration of reusability and composability of the different types of finetuned modules. We demonstrate how the reference architecture can be applied to understand properties and relative advantages of PEFT techniques, hence to inform selection of techniques for specific tasks, and design choices for new PEFT techniques.

This paper presents a comprehensive overview of the data preparation pipeline developed for the OpenGPT-X project, a large-scale initiative aimed at creating open and high-performance multilingual large language models (LLMs). The project goal is to deliver models that cover all major European languages, with a particular focus on real-world applications within the European Union. We explain all data processing steps, starting with the data selection and requirement definition to the preparation of the final datasets for model training. We distinguish between curated data and web data, as each of these categories is handled by distinct pipelines, with curated data undergoing minimal filtering and web data requiring extensive filtering and deduplication. This distinction guided the development of specialized algorithmic solutions for both pipelines. In addition to describing the processing methodologies, we provide an in-depth analysis of the datasets, increasing transparency and alignment with European data regulations. Finally, we share key insights and challenges faced during the project, offering recommendations for future endeavors in large-scale multilingual data preparation for LLMs.

The general capabilities of Large Language Models (LLM) highly rely on the composition and selection on extensive pretraining datasets, treated as commercial secrets by several institutions. To mitigate this issue, we open-source the details of a universally applicable data processing pipeline and validate its effectiveness and potential by introducing a competitive LLM baseline. Specifically, the data processing pipeline consists of broad collection to scale up and reweighting to improve quality. We then pretrain a 7B model BaichuanSEED with 3T tokens processed by our pipeline without any deliberate downstream task-related optimization, followed by an easy but effective supervised fine-tuning stage. BaichuanSEED demonstrates consistency and predictability throughout training and achieves comparable performance on comprehensive benchmarks with several commercial advanced large language models, such as Qwen1.5 and Llama3. We also conduct several heuristic experiments to discuss the potential for further optimization of downstream tasks, such as mathematics and coding.

Technical standards, or simply standards, are established documented guidelines and rules that facilitate the interoperability, quality, and accuracy of systems and processes. In recent years, we have witnessed an emerging paradigm shift where the adoption of generative AI (GenAI) models has increased tremendously, spreading implementation interests across standard-driven industries, including engineering, legal, healthcare, and education. In this paper, we assess the criticality levels of different standards across domains and sectors and complement them by grading the current compliance capabilities of state-of-the-art GenAI models. To support the discussion, we outline possible challenges and opportunities with integrating GenAI for standard compliance tasks while also providing actionable recommendations for entities involved with developing and using standards. Overall, we argue that aligning GenAI with standards through computational methods can help strengthen regulatory and operational compliance. We anticipate this area of research will play a central role in the management, oversight, and trustworthiness of larger, more powerful GenAI-based systems in the near future.

With easier access to powerful compute resources, there is a growing trend in the field of AI for software development to develop larger and larger language models (LLMs) to address a variety of programming tasks. Even LLMs applied to tasks from the high-performance computing (HPC) domain are huge in size (e.g., billions of parameters) and demand expensive compute resources for training. We found this design choice confusing - why do we need large LLMs trained on natural languages and programming languages unrelated to HPC for HPC-specific tasks? In this line of work, we aim to question design choices made by existing LLMs by developing smaller LLMs for specific domains - we call them domain-specific LLMs. Specifically, we start off with HPC as a domain and propose a novel tokenizer named Tokompiler, designed specifically for preprocessing code in HPC and compilation-centric tasks. Tokompiler leverages knowledge of language primitives to generate language-oriented tokens, providing a context-aware understanding of code structure while avoiding human semantics attributed to code structures completely. We applied Tokompiler to pre-train two state-of-the-art models, SPT-Code and Polycoder, for a Fortran code corpus mined from GitHub. We evaluate the performance of these models against the conventional LLMs. Results demonstrate that Tokompiler significantly enhances code completion accuracy and semantic understanding compared to traditional tokenizers in normalized-perplexity tests, down to ~1 perplexity score. This research opens avenues for further advancements in domain-specific LLMs, catering to the unique demands of HPC and compilation tasks.

Extensive LLM applications demand efficient structured generations, particularly for LR(1) grammars, to produce outputs in specified formats (e.g., JSON). Existing methods primarily parse LR(1) grammars into a pushdown automaton (PDA), leading to runtime execution overhead for context-dependent token processing, especially inefficient under large inference batches. To address these issues, we propose Pre^3 that exploits deterministic pushdown automata (DPDA) to optimize the constrained LLM decoding efficiency. First, by precomputing prefix-conditioned edges during the preprocessing, Pre^3 enables ahead-of-time edge analysis and thus makes parallel transition processing possible. Second, by leveraging the prefix-conditioned edges, Pre^3 introduces a novel approach that transforms LR(1) transition graphs into DPDA, eliminating the need for runtime path exploration and achieving edge transitions with minimal overhead. Pre^3 can be seamlessly integrated into standard LLM inference frameworks, reducing time per output token (TPOT) by up to 40% and increasing throughput by up to 36% in our experiments. Our code is available at https://github.com/ModelTC/lightllm.

Advancements in artificial intelligence, machine learning, and deep learning have catalyzed the transformation of big data analytics and management into pivotal domains for research and application. This work explores the theoretical foundations, methodological advancements, and practical implementations of these technologies, emphasizing their role in uncovering actionable insights from massive, high-dimensional datasets. The study presents a systematic overview of data preprocessing techniques, including data cleaning, normalization, integration, and dimensionality reduction, to prepare raw data for analysis. Core analytics methodologies such as classification, clustering, regression, and anomaly detection are examined, with a focus on algorithmic innovation and scalability. Furthermore, the text delves into state-of-the-art frameworks for data mining and predictive modeling, highlighting the role of neural networks, support vector machines, and ensemble methods in tackling complex analytical challenges. Special emphasis is placed on the convergence of big data with distributed computing paradigms, including cloud and edge computing, to address challenges in storage, computation, and real-time analytics. The integration of ethical considerations, including data privacy and compliance with global standards, ensures a holistic perspective on data management. Practical applications across healthcare, finance, marketing, and policy-making illustrate the real-world impact of these technologies. Through comprehensive case studies and Python-based implementations, this work equips researchers, practitioners, and data enthusiasts with the tools to navigate the complexities of modern data analytics. It bridges the gap between theory and practice, fostering the development of innovative solutions for managing and leveraging data in the era of artificial intelligence.

Language model pretraining has become almost synonymous with prohibitive cost, placing it out of reach for much of the academic and open-source communities. Although strong open-source efforts already exist, including open-weight models and open-source training recipes, a cost-efficient, hardware-accessible, and open-source pretraining recipe has long been missing. Even at a small scale, training Llama-3.2-3B costs over \1.5M, and reproducing SmolLM3-3B needs over 700K. In this report, we present an open pretraining recipe designed to lower this barrier. Using this recipe, we train a collection of Puro-2B models from scratch on up to 1.4 trillion tokens with FP8 precision on consumer-grade RTX 5090 GPUs. The models in the collection differ in token budgets and selected recipe variants. Our best model is trained at a compute cost of less than \6.9K and approaches Qwen2.5-1.5B performance under our evaluation protocol. This cost efficiency is enabled by a combination of approaches, including hardware selection, low-precision training, hyperball optimization, curriculum model averaging, and the data recipe. Beyond the recipe itself, we provide two additional results. First, across the Puro-2B collection, we derive a Puro Cost Scaling Law that relates training cost to average model performance; the fitted law suggests that about 4.4K, less than \$5,090, is sufficient to reach the performance of Qwen2-1.5B. Second, as an end-to-end case study, we examine how pretraining data curricula shape downstream performance after post-training. Such controlled studies are enabled by having access to the full pretraining pipeline rather than model weights alone. We release the full training recipe for Puro-2B, including data, code, and model weights under Apache 2.0 at https://huggingface.co/collections/thu-pacman/puro-2b.

Dealing with long and highly complex technical text is a challenge for Large Language Models (LLMs), which still have to unfold their potential in supporting expensive and timeintensive processes like patent drafting. Within patents, the description constitutes more than 90% of the document on average. Yet, its automatic generation remains understudied. When drafting patent applications, patent attorneys typically receive invention reports (IRs), which are usually confidential, hindering research on LLM-supported patent drafting. Often, prepublication research papers serve as IRs. We leverage this duality to build PAP2PAT, an open and realistic benchmark for patent drafting consisting of 1.8k patent-paper pairs describing the same inventions. To address the complex longdocument patent generation task, we propose chunk-based outline-guided generation using the research paper as invention specification. Our extensive evaluation using PAP2PAT and a human case study show that LLMs can effectively leverage information from the paper, but still struggle to provide the necessary level of detail. Fine-tuning leads to more patent-style language, but also to more hallucination. We release our data and code https://github.com/boschresearch/Pap2Pat.

The imperative need to scale computation across numerous nodes highlights the significance of efficient parallel computing, particularly in the realm of Message Passing Interface (MPI) integration. The challenging parallel programming task of generating MPI-based parallel programs has remained unexplored. This study first investigates the performance of state-of-the-art language models in generating MPI-based parallel programs. Findings reveal that widely used models such as GPT-3.5 and PolyCoder (specialized multi-lingual code models) exhibit notable performance degradation, when generating MPI-based programs compared to general-purpose programs. In contrast, domain-specific models such as MonoCoder, which are pretrained on MPI-related programming languages of C and C++, outperform larger models. Subsequently, we introduce a dedicated downstream task of MPI-based program generation by fine-tuning MonoCoder on HPCorpusMPI. We call the resulting model as MPIrigen. We propose an innovative preprocessing for completion only after observing the whole code, thus enabling better completion with a wider context. Comparative analysis against GPT-3.5 zero-shot performance, using a novel HPC-oriented evaluation method, demonstrates that MPIrigen excels in generating accurate MPI functions up to 0.8 accuracy in location and function predictions, and with more than 0.9 accuracy for argument predictions. The success of this tailored solution underscores the importance of domain-specific fine-tuning in optimizing language models for parallel computing code generation, paving the way for a new generation of automatic parallelization tools. The sources of this work are available at our GitHub MPIrigen repository: https://github.com/Scientific-Computing-Lab-NRCN/MPI-rigen

Modern large language model training is no longer limited by data availability, but by the inability of existing preprocessing pipelines to simultaneously achieve massive scale and high data quality. Current approaches are forced to sacrifice one for the other: either aggressively filtering to improve quality at the cost of severe token loss, or retaining large volumes of data while introducing substantial noise. In this work, we introduce FLUX, a preprocessing pipeline specifically designed to break this long-standing trade-off by maximizing token retention while enforcing rigorous quality control. Models trained on FLUX-curated data consistently outperform prior methods. A 3B-parameter model trained on 60B tokens with FLUX achieves 32.14% MMLU accuracy, surpassing the previous state-of-the-art pipeline DCLM (31.98%) and significantly outperforming FineWeb (29.88%). FLUX achieves the same aggregate score as a model trained on DCLM data using only 39B tokens, resulting in a 34.4% reduction in training compute. At the data level, FLUX extracts 50B usable tokens from a single dump (CC-MAIN-2025-51), compared to 40B from DCLM (+25% retention). FLUX-Base yields 192B tokens, exceeding FineWeb's 170B while still maintaining superior quality. Overall, FLUX establishes a new state of the art in web-scale data preprocessing by demonstrating that high retention, strong quality control, and computational efficiency can be achieved simultaneously, redefining the limits of scalable dataset construction for modern language models.

