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Sep 17

Molecular Implementation of the Machine-Learned Skala Exchange-Correlation Functional in CP2K through GauXC

Machine-learned exchange--correlation (XC) functionals offer a route to improve Kohn--Sham density-functional theory without incurring the cost of explicitly correlated electronic-structure methods. Their use in production simulation codes, however, requires a well-defined mapping between the learned model and the host-code density representation. We formulate and implement a Skala-1.1 interface in CP2K through the external GauXC library. CP2K supplies the geometry, Gaussian basis, spin-resolved atomic-orbital density matrix, and communicator, while GauXC evaluates the XC energy, atomic-orbital potential matrix, and available nuclear derivatives. The interface accepts both all-electron and valence-only density matrices. The latter may arise from separable dual-space pseudopotentials or molecular effective-core potentials. Implementation errors are isolated from functional differences by comparing the Perdew--Burke--Ernzerhof (PBE) functional evaluated through GauXC with native CP2K PBE. The resulting interface gives consistent energies, forces validated against finite-difference total-energy checks, and force-based molecular-virial diagnostics for representative molecular cases. The dietGMTKN55 benchmark suite is evaluated with an all-electron Gaussian augmented plane-wave treatment for elements up to bromine and def2 effective-core potentials for the heavier elements. The resulting aggregate mean absolute deviation of 1.255 kcal/mol is within 0.020 kcal/mol of the corresponding Skala reference value of 1.235 kcal/mol. This work establishes a validated molecular implementation of Skala in CP2K through GauXC.

  • 9 authors
·
Aug 18

A large collection of bioinformatics question-query pairs over federated knowledge graphs: methodology and applications

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.

  • 17 authors
·
Oct 8, 2024

EMBL AI Librarian: Life-Sciences Knowledge Layer for AI Agents

The web is increasingly accessed by AI agents rather than humans. Every agent needs knowledge, especially in the life-sciences, where agentic pipelines are growing fast. Access to the literature is a crucial part of that need, and resources such as Europe PMC, with over 40M indexed records, are widely used to meet it. Yet these resources were not built for AI agents: they take keywords and complex syntax and return whole papers, so every agent must learn the syntax, issue several searches, and read full papers to find the evidence it needs. We introduce EMBL AI Librarian, a knowledge layer that upgrades the Europe PMC interface for AI agents: an agent asks in natural language and receives evidence that answers it. A single LLM orchestrates the whole knowledge retrieval process: it plans complementary subqueries executed by the live Europe PMC search engine, then reads the selected papers and locates the relevant evidence. We evaluate Librarian across four benchmarks: literature synthesis, claim verification, open-domain question answering, and downstream biology tasks such as protocol questions and sequence manipulation. On ScholarQABench, Librarian improves Citation F1 by more than 16 points over strong recently published baselines. Used as the retrieval layer of an existing claim-verification pipeline, it increases agreement with expert consensus; and on the open-form LitQA2 benchmark, a GPT-5.4 agent scores about 8 points higher when grounded in Librarian than with web search. Overall, our results show that equipping life-science agents with the Librarian knowledge layer improves performance across a range of tasks. We release our code publicly at https://github.com/petroni-lab/librarian

Dense Text Retrieval based on Pretrained Language Models: A Survey

Text retrieval is a long-standing research topic on information seeking, where a system is required to return relevant information resources to user's queries in natural language. From classic retrieval methods to learning-based ranking functions, the underlying retrieval models have been continually evolved with the ever-lasting technical innovation. To design effective retrieval models, a key point lies in how to learn the text representation and model the relevance matching. The recent success of pretrained language models (PLMs) sheds light on developing more capable text retrieval approaches by leveraging the excellent modeling capacity of PLMs. With powerful PLMs, we can effectively learn the representations of queries and texts in the latent representation space, and further construct the semantic matching function between the dense vectors for relevance modeling. Such a retrieval approach is referred to as dense retrieval, since it employs dense vectors (a.k.a., embeddings) to represent the texts. Considering the rapid progress on dense retrieval, in this survey, we systematically review the recent advances on PLM-based dense retrieval. Different from previous surveys on dense retrieval, we take a new perspective to organize the related work by four major aspects, including architecture, training, indexing and integration, and summarize the mainstream techniques for each aspect. We thoroughly survey the literature, and include 300+ related reference papers on dense retrieval. To support our survey, we create a website for providing useful resources, and release a code repertory and toolkit for implementing dense retrieval models. This survey aims to provide a comprehensive, practical reference focused on the major progress for dense text retrieval.

