Daily Papers

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.

Extending the context window of large language models typically requires training on sequences at the target length, incurring quadratic memory and computational costs that make long-context adaptation expensive and difficult to reproduce. We propose EndPrompt, a method that achieves effective context extension using only short training sequences. The core insight is that exposing a model to long-range relative positional distances does not require constructing full-length inputs: we preserve the original short context as an intact first segment and append a brief terminal prompt as a second segment, assigning it positional indices near the target context length. This two-segment construction introduces both local and long-range relative distances within a short physical sequence while maintaining the semantic continuity of the training text--a property absent in chunk-based simulation approaches that split contiguous context. We provide a theoretical analysis grounded in Rotary Position Embedding and the Bernstein inequality, showing that position interpolation induces a rigorous smoothness constraint over the attention function, with shared Transformer parameters further suppressing unstable extrapolation to unobserved intermediate distances. Applied to LLaMA-family models extending the context window from 8K to 64K, EndPrompt achieves an average RULER score of 76.03 and the highest average on LongBench, surpassing LCEG (72.24), LongLoRA (72.95), and full-length fine-tuning (69.23) while requiring substantially less computation. These results demonstrate that long-context generalization can be induced from sparse positional supervision, challenging the prevailing assumption that dense long-sequence training is necessary for reliable context-window extension. The code is available at https://github.com/clx1415926/EndPrompt.

NVFP4 has grown increasingly popular as a 4-bit format for quantizing large language models due to its hardware support and its ability to retain useful information with relatively few bits per parameter. However, the format is not without limitations: recent work has shown that NVFP4 suffers from its error distribution, resulting in large amounts of quantization error on near-maximal values in each group of 16 values. In this work, we leverage this insight to design new Adaptive Block-Scaled Data Types that can adapt to the distribution of their input values. For four-bit quantization, our proposed IF4 (Int/Float 4) data type selects between FP4 and INT4 representations for each group of 16 values, which are then scaled by an E4M3 scale factor as is done with NVFP4. The selected data type is denoted using the scale factor's sign bit, which is currently unused in NVFP4, and we apply the same insight to design formats for other bit-widths, including IF3 and IF6. When used to quantize language models, we find that IF4 outperforms existing 4-bit block-scaled formats, achieving lower loss during quantized training and achieving higher accuracy on many tasks in post-training quantization. We additionally design and evaluate an IF4 Multiply-Accumulate (MAC) unit to demonstrate that IF4 can be implemented efficiently in next-generation hardware accelerators. Our code is available at https://github.com/mit-han-lab/fouroversix.

We present ForMaT (Format-Preserving Multilingual Translation), a parallel corpus of 3,956 PDFs across 15 language pairs that preserves original layout metadata proposed for multimodal machine translation. To ensure structural diversity in the dataset, we employ K-Medoids sampling over 45 geometric features, capturing complex elements like nested tables and formulas to focus only on visually diverse PDF documents. Our evaluation reveals that current MT systems struggle with spatial grounding and geometric synchronization, often losing the link between text and its visual context. ForMaT provides a benchmark for developing layout-aware translation models that integrate visual and textual context for high-fidelity document reconstruction.

End-to-end document parsers provide a unified interface, but serialize page layouts and regional contents into one autoregressive sequence. This formulation forces independent regions onto a decoding path whose length grows with the total content, whereas crop-based two-stage parsers expose region-level parallelism at the cost of repeated visual prefills and fragmented page context. To retain full-page context while removing dependencies, we propose PaDoc, a layout-grounded parser that treats the predicted layout as a branching structure over a shared page representation. Under a region-sufficiency assumption, we derive a prefix-conditioned factorization in which the layout stream and regional content branches advance concurrently, reducing the decoding depth to the longest layout-content path. We realize this factorization within a single MLLM: packed variable-length ancestor attention preserves the visibility under standard next-token training, while masked parallel decoding creates branches that the evaluated vLLM backend serves as concurrent requests with cache-resident shared-prefix reuse. On OmniDocBench Full, PaDoc attains an Overall layout F1 of 91.1 and, among end-to-end parsers, a top-tier Overall score of 94.24 together with the best Text Edit (0.038) and Formula CDM (95.59). On a 384-page subset and one A800 GPU, it is the fastest end-to-end parser at five concurrency levels, improving valid-page throughput by 67.4-118% and reducing P95 latency by 39.2-54.9% relative to a same-backbone Sequential SFT baseline. Code is available at https://github.com/Longin-Yu/Padoc

This paper introduces HiFloat4 (HiF4), a block floating-point data format tailored for deep learning. Each HiF4 unit packs 64 4-bit elements with 32 bits of shared scaling metadata, averaging 4.5 bits per value. The metadata specifies a three-level scaling hierarchy, capturing inter- and intra-group dynamic range while improving the utilization of the representational space. In addition, the large 64-element group size enables matrix multiplications to be executed in a highly fixed-point manner, significantly reducing hardware area and power consumption. To evaluate the proposed format, we conducted inference experiments on several language models, including LLaMA, Qwen, Mistral, DeepSeek-V3.1 and LongCat. Results show that HiF4 achieves higher average accuracy than the state-of-the-art NVFP4 format across multiple models and diverse downstream tasks.

