Daily Papers

Large Language Models (LLMs) have achieved remarkable success in automated code translation. While prior work has focused on improving translation accuracy through advanced prompting and iterative repair, the reliability of the underlying evaluation frameworks has received less attention. In this paper, we demonstrate that a significant number of reported failures in code translation are not due to incorrect logic, but rather evaluation-induced errors stemming from improper compilation flags, missing library links, and unconfigured runtime environments. We conduct a large-scale empirical study across five programming languages (C, C++, Java, Python, Go) and three benchmarks (Avatar, CodeNet, EvalPlus), covering 6,164 translations generated by GPT-4o, DeepSeek-Coder, and Magicoder. Our analysis identifies and categorizes common false negatives, distinguishing pipeline-induced failures that affect any model from model-dependent behaviors that vary across LLMs. Our findings highlight the necessity for transparent, configuration-aware evaluation standards to accurately assess progress in LLM-based code translation.

This report presents the Prime Collective Communications Library (PCCL), a novel fault-tolerant collective communication library designed for distributed ML workloads over the public internet. PCCL introduces a new programming model that enables dynamic peer joining and failure recovery. The library implements efficient collective operations like all-reduce while providing robust fault tolerance mechanisms that allow the system to continue operating even when peers fail or join during ongoing operations. We demonstrate that PCCL's design enables practical solutions to dynamic membership challenges in workloads with repeated operations and deterministic state advancement. Our implementation passes extensive stress tests across all major operating systems, showing reliable operation even under rapid peer churn and concurrent collective operations. By dispatching to multiple connections, we can efficiently utilize cross-continental long-fat-pipe TCP WAN links, in our experiments achieving up to 45 Gbit/s of bandwidth utilization across Europe and 25 Gbit/s across North America and Europe. PCCL's architecture enables easy implementation of distributed low-communication optimization strategies like DiLoCo, which significantly reduce communication frequency. Combined with quantization, this leads to a significant reduction in the bandwidth required for distributed training workloads. PCCL also allows for concurrent collective operations, which enables optimization strategies like async DiLoCo, which can completely hide communication overhead by implementing one-step delayed parameter updates. PCCL can facilitate exact bit-parity of the shared state across peers in all cases induced by graceful or abrupt peer churn. While PCCL exposes a C99 API, Python bindings are available which are compatible with PyTorch alongside FSDP. PCCL is available under the open source MIT license.

woma is a real-time foundation model for gastrointestinal endoscopy: a network trained without labels on about a million endoscopy frames, from which task models are fine-tuned. We contribute a systematic design for production. Requirements and pass marks were fixed before any run, eight candidates screened under pre-registered rules, self-supervised training taken to a stopping rule, then fine-tuning and deployment optimisation, all on one self-contained library, numbat. We also contribute woma itself with two fine-tuned models, every outcome reported met or missed. Our colonoscopy model finds and outlines polyps, names which colon segment is in view, suggests polyp type and grades bowel preparation. Our gastroscopy model names a station out of 22 protocol sites, flags and outlines lesions, and names one of seven findings. Every number was read on data never seen in training, and shipped weights were chosen on that record. In colonoscopy, 96% of polyps in a six-hospital PolypGen set are found at precision >=0.85, and 19 of 19 polyps across fifteen full REAL-Colon videos at 1.6 false alarms per procedure. In gastroscopy, landmark region is named correctly on 92% of frames from unseen patients, and 37 of 39 held-out neoplasia frames are flagged at specificity 0.91. On one workstation GPU every task runs over 1080p video at about 100 frames per second, faster than PyTorch, ONNX Runtime and TensorRT in all four precision regimes tested. TensorRT comes closest: one pass of our foundation model takes it 3 to 27% longer than ours, and we deliver 6 to 31% more frames per second from frame to results. A second build links no vendor library at all -- our own kernels over Vulkan -- so a site deploys two files and needs no toolkit, no cuDNN and no framework; in f32 it beats the CUDA build on the same card.

