Daily Papers

We introduce WorldVQA, a benchmark designed to evaluate the atomic visual world knowledge of Multimodal Large Language Models (MLLMs). Unlike current evaluations, which often conflate visual knowledge retrieval with reasoning, WorldVQA decouples these capabilities to strictly measure "what the model memorizes." The benchmark assesses the atomic capability of grounding and naming visual entities across a stratified taxonomy, spanning from common head-class objects to long-tail rarities. We expect WorldVQA to serve as a rigorous test for visual factuality, thereby establishing a standard for assessing the encyclopedic breadth and hallucination rates of current and next-generation frontier models.

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

Graph-based Retrieval-Augmented Generation (GraphRAG) organizes external knowledge as a hierarchical graph, enabling efficient retrieval and aggregation of scattered evidence across multiple documents. However, many existing benchmarks for GraphRAG rely on short, curated passages as external knowledge, failing to adequately evaluate systems in realistic settings involving long contexts and large-scale heterogeneous documents. To bridge this gap, we introduce WildGraphBench, a benchmark designed to assess GraphRAG performance in the wild. We leverage Wikipedia's unique structure, where cohesive narratives are grounded in long and heterogeneous external reference documents, to construct a benchmark reflecting real-word scenarios. Specifically, we sample articles across 12 top-level topics, using their external references as the retrieval corpus and citation-linked statements as ground truth, resulting in 1,100 questions spanning three levels of complexity: single-fact QA, multi-fact QA, and section-level summarization. Experiments across multiple baselines reveal that current GraphRAG pipelines help on multi-fact aggregation when evidence comes from a moderate number of sources, but this aggregation paradigm may overemphasize high-level statements at the expense of fine-grained details, leading to weaker performance on summarization tasks. Project page:https://github.com/BstWPY/WildGraphBench.

We present CoDEx, a set of knowledge graph completion datasets extracted from Wikidata and Wikipedia that improve upon existing knowledge graph completion benchmarks in scope and level of difficulty. In terms of scope, CoDEx comprises three knowledge graphs varying in size and structure, multilingual descriptions of entities and relations, and tens of thousands of hard negative triples that are plausible but verified to be false. To characterize CoDEx, we contribute thorough empirical analyses and benchmarking experiments. First, we analyze each CoDEx dataset in terms of logical relation patterns. Next, we report baseline link prediction and triple classification results on CoDEx for five extensively tuned embedding models. Finally, we differentiate CoDEx from the popular FB15K-237 knowledge graph completion dataset by showing that CoDEx covers more diverse and interpretable content, and is a more difficult link prediction benchmark. Data, code, and pretrained models are available at https://bit.ly/2EPbrJs.

Subject classification schemes are foundational to the organization, evaluation, and navigation of scientific knowledge. While expert-curated systems like Scopus provide widely used taxonomies, they often suffer from coarse granularity, subjectivity, and limited adaptability to emerging interdisciplinary fields. Data-driven alternatives based on citation networks show promise but lack rigorous, external validation against the semantic content of scientific literature. Here, we propose a novel quantitative framework that leverages classification tasks to evaluate the effectiveness of journal classification schemes. Using over 23 million paper abstracts, we demonstrate that labels derived from k-means clustering on Periodical2Vec (P2V)--a periodical embedding learned from paper-level citations--yield significantly higher classification performance than both Scopus and other data-driven baselines (e.g., citation, co-citation, and Node2Vec variants). By comparing journal partitions across classification schemes, two structural patterns emerge on the map of science: (1) the reorganization of disciplinary boundaries--splitting overly broad categories (e.g., "Medicine" into "Oncology", "Cardiology", and other specialties) while merging artificially fragmented ones (e.g., "Chemistry" and "Chemical Engineering"); and (2) the identification of coherent interdisciplinary clusters--such as "Biomedical Engineering", "Medical Ethics", and "Information Management"--that are dispersed across multiple categories but unified in citation space. These findings underscore that citation-derived periodical embeddings not only outperform traditional taxonomies in predictive validity but also offer a dynamic, fine-grained map of science that better reflects both the specialization and interdisciplinarity inherent in contemporary research.