Despite the power of Large Language Models (LLMs) like GPT-4, they still struggle with tasks that require generating complex, structured outputs. In this study, we assess the capability of Current LLMs in generating complex structured data and propose a structure-aware fine-tuning approach as a solution to improve this ability. To perform a comprehensive evaluation, we propose Struc-Bench, include five representative LLMs (i.e., GPT-NeoX 20B, GPT-3.5, GPT-4, and Vicuna) and evaluate them on our carefully constructed datasets spanning raw text, HTML, and LaTeX tables. Based on our analysis of current model performance, we identify specific common formatting errors and areas of potential improvement. To address complex formatting requirements, we utilize FormatCoT (Chain-of-Thought) to generate format instructions from target outputs. Our experiments show that our structure-aware fine-tuning method, when applied to LLaMA-7B, significantly improves adherence to natural language constraints, outperforming other evaluated LLMs. Based on these results, we present an ability map of model capabilities from six dimensions (i.e., coverage, formatting, reasoning, comprehension, pragmatics, and hallucination). This map highlights the weaknesses of LLMs in handling complex structured outputs and suggests promising directions for future work. Our code and models can be found at https://github.com/gersteinlab/Struc-Bench.

Numeric format proliferation in machine learning hardware -- FP8 (E4M3 and E5M2), BF16, MXFP4, microscaling block formats, and dozens of research variants -- has outpaced the availability of vendor-neutral, bit-exact reference material. Engineers porting models across accelerators encounter silent divergences that are difficult to diagnose without a shared ruler. This paper describes a catalog of 84 numeric formats spanning 13 families, a suite of six bit-exact conformance packs covering GF16, MXFP4 element, BF16, FP8 E4M3, FP8 E5M2, and E8M0 block scale, and an IEEE P3109 v3.2.0 cross-walk that maps each pack to its corresponding standards-track configured format. Each pack is a self-contained JSON document with a SHA-256 fingerprint, a shared row schema, and an anchor vector that encodes 3.0 -- the identity phi^2 + 1/phi^2 = 3 -- as a cross-pack sanity check. Packs are cross-validated against ml_dtypes 0.5.4 (Google/JAX); any divergence is documented explicitly and interpreted as a spec-permitted interpretation gap rather than hidden. The work is framed as registry filling: it does not propose new formats, make model-accuracy claims, or assert superiority over any vendor's implementation. All artifacts are publicly available at https://github.com/gHashTag/t27 under an open license.

As large language models continue to scale, fine-grained block-scaled low-precision formats such as NVFP4 are increasingly adopted for their substantial throughput and memory benefits. However, a single FP4 micro-format often mismatches heterogeneous block-level tensor statistics. To address this without changing the standard block-scaled MMA/GEMM execution path, we propose MixFP4, a mixed micro-format extension to NVFP4 that selects between two stored FP4 micro-formats (E2M1 and E1M2) per block. MixFP4 reuses NVFP4's scale hierarchy and encodes the format choice with zero additional metadata by repurposing the sign bit of the FP8 E4M3 block scale. By decoding both micro-formats into a unified internal E2M2 compute representation, MixFP4 avoids datapath duplication. Across representative LLM families, MixFP4 improves FP4 quantization robustness and accuracy over NVFP4 baselines with modest tensor-core overhead (3.1\% area, 1.5\% power).

Producing outputs that satisfy both semantic intent and format constraints is essential for deploying large language models in user-facing and system-integrated workflows. In this work, we focus on Markdown formatting, which is ubiquitous in assistants, documentation, and tool-augmented pipelines but still prone to subtle, hard-to-detect errors (e.g., broken lists, malformed tables, inconsistent headings, and invalid code blocks) that can significantly degrade downstream usability. We present FMBench, a benchmark for adaptive Markdown output formatting that evaluates models under a wide range of instruction-following scenarios with diverse structural requirements. FMBench emphasizes real-world formatting behaviors such as multi-level organization, mixed content (natural language interleaved with lists/tables/code), and strict adherence to user-specified layout constraints. To improve Markdown compliance without relying on hard decoding constraints, we propose a lightweight alignment pipeline that combines supervised fine-tuning (SFT) with reinforcement learning fine-tuning. Starting from a base model, we first perform SFT on instruction-response pairs, and then optimize a composite objective that balances semantic fidelity with structural correctness. Experiments on two model families (OpenPangu and Qwen) show that SFT consistently improves semantic alignment, while reinforcement learning provides additional gains in robustness to challenging Markdown instructions when initialized from a strong SFT policy. Our results also reveal an inherent trade-off between semantic and structural objectives, highlighting the importance of carefully designed rewards for reliable formatted generation. Code is available at: https://github.com/FudanCVL/FMBench.

As large language models have grown larger, interest has grown in low-precision numerical formats such as NVFP4 as a way to improve speed and reduce memory usage. However, quantizing models to NVFP4 remains difficult as the lack of precision generally degrades model performance. In this work, we address this issue with Four Over Six (4/6), a modification to the block-scaled NVFP4 quantization algorithm that yields reduced quantization error. Unlike integer formats, floating point formats have non-uniform step sizes which create larger quantization error on larger values. 4/6 takes advantage of this by adaptively scaling some blocks to smaller FP4 values, making the distribution of representable values more uniform and reducing quantization error for near-maximal values. We show that 4/6 can be implemented efficiently on NVIDIA Blackwell GPUs, resulting in performance gains during both pre-training and inference with minimal computational overhead. In pre-training experiments with the Nemotron 3 Nano 30B-A3B model architecture, we find that 4/6 brings training loss closer to BF16 compared to models trained with current state-of-the-art NVFP4 training recipes. Our code is available at http://github.com/mit-han-lab/fouroversix.