The exponential growth of scientific literature necessitates advanced tools for effective knowledge exploration. We present Knowledge Navigator, a system designed to enhance exploratory search abilities by organizing and structuring the retrieved documents from broad topical queries into a navigable, two-level hierarchy of named and descriptive scientific topics and subtopics. This structured organization provides an overall view of the research themes in a domain, while also enabling iterative search and deeper knowledge discovery within specific subtopics by allowing users to refine their focus and retrieve additional relevant documents. Knowledge Navigator combines LLM capabilities with cluster-based methods to enable an effective browsing method. We demonstrate our approach's effectiveness through automatic and manual evaluations on two novel benchmarks, CLUSTREC-COVID and SCITOC. Our code, prompts, and benchmarks are made publicly available.

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.

This data paper introduces MajinBook, an open catalogue designed to facilitate the use of shadow libraries--such as Library Genesis and Z-Library--for computational social science and cultural analytics. By linking metadata from these vast, crowd-sourced archives with structured bibliographic data from Goodreads, we create a high-precision corpus of over 539,000 references to English-language books spanning three centuries, enriched with first publication dates, genres, and popularity metrics like ratings and reviews. Our methodology prioritizes natively digital EPUB files to ensure machine-readable quality, while addressing biases in traditional corpora like HathiTrust, and includes secondary datasets for French, German, and Spanish. We evaluate the linkage strategy for accuracy, release all underlying data openly, and discuss the project's legal permissibility under EU and US frameworks for text and data mining in research.

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

Entity linking (mapping ambiguous mentions in text to entities in a knowledge base) is a foundational step in tasks such as knowledge graph construction, question-answering, and information extraction. Our method, LELA, is a modular coarse-to-fine approach that leverages the capabilities of large language models (LLMs), and works with different target domains, knowledge bases and LLMs, without any fine-tuning phase. Our experiments across various entity linking settings show that LELA is highly competitive with fine-tuned approaches, and substantially outperforms the non-fine-tuned ones.

Finding relevant literature underpins the practice of evidence-based medicine. From 2014 to 2016, TREC conducted a clinical decision support track, wherein participants were tasked with finding articles relevant to clinical questions posed by physicians. In total, 87 teams have participated over the past three years, generating 395 runs. During this period, each team has trialled a variety of methods. While there was significant overlap in the methods employed by different teams, the results were varied. Due to the diversity of the platforms used, the results arising from the different techniques are not directly comparable, reducing the ability to build on previous work. By using a stable platform, we have been able to compare different document and query processing techniques, allowing us to experiment with different search parameters. We have used our system to reproduce leading teams runs, and compare the results obtained. By benchmarking our indexing and search techniques, we can statistically test a variety of hypotheses, paving the way for further research.

The accessibility of documents within a collection holds a pivotal role in Information Retrieval, signifying the ease of locating specific content in a collection of documents. This accessibility can be achieved via two distinct avenues. The first is through some retrieval model using a keyword or other feature-based search, and the other is where a document can be navigated using links associated with them, if available. Metrics such as PageRank, Hub, and Authority illuminate the pathways through which documents can be discovered within the network of content while the concept of Retrievability is used to quantify the ease with which a document can be found by a retrieval model. In this paper, we compare these two perspectives, PageRank and retrievability, as they quantify the importance and discoverability of content in a corpus. Through empirical experimentation on benchmark datasets, we demonstrate a subtle similarity between retrievability and PageRank particularly distinguishable for larger datasets.

Diderot's Encyclop\'edie is a reference work from XVIIIth century in Europe that aimed at collecting the knowledge of its era. Wikipedia has the same ambition with a much greater scope. However, the lack of digital connection between the two encyclopedias may hinder their comparison and the study of how knowledge has evolved. A key element of Wikipedia is Wikidata that backs the articles with a graph of structured data. In this paper, we describe the annotation of more than 10,300 of the Encyclop\'edie entries with Wikidata identifiers enabling us to connect these entries to the graph. We considered geographic and human entities. The Encyclop\'edie does not contain biographic entries as they mostly appear as subentries of locations. We extracted all the geographic entries and we completely annotated all the entries containing a description of human entities. This represents more than 2,600 links referring to locations or human entities. In addition, we annotated more than 9,500 entries having a geographic content only. We describe the annotation process as well as application examples. This resource is available at https://github.com/pnugues/encyclopedie_1751

Mathematical symbols and descriptions appear in various forms across document section boundaries without explicit markup. In this paper, we present a new large-scale dataset that emphasizes extracting symbols and descriptions in scientific documents. Symlink annotates scientific papers of 5 different domains (i.e., computer science, biology, physics, mathematics, and economics). Our experiments on Symlink demonstrate the challenges of the symbol-description linking task for existing models and call for further research effort in this area. We will publicly release Symlink to facilitate future research.