As language models have scaled both their number of parameters and pretraining dataset sizes, the computational cost for pretraining has become intractable except for the most well-resourced teams. This increasing cost makes it ever more important to be able to reuse a model after it has completed pretraining; allowing for a model's abilities to further improve without needing to train from scratch. In this work, we detail a set of guidelines that cover how to design efficacious data distributions and learning rate schedules for continued pretraining of language models. When applying these findings within a continued pretraining run on top of a well-trained 15B parameter model, we show an improvement of 9\% in average model accuracy compared to the baseline of continued training on the pretraining set. The resulting recipe provides a practical starting point with which to begin developing language models through reuse rather than retraining.

During inference for transformer-based large language models (LLM), prefilling is the computation of the key-value (KV) cache for input tokens in the prompt prior to autoregressive generation. For longer input prompt lengths, prefilling will incur a significant overhead on decoding time. In this work, we highlight the following pitfall of prefilling: for batches containing high-varying prompt lengths, significant computation is wasted by the standard practice of padding sequences to the maximum length. As LLMs increasingly support longer context lengths, potentially up to 10 million tokens, variations in prompt lengths within a batch become more pronounced. To address this, we propose Prepacking, a simple yet effective method to optimize prefilling computation. To avoid redundant computation on pad tokens, prepacking combines prompts of varying lengths into a sequence and packs multiple sequences into a compact batch using a bin-packing algorithm. It then modifies the attention mask and positional encoding to compute multiple prefilled KV-caches for multiple prompts within a single sequence. On standard curated dataset containing prompts with varying lengths, we obtain a significant speed and memory efficiency improvements as compared to the default padding-based prefilling computation within Huggingface across a range of base model configurations and inference serving scenarios.

While frontier large language models demonstrate strong reasoning and mathematical capabilities, the practical process of training domain-specialized scientific language models from raw sources remains under-documented. In this work, we present a detailed case study of training a 1.36B-parameter scientific language model directly from raw arXiv LaTeX sources spanning mathematics, computer science, and theoretical physics. We describe an end-to-end pipeline covering metadata filtering, archive validation, LaTeX extraction, text normalization, domain-aware tokenization, and dense transformer training under constrained compute (2xA100 GPUs). Through 24 experimental runs, we analyze training stability, scaling behavior, data yield losses, and infrastructure bottlenecks. Our findings highlight how preprocessing decisions significantly affect usable token volume, how tokenization impacts symbolic stability, and how storage and I/O constraints can rival compute as limiting factors. We further analyze convergence dynamics and show stable training behavior in a data-rich regime (52B pretraining tokens). Rather than proposing a novel architecture, this work provides an engineering-grounded, transparent account of training a small scientific language model from scratch. We hope these insights support researchers operating under moderate compute budgets who seek to build domain-specialized models.

There is a compelling necessity from enterprises for fine tuning LLMs (Large Language Models) o get them trained on proprietary domain knowledge. The challenge is to imbibe the LLMs with domain specific knowledge using the most optimial resource and cost and in the best possible time. Many enterprises rely on RAG (Retrieval Augmented Generation) which does not need LLMs to be ine-tuned but they are limited by the quality of vector databases and their retrieval capabilities rather than the intrinsic capabilities of the LLMs themselves. In our current work we focus on fine tuning LLaMA, an open source LLM using proprietary documents and code from an enterprise repository and use the fine tuned models to evaluate the quality of responses. As part of this work, we aim to guide beginners on how to start with fine tuning an LLM for documentation and code by making educated guesses on size of GPU required and options that are available for formatting the data. We also propose pre processing recipes for both documentation and code to prepare dataset in different formats. The proposed methods of data preparation for document datasets are forming paragraph chunks, forming question and answer pairs and forming keyword and paragraph chunk pairs. For code dataset we propose forming summary and function pairs. Further, we qualitatively evaluate the results of the models for domain specific queries. Finally, we also propose practical guidelines and recommendations for fine tuning LLMs.

ProSper is a python library containing probabilistic algorithms to learn dictionaries. Given a set of data points, the implemented algorithms seek to learn the elementary components that have generated the data. The library widens the scope of dictionary learning approaches beyond implementations of standard approaches such as ICA, NMF or standard L1 sparse coding. The implemented algorithms are especially well-suited in cases when data consist of components that combine non-linearly and/or for data requiring flexible prior distributions. Furthermore, the implemented algorithms go beyond standard approaches by inferring prior and noise parameters of the data, and they provide rich a-posteriori approximations for inference. The library is designed to be extendable and it currently includes: Binary Sparse Coding (BSC), Ternary Sparse Coding (TSC), Discrete Sparse Coding (DSC), Maximal Causes Analysis (MCA), Maximum Magnitude Causes Analysis (MMCA), and Gaussian Sparse Coding (GSC, a recent spike-and-slab sparse coding approach). The algorithms are scalable due to a combination of variational approximations and parallelization. Implementations of all algorithms allow for parallel execution on multiple CPUs and multiple machines for medium to large-scale applications. Typical large-scale runs of the algorithms can use hundreds of CPUs to learn hundreds of dictionary elements from data with tens of millions of floating-point numbers such that models with several hundred thousand parameters can be optimized. The library is designed to have minimal dependencies and to be easy to use. It targets users of dictionary learning algorithms and Machine Learning researchers.

We present FOMO60K, a large-scale, heterogeneous dataset of 60,529 brain Magnetic Resonance Imaging (MRI) scans from 13,900 sessions and 11,187 subjects, aggregated from 16 publicly available sources. The dataset includes both clinical- and research-grade images, multiple MRI sequences, and a wide range of anatomical and pathological variability, including scans with large brain anomalies. Minimal preprocessing was applied to preserve the original image characteristics while reducing barriers to entry for new users. Accompanying code for self-supervised pretraining and finetuning is provided. FOMO60K is intended to support the development and benchmarking of self-supervised learning methods in medical imaging at scale.

Storing open-source fine-tuned models separately introduces redundancy and increases response times in applications utilizing multiple models. Delta-parameter pruning (DPP), particularly the random drop and rescale (DARE) method proposed by Yu et al., addresses this by pruning the majority of delta parameters--the differences between fine-tuned and pre-trained model weights--while typically maintaining minimal performance loss. However, DARE fails when either the pruning rate or the magnitude of the delta parameters is large. We highlight two key reasons for this failure: (1) an excessively large rescaling factor as pruning rates increase, and (2) high mean and variance in the delta parameters. To push DARE's limits, we introduce DAREx (DARE the eXtreme), which features two algorithmic improvements: (1) DAREx-q, a rescaling factor modification that significantly boosts performance at high pruning rates (e.g., >30 % on COLA and SST2 for encoder models, with even greater gains in decoder models), and (2) DAREx-L2, which combines DARE with AdamR, an in-training method that applies appropriate delta regularization before DPP. We also demonstrate that DAREx-q can be seamlessly combined with vanilla parameter-efficient fine-tuning techniques like LoRA and can facilitate structural DPP. Additionally, we revisit the application of importance-based pruning techniques within DPP, demonstrating that they outperform random-based methods when delta parameters are large. Through this comprehensive study, we develop a pipeline for selecting the most appropriate DPP method under various practical scenarios.

High-quality, large-scale corpora are the cornerstone of building foundation models. In this work, we introduce MathPile, a diverse and high-quality math-centric corpus comprising about 9.5 billion tokens. Throughout its creation, we adhered to the principle of ``less is more'', firmly believing in the supremacy of data quality over quantity, even in the pre-training phase. Our meticulous data collection and processing efforts included a complex suite of preprocessing, prefiltering, language identification, cleaning, filtering, and deduplication, ensuring the high quality of our corpus. Furthermore, we performed data contamination detection on downstream benchmark test sets to eliminate duplicates. We hope our MathPile can help to enhance the mathematical reasoning abilities of language models. We plan to open-source different versions of \mathpile with the scripts used for processing, to facilitate future developments in this field.

Autoformalization, the conversion of natural language mathematics into formal languages, offers significant potential for advancing mathematical reasoning. However, existing efforts are limited to formal languages with substantial online corpora and struggle to keep pace with rapidly evolving languages like Lean 4. To bridge this gap, we propose a new benchmark Formalization for Lean~4 (\name) designed to evaluate the autoformalization capabilities of large language models (LLMs). This benchmark encompasses a comprehensive assessment of questions, answers, formal statements, and proofs. Additionally, we introduce a Process-Supervised Verifier (PSV) model that leverages the precise feedback from Lean 4 compilers to enhance autoformalization. Our experiments demonstrate that the PSV method improves autoformalization, enabling higher accuracy using less filtered training data. Furthermore, when fine-tuned with data containing detailed process information, PSV can leverage the data more effectively, leading to more significant improvements in autoformalization for Lean 4. Our dataset and code are available at https://github.com/rookie-joe/PDA.

The quality of training data fundamentally determines the capabilities of large language models (LLMs), yet no unified benchmark exists to measure how well LLMs, agents, and data-centric workflows actually prepare training data end to end. We view LLM-driven data preparation as comprising two complementary capabilities: data construction, which transforms raw sources into supervised training data, and data quality evaluation, which predicts the training value of candidate datasets before downstream training; throughout, "quality" refers to downstream training utility rather than surface-level textual properties. We introduce DataPrep-Bench, the first unified benchmark that jointly evaluates both capabilities under a shared downstream-grounded protocol over six domains and multiple base models. For data construction, methods consume identical raw sources and are scored by fine-tuning a base model on their outputs jointly with Dolly-15k; alongside this track we release Data-Construction-Skill, a skill-guided agent that lifts the Dolly-only baseline by nearly 20 points absolute on Llama-3.1-8B Finance and is competitive with the strongest agent- and DataFlow-based methods in knowledge-extraction-dense domains. For data quality evaluation, scoring functions are scored by Pearson correlation with downstream performance on a shared candidate pool; we release the Distributional Alignment Score (DAS), a distribution-based evaluator that uses MMD between a candidate dataset and a domain proxy. DAS attains the strongest cross-model correlation in four of six domains and is the only metric clearing r > 0.70 simultaneously in Math, Science, and Medical, outperforming existing quality-, diversity-, and heuristic-based evaluators. DataPrep-Bench provides a unified, downstream-grounded framework for measuring progress on both capabilities as co-equal targets of LLM-driven data preparation.

Feature preprocessing continues to play a critical role when applying machine learning and statistical methods to tabular data. In this paper, we propose the use of the kernel density integral transformation as a feature preprocessing step. Our approach subsumes the two leading feature preprocessing methods as limiting cases: linear min-max scaling and quantile transformation. We demonstrate that, without hyperparameter tuning, the kernel density integral transformation can be used as a simple drop-in replacement for either method, offering protection from the weaknesses of each. Alternatively, with tuning of a single continuous hyperparameter, we frequently outperform both of these methods. Finally, we show that the kernel density transformation can be profitably applied to statistical data analysis, particularly in correlation analysis and univariate clustering.

Real-world model deployments demand strong performance on narrow domains where data is often scarce. Typically, practitioners finetune models to specialize them, but this risks overfitting to the domain and forgetting general knowledge. We study a simple strategy, specialized pretraining (SPT), where a small domain dataset, typically reserved for finetuning, is repeated starting from pretraining as a fraction of the total tokens. Across three specialized domains (ChemPile, MusicPile, and ProofPile), SPT improves domain performance and preserves general capabilities after finetuning compared to standard pretraining. In our experiments, SPT reduces the pretraining tokens needed to reach a given domain performance by up to 1.75x. These gains grow when the target domain is underrepresented in the pretraining corpus: on domains far from web text, a 1B SPT model outperforms a 3B standard pretrained model. Beyond these empirical gains, we derive overfitting scaling laws to guide practitioners in selecting the optimal domain-data repetition for a given pretraining compute budget. Our observations reveal the finetuner's fallacy: while finetuning may appear to be the cheapest path to domain adaptation, introducing specialized domain data during pretraining stretches its utility. SPT yields better specialized domain performance (via reduced overfitting across repeated exposures) and better general domain performance (via reduced forgetting during finetuning), ultimately achieving stronger results with fewer parameters and less total compute when amortized over inference. To get the most out of domain data, incorporate it as early in training as possible.