Background. In the last decades, several life science resources have structured data using the same framework and made these accessible using the same query language to facilitate interoperability. Knowledge graphs have seen increased adoption in bioinformatics due to their advantages for representing data in a generic graph format. For example, yummydata.org catalogs more than 60 knowledge graphs accessible through SPARQL, a technical query language. Although SPARQL allows powerful, expressive queries, even across physically distributed knowledge graphs, formulating such queries is a challenge for most users. Therefore, to guide users in retrieving the relevant data, many of these resources provide representative examples. These examples can also be an important source of information for machine learning, if a sufficiently large number of examples are provided and published in a common, machine-readable and standardized format across different resources. Findings. We introduce a large collection of human-written natural language questions and their corresponding SPARQL queries over federated bioinformatics knowledge graphs (KGs) collected for several years across different research groups at the SIB Swiss Institute of Bioinformatics. The collection comprises more than 1000 example questions and queries, including 65 federated queries. We propose a methodology to uniformly represent the examples with minimal metadata, based on existing standards. Furthermore, we introduce an extensive set of open-source applications, including query graph visualizations and smart query editors, easily reusable by KG maintainers who adopt the proposed methodology. Conclusions. We encourage the community to adopt and extend the proposed methodology, towards richer KG metadata and improved Semantic Web services.

Clark Hash is a small method for storing neural embeddings in less space. It normalizes each database vector, applies a deterministic sparse signed Johnson-Lindenstrauss projection, clips the result, and stores a fixed-width scalar-quantized code. Queries stay in floating point and are scored against the stored sketches. In the default 384-dimensional sentence-embedding setting, Clark Hash stores a cosine-search vector in 48 bytes instead of 1536 bytes for dense f32 storage. This is 32x smaller. The method does not need a training pass, learned codebooks, rotations, or corpus statistics before new vectors can be stored. We describe the codec, the Rust implementation, and a multilingual sentence-similarity evaluation on 9,304 labeled pairs from 29 subsets. With a multilingual MiniLM encoder, the 48-byte sketches reached 0.910 and 0.946 macro Pearson correlation with dense cosine scores on STS17 and STS22. Clark Hash is not a new Johnson-Lindenstrauss theorem and it is not a replacement for approximate nearest-neighbor indexes. It is a simple stateless codec for compact embedding storage.

Accurately identifying the synthesis conditions of metal-organic frameworks (MOFs) is essential for guiding experimental design, yet remains challenging because relevant information in the literature is often scattered, inconsistent, and difficult to interpret. We present MOFh6, a large language model driven system that reads raw articles or crystal codes and converts them into standardized synthesis tables. It links related descriptions across paragraphs, unifies ligand abbreviations with full names, and outputs structured parameters ready for use. MOFh6 achieved 99% extraction accuracy, resolved 94.1% of abbreviation cases across five major publishers, and maintained a precision of 0.93 +/- 0.01. Processing a full text takes 9.6 s, locating synthesis descriptions 36 s, with 100 papers processed for USD 4.24. By replacing static database lookups with real-time extraction, MOFh6 reshapes MOF synthesis research, accelerating the conversion of literature knowledge into practical synthesis protocols and enabling scalable, data-driven materials discovery.

In the English speech-to-text (STT) machine learning task, acoustic models are conventionally trained on uncased Latin characters, and any necessary orthography (such as capitalization, punctuation, and denormalization of non-standard words) is imputed by separate post-processing models. This adds complexity and limits performance, as many formatting tasks benefit from semantic information present in the acoustic signal but absent in transcription. Here we propose a new STT task: end-to-end neural transcription with fully formatted text for target labels. We present baseline Conformer-based models trained on a corpus of 5,000 hours of professionally transcribed earnings calls, achieving a CER of 1.7. As a contribution to the STT research community, we release the corpus free for non-commercial use at https://datasets.kensho.com/datasets/scribe.

Existing diffusion codecs typically build on text-to-image diffusion foundation models like Stable Diffusion. However, text conditioning is suboptimal from a compression perspective, hindering the potential of downstream diffusion codecs, particularly at ultra-low bitrates. To address it, we introduce CoD, the first Compression-oriented Diffusion foundation model, trained from scratch to enable end-to-end optimization of both compression and generation. CoD is not a fixed codec but a general foundation model designed for various diffusion-based codecs. It offers several advantages: High compression efficiency, replacing Stable Diffusion with CoD in downstream codecs like DiffC achieves SOTA results, especially at ultra-low bitrates (e.g., 0.0039 bpp); Low-cost and reproducible training, 300times faster training than Stable Diffusion (sim 20 vs. sim 6,250 A100 GPU days) on entirely open image-only datasets; Providing new insights, e.g., We find pixel-space diffusion can achieve VTM-level PSNR with high perceptual quality and can outperform GAN-based codecs using fewer parameters. We hope CoD lays the foundation for future diffusion codec research. Codes will be released.

In this paper, we propose an end-to-end deep learning model, called E2Efold, for RNA secondary structure prediction which can effectively take into account the inherent constraints in the problem. The key idea of E2Efold is to directly predict the RNA base-pairing matrix, and use an unrolled algorithm for constrained programming as the template for deep architectures to enforce constraints. With comprehensive experiments on benchmark datasets, we demonstrate the superior performance of E2Efold: it predicts significantly better structures compared to previous SOTA (especially for pseudoknotted structures), while being as efficient as the fastest algorithms in terms of inference time.

This study investigates whether Compressed-Language Models (CLMs), i.e. language models operating on raw byte streams from Compressed File Formats~(CFFs), can understand files compressed by CFFs. We focus on the JPEG format as a representative CFF, given its commonality and its representativeness of key concepts in compression, such as entropy coding and run-length encoding. We test if CLMs understand the JPEG format by probing their capabilities to perform along three axes: recognition of inherent file properties, handling of files with anomalies, and generation of new files. Our findings demonstrate that CLMs can effectively perform these tasks. These results suggest that CLMs can understand the semantics of compressed data when directly operating on the byte streams of files produced by CFFs. The possibility to directly operate on raw compressed files offers the promise to leverage some of their remarkable characteristics, such as their ubiquity, compactness, multi-modality and segment-nature.