As part of its scholarly data efforts, the Internet Archive (IA) releases a first version of a citation graph dataset, named refcat, derived from scholarly publications and additional data sources. It is composed of data gathered by the fatcat cataloging project (the catalog that underpins IA Scholar), related web-scale crawls targeting primary and secondary scholarly outputs, as well as metadata from the Open Library project and Wikipedia. This first version of the graph consists of over 1.3B citations. We release this dataset under a CC0 Public Domain Dedication, accessible through Internet Archive. The source code used for the derivation process, including exact and fuzzy citation matching, is released under an MIT license. The goal of this report is to describe briefly the current contents and the derivation of the dataset.

There are a few prominent practices for conducting reviews of academic literature, including searching for specific keywords on Google Scholar or checking citations from some initial seed paper(s). These approaches serve a critical purpose for academic literature reviews, yet there remain challenges in identifying relevant literature when similar work may utilize different terminology (e.g., mixed-initiative visual analytics papers may not use the same terminology as papers on model-steering, yet the two topics are relevant to one another). In this paper, we introduce a system, VitaLITy, intended to complement existing practices. In particular, VitaLITy promotes serendipitous discovery of relevant literature using transformer language models, allowing users to find semantically similar papers in a word embedding space given (1) a list of input paper(s) or (2) a working abstract. VitaLITy visualizes this document-level embedding space in an interactive 2-D scatterplot using dimension reduction. VitaLITy also summarizes meta information about the document corpus or search query, including keywords and co-authors, and allows users to save and export papers for use in a literature review. We present qualitative findings from an evaluation of VitaLITy, suggesting it can be a promising complementary technique for conducting academic literature reviews. Furthermore, we contribute data from 38 popular data visualization publication venues in VitaLITy, and we provide scrapers for the open-source community to continue to grow the list of supported venues.

We present a collection of open, machine-readable document datasets covering parliamentary proceedings, legal judgments, government publications, news, and tourism statistics from Sri Lanka. As of v20251005, the collection currently comprises 215,670 documents (60.3 GB) across 13 datasets in Sinhala, Tamil, and English. The datasets are updated daily and mirrored on GitHub and Hugging Face. These resources aim to support research in computational linguistics, legal analytics, socio-political studies, and multilingual natural language processing. We describe the data sources, collection pipeline, formats, and potential use cases, while discussing licensing and ethical considerations.

Humanities scholars commonly provide evidence for claims that they make about a work of literature (e.g., a novel) in the form of quotations from the work. We collect a large-scale dataset (RELiC) of 78K literary quotations and surrounding critical analysis and use it to formulate the novel task of literary evidence retrieval, in which models are given an excerpt of literary analysis surrounding a masked quotation and asked to retrieve the quoted passage from the set of all passages in the work. Solving this retrieval task requires a deep understanding of complex literary and linguistic phenomena, which proves challenging to methods that overwhelmingly rely on lexical and semantic similarity matching. We implement a RoBERTa-based dense passage retriever for this task that outperforms existing pretrained information retrieval baselines; however, experiments and analysis by human domain experts indicate that there is substantial room for improvement over our dense retriever.

Academic literature reviews have traditionally relied on techniques such as keyword searches and accumulation of relevant back-references, using databases like Google Scholar or IEEEXplore. However, both the precision and accuracy of these search techniques is limited by the presence or absence of specific keywords, making literature review akin to searching for needles in a haystack. We present vitaLITy 2, a solution that uses a Large Language Model or LLM-based approach to identify semantically relevant literature in a textual embedding space. We include a corpus of 66,692 papers from 1970-2023 which are searchable through text embeddings created by three language models. vitaLITy 2 contributes a novel Retrieval Augmented Generation (RAG) architecture and can be interacted with through an LLM with augmented prompts, including summarization of a collection of papers. vitaLITy 2 also provides a chat interface that allow users to perform complex queries without learning any new programming language. This also enables users to take advantage of the knowledge captured in the LLM from its enormous training corpus. Finally, we demonstrate the applicability of vitaLITy 2 through two usage scenarios. vitaLITy 2 is available as open-source software at https://vitality-vis.github.io.