This paper presents NT-Java-1.1B, an open-source specialized code language model built on StarCoderBase-1.1B, designed for coding tasks in Java programming. NT-Java-1.1B achieves state-of-the-art performance, surpassing its base model and majority of other models of similar size on MultiPL-E Java code benchmark. While there have been studies on extending large, generic pre-trained models to improve proficiency in specific programming languages like Python, similar investigations on small code models for other programming languages are lacking. Large code models require specialized hardware like GPUs for inference, highlighting the need for research into building small code models that can be deployed on developer desktops. This paper addresses this research gap by focusing on the development of a small Java code model, NT-Java-1.1B, and its quantized versions, which performs comparably to open models around 1.1B on MultiPL-E Java code benchmarks, making them ideal for desktop deployment. This paper establishes the foundation for specialized models across languages and sizes for a family of NT Models.

Reproducing machine learning experiments requires reconstructing procedures from information scattered across papers, released code, and supporting artifacts. For coding agents, reproduction success can therefore depend on their ability to fill in missing details, rather than on the released artifacts alone. We ask whether preserving recovered procedures and decisions improves subsequent independent reproduction. We define a standardized artifact design comprising a refined codebase, environment setup, experiment launchers, and a reproduction guide, and introduce ReproBridge, an agent workflow for constructing these refined reproducible artifacts. ReproBridge-Bench provides 1,029 tasks from 387 experiments across 36 papers, anchored by five human-verified reference scores per task. Agents attempt tasks in fresh sessions with raw code or refined artifacts; a separate Auditor checks execution evidence. Across four evaluated models, refined artifacts raise mean reproduction success from 76.4% to 92.6% and reduce downstream API spending by 19.7% on average. The cross-model success-rate spread narrows from 21.6 to 3.9 percentage points, with all four models achieving mean success rates above 90%. Removing any component reduces success in the ablation study, with the largest losses from code and environment removal. These results suggest that preserving execution knowledge helps even models with lower raw-code success reproduce experiments more reliably and at lower API cost.

Adapting large-scale pretrained language models to downstream tasks via fine-tuning is the standard method for achieving state-of-the-art performance on NLP benchmarks. However, fine-tuning all weights of models with millions or billions of parameters is sample-inefficient, unstable in low-resource settings, and wasteful as it requires storing a separate copy of the model for each task. Recent work has developed parameter-efficient fine-tuning methods, but these approaches either still require a relatively large number of parameters or underperform standard fine-tuning. In this work, we propose Compacter, a method for fine-tuning large-scale language models with a better trade-off between task performance and the number of trainable parameters than prior work. Compacter accomplishes this by building on top of ideas from adapters, low-rank optimization, and parameterized hypercomplex multiplication layers. Specifically, Compacter inserts task-specific weight matrices into a pretrained model's weights, which are computed efficiently as a sum of Kronecker products between shared "slow" weights and "fast" rank-one matrices defined per Compacter layer. By only training 0.047% of a pretrained model's parameters, Compacter performs on par with standard fine-tuning on GLUE and outperforms standard fine-tuning on SuperGLUE and low-resource settings. Our code is publicly available at~https://github.com/rabeehk/compacter.

Recent work has demonstrated that coding agents can formalize entire advanced mathematics textbooks in Lean 4, yet existing efforts concentrate on branches of mathematics already well-represented in mathlib and measure success solely through kernel acceptance. We address both limitations by applying a coding agent to formalize Numerical Methods for Ordinary Differential Equations, a textbook in numerical analysis that is largely absent from mathlib, stressing the agent's capacity to develop new theory from scratch. We further introduce a systematic, reproducible three-dimensional framework for evaluating the quality of agent-produced formalizations beyond compilation: semantic correctness, Mathlib reuse, and cross-file reuse via LLM-as-judge methods. Applying this framework to our own formalization and to the released outputs of RepoProver and M2F, we uncover recurring unfaithful formalization patterns, including incomplete multi-part statements, added weakening hypotheses, and parameter restrictions, that kernel acceptance entirely obscures. Our results suggest that compilation-based metrics substantially overstate formalization quality, and we provide a reproducible audit methodology to support more rigorous evaluation of future autoformalization systems.

In the dynamic landscape of generative NLP, traditional text processing pipelines limit research flexibility and reproducibility, as they are tailored to specific dataset, task, and model combinations. The escalating complexity, involving system prompts, model-specific formats, instructions, and more, calls for a shift to a structured, modular, and customizable solution. Addressing this need, we present Unitxt, an innovative library for customizable textual data preparation and evaluation tailored to generative language models. Unitxt natively integrates with common libraries like HuggingFace and LM-eval-harness and deconstructs processing flows into modular components, enabling easy customization and sharing between practitioners. These components encompass model-specific formats, task prompts, and many other comprehensive dataset processing definitions. The Unitxt-Catalog centralizes these components, fostering collaboration and exploration in modern textual data workflows. Beyond being a tool, Unitxt is a community-driven platform, empowering users to build, share, and advance their pipelines collaboratively. Join the Unitxt community at https://github.com/IBM/unitxt!

Large language models are strong general-purpose code generators, but executable algorithmic trading remains a demanding specialization target: a model must translate a natural-language strategy specification into correct program logic for a specialized trading framework, execute on historical data, produce trades, and remain semantically faithful to the request. We study two complementary mechanisms for specializing language models for this setting: continued pretraining on algorithmic-trading framework code and supervised fine-tuning (SFT) on agent-validated request-to-code pairs. Evaluation is centered on QuantCode-Bench, our 400-task benchmark for Backtrader strategy generation, together with a repository-level SWE-bench-like track. Continued pretraining improves single-turn Judge Pass from 41.5% to 47.5% for Qwen3.5-397B-A17B and from 27.8% to 33.0% for Qwen3.6-35B-A3B. SFT applied after continued pretraining yields a larger gain for Qwen3.6-35B-A3B, reaching 58.2% Judge Pass and 83.5% successful backtests; in agentic evaluation it raises first-turn success from 22.3% to 58.3% and final success after up to 10 turns from 47.5% to 79.5%. Continued pretraining alone improves first-turn agentic success but lowers final success after repair from 47.5% to 32.5%, consistent with degraded instruction following, whereas SFT improves both. We also identify a capability-retention failure: domain specialization degrades parser-conformant structured tool calling, and targeted recovery SFT restores tool-call formatting but not the base checkpoint's repository-level agent performance. The results show that framework-oriented pretraining, validated SFT, and explicit capability-retention evaluation address distinct failure modes in domain-specific executable code generation.

The field of Deep Learning (DL) has undergone explosive growth during the last decade, with a substantial impact on Natural Language Processing (NLP) as well. Yet, compared to more established disciplines, a lack of common experimental standards remains an open challenge to the field at large. Starting from fundamental scientific principles, we distill ongoing discussions on experimental standards in NLP into a single, widely-applicable methodology. Following these best practices is crucial to strengthen experimental evidence, improve reproducibility and support scientific progress. These standards are further collected in a public repository to help them transparently adapt to future needs.

We present Statistical Calibrated Activation Pruning (SCAP), a post-training activation pruning framework that (1) generalizes sparsification by input activations of Fully-Connected layers for generic and flexible application across Transformers, and (2) features a simple Mode-Centering technique to pre-calibrate activation distributions for maximizing post-training sparsity. Our results demonstrate robust Pareto efficiency compared to prior methods, translating to a 1.5x additional LLM decoding speedup against CATS at iso model quality. SCAP effectiveness is empirically verified across a wide range of models, including recent Transformer Decoders, MoE, Mamba2, Encoding Transformer, and pre-quantized models, highlighting its practicality and scalability. The code is available at: https://github.com/IntelLabs/SCAP.

We introduce Post-Optimization Model Edit (POME), a new algorithm that enhances the performance of fine-tuned large language models using only their pretrained and fine-tuned checkpoints, without requiring extra data or further optimization. The core idea is to apply a muon-style projection to ΔW, the difference between the fine-tuned and pretrained weights. This projection uses truncated singular value decomposition (SVD) to equalize the influence of dominant update directions and prune small singular values, which often represent noise. As a simple post-processing step, POME is completely decoupled from the training pipeline. It requires zero modifications and imposes no overhead, making it universally compatible with any optimizer or distributed framework. POME delivers consistent gains, boosting average performance by +2.5\% on GSM8K and +1.0\% on code generation. Its broad applicability -- from 7B foundation models to 72B RLHF-instructed models -- establishes it as a practical, zero-cost enhancement for any fine-tuning pipeline. Code is available at https://github.com/NUS-HPC-AI-Lab/POME.

Large Language Models (LLMs) are often asked to generate structured outputs that obey precise syntactic rules, such as code snippets or formatted data. Grammar-constrained decoding (GCD) can guarantee that LLM outputs matches such rules by masking out tokens that will provably lead to outputs that do not belong to a specified context-free grammar (CFG). To guarantee soundness, GCD algorithms have to compute how a given LLM subword tokenizer can align with the tokens used by a given context-free grammar and compute token masks based on this information. Doing so efficiently is challenging and existing GCD algorithms require tens of minutes to preprocess common grammars. We present a new GCD algorithm together with an implementation that offers 17.71x faster offline preprocessing than existing approaches while preserving state-of-the-art efficiency in online mask computation.

The use of Project Gutenberg (PG) as a text corpus has been extremely popular in statistical analysis of language for more than 25 years. However, in contrast to other major linguistic datasets of similar importance, no consensual full version of PG exists to date. In fact, most PG studies so far either consider only a small number of manually selected books, leading to potential biased subsets, or employ vastly different pre-processing strategies (often specified in insufficient details), raising concerns regarding the reproducibility of published results. In order to address these shortcomings, here we present the Standardized Project Gutenberg Corpus (SPGC), an open science approach to a curated version of the complete PG data containing more than 50,000 books and more than 3 times 10^9 word-tokens. Using different sources of annotated metadata, we not only provide a broad characterization of the content of PG, but also show different examples highlighting the potential of SPGC for investigating language variability across time, subjects, and authors. We publish our methodology in detail, the code to download and process the data, as well as the obtained corpus itself on 3 different levels of granularity (raw text, timeseries of word tokens, and counts of words). In this way, we provide a reproducible, pre-processed, full-size version of Project Gutenberg as a new scientific resource for corpus linguistics, natural language processing, and information retrieval.

Human feedback plays a pivotal role in aligning large language models (LLMs) with human preferences. However, such feedback is often noisy or inconsistent, which can degrade the quality of reward models and hinder alignment. While various automated data cleaning methods have been proposed to mitigate this issue, a systematic evaluation of their effectiveness and generalizability remains lacking. To bridge this gap, we introduce the first comprehensive benchmark for evaluating 13 preference data cleaning methods in the context of LLM alignment. PrefCleanBench offers a standardized protocol to assess cleaning strategies in terms of alignment performance and generalizability across diverse datasets, model architectures, and optimization algorithms. By unifying disparate methods and rigorously comparing them, we uncover key factors that determine the success of data cleaning in alignment tasks. This benchmark lays the groundwork for principled and reproducible approaches to improving LLM alignment through better data quality-highlighting the crucial but underexplored role of data preprocessing in responsible AI development. We release modular implementations of all methods to catalyze further research: https://github.com/deeplearning-wisc/PrefCleanBench.