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.

Function calling is a core capability of large language models, essential for AI agents. Existing benchmarks such as the Berkeley Function Calling Leaderboard (BFCL), tau^2-Bench (arXiv:2506.07982), and ACEBench (arXiv:2501.12851) evaluate argument correctness but do not test adherence to format instructions embedded in parameter descriptions, such as enclosing values in double quotes or using ISO date formats. We introduce IFEval-FC, a benchmark inspired by IFEval (arXiv:2311.07911) that assesses precise instruction following in function calling. IFEval-FC encodes verifiable formats directly within JSON schema descriptions, for example specifying that a value must not contain punctuation. It includes 750 test cases, each consisting of a function with an embedded format for one of its input parameters and a corresponding user query. Evaluation is fully algorithmic, ensuring objectivity, reproducibility, and scalability. Our results show that even state-of-the-art proprietary models, including GPT-5 and Claude 4.1 Opus, frequently fail to follow basic formatting rules, highlighting a practical limitation for real-world agent systems. The complete codebase and data are publicly available at https://github.com/Skripkon/IFEval-FC.

In the era of Large Language Models (LLMs), the code summarization technique boosts a lot, along with the emergence of many new significant works. However, the potential of code summarization in the Computer Security Area still remains explored. Can we generate a code summary of a code snippet for its security intention? Thus, this work proposes an innovative large-scale multi-perspective Code Intent Summary Dataset named BADS , aiming to increase the understanding of a given code snippet and reduce the risk in the code developing process. The procedure of establishing a dataset can be divided into four steps: First, we collect samples of codes with known vulnerabilities as well as code generated by AI from multiple sources. Second, we do the data clean and format unification, then do the data combination. Third, we utilize the LLM to automatically Annotate the code snippet. Last, We do the human evaluation to double-check. The dataset contains X code examples which cover Y categories of vulnerability. Our data are from Z open-source projects and CVE entries, and compared to existing work, our dataset not only contains original code but also code function summary and security intent summary, providing context information for research in code security analysis. All information is in CSV format. The contributions of this paper are four-fold: the establishment of a high-quality, multi-perspective Code Intent Summary Dataset; an innovative method in data collection and processing; A new multi-perspective code analysis framework that promotes cross-disciplinary research in the fields of software engineering and cybersecurity; improving the practicality and scalability of the research outcomes by considering the code length limitations in real-world applications. Our dataset and related tools have been publicly released on GitHub.

Background: Dutch medical corpora are scarce, limiting NLP development. \\ Methods: We translated English datasets, identified medical text in generic corpora, and extracted open Dutch medical resources. \\ Results: The resulting corpus comprises pm 35 billion tokens across the medical domain in about 100 million documents, freely available on Hugging Face. \\ Conclusion: This work establishes the first large-scale Dutch medical language corpus for pre-training and downstream NLP tasks.

The goal of decompilation is to convert compiled low-level code (e.g., assembly code) back into high-level programming languages, enabling analysis in scenarios where source code is unavailable. This task supports various reverse engineering applications, such as vulnerability identification, malware analysis, and legacy software migration. The end-to-end decompile method based on large langauge models (LLMs) reduces reliance on additional tools and minimizes manual intervention due to its inherent properties. However, previous end-to-end methods often lose critical information necessary for reconstructing control flow structures and variables when processing binary files, making it challenging to accurately recover the program's logic. To address these issues, we propose the ReF Decompile method, which incorporates the following innovations: (1) The Relabelling strategy replaces jump target addresses with labels, preserving control flow clarity. (2) The Function Call strategy infers variable types and retrieves missing variable information from binary files. Experimental results on the Humaneval-Decompile Benchmark demonstrate that ReF Decompile surpasses comparable baselines and achieves state-of-the-art (SOTA) performance of 61.43%.

Purpose: In radiology, large language models (LLMs), including ChatGPT, have recently gained attention, and their utility is being rapidly evaluated. However, concerns have emerged regarding their reliability in clinical applications due to limitations such as hallucinations and insufficient referencing. To address these issues, we focus on the latest technology, retrieval-augmented generation (RAG), which enables LLMs to reference reliable external knowledge (REK). Specifically, this study examines the utility and reliability of a recently released RAG-equipped LLM (RAG-LLM), NotebookLM, for staging lung cancer. Materials and methods: We summarized the current lung cancer staging guideline in Japan and provided this as REK to NotebookLM. We then tasked NotebookLM with staging 100 fictional lung cancer cases based on CT findings and evaluated its accuracy. For comparison, we performed the same task using a gold-standard LLM, GPT-4 Omni (GPT-4o), both with and without the REK. Results: NotebookLM achieved 86% diagnostic accuracy in the lung cancer staging experiment, outperforming GPT-4o, which recorded 39% accuracy with the REK and 25% without it. Moreover, NotebookLM demonstrated 95% accuracy in searching reference locations within the REK. Conclusion: NotebookLM successfully performed lung cancer staging by utilizing the REK, demonstrating superior performance compared to GPT-4o. Additionally, it provided highly accurate reference locations within the REK, allowing radiologists to efficiently evaluate the reliability of NotebookLM's responses and detect possible hallucinations. Overall, this study highlights the potential of NotebookLM, a RAG-LLM, in image diagnosis.

Despite the rapid growth of context length of large language models (LLMs) , LLMs still perform poorly in long document summarization. An important reason for this is that relevant information about an event is scattered throughout long documents, and the messy narrative order impairs the accurate understanding and utilization of LLMs for long documents. To address these issues, we propose a novel summary generation framework, called HERA. Specifically, we first segment a long document by its semantic structure and retrieve text segments about the same event, and finally reorder them to form the input context. We evaluate our approach on two long document summarization datasets. The experimental results show that HERA outperforms foundation models in ROUGE, BERTScore and faithfulness metrics, while HERA does not require additional fine-tuning and resources.