  • 4 authors
·
Nov 27, 2022

Ragnarök: A Reusable RAG Framework and Baselines for TREC 2024 Retrieval-Augmented Generation Track

Did you try out the new Bing Search? Or maybe you fiddled around with Google AI~Overviews? These might sound familiar because the modern-day search stack has recently evolved to include retrieval-augmented generation (RAG) systems. They allow searching and incorporating real-time data into large language models (LLMs) to provide a well-informed, attributed, concise summary in contrast to the traditional search paradigm that relies on displaying a ranked list of documents. Therefore, given these recent advancements, it is crucial to have an arena to build, test, visualize, and systematically evaluate RAG-based search systems. With this in mind, we propose the TREC 2024 RAG Track to foster innovation in evaluating RAG systems. In our work, we lay out the steps we've made towards making this track a reality -- we describe the details of our reusable framework, Ragnar\"ok, explain the curation of the new MS MARCO V2.1 collection choice, release the development topics for the track, and standardize the I/O definitions which assist the end user. Next, using Ragnar\"ok, we identify and provide key industrial baselines such as OpenAI's GPT-4o or Cohere's Command R+. Further, we introduce a web-based user interface for an interactive arena allowing benchmarking pairwise RAG systems by crowdsourcing. We open-source our Ragnar\"ok framework and baselines to achieve a unified standard for future RAG systems.

  • 8 authors
·
Jun 24, 2024

Beyond Ten Turns: Unlocking Long-Horizon Agentic Search with Large-Scale Asynchronous RL

Recent advancements in LLM-based agents have demonstrated remarkable capabilities in handling complex, knowledge-intensive tasks by integrating external tools. Among diverse choices of tools, search tools play a pivotal role in accessing vast external knowledge. However, open-source agents still fall short of achieving expert-level Search Intelligence, the ability to resolve ambiguous queries, generate precise searches, analyze results, and conduct thorough exploration. Existing approaches fall short in scalability, efficiency, and data quality. For example, small turn limits in existing online RL methods, e.g. <=10, restrict complex strategy learning. This paper introduces ASearcher, an open-source project for large-scale RL training of search agents. Our key contributions include: (1) Scalable fully asynchronous RL training that enables long-horizon search while maintaining high training efficiency. (2) A prompt-based LLM agent that autonomously synthesizes high-quality and challenging QAs, creating a large-scale QA dataset. Through RL training, our prompt-based QwQ-32B agent achieves substantial improvements, with 46.7% and 20.8% Avg@4 gains on xBench and GAIA, respectively. Notably, our agent exhibits extreme long-horizon search, with tool calls exceeding 40 turns and output tokens exceeding 150k during training time. With a simple agent design and no external LLMs, ASearcher-Web-QwQ achieves Avg@4 scores of 42.1 on xBench and 52.8 on GAIA, surpassing existing open-source 32B agents. We open-source our models, training data, and codes in https://github.com/inclusionAI/ASearcher.

  • 8 authors
·
Aug 11, 2025 3

Étude cognitive des processus de construction d'une requête dans un système de gestion de connaissances médicales

This article presents the Cogni-CISMeF project, which aims at improving medical information search in the CISMeF system (Catalog and Index of French-language health resources) by including a conversational agent to interact with the user in natural language. To study the cognitive processes involved during the information search, a bottom-up methodology was adopted. Experimentation has been set up to obtain human dialogs between a user (playing the role of patient) dealing with medical information search and a CISMeF expert refining the request. The analysis of these dialogs underlined the use of discursive evidence: vocabulary, reformulation, implicit or explicit expression of user intentions, conversational sequences, etc. A model of artificial agent is proposed. It leads the user in its information search by proposing to him examples, assistance and choices. This model was implemented and integrated in the CISMeF system. ---- Cet article d\'ecrit le projet Cogni-CISMeF qui propose un module de dialogue Homme-Machine \`a int\'egrer dans le syst\`eme d'indexation de connaissances m\'edicales CISMeF (Catalogue et Index des Sites M\'edicaux Francophones). Nous avons adopt\'e une d\'emarche de mod\'elisation cognitive en proc\'edant \`a un recueil de corpus de dialogues entre un utilisateur (jouant le r\^ole d'un patient) d\'esirant une information m\'edicale et un expert CISMeF af inant cette demande pour construire la requ\^ete. Nous avons analys\'e la structure des dialogues ainsi obtenus et avons \'etudi\'e un certain nombre d'indices discursifs : vocabulaire employ\'e, marques de reformulation, commentaires m\'eta et \'epilinguistiques, expression implicite ou explicite des intentions de l'utilisateur, encha\^inement conversationnel, etc. De cette analyse, nous avons construit un mod\`ele d'agent artificiel dot\'e de capacit\'es cognitives capables d'aider l'utilisateur dans sa t\^ache de recherche d'information. Ce mod\`ele a \'et\'e impl\'ement\'e et int\'egr\'e dans le syst\`eme CISMeF.