Large Language Models (LLMs), typified by OpenAI's GPT series and Meta's LLaMA variants, have marked a significant advancement in artificial intelligence. Trained on vast amounts of text data, LLMs are capable of understanding and generating human-like text across a diverse range of topics. This study expands on the applications of LLMs, exploring their potential in data preprocessing, a critical stage in data mining and analytics applications. We delve into the applicability of state-of-the-art LLMs such as GPT-3.5, GPT-4, and Vicuna-13B for error detection, data imputation, schema matching, and entity matching tasks. Alongside showcasing the inherent capabilities of LLMs, we highlight their limitations, particularly in terms of computational expense and inefficiency. We propose an LLM-based framework for data preprocessing, which integrates cutting-edge prompt engineering techniques, coupled with traditional methods like contextualization and feature selection, to improve the performance and efficiency of these models. The effectiveness of LLMs in data preprocessing is evaluated through an experimental study spanning 12 datasets. GPT-4 emerged as a standout, achieving 100\% accuracy or F1 score on 4 datasets, suggesting LLMs' immense potential in these tasks. Despite certain limitations, our study underscores the promise of LLMs in this domain and anticipates future developments to overcome current hurdles.

Released in 2025, Institutional Books: Harvard Library (IB-HL) is a collection of 983,004 volumes (242B o200k_base tokens), originally digitized through Harvard Library's participation in the Google Books Library project. As researchers and developers have begun to use IB-HL, a tension has emerged between standard large-scale preprocessing practices and the goals of careful information stewardship. Many existing pipelines optimize for web text: as a result, they tend to aggressively filter, deduplicate, restrict by language, and sometimes discard meaningful metadata. Meanwhile, researchers seeking to use IB-HL duplicate effort while performing similar processing and analysis. We describe an approach that we call Enriched Text. Instead of producing a single 'complete' stream of tokens, we normalize the text while preserving metadata through annotations. We separate endmatter, detect per-paragraph language, identify clusters of duplicate paragraphs, and compute per-paragraph bits-per-byte scores. We provide this information through HTML-like annotations layered on top of the text. By parsing these annotations, users can tailor the output to their own needs instead of accepting a global editorial decision on content. The pipeline applies to all approx250 languages in the collection. This report describes this project's goals, implementation, and design rationale. The release includes IB-HL-ET (an enriched-text version of IB-HL containing 217B o200k_base tokens across 983,003 volumes, organized into 1.39B annotated subtopic paragraphs) and the pipeline that produced it. These serve to make the collection easier for machines to parse and for humans to study.

As researchers and practitioners apply Machine Learning to increasingly more software engineering problems, the approaches they use become more sophisticated. A lot of modern approaches utilize internal code structure in the form of an abstract syntax tree (AST) or its extensions: path-based representation, complex graph combining AST with additional edges. Even though the process of extracting ASTs from code can be done with different parsers, the impact of choosing a parser on the final model quality remains unstudied. Moreover, researchers often omit the exact details of extracting particular code representations. In this work, we evaluate two models, namely Code2Seq and TreeLSTM, in the method name prediction task backed by eight different parsers for the Java language. To unify the process of data preparation with different parsers, we develop SuperParser, a multi-language parser-agnostic library based on PathMiner. SuperParser facilitates the end-to-end creation of datasets suitable for training and evaluation of ML models that work with structural information from source code. Our results demonstrate that trees built by different parsers vary in their structure and content. We then analyze how this diversity affects the models' quality and show that the quality gap between the most and least suitable parsers for both models turns out to be significant. Finally, we discuss other features of the parsers that researchers and practitioners should take into account when selecting a parser along with the impact on the models' quality. The code of SuperParser is publicly available at https://doi.org/10.5281/zenodo.6366591. We also publish Java-norm, the dataset we use to evaluate the models: https://doi.org/10.5281/zenodo.6366599.

Ex-post harmonisation is one of many data preprocessing processes used to combine the increasingly vast and diverse sources of data available for research and analysis. Documenting provenance and ensuring the quality of multi-source datasets is vital for ensuring trustworthy scientific research and encouraging reuse of existing harmonisation efforts. However, capturing and communicating statistically relevant properties of harmonised datasets is difficult without a universal standard for describing harmonisation operations. Our paper combines mathematical and computer science perspectives to address this need. The Crossmaps Framework defines a new approach for transforming existing variables collected under a specific measurement or classification standard to an imputed counterfactual variable indexed by some target standard. It uses computational graphs to separate intended transformation logic from actual data transformations, and avoid the risk of syntactically valid data manipulation scripts resulting in statistically questionable data. In this paper, we introduce the Crossmaps Framework through the example of ex-post harmonisation of aggregated statistics in the social sciences. We define a new provenance task abstraction, the crossmap transform, and formalise two associated objects, the shared mass array and the crossmap. We further define graph, matrix and list encodings of crossmaps and discuss resulting implications for understanding statistical properties of ex-post harmonisation and designing error minimising workflows.

Data preparation aims to denoise raw datasets, uncover cross-dataset relationships, and extract valuable insights from them, which is essential for a wide range of data-centric applications. Driven by (i) rising demands for application-ready data (e.g., for analytics, visualization, decision-making), (ii) increasingly powerful LLM techniques, and (iii) the emergence of infrastructures that facilitate flexible agent construction (e.g., using Databricks Unity Catalog), LLM-enhanced methods are rapidly becoming a transformative and potentially dominant paradigm for data preparation. By investigating hundreds of recent literature works, this paper presents a systematic review of this evolving landscape, focusing on the use of LLM techniques to prepare data for diverse downstream tasks. First, we characterize the fundamental paradigm shift, from rule-based, model-specific pipelines to prompt-driven, context-aware, and agentic preparation workflows. Next, we introduce a task-centric taxonomy that organizes the field into three major tasks: data cleaning (e.g., standardization, error processing, imputation), data integration (e.g., entity matching, schema matching), and data enrichment (e.g., data annotation, profiling). For each task, we survey representative techniques, and highlight their respective strengths (e.g., improved generalization, semantic understanding) and limitations (e.g., the prohibitive cost of scaling LLMs, persistent hallucinations even in advanced agents, the mismatch between advanced methods and weak evaluation). Moreover, we analyze commonly used datasets and evaluation metrics (the empirical part). Finally, we discuss open research challenges and outline a forward-looking roadmap that emphasizes scalable LLM-data systems, principled designs for reliable agentic workflows, and robust evaluation protocols.

Medical vision-language pretraining increasingly relies on medical reports as large-scale supervisory signals; however, raw reports often exhibit substantial stylistic heterogeneity, variable length, and a considerable amount of image-irrelevant content. Although text normalization is frequently adopted as a preprocessing step in prior work, its design principles and empirical impact on vision-language pretraining remain insufficiently and systematically examined. In this study, we present MedTri, a deployable normalization framework for medical vision-language pretraining that converts free-text reports into a unified [Anatomical Entity: Radiologic Description + Diagnosis Category] triplet. This structured, anatomy-grounded normalization preserves essential morphological and spatial information while removing stylistic noise and image-irrelevant content, providing consistent and image-grounded textual supervision at scale. Across multiple datasets spanning both X-ray and computed tomography (CT) modalities, we demonstrate that structured, anatomy-grounded text normalization is an important factor in medical vision-language pretraining quality, yielding consistent improvements over raw reports and existing normalization baselines. In addition, we illustrate how this normalization can easily support modular text-level augmentation strategies, including knowledge enrichment and anatomy-grounded counterfactual supervision, which provide complementary gains in robustness and generalization without altering the core normalization process. Together, our results position structured text normalization as a critical and generalizable preprocessing component for medical vision-language learning, while MedTri provides this normalization platform. Code and data will be released at https://github.com/Arturia-Pendragon-Iris/MedTri.

Recent advancements in NLP have witnessed the groundbreaking impact of pretrained models, yielding impressive outcomes across various tasks. This study seeks to extend the power of pretraining methodologies to facilitating the prediction over tables in data science, a domain traditionally overlooked, yet inherently challenging due to the plethora of table schemas intrinsic to different tasks. The primary research questions underpinning this work revolve around the establishment of a universal pretraining protocol for tables with varied structures, the generalizability and transferability of learned knowledge across tasks, the adaptation to diverse downstream applications, and the incorporation of incremental columns over time. In response to these challenges, we introduce UniTabE, a straightforward yet effective method designed to process tables in a uniform manner, devoid of constraints imposed by specific table structures. UniTabE's core concept relies on representing each basic table element with a module, termed TabUnit. This is subsequently followed by a Transformer encoder to refine the representation. Moreover, our model is designed to facilitate pretraining and finetuning through the utilization of free-form prompts. In order to implement the pretraining phase, we curated an expansive tabular dataset comprising approximately 13B samples, meticulously gathered from the Kaggle platform. This research primarily centers on classification and regression tasks involving tabular data, and conducts rigorous experimental testing and analyses to validate the effectiveness of our methodology. The experimental results demonstrate UniTabE's superior performance against several baselines across massive benchmarks. This, therefore, underscores UniTabE's potential to significantly enhance the semantic representation of tabular data, thereby marking a significant stride for tabular data analysis.

Structural pruning has emerged as a promising approach for producing more efficient models. Nevertheless, the community suffers from a lack of standardized benchmarks and metrics, leaving the progress in this area not fully comprehended. To fill this gap, we present the first comprehensive benchmark, termed PruningBench, for structural pruning. PruningBench showcases the following three characteristics: 1) PruningBench employs a unified and consistent framework for evaluating the effectiveness of diverse structural pruning techniques; 2) PruningBench systematically evaluates 16 existing pruning methods, encompassing a wide array of models (e.g., CNNs and ViTs) and tasks (e.g., classification and detection); 3) PruningBench provides easily implementable interfaces to facilitate the implementation of future pruning methods, and enables the subsequent researchers to incorporate their work into our leaderboards. We provide an online pruning platform for customizing pruning tasks and reproducing all results in this paper. Leaderboard results can also be available.

There is growing evidence that pretraining on high quality, carefully thought-out tokens such as code or mathematics plays an important role in improving the reasoning abilities of large language models. For example, Minerva, a PaLM model finetuned on billions of tokens of mathematical documents from arXiv and the web, reported dramatically improved performance on problems that require quantitative reasoning. However, because all known open source web datasets employ preprocessing that does not faithfully preserve mathematical notation, the benefits of large scale training on quantitive web documents are unavailable to the research community. We introduce OpenWebMath, an open dataset inspired by these works containing 14.7B tokens of mathematical webpages from Common Crawl. We describe in detail our method for extracting text and LaTeX content and removing boilerplate from HTML documents, as well as our methods for quality filtering and deduplication. Additionally, we run small-scale experiments by training 1.4B parameter language models on OpenWebMath, showing that models trained on 14.7B tokens of our dataset surpass the performance of models trained on over 20x the amount of general language data. We hope that our dataset, openly released on the Hugging Face Hub, will help spur advances in the reasoning abilities of large language models.

Tokenization is the first -- and often least scrutinized -- step of most NLP pipelines. Standard algorithms for learning tokenizers rely on frequency-based objectives, which favor languages dominant in the training data and consequently leave lower-resource languages with tokenizations that are disproportionately longer, morphologically implausible, or even riddled with <UNK> placeholders. This phenomenon ultimately amplifies computational and financial inequalities between users from different language backgrounds. To remedy this, we introduce Parity-aware Byte Pair Encoding (BPE), a variant of the widely-used BPE algorithm. At every merge step, Parity-aware BPE maximizes the compression gain of the currently worst-compressed language, trading a small amount of global compression for cross-lingual parity. We find empirically that Parity-aware BPE leads to more equitable token counts across languages, with negligible impact on global compression rate and no substantial effect on language-model performance in downstream tasks.