In this work, we study how URL extraction results depend on input format. We compiled a pilot dataset by extracting URLs from 10 arXiv papers and used the same heuristic method to extract URLs from four formats derived from the PDF files or the source LaTeX files. We found that accurate and complete URL extraction from any single format or a combination of multiple formats is challenging, with the best F1-score of 0.71. Using the pilot dataset, we evaluate extraction performance across formats and show that structured formats like HTML and XML produce more accurate results than PDFs or Text. Combining multiple formats improves coverage, especially when targeting research-critical resources. We further apply URL extraction on two tasks, namely classifying URLs into open-access datasets and software and the others, and analyzing the trend of URLs usage in arXiv papers from 1992 to 2024. These results suggest that using a combination of multiple formats achieves better performance on URL extraction than a single format, and the number of URLs in arXiv papers has been steadily increasing since 1992 to 2014 and has been drastically increasing from 2014 to 2024. The dataset and the Jupyter notebooks used for the preliminary analysis are publicly available at https://github.com/lamps-lab/arxiv-urls

Fill-in-the-Middle (FIM) models play a vital role in code completion tasks, leveraging both prefix and suffix context to provide more accurate and contextually relevant suggestions. This paper presents approaches to improve FIM code completion while addressing the challenge of maintaining low latency for real-time coding assistance. We enhance FIM code completion by incorporating context and curriculum examples in the training process. We identify patterns where completion suggestions fail more frequently, revealing complexities that smaller language models struggle with. To address these challenges, we develop a curriculum dataset by extracting hard-to-complete patterns from code repositories and generate context examples using semantic and static analysis tools (e.g. TSC compiler). We fine-tune various sized models, including StarCoder and DeepSeek, on this enhanced dataset. Our evaluation encompasses three key dimensions: the Santa Coder FIM task, the Amazon CCEval benchmark, and a new Multi-Line Infilling evaluation benchmark derived from SWE-bench. Comprehensive ablation studies across multiple model sizes reveal that while all fine-tuned models show improvements, the performance gains are more pronounced for smaller parameter models and incorporating difficult-to-complete examples, as part of curriculum learning, improves the code completion performance. This finding is particularly significant given the latency constraints of code completion tasks. While larger models like GPT and Claude perform well in multi-line completions but are prohibitively challenging to use given high latency, and our fine-tuned models achieve a balance between performance and latency. Finally, we validate our approach through online A/B testing, demonstrating tangible improvements in Completion Acceptance Rate (CAR) and Completion Persistence Rate (CPR), with zero latency impact.

This study examines 4-bit quantization methods like GPTQ in large language models (LLMs), highlighting GPTQ's overfitting and limited enhancement in Zero-Shot tasks. While prior works merely focusing on zero-shot measurement, we extend task scope to more generative categories such as code generation and abstractive summarization, in which we found that INT4 quantization can significantly underperform. However, simply shifting to higher precision formats like FP6 has been particularly challenging, thus overlooked, due to poor performance caused by the lack of sophisticated integration and system acceleration strategies on current AI hardware. Our results show that FP6, even with a coarse-grain quantization scheme, performs robustly across various algorithms and tasks, demonstrating its superiority in accuracy and versatility. Notably, with the FP6 quantization, \codestar-15B model performs comparably to its FP16 counterpart in code generation, and for smaller models like the 406M it closely matches their baselines in summarization. Neither can be achieved by INT4. To better accommodate various AI hardware and achieve the best system performance, we propose a novel 4+2 design for FP6 to achieve similar latency to the state-of-the-art INT4 fine-grain quantization. With our design, FP6 can become a promising solution to the current 4-bit quantization methods used in LLMs.

LLMs are widely used in complex AI applications. These applications underscore the need for LLM outputs to adhere to a specific format, for their integration with other components in the systems. Typically the format rules e.g., for data serialization formats such as JSON, YAML, or Code in Programming Language are expressed as context-free grammar (CFG). Due to the hallucinations and unreliability of LLMs, instructing LLMs to adhere to specified syntax becomes an increasingly important challenge. We present SynCode, a novel framework for efficient and general syntactical decoding with LLMs, to address this challenge. SynCode leverages the CFG of a formal language, utilizing an offline-constructed efficient lookup table called DFA mask store based on the discrete finite automaton (DFA) of the language grammar terminals. We demonstrate SynCode's soundness and completeness given the CFG of the formal language, presenting its ability to retain syntactically valid tokens while rejecting invalid ones. SynCode seamlessly integrates with any language defined by CFG, as evidenced by experiments focusing on generating JSON, Python, and Go outputs. Our experiments evaluating the effectiveness of SynCode for JSON generation demonstrate that SynCode eliminates all syntax errors and significantly outperforms state-of-the-art baselines. Furthermore, our results underscore how SynCode significantly reduces 96.07% of syntax errors in generated Python and Go code, showcasing its substantial impact on enhancing syntactical precision in LLM generation. Our code is available at https://github.com/uiuc-focal-lab/syncode

Fundamental experimental measurements of quantities such as ignition delay times, laminar flame speeds, and species profiles (among others) serve important roles in understanding fuel chemistry and validating chemical kinetic models. However, despite both the importance and abundance of such information in the literature, the community lacks a widely adopted standard format for this data. This impedes both sharing and wide use by the community. Here we introduce a new chemical kinetics experimental data format, ChemKED, and the related Python-based package for validating and working with ChemKED-formatted files called PyKED. We also review past and related efforts, and motivate the need for a new solution. ChemKED currently supports the representation of autoignition delay time measurements from shock tubes and rapid compression machines. ChemKED-formatted files contain all of the information needed to simulate experimental data points, including the uncertainty of the data. ChemKED is based on the YAML data serialization language, and is intended as a human- and machine-readable standard for easy creation and automated use. Development of ChemKED and PyKED occurs openly on GitHub under the BSD 3-clause license, and contributions from the community are welcome. Plans for future development include support for experimental data from laminar flame, jet stirred reactor, and speciation measurements.