  • 5 authors
·
Feb 10, 2014

LitSearch: A Retrieval Benchmark for Scientific Literature Search

Literature search questions, such as "where can I find research on the evaluation of consistency in generated summaries?" pose significant challenges for modern search engines and retrieval systems. These questions often require a deep understanding of research concepts and the ability to reason over entire articles. In this work, we introduce LitSearch, a retrieval benchmark comprising 597 realistic literature search queries about recent ML and NLP papers. LitSearch is constructed using a combination of (1) questions generated by GPT-4 based on paragraphs containing inline citations from research papers and (2) questions about recently published papers, manually written by their authors. All LitSearch questions were manually examined or edited by experts to ensure high quality. We extensively benchmark state-of-the-art retrieval models and also evaluate two LLM-based reranking pipelines. We find a significant performance gap between BM25 and state-of-the-art dense retrievers, with a 24.8% difference in absolute recall@5. The LLM-based reranking strategies further improve the best-performing dense retriever by 4.4%. Additionally, commercial search engines and research tools like Google Search perform poorly on LitSearch, lagging behind the best dense retriever by 32 points. Taken together, these results show that LitSearch is an informative new testbed for retrieval systems while catering to a real-world use case.

  • 6 authors
·
Jul 10, 2024

SiDiaC-v.2.0: Sinhala Diachronic Corpus Version 2.0

SiDiaC-v.2.0 is the largest comprehensive Sinhala Diachronic Corpus to date, covering a period from 1800 CE to 1955 CE in terms of publication dates, and a historical span from the 5th to the 20th century CE in terms of written dates. The corpus consists of 244k words across 185 literary works that underwent thorough filtering, preprocessing, and copyright compliance checks, followed by extensive post-processing. Additionally, a subset of 59 documents totalling 70k words was annotated based on their written dates. Texts from the National Library of Sri Lanka were selected from the SiDiaC-v.1.0 non-filtered list, which was digitised using Google Document AI OCR. This was followed by post-processing to correct formatting issues, address code-mixing, include special tokens, and fix malformed tokens. The construction of SiDiaC-v.2.0 was informed by practices from other corpora, such as FarPaHC, SiDiaC-v.1.0, and CCOHA. This was particularly relevant for syntactic annotation and text normalisation strategies, given the shared characteristics of low-resource language status between Faroese and the similar cleaning strategies utilised in CCOHA. This corpus is categorised into two layers based on genres: primary and secondary. The primary categorisation is binary, assigning each book to either Non-Fiction or Fiction. The secondary categorisation is more detailed, grouping texts under specific genres such as Religious, History, Poetry, Language, and Medical. Despite facing challenges due to limited resources, SiDiaC-v.2.0 serves as a comprehensive resource for Sinhala NLP, building upon the work previously done in SiDiaC-v.1.0.

  • 6 authors
·
Mar 10

130k Lines of Formal Topology in Two Weeks: Simple and Cheap Autoformalization for Everyone?

This is a brief description of a project that has already autoformalized a large portion of the general topology from the Munkres textbook (which has in total 241 pages in 7 chapters and 39 sections). The project has been running since November 21, 2025 and has as of January 4, 2026, produced 160k lines of formalized topology. Most of it (about 130k lines) have been done in two weeks,from December 22 to January 4, for an LLM subscription cost of about \$100. This includes a 3k-line proof of Urysohn's lemma, a 2k-line proof of Urysohn's Metrization theorem, over 10k-line proof of the Tietze extension theorem, and many more (in total over 1.5k lemmas/theorems). The approach is quite simple and cheap: build a long-running feedback loop between an LLM and a reasonably fast proof checker equipped with a core foundational library. The LLM is now instantiated as ChatGPT (mostly 5.2) or Claude Sonnet (4.5) run through the respective Codex or Claude Code command line interfaces. The proof checker is Chad Brown's higher-order set theory system Megalodon, and the core library is Brown's formalization of basic set theory and surreal numbers (including reals, etc). The rest is some prompt engineering and technical choices which we describe here. Based on the fast progress, low cost, virtually unknown ITP/library, and the simple setup available to everyone, we believe that (auto)formalization may become quite easy and ubiquitous in 2026, regardless of which proof assistant is used.