Tracing connections between historical texts is an important part of intertextual research, enabling scholars to reconstruct the virtual library of a writer and identify the sources influencing their creative process. These intertextual links manifest in diverse forms, ranging from direct verbatim quotations to subtle allusions and paraphrases disguised by morphological variation. Language models offer a promising path forward due to their capability of capturing semantic similarity beyond lexical overlap. However, the development of new methods for this task is held back by the scarcity of standardized benchmarks and easy-to-use datasets. We address this gap by introducing Loci Similes, a benchmark for Latin intertextuality detection comprising of a curated dataset of ~172k text segments containing 545 expert-verified parallels linking Late Antique authors to a corpus of classical authors. Using this data, we establish baselines for retrieval and classification of intertextualities with state-of-the-art LLMs.

We present PyThaiNLP, a free and open-source natural language processing (NLP) library for Thai language implemented in Python. It provides a wide range of software, models, and datasets for Thai language. We first provide a brief historical context of tools for Thai language prior to the development of PyThaiNLP. We then outline the functionalities it provided as well as datasets and pre-trained language models. We later summarize its development milestones and discuss our experience during its development. We conclude by demonstrating how industrial and research communities utilize PyThaiNLP in their work. The library is freely available at https://github.com/pythainlp/pythainlp.

Identifying the intent of a citation in scientific papers (e.g., background information, use of methods, comparing results) is critical for machine reading of individual publications and automated analysis of the scientific literature. We propose structural scaffolds, a multitask model to incorporate structural information of scientific papers into citations for effective classification of citation intents. Our model achieves a new state-of-the-art on an existing ACL anthology dataset (ACL-ARC) with a 13.3% absolute increase in F1 score, without relying on external linguistic resources or hand-engineered features as done in existing methods. In addition, we introduce a new dataset of citation intents (SciCite) which is more than five times larger and covers multiple scientific domains compared with existing datasets. Our code and data are available at: https://github.com/allenai/scicite.

Large language models (LLMs) have grown in their usage to provide support for question answering across numerous disciplines. The models on their own have already shown promise for answering basic questions, however fail quickly where expert domain knowledge is required or the question is nuanced. Scientific research often involves searching for relevant literature, distilling pertinent information from that literature and analysing how the findings support or contradict one another. The information is often encapsulated in the full text body of research articles, rather than just in the abstracts. Statements within these articles frequently require the wider article context to be fully understood. We have built an LLM-based system that performs such search and distillation of information encapsulated in scientific literature, and we evaluate our keyword based search and information distillation system against a set of biology related questions from previously released literature benchmarks. We demonstrate sparse retrieval methods exhibit results close to state of the art without the need for dense retrieval, with its associated infrastructure and complexity overhead. We also show how to increase the coverage of relevant documents for literature review generation.

We propose a simple Named Entity Linking system that can be trained from Wikidata only. This demonstrates the strengths and weaknesses of this data source for this task and provides an easily reproducible baseline to compare other systems against. Our model is lightweight to train, to run and to keep synchronous with Wikidata in real time.

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.

This paper presents teaching materials, particularly assignments and ideas for classroom activities, from a new course on large language models (LLMs) taught at Charles University. The assignments include experiments with LLM inference for weather report generation and machine translation. The classroom activities include class quizzes, focused research on downstream tasks and datasets, and an interactive "best paper" session aimed at reading and comprehension of research papers.

We present our submission to the Task 5 of SemEval-2025 that aims to aid librarians in assigning subject tags to the library records by producing a list of likely relevant tags for a given document. We frame the task as an information retrieval problem, where the document content is used to retrieve subject tags from a large subject taxonomy. We leverage two types of encoder models to build a two-stage information retrieval system -- a bi-encoder for coarse-grained candidate extraction at the first stage, and a cross-encoder for fine-grained re-ranking at the second stage. This approach proved effective, demonstrating significant improvements in recall compared to single-stage methods and showing competitive results according to qualitative evaluation.