Large foundation models have become central to modern machine learning, with performance scaling predictably with model size and data. However, training and deploying such models incur substantial computational and memory costs, motivating the development of low-precision training techniques. Recent work has demonstrated that 4-bit floating-point (FP4) formats--such as MXFP4 and NVFP4--can be successfully applied to linear GEMM operations in large language models (LLMs), achieving up to 4x improvements in compute throughput and memory efficiency compared to higher-precision baselines. In this work, we investigate the recently proposed HiFloat4 FP4 format for Huawei Ascend NPUs and systematically compare it with MXFP4 in large-scale training settings. All experiments are conducted on Ascend NPU clusters, with linear and expert GEMM operations performed entirely in FP4 precision. We evaluate both dense architectures (e.g., Pangu and LLaMA-style models) and mixture-of-experts (MoE) models, where both standard linear layers and expert-specific GEMMs operate in FP4. Furthermore, we explore stabilization techniques tailored to FP4 training that significantly reduce numerical degradation, maintaining relative error within 1% of full-precision baselines while preserving the efficiency benefits of 4-bit computation. Our results provide a comprehensive empirical study of FP4 training on NPUs and highlight the practical trade-offs between FP4 formats in large-scale dense and MoE models.

Large Language Model agents increasingly operate external systems through programmatic interfaces, yet practitioners lack empirical guidance on how to structure the context these agents consume. Using SQL generation as a proxy for programmatic agent operations, we present a systematic study of context engineering for structured data, comprising 9,649 experiments across 11 models, 4 formats (YAML, Markdown, JSON, Token-Oriented Object Notation [TOON]), and schemas ranging from 10 to 10,000 tables. Our findings challenge common assumptions. First, architecture choice is model-dependent: file-based context retrieval improves accuracy for frontier-tier models (Claude, GPT, Gemini; +2.7%, p=0.029) but shows mixed results for open source models (aggregate -7.7%, p<0.001), with deficits varying substantially by model. Second, format does not significantly affect aggregate accuracy (chi-squared=2.45, p=0.484), though individual models, particularly open source, exhibit format-specific sensitivities. Third, model capability is the dominant factor, with a 21 percentage point accuracy gap between frontier and open source tiers that dwarfs any format or architecture effect. Fourth, file-native agents scale to 10,000 tables through domain-partitioned schemas while maintaining high navigation accuracy. Fifth, file size does not predict runtime efficiency: compact or novel formats can incur a token overhead driven by grep output density and pattern unfamiliarity, with the magnitude depending on model capability. These findings provide practitioners with evidence-based guidance for deploying LLM agents on structured systems, demonstrating that architectural decisions should be tailored to model capability rather than assuming universal best practices.

Model families train every size from scratch. Can a pretrained large model be converted into a smaller sibling? We characterize the 1.4B->410M conversion in the Pythia family end-to-end: (i) representations align strongly across sizes (ridge R^2=0.84) while parameters align weakly; (ii) dense weight projection is functionally destructive -- provably not an assembly artifact -- because basis mixing breaks rotary, per-head, GELU, and LayerNorm structure; (iii) after the best-fit linear operator, weight residuals are statistically indistinguishable from noise under shuffle controls; (iv) conversion value therefore lives in initialization. In matched-budget continued pre-training we decompose conversion into two independent levers -- least-squares compensation (function: best zero-shot) and variance-preserving rescale (dynamics: best endpoints). Compensation is a token-efficient, low-budget win rather than a universal one: at 30M tokens it beats the strongest subcloning variant on both a width-reduced pair (84.0 +/- 1.8 vs. 89.7 +/- 3.7, 3/3 seeds) and a held-out depth-reduced pair (109.3 vs. 117.9, 3/3 seeds), reaching a given quality with fewer tokens; at a 33x larger budget the two converge to parity (40.0 vs. 40.0), both far ahead of from-scratch, which transfer initialization always beats -- by up to 18x at low budget, the margin narrowing at convergence and at the largest scale. We further map the method's boundary: at ~5x the donor scale (6.9B->1.4B) stacking both levers over-corrects, which we trace to ill-conditioning of the compensation solve at large width, pointing to dimension-aware regularization as the fix. Code, checkpoints, and the frozen evaluation corpus are released.

Recent developments show that Large Language Models (LLMs) produce state-of-the-art performance on natural language (NL) to code generation for resource-rich general-purpose languages like C++, Java, and Python. However, their practical usage for structured domain-specific languages (DSLs) such as YAML, JSON is limited due to domain-specific schema, grammar, and customizations generally unseen by LLMs during pre-training. Efforts have been made to mitigate this challenge via in-context learning through relevant examples or by fine-tuning. However, it suffers from problems, such as limited DSL samples and prompt sensitivity but enterprises maintain good documentation of the DSLs. Therefore, we propose DocCGen, a framework that can leverage such rich knowledge by breaking the NL-to-Code generation task for structured code languages into a two-step process. First, it detects the correct libraries using the library documentation that best matches the NL query. Then, it utilizes schema rules extracted from the documentation of these libraries to constrain the decoding. We evaluate our framework for two complex structured languages, Ansible YAML and Bash command, consisting of two settings: Out-of-domain (OOD) and In-domain (ID). Our extensive experiments show that DocCGen consistently improves different-sized language models across all six evaluation metrics, reducing syntactic and semantic errors in structured code. We plan to open-source the datasets and code to motivate research in constrained code generation.