Structured pruning is a hardware-friendly way to compress LLMs, but it is mostly validated on multiple-choice recognition tasks, while the same compressed checkpoints can collapse on the free-form generation that deployment actually requires. Two observations trace this gap. First, greedy pass@1 nearly vanishes after compression, yet pass@k recovers substantially under repeated sampling: useful generations are demoted, not erased. Second, the recoverable regime fails mainly through suffix repetition. Recovery should therefore train on the compressed model's own on-policy states with dense token-level supervision, which On-Policy Distillation (OPD) provides by reusing the pre-compression model as a frozen teacher. However, long on-policy rollouts spend early recovery budget on low-information repetitive suffixes, delaying loss descent. To mitigate this waste, we propose \shortopd, a short-to-long OPD schedule that detects teacher-confirmed repetitive suffixes, treats the surviving prefix as each rollout's effective length, and allocates future rollout budgets to the effective lengths the policy can currently use. Across math, code, and open-ended generation, \shortopd\ raises the compressed model's score to about 9times its unrecovered value and 1.6--4.4times standard recovery recipes (SFT w/o KD, KD, and SeqKD), and it matches a fixed 8192-token rollout horizon within two points using a quarter of the training time (8.5 vs.\ 35.9 hours) and 71% fewer rollout tokens. We hope this recipe helps move structured pruning beyond marginal gains on perplexity and multiple-choice benchmarks, a step closer to deployment-ready generation quality.

Tables stored in databases and tables which are present in web pages and articles account for a large part of semi-structured data that is available on the internet. It then becomes pertinent to develop a modeling approach with large language models (LLMs) that can be used to solve diverse table tasks such as semantic parsing, question answering as well as classification problems. Traditionally, there existed separate models specialized for each task individually. It raises the question of how far can we go to build a unified model that works well on some table tasks without significant degradation on others. To that end, we attempt at creating a shared modeling approach in the pretraining stage with encoder-decoder style LLMs that can cater to diverse tasks. We evaluate our approach that continually pretrains and finetunes different model families of T5 with data from tables and surrounding context, on these downstream tasks at different model scales. Through multiple ablation studies, we observe that our pretraining with self-supervised objectives can significantly boost the performance of the models on these tasks. As an example of one improvement, we observe that the instruction finetuned public models which come specialized on text question answering (QA) and have been trained on table data still have room for improvement when it comes to table specific QA. Our work is the first attempt at studying the advantages of a unified approach to table specific pretraining when scaled from 770M to 11B sequence to sequence models while also comparing the instruction finetuned variants of the models.

The BigCode project is an open-scientific collaboration working on the responsible development of large language models for code. This tech report describes the progress of the collaboration until December 2022, outlining the current state of the Personally Identifiable Information (PII) redaction pipeline, the experiments conducted to de-risk the model architecture, and the experiments investigating better preprocessing methods for the training data. We train 1.1B parameter models on the Java, JavaScript, and Python subsets of The Stack and evaluate them on the MultiPL-E text-to-code benchmark. We find that more aggressive filtering of near-duplicates can further boost performance and, surprisingly, that selecting files from repositories with 5+ GitHub stars deteriorates performance significantly. Our best model outperforms previous open-source multilingual code generation models (InCoder-6.7B and CodeGen-Multi-2.7B) in both left-to-right generation and infilling on the Java, JavaScript, and Python portions of MultiPL-E, despite being a substantially smaller model. All models are released under an OpenRAIL license at https://hf.co/bigcode.

Byte Pair Encoding (BPE) tokenizers, widely used in Large Language Models, face challenges in multilingual settings, including penalization of non-Western scripts and the creation of tokens with partial UTF-8 sequences. Pretokenization, often reliant on complex regular expressions, can also introduce fragility and unexpected edge cases. We propose SCRIPT (Script Category Representation in PreTokenization), a novel encoding scheme that bypasses UTF-8 byte conversion by using initial tokens based on Unicode script and category properties. This approach enables a simple, rule-based pretokenization strategy that respects script boundaries, offering a robust alternative to pretokenization strategies based on regular expressions. We also introduce and validate a constrained BPE merging strategy that enforces character integrity, applicable to both SCRIPT-BPE and byte-based BPE. Our experiments demonstrate that SCRIPT-BPE achieves competitive compression while eliminating encoding-based penalties for non-Latin-script languages.

Medical applications of machine learning (ML) have experienced a surge in popularity in recent years. The intensive care unit (ICU) is a natural habitat for ML given the abundance of available data from electronic health records. Models have been proposed to address numerous ICU prediction tasks like the early detection of complications. While authors frequently report state-of-the-art performance, it is challenging to verify claims of superiority. Datasets and code are not always published, and cohort definitions, preprocessing pipelines, and training setups are difficult to reproduce. This work introduces Yet Another ICU Benchmark (YAIB), a modular framework that allows researchers to define reproducible and comparable clinical ML experiments; we offer an end-to-end solution from cohort definition to model evaluation. The framework natively supports most open-access ICU datasets (MIMIC III/IV, eICU, HiRID, AUMCdb) and is easily adaptable to future ICU datasets. Combined with a transparent preprocessing pipeline and extensible training code for multiple ML and deep learning models, YAIB enables unified model development. Our benchmark comes with five predefined established prediction tasks (mortality, acute kidney injury, sepsis, kidney function, and length of stay) developed in collaboration with clinicians. Adding further tasks is straightforward by design. Using YAIB, we demonstrate that the choice of dataset, cohort definition, and preprocessing have a major impact on the prediction performance - often more so than model class - indicating an urgent need for YAIB as a holistic benchmarking tool. We provide our work to the clinical ML community to accelerate method development and enable real-world clinical implementations. Software Repository: https://github.com/rvandewater/YAIB.

Pretraining large language models (LLMs) on high-quality, structured data such as mathematics and code substantially enhances reasoning capabilities. However, existing math-focused datasets built from Common Crawl suffer from degraded quality due to brittle extraction heuristics, lossy HTML-to-text conversion, and the failure to reliably preserve mathematical structure. In this work, we introduce Nemotron-CC-Math, a large-scale, high-quality mathematical corpus constructed from Common Crawl using a novel, domain-agnostic pipeline specifically designed for robust scientific text extraction. Unlike previous efforts, our pipeline recovers math across various formats (e.g., MathJax, KaTeX, MathML) by leveraging layout-aware rendering with lynx and a targeted LLM-based cleaning stage. This approach preserves the structural integrity of equations and code blocks while removing boilerplate, standardizing notation into LaTeX representation, and correcting inconsistencies. We collected a large, high-quality math corpus, namely Nemotron-CC-Math-3+ (133B tokens) and Nemotron-CC-Math-4+ (52B tokens). Notably, Nemotron-CC-Math-4+ not only surpasses all prior open math datasets-including MegaMath, FineMath, and OpenWebMath-but also contains 5.5 times more tokens than FineMath-4+, which was previously the highest-quality math pretraining dataset. When used to pretrain a Nemotron-T 8B model, our corpus yields +4.8 to +12.6 gains on MATH and +4.6 to +14.3 gains on MBPP+ over strong baselines, while also improving general-domain performance on MMLU and MMLU-Stem. We present the first pipeline to reliably extract scientific content--including math--from noisy web-scale data, yielding measurable gains in math, code, and general reasoning, and setting a new state of the art among open math pretraining corpora. To support open-source efforts, we release our code and datasets.

The rapid advancement of Large Language Models (LLMs) has resulted in a significant knowledge gap between the open-source community and industry, primarily because the latter relies on closed-source, high-quality data and training recipes. To address this, we introduce PCMind-2.1-Kaiyuan-2B, a fully open-source 2-billion-parameter model focused on improving training efficiency and effectiveness under resource constraints. Our methodology includes three key innovations: a Quantile Data Benchmarking method for systematically comparing heterogeneous open-source datasets and providing insights on data mixing strategies; a Strategic Selective Repetition scheme within a multi-phase paradigm to effectively leverage sparse, high-quality data; and a Multi-Domain Curriculum Training policy that orders samples by quality. Supported by a highly optimized data preprocessing pipeline and architectural modifications for FP16 stability, Kaiyuan-2B achieves performance competitive with state-of-the-art fully open-source models, demonstrating practical and scalable solutions for resource-limited pretraining. We release all assets (including model weights, data, and code) under Apache 2.0 license at https://huggingface.co/thu-pacman/PCMind-2.1-Kaiyuan-2B.

Meta-learning researchers face two fundamental issues in their empirical work: prototyping and reproducibility. Researchers are prone to make mistakes when prototyping new algorithms and tasks because modern meta-learning methods rely on unconventional functionalities of machine learning frameworks. In turn, reproducing existing results becomes a tedious endeavour -- a situation exacerbated by the lack of standardized implementations and benchmarks. As a result, researchers spend inordinate amounts of time on implementing software rather than understanding and developing new ideas. This manuscript introduces learn2learn, a library for meta-learning research focused on solving those prototyping and reproducibility issues. learn2learn provides low-level routines common across a wide-range of meta-learning techniques (e.g. meta-descent, meta-reinforcement learning, few-shot learning), and builds standardized interfaces to algorithms and benchmarks on top of them. In releasing learn2learn under a free and open source license, we hope to foster a community around standardized software for meta-learning research.

Pre-tokenization, the initial step in many modern tokenization pipelines, segments text into smaller units called pretokens, typically splitting on whitespace and punctuation. While this process encourages having full, individual words as tokens, it introduces a fundamental limitation in most tokenization algorithms such as Byte Pair Encoding (BPE). Specifically, pre-tokenization causes the distribution of tokens in a corpus to heavily skew towards common, full-length words. This skewed distribution limits the benefits of expanding to larger vocabularies, since the additional tokens appear with progressively lower counts. To overcome this barrier, we propose BoundlessBPE, a modified BPE algorithm that relaxes the pretoken boundary constraint. Our approach selectively merges two complete pretokens into a larger unit we term a superword. Superwords are not necessarily semantically cohesive. For example, the pretokens " of" and " the" might be combined to form the superword " of the". This merging strategy results in a substantially more uniform distribution of tokens across a corpus than standard BPE, and compresses text more effectively, with an approximate 20% increase in bytes per token.

Developing documentation guidelines and easy-to-use templates for datasets and models is a challenging task, especially given the variety of backgrounds, skills, and incentives of the people involved in the building of natural language processing (NLP) tools. Nevertheless, the adoption of standard documentation practices across the field of NLP promotes more accessible and detailed descriptions of NLP datasets and models, while supporting researchers and developers in reflecting on their work. To help with the standardization of documentation, we present two case studies of efforts that aim to develop reusable documentation templates -- the HuggingFace data card, a general purpose card for datasets in NLP, and the GEM benchmark data and model cards with a focus on natural language generation. We describe our process for developing these templates, including the identification of relevant stakeholder groups, the definition of a set of guiding principles, the use of existing templates as our foundation, and iterative revisions based on feedback.

Process mining, i.e., a sub-field of data science focusing on the analysis of event data generated during the execution of (business) processes, has seen a tremendous change over the past two decades. Starting off in the early 2000's, with limited to no tool support, nowadays, several software tools, i.e., both open-source, e.g., ProM and Apromore, and commercial, e.g., Disco, Celonis, ProcessGold, etc., exist. The commercial process mining tools provide limited support for implementing custom algorithms. Moreover, both commercial and open-source process mining tools are often only accessible through a graphical user interface, which hampers their usage in large-scale experimental settings. Initiatives such as RapidProM provide process mining support in the scientific workflow-based data science suite RapidMiner. However, these offer limited to no support for algorithmic customization. In the light of the aforementioned, in this paper, we present a novel process mining library, i.e. Process Mining for Python (PM4Py) that aims to bridge this gap, providing integration with state-of-the-art data science libraries, e.g., pandas, numpy, scipy and scikit-learn. We provide a global overview of the architecture and functionality of PM4Py, accompanied by some representative examples of its usage.