  • 1 authors
·
Jan 5

Evaluating Large Language Models for Code Review

Context: Code reviews are crucial for software quality. Recent AI advances have allowed large language models (LLMs) to review and fix code; now, there are tools that perform these reviews. However, their reliability and accuracy have not yet been systematically evaluated. Objective: This study compares different LLMs' performance in detecting code correctness and suggesting improvements. Method: We tested GPT4o and Gemini 2.0 Flash on 492 AI generated code blocks of varying correctness, along with 164 canonical code blocks from the HumanEval benchmark. To simulate the code review task objectively, we expected LLMs to assess code correctness and improve the code if needed. We ran experiments with different configurations and reported on the results. Results: With problem descriptions, GPT4o and Gemini 2.0 Flash correctly classified code correctness 68.50% and 63.89% of the time, respectively, and corrected the code 67.83% and 54.26% of the time for the 492 code blocks of varying correctness. Without problem descriptions, performance declined. The results for the 164 canonical code blocks differed, suggesting that performance depends on the type of code. Conclusion: LLM code reviews can help suggest improvements and assess correctness, but there is a risk of faulty outputs. We propose a process that involves humans, called the "Human in the loop LLM Code Review" to promote knowledge sharing while mitigating the risk of faulty outputs.

  • 4 authors
·
May 26, 2025

FAIR Jupyter: a knowledge graph approach to semantic sharing and granular exploration of a computational notebook reproducibility dataset

The way in which data are shared can affect their utility and reusability. Here, we demonstrate how data that we had previously shared in bulk can be mobilized further through a knowledge graph that allows for much more granular exploration and interrogation. The original dataset is about the computational reproducibility of GitHub-hosted Jupyter notebooks associated with biomedical publications. It contains rich metadata about the publications, associated GitHub repositories and Jupyter notebooks, and the notebooks' reproducibility. We took this dataset, converted it into semantic triples and loaded these into a triple store to create a knowledge graph, FAIR Jupyter, that we made accessible via a web service. This enables granular data exploration and analysis through queries that can be tailored to specific use cases. Such queries may provide details about any of the variables from the original dataset, highlight relationships between them or combine some of the graph's content with materials from corresponding external resources. We provide a collection of example queries addressing a range of use cases in research and education. We also outline how sets of such queries can be used to profile specific content types, either individually or by class. We conclude by discussing how such a semantically enhanced sharing of complex datasets can both enhance their FAIRness, i.e., their findability, accessibility, interoperability, and reusability, and help identify and communicate best practices, particularly with regards to data quality, standardization, automation and reproducibility.

  • 2 authors
·
Apr 19, 2024

A standardized Project Gutenberg corpus for statistical analysis of natural language and quantitative linguistics

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.

  • 2 authors
·
Dec 19, 2018

Gaia Data Release 3: Summary of the content and survey properties

We present the third data release of the European Space Agency's Gaia mission, GDR3. The GDR3 catalogue is the outcome of the processing of raw data collected with the Gaia instruments during the first 34 months of the mission by the Gaia Data Processing and Analysis Consortium. The GDR3 catalogue contains the same source list, celestial positions, proper motions, parallaxes, and broad band photometry in the G, G_{BP}, and G_{RP} pass-bands already present in the Early Third Data Release. GDR3 introduces an impressive wealth of new data products. More than 33 million objects in the ranges G_{rvs} < 14 and 3100 <T_{eff} <14500 , have new determinations of their mean radial velocities based on data collected by Gaia. We provide G_{rvs} magnitudes for most sources with radial velocities, and a line broadening parameter is listed for a subset of these. Mean Gaia spectra are made available to the community. The GDR3 catalogue includes about 1 million mean spectra from the radial velocity spectrometer, and about 220 million low-resolution blue and red prism photometer BPRP mean spectra. The results of the analysis of epoch photometry are provided for some 10 million sources across 24 variability types. GDR3 includes astrophysical parameters and source class probabilities for about 470 million and 1500 million sources, respectively, including stars, galaxies, and quasars. Orbital elements and trend parameters are provided for some 800,000 astrometric, spectroscopic and eclipsing binaries. More than 150,000 Solar System objects, including new discoveries, with preliminary orbital solutions and individual epoch observations are part of this release. Reflectance spectra derived from the epoch BPRP spectral data are published for about 60\,000 asteroids. Finally, an additional data set is provided, namely the Gaia Andromeda Photometric Survey (abridged)