Quantization addresses the high resource demand for large language models (LLMs) by alleviating memory pressure and bandwidth congestion and providing significantly scaled compute power with a tolerable impact on accuracy. Four-bit floating point (FP4), the lowest-precision format that preserves essential numerical properties such as exponent and sign, has begun to be adopted in cutting-edge architectures, including Blackwell and AMD CDNA, to support LLM quantization and reduce deployment costs. Although aggressive quantization can yield efficiency gains, the quantization sensitivity of within-transformer layers and whether these sensitivities generalize across existing FP4 formats and model scales remain underexplored. To elucidate quantization sensitivity, this study conducts a systematic analysis of two FP4 formats, MXFP4 and NVFP4, across three Qwen2.5 model scales (0.5B, 7B, and 14B), using controlled component-wise and block-wise isolation methodologies. We observe that MLP up- and down-projection layers consistently dominate in terms of sensitivity, while gate and attention projections are moderately and substantially less sensitive to FP4 quantization, respectively. We further find that sensitivity does not universally localize to the final blocks, but early blocks can be highly sensitive, particularly under MXFP4. Our results provide a diagnostic characterization of the inference behavior of FP4 across components, depths, and FP4 formats.

Asking a large language model to respond in JSON should be a formatting choice, not a capability tax. Yet we find that structured output requirements -- JSON, XML, LaTeX, Markdown -- substantially degrade reasoning and writing performance across open-weight models. The research response has focused on constrained decoding, but sampling bias accounts for only a fraction of the degradation. The dominant cost enters at the prompt: format-requesting instructions alone cause most of the accuracy loss, before any decoder constraint is applied. This diagnosis points to a simple principle: decouple reasoning from formatting. Whether by generating freeform first and reformatting in a second pass, or by enabling extended thinking within a single generation, separating the two concerns substantially recovers lost accuracy. Across six open-weight models, four API models, four formats, and tasks spanning math, science, logic, and writing, decoupling recovers most lost accuracy. Notably, most recent closed-weight models show little to no format tax, suggesting the problem is not inherent to structured generation but a gap that current open-weight models have yet to close. Code is available at https://github.com/ivnle/the-format-tax.

We present the new parton distribution functions (PDFs) from the CTEQ-TEA collaboration, obtained using a wide variety of high-precision Large Hadron Collider (LHC) data, in addition to the combined HERA I+II deep-inelastic scattering data set, along with the data sets present in the CT14 global QCD analysis. New LHC measurements in single-inclusive jet production with the full rapidity coverage, as well as production of Drell-Yan pairs, top-quark pairs, and high-p_T Z bosons, are included to achieve the greatest sensitivity to the PDFs. The parton distributions are determined at NLO and NNLO, with each of these PDFs accompanied by error sets determined using the Hessian method. Fast PDF survey techniques, based on the Hessian representation and the Lagrange Multiplier method, are used to quantify the preference of each data set to quantities such as α_s(m_Z), and the gluon and strange quark distributions. We designate the main resulting PDF set as CT18. The ATLAS 7 TeV precision W/Z data are not included in CT18, due to their tension with other data sets in the global fit. Alternate PDF sets are generated including the ATLAS precision 7 TeV W/Z data (CT18A), a new scale choice for low-x DIS data (CT18X), or all of the above with a slightly higher choice for the charm mass (CT18Z). Theoretical calculations of standard candle cross sections at the LHC (such as the gg fusion Higgs boson cross section) are presented.

Embedding models play a pivot role in modern NLP applications such as IR and RAG. While the context limit of LLMs has been pushed beyond 1 million tokens, embedding models are still confined to a narrow context window not exceeding 8k tokens, refrained from application scenarios requiring long inputs such as legal contracts. This paper explores context window extension of existing embedding models, pushing the limit to 32k without requiring additional training. First, we examine the performance of current embedding models for long context retrieval on our newly constructed LongEmbed benchmark. LongEmbed comprises two synthetic tasks and four carefully chosen real-world tasks, featuring documents of varying length and dispersed target information. Benchmarking results underscore huge room for improvement in these models. Based on this, comprehensive experiments show that training-free context window extension strategies like position interpolation can effectively extend the context window of existing embedding models by several folds, regardless of their original context being 512 or beyond 4k. Furthermore, for models employing absolute position encoding (APE), we show the possibility of further fine-tuning to harvest notable performance gains while strictly preserving original behavior for short inputs. For models using rotary position embedding (RoPE), significant enhancements are observed when employing RoPE-specific methods, such as NTK and SelfExtend, indicating RoPE's superiority over APE for context window extension. To facilitate future research, we release E5-Base-4k and E5-RoPE-Base, along with the LongEmbed benchmark.

The article presents a new multi-label comprehensive image dataset from flexible endoscopy, colonoscopy and capsule endoscopy, named ERS. The collection has been labeled according to the full medical specification of 'Minimum Standard Terminology 3.0' (MST 3.0), describing all possible findings in the gastrointestinal tract (104 possible labels), extended with an additional 19 labels useful in common machine learning applications. The dataset contains around 6000 precisely and 115,000 approximately labeled frames from endoscopy videos, 3600 precise and 22,600 approximate segmentation masks, and 1.23 million unlabeled frames from flexible and capsule endoscopy videos. The labeled data cover almost entirely the MST 3.0 standard. The data came from 1520 videos of 1135 patients. Additionally, this paper proposes and describes four exemplary experiments in gastrointestinal image classification task performed using the created dataset. The obtained results indicate the high usefulness and flexibility of the dataset in training and testing machine learning algorithms in the field of endoscopic data analysis.