Tokenization is a critical preprocessing step for large language models (LLMs), directly impacting training efficiency and downstream performance. General-purpose tokenizers trained predominantly on English and Latin-script languages exhibit suboptimal performance on morphologically rich languages such as Arabic, resulting in inflated token sequences and reduced compression efficiency. In this work, we present AraToken, an Arabic-optimized tokenizer built on SentencePiece Unigram algorithm with a comprehensive normalization pipeline addressing Arabic-specific orthographic variations including Alif variants, diacritics, and Arabic-Indic numerals. We systematically compare BPE, WordPiece, and SentencePiece algorithms across multiple configurations, demonstrating that SentencePiece with normalization achieves 18% lower fertility (1.199 vs 1.35 tokens/word) compared to unnormalized baselines. Furthermore, we introduce the Language Extension Pipeline (LEP), a method for integrating the optimized tokenizer into Qwen3-0.6B through vocabulary extension with mean subtoken initialization and selective transformer layer unfreezing. Our experiments show that LEP reduces evaluation loss from 8.28 to 2.43 within 800 training steps on 100K Arabic samples. We release our tokenizer, training scripts, and model checkpoints to facilitate Arabic NLP research.

The high computational cost associated with pretraining large language models limits their research. Two strategies have emerged to address this issue: domain specialization and pretraining with high-quality data. To explore these strategies, we specialized the Sabi\'a-2 Small model with 1.9 billion unique tokens from reputable Brazilian legal sources and conducted few-shot evaluations on legal and general knowledge exams. Our model, Juru, demonstrates the benefits of domain specialization with a reduced amount of pretraining data. However, this specialization comes at the expense of degrading performance in other knowledge areas within the same language. This study contributes to the growing body of scientific evidence showing that pretraining data selection may enhance the performance of large language models, enabling the exploration of these models at a lower cost.

Faithfully translating research papers into repository-level implementations remains challenging because papers often describe methods at a high level, leave implementation assumptions implicit, and require generated repositories to preserve method logic, evaluation protocols, and cross-file consistency. Despite recent advances in paper-to-code agents, their intermediate outputs are often presented as free-form plans or summaries that downstream coding agents may ignore, reinterpret, or compress, leading to algorithmic simplification and inconsistent repository structure. To address these challenges, we introduce PaperCompiler, a paper-to-code generation framework that compiles paper-grounded evidence into explicit repository-level implementation specifications. PaperCompiler grounds implementation-relevant evidence while preserving source provenance and distinguishing paper-supported, inferred, externally delegated, and unresolved information. The resulting specifications encode non-degradation requirements, ownership assignments, cross-file dependencies, and file-level constraints. Repository generation proceeds under these compiled specifications while retaining flexibility over local engineering choices not fixed by the paper. PaperCompiler outperforms strong baselines on Paper2CodeBench, achieving a 13.8% relative improvement in reference-based fidelity (from 3.64 to 4.15) and reducing high-severity evaluator critiques (from 13.2% to 6.1%).

The web contains large-scale, diverse, and abundant information to satisfy the information-seeking needs of humans. Through meticulous data collection, preprocessing, and curation, webpages can be used as a fundamental data resource for language model pretraining. However, when confronted with the progressively revolutionized and intricate nature of webpages, rule-based/feature-based web scrapers are becoming increasingly inadequate. This paper presents a simple, fast, and effective Neural web Scraper (NeuScraper) to help extract primary and clean text contents from webpages. Experimental results show that NeuScraper surpasses the baseline scrapers by achieving more than a 20% improvement, demonstrating its potential in extracting higher-quality data to facilitate the language model pretraining. All of the code is available at https://github.com/OpenMatch/NeuScraper.

The performance of large language models (LLMs) is deeply influenced by the quality and composition of their training data. While much of the existing work has centered on English, there remains a gap in understanding how to construct effective training corpora for other languages. We explore scalable methods for building web-based corpora for LLMs. We apply them to build a new 120B token corpus in Portuguese that achieves competitive results to an industrial-grade corpus. Using a continual pretraining setup, we study how different data selection and preprocessing strategies affect LLM performance when transitioning a model originally trained in English to another language. Our findings demonstrate the value of language-specific filtering pipelines, including classifiers for education, science, technology, engineering, and mathematics (STEM), as well as toxic content. We show that adapting a model to the target language leads to performance improvements, reinforcing the importance of high-quality, language-specific data. While our case study focuses on Portuguese, our methods are applicable to other languages, offering insights for multilingual LLM development.

Overparameterized Neural Networks (NN) display state-of-the-art performance. However, there is a growing need for smaller, energy-efficient, neural networks tobe able to use machine learning applications on devices with limited computational resources. A popular approach consists of using pruning techniques. While these techniques have traditionally focused on pruning pre-trained NN (LeCun et al.,1990; Hassibi et al., 1993), recent work by Lee et al. (2018) has shown promising results when pruning at initialization. However, for Deep NNs, such procedures remain unsatisfactory as the resulting pruned networks can be difficult to train and, for instance, they do not prevent one layer from being fully pruned. In this paper, we provide a comprehensive theoretical analysis of Magnitude and Gradient based pruning at initialization and training of sparse architectures. This allows us to propose novel principled approaches which we validate experimentally on a variety of NN architectures.

Reproducibility is central to research credibility, yet large-scale reanalysis of empricial data remains costly because replication packages vary widely in structure, software environment, and documentation. We develop and evaluate an agentic AI workflow that addresses this execution bottleneck while preserving scientific rigor. The system separates scientific reasoning from computational execution: researchers design fixed diagnostic templates, and the workflow automates the acquisition, harmonization, and execution of replication materials using pre-specified, version-controlled code. A structured knowledge layer records resolved failure patterns, enabling adaptation across heterogeneous studies while keeping each pipeline version transparent and stable. We evaluate this workflow on 92 instrumental variable (IV) studies, including 67 with manually verified reproducible 2SLS estimates and 25 newly published IV studies under identical criteria. For each paper, we analyze up to three two-stage least squares (2SLS) specifications, totaling 215. Across the 92 papers, the system achieves 87% end-to-end success overall. Conditional on accessible data and code, reproducibility is 100% at both the paper and specification levels. The framework substantially lowers the cost of executing established empirical protocols and can be adapted in empirical settings where analytic templates and norms of transparency are well established.

Obtaining text datasets with semantic annotations is an effortful process, yet crucial for supervised training in natural language processsing (NLP). In general, developing and applying new NLP pipelines in domain-specific contexts for tasks often requires custom designed datasets to address NLP tasks in supervised machine learning fashion. When operating in non-English languages for medical data processing, this exposes several minor and major, interconnected problems such as lack of task-matching datasets as well as task-specific pre-trained models. In our work we suggest to leverage pretrained language models for training data acquisition in order to retrieve sufficiently large datasets for training smaller and more efficient models for use-case specific tasks. To demonstrate the effectiveness of your approach, we create a custom dataset which we use to train a medical NER model for German texts, GPTNERMED, yet our method remains language-independent in principle. Our obtained dataset as well as our pre-trained models are publicly available at: https://github.com/frankkramer-lab/GPTNERMED

Since compute grows much faster than web text available for language model pre-training, we ask how one should approach pre-training under fixed data and no compute constraints. We first show that existing data-constrained approaches of increasing epoch count and parameter count eventually overfit, and we significantly improve upon such recipes by properly tuning regularization, finding that the optimal weight decay is 30times larger than standard practice. Since our regularized recipe monotonically decreases loss following a simple power law in parameter count, we estimate its best possible performance via the asymptote of its scaling law rather than the performance at a fixed compute budget. We then identify that ensembling independently trained models achieves a significantly lower loss asymptote than the regularized recipe. Our best intervention combining epoching, regularization, parameter scaling, and ensemble scaling achieves an asymptote at 200M tokens using 5.17times less data than our baseline, and our data scaling laws predict that this improvement persists at higher token budgets. We find that our data efficiency gains can be realized at much smaller parameter counts as we can distill an ensemble into a student model that is 8times smaller and retains 83% of the ensembling benefit. Finally, our interventions designed for validation loss generalize to downstream benchmarks, achieving a 9% improvement for pre-training evals and a 17.5times data efficiency improvement over continued pre-training on math mid-training data. Our results show that simple algorithmic improvements can enable significantly more data-efficient pre-training in a compute-rich future.

Modern deep neural networks, particularly recent large language models, come with massive model sizes that require significant computational and storage resources. To enable the deployment of modern models on resource-constrained environments and accelerate inference time, researchers have increasingly explored pruning techniques as a popular research direction in neural network compression. However, there is a dearth of up-to-date comprehensive review papers on pruning. To address this issue, in this survey, we provide a comprehensive review of existing research works on deep neural network pruning in a taxonomy of 1) universal/specific speedup, 2) when to prune, 3) how to prune, and 4) fusion of pruning and other compression techniques. We then provide a thorough comparative analysis of seven pairs of contrast settings for pruning (e.g., unstructured/structured) and explore emerging topics, including post-training pruning, different levels of supervision for pruning, and broader applications (e.g., adversarial robustness) to shed light on the commonalities and differences of existing methods and lay the foundation for further method development. To facilitate future research, we build a curated collection of datasets, networks, and evaluations on different applications. Finally, we provide some valuable recommendations on selecting pruning methods and prospect promising research directions. We build a repository at https://github.com/hrcheng1066/awesome-pruning.

Language models for scientific tasks are trained on text from scientific publications, most distributed as PDFs that require parsing. PDF parsing approaches range from inexpensive heuristics (for simple documents) to computationally intensive ML-driven systems (for complex or degraded ones). The choice of the "best" parser for a particular document depends on its computational cost and the accuracy of its output. To address these issues, we introduce an Adaptive Parallel PDF Parsing and Resource Scaling Engine (AdaParse), a data-driven strategy for assigning an appropriate parser to each document. We enlist scientists to select preferred parser outputs and incorporate this information through direct preference optimization (DPO) into AdaParse, thereby aligning its selection process with human judgment. AdaParse then incorporates hardware requirements and predicted accuracy of each parser to orchestrate computational resources efficiently for large-scale parsing campaigns. We demonstrate that AdaParse, when compared to state-of-the-art parsers, improves throughput by 17times while still achieving comparable accuracy (0.2 percent better) on a benchmark set of 1000 scientific documents. AdaParse's combination of high accuracy and parallel scalability makes it feasible to parse large-scale scientific document corpora to support the development of high-quality, trillion-token-scale text datasets. The implementation is available at https://github.com/7shoe/AdaParse/

Structural neural network pruning aims to remove the redundant channels in the deep convolutional neural networks (CNNs) by pruning the filters of less importance to the final output accuracy. To reduce the degradation of performance after pruning, many methods utilize the loss with sparse regularization to produce structured sparsity. In this paper, we analyze these sparsity-training-based methods and find that the regularization of unpruned channels is unnecessary. Moreover, it restricts the network's capacity, which leads to under-fitting. To solve this problem, we propose a novel pruning method, named MaskSparsity, with pruning-aware sparse regularization. MaskSparsity imposes the fine-grained sparse regularization on the specific filters selected by a pruning mask, rather than all the filters of the model. Before the fine-grained sparse regularization of MaskSparity, we can use many methods to get the pruning mask, such as running the global sparse regularization. MaskSparsity achieves 63.03%-FLOPs reduction on ResNet-110 by removing 60.34% of the parameters, with no top-1 accuracy loss on CIFAR-10. On ILSVRC-2012, MaskSparsity reduces more than 51.07% FLOPs on ResNet-50, with only a loss of 0.76% in the top-1 accuracy. The code is released at https://github.com/CASIA-IVA-Lab/MaskSparsity. Moreover, we have integrated the code of MaskSparity into a PyTorch pruning toolkit, EasyPruner, at https://gitee.com/casia_iva_engineer/easypruner.