  • 456 authors
·
Jul 30, 2022

ChatGPT in the Age of Generative AI and Large Language Models: A Concise Survey

ChatGPT is a large language model (LLM) created by OpenAI that has been carefully trained on a large amount of data. It has revolutionized the field of natural language processing (NLP) and has pushed the boundaries of LLM capabilities. ChatGPT has played a pivotal role in enabling widespread public interaction with generative artificial intelligence (GAI) on a large scale. It has also sparked research interest in developing similar technologies and investigating their applications and implications. In this paper, our primary goal is to provide a concise survey on the current lines of research on ChatGPT and its evolution. We considered both the glass box and black box views of ChatGPT, encompassing the components and foundational elements of the technology, as well as its applications, impacts, and implications. The glass box approach focuses on understanding the inner workings of the technology, and the black box approach embraces it as a complex system, and thus examines its inputs, outputs, and effects. This paves the way for a comprehensive exploration of the technology and provides a road map for further research and experimentation. We also lay out essential foundational literature on LLMs and GAI in general and their connection with ChatGPT. This overview sheds light on existing and missing research lines in the emerging field of LLMs, benefiting both public users and developers. Furthermore, the paper delves into the broad spectrum of applications and significant concerns in fields such as education, research, healthcare, finance, etc.

  • 5 authors
·
Jul 9, 2023

A Complete Survey on Generative AI (AIGC): Is ChatGPT from GPT-4 to GPT-5 All You Need?

As ChatGPT goes viral, generative AI (AIGC, a.k.a AI-generated content) has made headlines everywhere because of its ability to analyze and create text, images, and beyond. With such overwhelming media coverage, it is almost impossible for us to miss the opportunity to glimpse AIGC from a certain angle. In the era of AI transitioning from pure analysis to creation, it is worth noting that ChatGPT, with its most recent language model GPT-4, is just a tool out of numerous AIGC tasks. Impressed by the capability of the ChatGPT, many people are wondering about its limits: can GPT-5 (or other future GPT variants) help ChatGPT unify all AIGC tasks for diversified content creation? Toward answering this question, a comprehensive review of existing AIGC tasks is needed. As such, our work comes to fill this gap promptly by offering a first look at AIGC, ranging from its techniques to applications. Modern generative AI relies on various technical foundations, ranging from model architecture and self-supervised pretraining to generative modeling methods (like GAN and diffusion models). After introducing the fundamental techniques, this work focuses on the technological development of various AIGC tasks based on their output type, including text, images, videos, 3D content, etc., which depicts the full potential of ChatGPT's future. Moreover, we summarize their significant applications in some mainstream industries, such as education and creativity content. Finally, we discuss the challenges currently faced and present an outlook on how generative AI might evolve in the near future.

  • 17 authors
·
Mar 21, 2023

GDC Cohort Copilot: An AI Copilot for Curating Cohorts from the Genomic Data Commons

Motivation: The Genomic Data Commons (GDC) provides access to high quality, harmonized cancer genomics data through a unified curation and analysis platform centered around patient cohorts. While GDC users can interactively create complex cohorts through the graphical Cohort Builder, users (especially new ones) may struggle to find specific cohort descriptors across hundreds of possible fields and properties. However, users may be better able to describe their desired cohort in free-text natural language. Results: We introduce GDC Cohort Copilot, an open-source copilot tool for curating cohorts from the GDC. GDC Cohort Copilot automatically generates the GDC cohort filter corresponding to a user-input natural language description of their desired cohort, before exporting the cohort back to the GDC for further analysis. An interactive user interface allows users to further refine the generated cohort. We develop and evaluate multiple large language models (LLMs) for GDC Cohort Copilot and demonstrate that our locally-served, open-source GDC Cohort LLM achieves better results than GPT-4o prompting in generating GDC cohorts. Availability and implementation: The standalone docker image for GDC Cohort Copilot is available at https://quay.io/repository/cdis/gdc-cohort-copilot. Source code is available at https://github.com/uc-cdis/gdc-cohort-copilot. GDC Cohort LLM weights are available at https://huggingface.co/uc-ctds.