Identifying and reconstructing hadronic τ decays (τ_{h}) is an important task at current and future high-energy physics experiments, as τ_{h} represent an important tool to analyze the production of Higgs and electroweak bosons as well as to search for physics beyond the Standard Model. The identification of τ_{h} can be viewed as a generalization and extension of jet-flavour tagging, which has in the recent years undergone significant progress due to the use of deep learning. Based on a granular simulation with realistic detector effects and a particle flow-based event reconstruction, we show in this paper that deep learning-based jet-flavour-tagging algorithms are powerful τ_{h} identifiers. Specifically, we show that jet-flavour-tagging algorithms such as LorentzNet and ParticleTransformer can be adapted in an end-to-end fashion for discriminating τ_{h} from quark and gluon jets. We find that the end-to-end transformer-based approach significantly outperforms contemporary state-of-the-art τ_{h} reconstruction and identification algorithms currently in use at the Large Hadron Collider.

The Vera C. Rubin Observatory will generate an unprecedented volume of data, including approximately 60 petabytes of raw data and around 30 trillion observed sources, posing a significant challenge for large-scale and end-user scientific analysis. As part of the LINCC Frameworks Project we are addressing these challenges with the development of the HATS (Hierarchical Adaptive Tiling Scheme) format and analysis package LSDB. HATS partitions data adaptively using a hierarchical tiling system to balance the file sizes, enabling efficient parallel analysis. Recent updates include improved metadata consistency, support for incremental updates, and enhanced compatibility with evolving datasets. LSDB complements HATS by providing a scalable, user-friendly interface for large catalog analysis, integrating spatial queries, crossmatching, and time-series tools while utilizing Dask for parallelization. We have successfully demonstrated the use of these tools with datasets such as ZTF and Pan-STARRS data releases on both cluster and cloud environments. We are deeply involved in several ongoing collaborations to ensure alignment with community needs, with future plans for IVOA standardization and support for upcoming Rubin, Euclid and Roman data. We provide our code and materials at lsdb.io.

Case Report Forms (CRFs) are largely used in medical research as they ensure accuracy, reliability, and validity of results in clinical studies. However, publicly available, wellannotated CRF datasets are scarce, limiting the development of CRF slot filling systems able to fill in a CRF from clinical notes. To mitigate the scarcity of CRF datasets, we propose to take advantage of available datasets annotated for information extraction tasks and to convert them into structured CRFs. We present a semi-automatic conversion methodology, which has been applied to the E3C dataset in two languages (English and Italian), resulting in a new, high-quality dataset for CRF slot filling. Through several experiments on the created dataset, we report that slot filling achieves 59.7% for Italian and 67.3% for English on a closed Large Language Models (zero-shot) and worse performances on three families of open-source models, showing that filling CRFs is challenging even for recent state-of-the-art LLMs. We release the datest at https://huggingface.co/collections/NLP-FBK/e3c-to-crf-67b9844065460cbe42f80166

A proper code evaluation metric (CEM) profoundly impacts the evolution of code generation, which is an important research field in NLP and software engineering. Prevailing match-based CEMs (e.g., BLEU, Accuracy, and CodeBLEU) suffer from two significant drawbacks. 1. They primarily measure the surface differences between codes without considering their functional equivalence. However, functional equivalence is pivotal in evaluating the effectiveness of code generation, as different codes can perform identical operations. 2. They are predominantly designed for the Ref-only input format. However, code evaluation necessitates versatility in input formats. Aside from Ref-only, there are NL-only and Ref\&NL formats, which existing match-based CEMs cannot effectively accommodate. In this paper, we propose CodeScore, a large language model (LLM)-based CEM, which estimates the functional correctness of generated code on three input types. To acquire CodeScore, we present UniCE, a unified code generation learning framework, for LLMs to learn code execution (i.e., learning PassRatio and Executability of generated code) with unified input. Extensive experimental results on multiple code evaluation datasets demonstrate that CodeScore absolutely improves up to 58.87% correlation with functional correctness compared to other CEMs, achieves state-of-the-art performance, and effectively handles three input formats.

The stereo correspondence and reconstruction of endoscopic data sub-challenge was organized during the Endovis challenge at MICCAI 2019 in Shenzhen, China. The task was to perform dense depth estimation using 7 training datasets and 2 test sets of structured light data captured using porcine cadavers. These were provided by a team at Intuitive Surgical. 10 teams participated in the challenge day. This paper contains 3 additional methods which were submitted after the challenge finished as well as a supplemental section from these teams on issues they found with the dataset.

Previous work mainly focuses on improving cross-lingual transfer for NLU tasks with a multilingual pretrained encoder (MPE), or improving the performance on supervised machine translation with BERT. However, it is under-explored that whether the MPE can help to facilitate the cross-lingual transferability of NMT model. In this paper, we focus on a zero-shot cross-lingual transfer task in NMT. In this task, the NMT model is trained with parallel dataset of only one language pair and an off-the-shelf MPE, then it is directly tested on zero-shot language pairs. We propose SixT, a simple yet effective model for this task. SixT leverages the MPE with a two-stage training schedule and gets further improvement with a position disentangled encoder and a capacity-enhanced decoder. Using this method, SixT significantly outperforms mBART, a pretrained multilingual encoder-decoder model explicitly designed for NMT, with an average improvement of 7.1 BLEU on zero-shot any-to-English test sets across 14 source languages. Furthermore, with much less training computation cost and training data, our model achieves better performance on 15 any-to-English test sets than CRISS and m2m-100, two strong multilingual NMT baselines.