Dataset Condensation is a newly emerging technique aiming at learning a tiny dataset that captures the rich information encoded in the original dataset. As the size of datasets contemporary machine learning models rely on becomes increasingly large, condensation methods become a prominent direction for accelerating network training and reducing data storage. Despite numerous methods have been proposed in this rapidly growing field, evaluating and comparing different condensation methods is non-trivial and still remains an open issue. The quality of condensed dataset are often shadowed by many critical contributing factors to the end performance, such as data augmentation and model architectures. The lack of a systematic way to evaluate and compare condensation methods not only hinders our understanding of existing techniques, but also discourages practical usage of the synthesized datasets. This work provides the first large-scale standardized benchmark on Dataset Condensation. It consists of a suite of evaluations to comprehensively reflect the generability and effectiveness of condensation methods through the lens of their generated dataset. Leveraging this benchmark, we conduct a large-scale study of current condensation methods, and report many insightful findings that open up new possibilities for future development. The benchmark library, including evaluators, baseline methods, and generated datasets, is open-sourced to facilitate future research and application.

For patients suffering from central nervous system tumors, prognosis estimation, treatment decisions, and postoperative assessments are made from the analysis of a set of magnetic resonance (MR) scans. Currently, the lack of open tools for standardized and automatic tumor segmentation and generation of clinical reports, incorporating relevant tumor characteristics, leads to potential risks from inherent decisions' subjectivity. To tackle this problem, the proposed Raidionics open-source software has been developed, offering both a user-friendly graphical user interface and stable processing backend. The software includes preoperative segmentation models for each of the most common tumor types (i.e., glioblastomas, lower grade gliomas, meningiomas, and metastases), together with one early postoperative glioblastoma segmentation model. Preoperative segmentation performances were quite homogeneous across the four different brain tumor types, with an average Dice around 85% and patient-wise recall and precision around 95%. Postoperatively, performances were lower with an average Dice of 41%. Overall, the generation of a standardized clinical report, including the tumor segmentation and features computation, requires about ten minutes on a regular laptop. The proposed Raidionics software is the first open solution enabling an easy use of state-of-the-art segmentation models for all major tumor types, including preoperative and postsurgical standardized reports.

Supervised fine-tuning (SFT) data selection is commonly formulated as instance ranking: score each example and retain a top-k subset. However, effective SFT training subsets are often produced through ordered curation recipes, where filtering, mixing, and deduplication operators jointly shape the final data distribution. We formulate this problem as fixed-pool data recipe search: given a raw instruction pool and a library of grounded operators, the goal is to discover an executable recipe that constructs a high-quality selected subset under a limited budget of full SFT evaluations, without generating, rewriting, or augmenting training samples. We introduce AutoSelection, a two-layer solver that decouples fixed-pool materialization based on cached task-, data-, and model-side signals from expensive full evaluation, using warmup probes, realized subset states, local recipe edits, Gaussian-process-assisted ranking, and stagnation-triggered reseeding. Experiments on a 90K instruction pool show that AutoSelection achieves the strongest in-distribution reasoning average across three base models, outperforming full-data training, random recipe search, random top-k, and single-operator selectors. Additional Out-of-distribution graph-reasoning results, search-stability analyses, structural ablations, and 1.5B-to-7B transfer checks further show that recipe structure matters beyond individual selection operators. Code is available at https://github.com/w253/AutoSelection.

The ENDF-6 format, widely used worldwide for storing and disseminating nuclear data, is managed by the Cross Sections Evaluation Working Group (CSEWG) and fully documented in the ENDF-6 formats manual. This manual employs a combination of formal and natural language, introducing the possibility of ambiguity in certain parts of the format specification. To eliminate the possibility of ambiguity, this contribution proposes a generalization of the formal language used in the ENDF-6 formats manual, which is precisely defined in extended Backus-Naur form (EBNF). This formalization also offers several other advantages, notably reducing the complexity of creating and updating parsing and validation programs for ENDF-6 formatted files. Moreover, the availability of a formal description enables the automatic mapping of the low-level ENDF-6 representation, provided by a sequence of numbers, to a more human-friendly hierarchical representation with variable names. Demonstrating these advantages, almost the entire ENDF-6 format description has been translated into the proposed formal language, accompanied by a reference implementation of a parser/translator. This implementation leverages the formal format specification to enable reading, writing, and validating ENDF-6 formatted files.

Modernizing legacy COBOL systems remains difficult due to scarce expertise, large and long-lived codebases, and strict correctness requirements. Recent large language model (LLM)-based modernization systems increasingly rely on agentic workflows in which the model controls multi-step tool execution. However, it remains unclear whether delegating execution control to the LLM improves correctness, robustness, or efficiency in structured software engineering workflows. We present a controlled empirical study of deterministic and LLM-controlled orchestration for COBOL-to-Python modernization. Using a unified experimental framework, we hold the language models, prompts, tools, configurations, and source programs constant while varying only the execution control strategy. This isolates orchestration as the sole experimental variable. We evaluate both approaches using functional correctness, robustness across repeated stochastic runs, and computational efficiency. Across multiple models, deterministic orchestration achieves comparable computational accuracy to LLM-controlled orchestration while improving worst-case robustness and reducing performance variability across runs. Deterministic execution also reduces token consumption by up to 3.5x, leading to substantially lower operational cost. These results suggest that, in structured modernization workflows with explicit validation stages, fixed execution policies provide more stable and cost-efficient behavior than fully agentic orchestration without reducing translation quality.

Brazilian Portuguese remains under-served by open language models, and the few that exist are difficult to reproduce and are often compared without measures of uncertainty. We release Manacá-1B, an open decoder-only model of 1.72 billion parameters trained from scratch for Brazilian Portuguese with a fully containerized, reproducible pipeline. The pretraining is stable, with zero skipped or NaN steps and self-recovering loss spikes, and we release its full log and dynamics. We evaluate the model against nine open baselines on four Portuguese benchmarks under a single harness. Every comparison reports a standard error and a paired significance test, and the harness is validated against previously published numbers. On last-word prediction Manacá-1B is the strongest model below the 7B scale, exceeding both Tucano-1b1 and Tucano-2b4 on LAMBADA-PT with large paired margins; it is competitive on commonsense completion and near chance on multiple-choice reasoning, as are all small base models. Along the way we document a concrete evaluation pitfall: converting a SentencePiece tokenizer with case-folding normalization to the HuggingFace fast format silently drops the normalizer, routing every capitalized token to byte-fallback and depressing scores in a way that is invisible in aggregate metrics. The uncorrected tokenizer lowered LAMBADA-PT accuracy from 45.3 to 25.0; we quantify the effect and provide a one-line fix that reproduces the training tokenizer exactly. Code, raw training and evaluation logs, per-example prediction vectors, the model weights, and the corrected tokenizer are released so that every number in this paper can be recomputed.

Procedural videos, exemplified by recipe demonstrations, are instrumental in conveying step-by-step instructions. However, understanding such videos is challenging as it involves the precise localization of steps and the generation of textual instructions. Manually annotating steps and writing instructions is costly, which limits the size of current datasets and hinders effective learning. Leveraging large but noisy video-transcript datasets for pre-training can boost performance but demands significant computational resources. Furthermore, transcripts contain irrelevant content and differ in style from human-written instructions. To mitigate these issues, we propose a novel technique, Sieve-&-Swap, to automatically generate high-quality training data for the recipe domain: (i) Sieve: filters irrelevant transcripts and (ii) Swap: acquires high-quality text by replacing transcripts with human-written instruction from a text-only recipe dataset. The resulting dataset is three orders of magnitude smaller than current web-scale datasets but enables efficient training of large-scale models. Alongside Sieve-&-Swap, we propose Procedure Transformer (ProcX), a model for end-to-end step localization and instruction generation for procedural videos. When pre-trained on our curated dataset, this model achieves state-of-the-art performance on YouCook2 and Tasty while using a fraction of the training data. We have released code and dataset.

A research idea may be novel, coherent, and scientifically plausible, yet its proposed method may remain insufficiently specified for faithful implementation. We study the codification readiness of implementation-facing research-method specifications, defined by whether they provide sufficient methodological information for a competent implementer or coding agent to construct the intended method without unsupported assumptions. We construct evidence-grounded specifications and their supported resolutions from papers, codebases, issue threads, and reproduction artifacts. We introduce IdeaAMBIG, a benchmark of 660 evidence-grounded instances: 163 real-world gaps from reproducibility reports and GitHub issues, and 497 controlled synthetic gaps injected into codification-ready references. IdeaAMBIG evaluates three capabilities: codification-readiness assessment, defect localization, and clarification action generation. Defect localization receives only the specification, whereas clarification additionally receives the annotated defect. Across 13 LLMs, the best model achieves 9.6% Macro Defect Recovery Rate on real-world instances but 80.6% Macro Clarification Action Success Rate when given the defect. In an oracle study, supplying the gold resolution raises the downstream codification-ready rate from 14% to 98%. Across all evaluated models, defect localization is the main bottleneck, with stronger clarification given the defect.

We present ELMOD - Efficient Language Model for On-Device Deployment - a compact (2.7B) German language model designed for efficient inference on resource-constrained hardware. ELMOD was trained on a limited computational budget (55k H100 GPU hours) using exclusively publicly available data. We developed a suite of German-specific data pre-processing, which differ from English-oriented counterparts in their handling of morphological variation, compounding, and orthographic conventions. Furthermore, we introduced a quality filtering and rephrasing step, which increased the instructional quality of the data, improved performance during the annealing phase, and reduced overall compute requirements. Thanks to our architectural model and data choices, including prefiltering, our educational-quality filtering and rephrasal to raise the educational-quality, ELMOD is the strongest performer in its size class (<3B), matching the performance of 7B-parameter models in German.

Autoformalization is commonly framed as translating natural-language mathematical statements into machine-verifiable formal languages such as Lean 4. However, faithful formalization requires more than translation. Models must map mathematical concepts to the complex hierarchy of types and definitions in formal libraries such as Mathlib, while ensuring that generated statements preserve the meaning of the source propositions. Existing approaches struggle because they rely heavily on the model's parametric memory for library-specific knowledge, while common data construction pipelines often resort to filtering single-pass outputs and lack mechanisms for feedback-driven revision. To address these challenges, we introduce MathForm, an autoformalization framework for constructing verified training data through Mathlib knowledge retrieval and verification-guided iterative refinement. Before generation, a retrieval planner gathers relevant definitions and existing formalizations from Mathlib to guide the formalization generator. Generated statements are then revised using compiler diagnostics and semantic-consistency feedback. Using this framework, we construct FormalVerse, a Lean 4 dataset containing approximately 367K verified examples across diverse mathematical domains and sources. We then train MathForm-8B through supervised fine-tuning followed by reinforcement learning. Across six benchmarks, MathForm-8B achieves average Pass@8 rates of 88.06% under Syntax Check (SC) and 72.37% under Consistency Check (CC), outperforming multiple specialized 32B autoformalizers. On the challenging FATE-H and FATE-X subsets, it attains CC pass rates of 63% and 37%, exceeding the strongest specialized baselines in both cases.