  • 5 authors
·
Jul 2, 2025

Retrieval Augmented Generation Evaluation for Health Documents

Safe and trustworthy use of Large Language Models (LLM) in the processing of healthcare documents and scientific papers could substantially help clinicians, scientists and policymakers in overcoming information overload and focusing on the most relevant information at a given moment. Retrieval Augmented Generation (RAG) is a promising method to leverage the potential of LLMs while enhancing the accuracy of their outcomes. This report assesses the potentials and shortcomings of such approaches in the automatic knowledge synthesis of different types of documents in the health domain. To this end, it describes: (1) an internally developed proof of concept pipeline that employs state-of-the-art practices to deliver safe and trustable analysis for healthcare documents and scientific papers called RAGEv (Retrieval Augmented Generation Evaluation); (2) a set of evaluation tools for LLM-based document retrieval and generation; (3) a benchmark dataset to verify the accuracy and veracity of the results called RAGEv-Bench. It concludes that careful implementations of RAG techniques could minimize most of the common problems in the use of LLMs for document processing in the health domain, obtaining very high scores both on short yes/no answers and long answers. There is a high potential for incorporating it into the day-to-day work of policy support tasks, but additional efforts are required to obtain a consistent and trustworthy tool.

  • 11 authors
·
May 7, 2025

Institutional Books - Enriched Text: A customizable multilingual open-source pipeline for denoising, deduplicating, and annotating OCR text at scale

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.

RareBench: Can LLMs Serve as Rare Diseases Specialists?

Generalist Large Language Models (LLMs), such as GPT-4, have shown considerable promise in various domains, including medical diagnosis. Rare diseases, affecting approximately 300 million people worldwide, often have unsatisfactory clinical diagnosis rates primarily due to a lack of experienced physicians and the complexity of differentiating among many rare diseases. In this context, recent news such as "ChatGPT correctly diagnosed a 4-year-old's rare disease after 17 doctors failed" underscore LLMs' potential, yet underexplored, role in clinically diagnosing rare diseases. To bridge this research gap, we introduce RareBench, a pioneering benchmark designed to systematically evaluate the capabilities of LLMs on 4 critical dimensions within the realm of rare diseases. Meanwhile, we have compiled the largest open-source dataset on rare disease patients, establishing a benchmark for future studies in this domain. To facilitate differential diagnosis of rare diseases, we develop a dynamic few-shot prompt methodology, leveraging a comprehensive rare disease knowledge graph synthesized from multiple knowledge bases, significantly enhancing LLMs' diagnostic performance. Moreover, we present an exhaustive comparative study of GPT-4's diagnostic capabilities against those of specialist physicians. Our experimental findings underscore the promising potential of integrating LLMs into the clinical diagnostic process for rare diseases. This paves the way for exciting possibilities in future advancements in this field.

  • 6 authors
·
Feb 9, 2024

Application of NotebookLM, a Large Language Model with Retrieval-Augmented Generation, for Lung Cancer Staging

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.

  • 8 authors
·
Oct 8, 2024

SymbioticRAG: Enhancing Document Intelligence Through Human-LLM Symbiotic Collaboration

We present SymbioticRAG, a novel framework that fundamentally reimagines Retrieval-Augmented Generation~(RAG) systems by establishing a bidirectional learning relationship between humans and machines. Our approach addresses two critical challenges in current RAG systems: the inherently human-centered nature of relevance determination and users' progression from "unconscious incompetence" in query formulation. SymbioticRAG introduces a two-tier solution where Level 1 enables direct human curation of retrieved content through interactive source document exploration, while Level 2 aims to build personalized retrieval models based on captured user interactions. We implement Level 1 through three key components: (1)~a comprehensive document processing pipeline with specialized models for layout detection, OCR, and extraction of tables, formulas, and figures; (2)~an extensible retriever module supporting multiple retrieval strategies; and (3)~an interactive interface that facilitates both user engagement and interaction data logging. We experiment Level 2 implementation via a retriever strategy incorporated LLM summarized user intention from user interaction logs. To maintain high-quality data preparation, we develop a human-on-the-loop validation interface that improves pipeline output while advancing research in specialized extraction tasks. Evaluation across three scenarios (literature review, geological exploration, and education) demonstrates significant improvements in retrieval relevance and user satisfaction compared to traditional RAG approaches. To facilitate broader research and further advancement of SymbioticRAG Level 2 implementation, we will make our system openly accessible to the research community.

  • 7 authors
·
May 5, 2025

Institutional Books 1.0: A 242B token dataset from Harvard Library's collections, refined for accuracy and usability

Large language models (LLMs) use data to learn about the world in order to produce meaningful correlations and predictions. As such, the nature, scale, quality, and diversity of the datasets used to train these models, or to support their work at inference time, have a direct impact on their quality. The rapid development and adoption of LLMs of varying quality has brought into focus the scarcity of publicly available, high-quality training data and revealed an urgent need to ground the stewardship of these datasets in sustainable practices with clear provenance chains. To that end, this technical report introduces Institutional Books 1.0, a large collection of public domain books originally digitized through Harvard Library's participation in the Google Books project, beginning in 2006. Working with Harvard Library, we extracted, analyzed, and processed these volumes into an extensively-documented dataset of historic texts. This analysis covers the entirety of Harvard Library's collection scanned as part of that project, originally spanning 1,075,899 volumes written in over 250 different languages for a total of approximately 250 billion tokens. As part of this initial release, the OCR-extracted text (original and post-processed) as well as the metadata (bibliographic, source, and generated) of the 983,004 volumes, or 242B tokens, identified as being in the public domain have been made available. This report describes this project's goals and methods as well as the results of the analyses we performed, all in service of making this historical collection more accessible and easier for humans and machines alike to filter, read and use.

Red Teaming for Generative AI, Report on a Copyright-Focused Exercise Completed in an Academic Medical Center

Background: Generative artificial intelligence (AI) deployment in academic medical settings raises copyright compliance concerns. Dana-Farber Cancer Institute implemented GPT4DFCI, an internal generative AI tool utilizing OpenAI models, that is approved for enterprise use in research and operations. Given (1) the exceptionally broad adoption of the tool in our organization, (2) our research mission, and (3) the shared responsibility model required to benefit from Customer Copyright Commitment in Azure OpenAI Service products, we deemed rigorous copyright compliance testing necessary. Case Description: We conducted a structured red teaming exercise in Nov. 2024, with 42 participants from academic, industry, and government institutions. Four teams attempted to extract copyrighted content from GPT4DFCI across four domains: literary works, news articles, scientific publications, and access-restricted clinical notes. Teams successfully extracted verbatim book dedications and near-exact passages through various strategies. News article extraction failed despite jailbreak attempts. Scientific article reproduction yielded only high-level summaries. Clinical note testing revealed appropriate privacy safeguards. Discussion: The successful extraction of literary content indicates potential copyrighted material presence in training data, necessitating inference-time filtering. Differential success rates across content types suggest varying protective mechanisms. The event led to implementation of a copyright-specific meta-prompt in GPT4DFCI; this mitigation has been in production since Jan. 2025. Conclusion: Systematic red teaming revealed specific vulnerabilities in generative AI copyright compliance, leading to concrete mitigation strategies. Academic medical institutions deploying generative AI should implement continuous testing protocols to ensure legal and ethical compliance.

  • 41 authors
·
Jun 26, 2025

Legal RAG Bench: an end-to-end benchmark for legal RAG

We introduce Legal RAG Bench, a benchmark and evaluation methodology for assessing the end-to-end performance of legal RAG systems. As a benchmark, Legal RAG Bench consists of 4,876 passages from the Victorian Criminal Charge Book alongside 100 complex, hand-crafted questions demanding expert knowledge of criminal law and procedure. Both long-form answers and supporting passages are provided. As an evaluation methodology, Legal RAG Bench leverages a full factorial design and novel hierarchical error decomposition framework, enabling apples-to-apples comparisons of the contributions of retrieval and reasoning models in RAG. We evaluate three state-of-the-art embedding models (Isaacus' Kanon 2 Embedder, Google's Gemini Embedding 001, and OpenAI's Text Embedding 3 Large) and two frontier LLMs (Gemini 3.1 Pro and GPT-5.2), finding that information retrieval is the primary driver of legal RAG performance, with LLMs exerting a more moderate effect on correctness and groundedness. Kanon 2 Embedder, in particular, had the largest positive impact on performance, improving average correctness by 17.5 points, groundedness by 4.5 points, and retrieval accuracy by 34 points. We observe that many errors attributed to hallucinations in legal RAG systems are in fact triggered by retrieval failures, concluding that retrieval sets the ceiling for the performance of many modern legal RAG systems. We document why and how we built Legal RAG Bench alongside the results of our evaluations. We also openly release our code and data to assist with reproduction of our findings.