While large general-purpose Transformer-based encoders excel at general language understanding, their performance diminishes in specialized domains like manufacturing due to a lack of exposure to domain-specific terminology and semantics. In this paper, we address this gap by introducing ManufactuBERT, a RoBERTa model continually pretrained on a large-scale corpus curated for the manufacturing domain. We present a comprehensive data processing pipeline to create this corpus from web data, involving an initial domain-specific filtering step followed by a multi-stage deduplication process that removes redundancies. Our experiments show that ManufactuBERT establishes a new state-of-the-art on a range of manufacturing-related NLP tasks, outperforming strong specialized baselines. More importantly, we demonstrate that training on our carefully deduplicated corpus significantly accelerates convergence, leading to a 33\% reduction in training time and computational cost compared to training on the non-deduplicated dataset. The proposed pipeline offers a reproducible example for developing high-performing encoders in other specialized domains. We will release our model and curated corpus at https://huggingface.co/cea-list-ia.

Supervised fine-tuning (SFT) followed by Group Relative Policy Optimization (GRPO) is a common post-training recipe. We conduct a controlled ablation over SFT-GRPO data overlap, evaluating Qwen3-8B (thinking disabled) post-trained for Lean 4 autoformalization under six conditions that differ solely in training recipe: a base model, SFT-only, GRPO-only, and three SFT+GRPO configurations where 0 percent, 30 percent, or 100 percent of the GRPO prompts coincide with the SFT corpus. Keeping SFT and GRPO data disjoint consistently outperforms full overlap at zero additional compute cost. Evaluating on Gaokao-Formal and PutnamBench under both compile pass at k and semantic pass at k assessed by an LLM judge, we find that lower overlap is monotonically associated with higher compilation and semantic accuracy. At 0 percent overlap, GRPO yields a 10.4 percentage point semantic gain over SFT alone on Gaokao, while at 100 percent overlap both metrics remain flat, rendering the GRPO stage effectively redundant. We further show that dual-metric evaluation reveals compile semantic gaps exceeding 30 percentage points for the highest compiling models, a disparity invisible under compile-only benchmarking. To our knowledge, this is the first controlled investigation of SFT-GRPO data overlap as a post-training hyperparameter, demonstrating how model behavior varies based on the degree of data sharing between training stages.

Large Language Models (LLMs) have achieved significant success across various NLP tasks. However, their massive computational costs limit their widespread use, particularly in real-time applications. Structured pruning offers an effective solution by compressing models and directly providing end-to-end speed improvements, regardless of the hardware environment. Meanwhile, different components of the model exhibit varying sensitivities towards pruning, calling for non-uniform model compression. However, a pruning method should not only identify a capable substructure, but also account for post-compression training. To this end, we propose \sysname, a method for training-aware structured pruning. \sysname builds upon an evolutionary search process, generating multiple offspring models in each generation through mutation, and selecting the fittest for survival. To assess the effect of post-training, we incorporate a lightweight, multistep training process within the offspring population, progressively increasing the number of tokens and eliminating poorly performing models in each selection stage. We validate our method through extensive experiments on Llama-2-7B, Llama-3.1-8B and Qwen-2.5-14B-Instruct, achieving state-of-the-art performance for structured pruning. For instance, \sysname surpasses ShearedLlama while requiring 5times less training data during post-compression training.

The performance of large language models (LLMs) in program synthesis and mathematical reasoning is fundamentally limited by the quality of their pre-training corpora. We introduce two openly licensed datasets, released under the Llama 3.3 Community License, that significantly enhance LLM performance by systematically rewriting public data. SwallowCode (approximately 16.1 billion tokens) refines Python snippets from The-Stack-v2 through a novel four-stage pipeline: syntax validation, pylint-based style filtering, and a two-stage LLM rewriting process that enforces style conformity and transforms snippets into self-contained, algorithmically efficient examples. Unlike prior methods that rely on exclusionary filtering or limited transformations, our transform-and-retain approach upgrades low-quality code, maximizing data utility. SwallowMath (approximately 2.3 billion tokens) enhances Finemath-4+ by removing boilerplate, restoring context, and reformatting solutions into concise, step-by-step explanations. Within a fixed 50 billion token training budget, continual pre-training of Llama-3.1-8B with SwallowCode boosts pass@1 by +17.0 on HumanEval and +17.7 on HumanEval+ compared to Stack-Edu, surpassing the baseline model's code generation capabilities. Similarly, substituting SwallowMath yields +12.4 accuracy on GSM8K and +7.6 on MATH. Ablation studies confirm that each pipeline stage contributes incrementally, with rewriting delivering the largest gains. All datasets, prompts, and checkpoints are publicly available, enabling reproducible research and advancing LLM pre-training for specialized domains.

While data are the primary fuel for machine learning models, they often suffer from missing values, especially when collected in real-world scenarios. However, many off-the-shelf machine learning models, including artificial neural network models, are unable to handle these missing values directly. Therefore, extra data preprocessing and curation steps, such as data imputation, are inevitable before learning and prediction processes. In this study, we propose a simple and intuitive yet effective method for pruning missing values (PROMISSING) during learning and inference steps in neural networks. In this method, there is no need to remove or impute the missing values; instead, the missing values are treated as a new source of information (representing what we do not know). Our experiments on simulated data, several classification and regression benchmarks, and a multi-modal clinical dataset show that PROMISSING results in similar prediction performance compared to various imputation techniques. In addition, our experiments show models trained using PROMISSING techniques are becoming less decisive in their predictions when facing incomplete samples with many unknowns. This finding hopefully advances machine learning models from being pure predicting machines to more realistic thinkers that can also say "I do not know" when facing incomplete sources of information.

Large language model pre-training has traditionally relied on human experts to craft heuristics for improving the corpora quality, resulting in numerous rules developed to date. However, these rules lack the flexibility to address the unique characteristics of individual example effectively. Meanwhile, applying tailored rules to every example is impractical for human experts. In this paper, we demonstrate that even small language models, with as few as 0.3B parameters, can exhibit substantial data refining capabilities comparable to those of human experts. We introduce Programming Every Example (ProX), a novel framework that treats data refinement as a programming task, enabling models to refine corpora by generating and executing fine-grained operations, such as string normalization, for each individual example at scale. Experimental results show that models pre-trained on ProX-curated data outperform either original data or data filtered by other selection methods by more than 2% across various downstream benchmarks. Its effectiveness spans various model sizes and pre-training corpora, including C4, RedPajama-V2, and FineWeb. Furthermore, ProX exhibits significant potential in domain-specific continual pre-training: without domain specific design, models trained on OpenWebMath refined by ProX outperform human-crafted rule-based methods, improving average accuracy by 7.6% over Mistral-7B, with 14.6% for Llama-2-7B and 20.3% for CodeLlama-7B, all within 10B tokens to be comparable to models like Llemma-7B trained on 200B tokens. Further analysis highlights that ProX significantly saves training FLOPs, offering a promising path for efficient LLM pre-training.We are open-sourcing ProX with >100B corpus, models, and sharing all training and implementation details for reproducible research and future innovation. Code: https://github.com/GAIR-NLP/ProX

Autoformalization, which translates natural language mathematics into machine-verifiable formal statements, is critical for using formal mathematical reasoning to solve math problems stated in natural language. While Large Language Models can generate syntactically correct formal statements, they often fail to preserve the original problem's semantic intent. This limitation arises from the LLM approaches' treating autoformalization as a simplistic translation task which lacks mechanisms for self-reflection and iterative refinement that human experts naturally employ. To address these issues, we propose ReForm, a Reflective Autoformalization method that tightly integrates semantic consistency evaluation into the autoformalization process. This enables the model to iteratively generate formal statements, assess its semantic fidelity, and self-correct identified errors through progressive refinement. To effectively train this reflective model, we introduce Prospective Bounded Sequence Optimization (PBSO), which employs different rewards at different sequence positions to ensure that the model develops both accurate autoformalization and correct semantic validations, preventing superficial critiques that would undermine the purpose of reflection. Extensive experiments across four autoformalization benchmarks demonstrate that ReForm achieves an average improvement of 17.2 percentage points over the strongest baselines. To further ensure evaluation reliability, we introduce ConsistencyCheck, a benchmark of 859 expert-annotated items that not only validates LLMs as judges but also reveals that autoformalization is inherently difficult: even human experts produce semantic errors in up to 38.5% of cases.

Tokenization is a fundamental preprocessing step in Natural Language Processing (NLP), significantly impacting the capability of large language models (LLMs) to capture linguistic and semantic nuances. This study introduces a novel evaluation framework addressing tokenization challenges specific to morphologically-rich and low-resource languages such as Turkish. Utilizing the Turkish MMLU (TR-MMLU) dataset, comprising 6,200 multiple-choice questions from the Turkish education system, we assessed tokenizers based on vocabulary size, token count, processing time, language-specific token percentages (\%TR), and token purity (\%Pure). These newly proposed metrics measure how effectively tokenizers preserve linguistic structures. Our analysis reveals that language-specific token percentages exhibit a stronger correlation with downstream performance (e.g., MMLU scores) than token purity. Furthermore, increasing model parameters alone does not necessarily enhance linguistic performance, underscoring the importance of tailored, language-specific tokenization methods. The proposed framework establishes robust and practical tokenization standards for morphologically complex languages.

Tokenization is an understudied and often neglected component of modern LLMs. Most published works use a single tokenizer for all experiments, often borrowed from another model, without performing ablations or analysis to optimize tokenization. Moreover, the tokenizer is generally kept unchanged when fine-tuning a base model. In this paper, we show that the size, pre-tokenization regular expression, and training data of a tokenizer can significantly impact the model's generation speed, effective context size, memory usage, and downstream performance. We train specialized Byte-Pair Encoding code tokenizers, and conduct extensive ablations on the impact of tokenizer design on the performance of LLMs for code generation tasks such as HumanEval and MBPP, and provide recommendations for tokenizer hyper-parameters selection and switching the tokenizer in a pre-trained LLM. We perform our experiments on models trained from scratch and from pre-trained models, verifying their applicability to a wide range of use-cases. We find that when fine-tuning on more than 50 billion tokens, we can specialize the tokenizer of a pre-trained LLM to obtain large gains in generation speed and effective context size.

Pre-trained language models (PLM) based on transformer neural networks developed in the field of natural language processing (NLP) offer great opportunities to improve automatic content analysis in communication science, especially for the coding of complex semantic categories in large datasets via supervised machine learning. However, three characteristics so far impeded the widespread adoption of the methods in the applying disciplines: the dominance of English language models in NLP research, the necessary computing resources, and the effort required to produce training data to fine-tune PLMs. In this study, we address these challenges by using a multilingual transformer model in combination with the adapter extension to transformers, and few-shot learning methods. We test our approach on a realistic use case from communication science to automatically detect claims and arguments together with their stance in the German news debate on arms deliveries to Ukraine. In three experiments, we evaluate (1) data preprocessing strategies and model variants for this task, (2) the performance of different few-shot learning methods, and (3) how well the best setup performs on varying training set sizes in terms of validity, reliability, replicability and reproducibility of the results. We find that our proposed combination of transformer adapters with pattern exploiting training provides a parameter-efficient and easily shareable alternative to fully fine-tuning PLMs. It performs on par in terms of validity, while overall, provides better properties for application in communication studies. The results also show that pre-fine-tuning for a task on a near-domain dataset leads to substantial improvement, in particular in the few-shot setting. Further, the results indicate that it is useful to bias the dataset away from the viewpoints of specific prominent individuals.