isaacus Isaacus
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Mar 2 2

OpenAI GPT-5 System Card

This is the system card published alongside the OpenAI GPT-5 launch, August 2025. GPT-5 is a unified system with a smart and fast model that answers most questions, a deeper reasoning model for harder problems, and a real-time router that quickly decides which model to use based on conversation type, complexity, tool needs, and explicit intent (for example, if you say 'think hard about this' in the prompt). The router is continuously trained on real signals, including when users switch models, preference rates for responses, and measured correctness, improving over time. Once usage limits are reached, a mini version of each model handles remaining queries. This system card focuses primarily on gpt-5-thinking and gpt-5-main, while evaluations for other models are available in the appendix. The GPT-5 system not only outperforms previous models on benchmarks and answers questions more quickly, but -- more importantly -- is more useful for real-world queries. We've made significant advances in reducing hallucinations, improving instruction following, and minimizing sycophancy, and have leveled up GPT-5's performance in three of ChatGPT's most common uses: writing, coding, and health. All of the GPT-5 models additionally feature safe-completions, our latest approach to safety training to prevent disallowed content. Similarly to ChatGPT agent, we have decided to treat gpt-5-thinking as High capability in the Biological and Chemical domain under our Preparedness Framework, activating the associated safeguards. While we do not have definitive evidence that this model could meaningfully help a novice to create severe biological harm -- our defined threshold for High capability -- we have chosen to take a precautionary approach.

  • 484 authors
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Dec 19, 2025

LeanSearch v2: Global Premise Retrieval for Lean 4 Theorem Proving

Proving theorems in Lean 4 often requires identifying a scattered set of library lemmas whose joint use enables a concise proof -- a task we call global premise retrieval. Existing tools address adjacent problems: semantic search engines find individual declarations matching a query, while premise-selection systems predict useful lemmas one tactic step at a time. Neither recovers the full premise set an entire theorem requires. We present LeanSearch v2, a two-mode retrieval system for this task. Its standard mode applies a hierarchy-informalized Mathlib corpus with an embedding-reranker pipeline, achieving state-of-the-art single-query retrieval without domain-specific fine-tuning (nDCG@10 of 0.62 vs. 0.53 for the next-best system). Its reasoning mode builds on standard mode as its retrieval substrate, targeting global premise retrieval through iterative sketch-retrieve-reflect cycles. On a 69-query benchmark of research-level Mathlib theorems, reasoning mode recovers 46.1% of ground-truth premise groups within 10 retrieved candidates, outperforming strong reasoning retrieval systems (38.0%) and premise-selection baselines (9.3%) on the same benchmark. In a controlled downstream evaluation with a fixed prover loop, replacing alternative retrievers with LeanSearch v2 yields the highest proof success (20% vs. 16% for the next-best system and 4% without retrieval), confirming that retrieval quality propagates to proof generation. We have open-sourced all code, data, and benchmarks. Code and data: https://github.com/frenzymath/LeanSearch-v2 . The standard mode is publicly available with API access at https://leansearch.net/ .

  • 8 authors
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May 13

A Comprehensive Survey of AI-Generated Content (AIGC): A History of Generative AI from GAN to ChatGPT

Recently, ChatGPT, along with DALL-E-2 and Codex,has been gaining significant attention from society. As a result, many individuals have become interested in related resources and are seeking to uncover the background and secrets behind its impressive performance. In fact, ChatGPT and other Generative AI (GAI) techniques belong to the category of Artificial Intelligence Generated Content (AIGC), which involves the creation of digital content, such as images, music, and natural language, through AI models. The goal of AIGC is to make the content creation process more efficient and accessible, allowing for the production of high-quality content at a faster pace. AIGC is achieved by extracting and understanding intent information from instructions provided by human, and generating the content according to its knowledge and the intent information. In recent years, large-scale models have become increasingly important in AIGC as they provide better intent extraction and thus, improved generation results. With the growth of data and the size of the models, the distribution that the model can learn becomes more comprehensive and closer to reality, leading to more realistic and high-quality content generation. This survey provides a comprehensive review on the history of generative models, and basic components, recent advances in AIGC from unimodal interaction and multimodal interaction. From the perspective of unimodality, we introduce the generation tasks and relative models of text and image. From the perspective of multimodality, we introduce the cross-application between the modalities mentioned above. Finally, we discuss the existing open problems and future challenges in AIGC.

  • 7 authors
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Mar 7, 2023