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.

Most scientific materials compress reasoning, presenting conclusions while omitting the derivational chains that justify them. This compression hinders verification by lacking explicit, step-wise justifications and inhibits cross-domain links by collapsing the very pathways that establish the logical and causal connections between concepts. We introduce a scalable framework that decompresses scientific reasoning, constructing a verifiable Long Chain-of-Thought (LCoT) knowledge base and projecting it into an emergent encyclopedia, SciencePedia. Our pipeline operationalizes an endpoint-driven, reductionist strategy: a Socratic agent, guided by a curriculum of around 200 courses, generates approximately 3 million first-principles questions. To ensure high fidelity, multiple independent solver models generate LCoTs, which are then rigorously filtered by prompt sanitization and cross-model answer consensus, retaining only those with verifiable endpoints. This verified corpus powers the Brainstorm Search Engine, which performs inverse knowledge search -- retrieving diverse, first-principles derivations that culminate in a target concept. This engine, in turn, feeds the Plato synthesizer, which narrates these verified chains into coherent articles. The initial SciencePedia comprises approximately 200,000 fine-grained entries spanning mathematics, physics, chemistry, biology, engineering, and computation. In evaluations across six disciplines, Plato-synthesized articles (conditioned on retrieved LCoTs) exhibit substantially higher knowledge-point density and significantly lower factual error rates than an equally-prompted baseline without retrieval (as judged by an external LLM). Built on this verifiable LCoT knowledge base, this reasoning-centric approach enables trustworthy, cross-domain scientific synthesis at scale and establishes the foundation for an ever-expanding encyclopedia.

Information overload is a major obstacle to scientific progress. The explosive growth in scientific literature and data has made it ever harder to discover useful insights in a large mass of information. Today scientific knowledge is accessed through search engines, but they are unable to organize scientific knowledge alone. In this paper we introduce Galactica: a large language model that can store, combine and reason about scientific knowledge. We train on a large scientific corpus of papers, reference material, knowledge bases and many other sources. We outperform existing models on a range of scientific tasks. On technical knowledge probes such as LaTeX equations, Galactica outperforms the latest GPT-3 by 68.2% versus 49.0%. Galactica also performs well on reasoning, outperforming Chinchilla on mathematical MMLU by 41.3% to 35.7%, and PaLM 540B on MATH with a score of 20.4% versus 8.8%. It also sets a new state-of-the-art on downstream tasks such as PubMedQA and MedMCQA dev of 77.6% and 52.9%. And despite not being trained on a general corpus, Galactica outperforms BLOOM and OPT-175B on BIG-bench. We believe these results demonstrate the potential for language models as a new interface for science. We open source the model for the benefit of the scientific community.

Large language model (LLM) contexts are typically constructed using retrieval-augmented generation (RAG), which involves ranking and selecting the top-k passages. The approach causes fragmentation in information graphs in document structures, over-retrieval, and duplication of content alongside insufficient query context, including 2nd and 3rd order facets. In this paper, a structure-informed and diversity-constrained context bubble construction framework is proposed that assembles coherent, citable bundles of spans under a strict token budget. The method preserves and exploits inherent document structure by organising multi-granular spans (e.g., sections and rows) and using task-conditioned structural priors to guide retrieval. Starting from high-relevance anchor spans, a context bubble is constructed through constrained selection that balances query relevance, marginal coverage, and redundancy penalties. It will explicitly constrain diversity and budget, producing compact and informative context sets, unlike top-k retrieval. Moreover, a full retrieval is emitted that traces the scoring and selection choices of the records, thus providing auditability and deterministic tuning. Experiments on enterprise documents demonstrate the efficiency of context bubble as it significantly reduces redundant context, is better able to cover secondary facets and has a better answer quality and citation faithfulness within a limited context window. Ablation studies demonstrate that both structural priors as well as diversity constraint selection are necessary; removing either component results in a decline in coverage and an increase in redundant or incomplete context.

We present a corpus of 5,000 richly annotated abstracts of medical articles describing clinical randomized controlled trials. Annotations include demarcations of text spans that describe the Patient population enrolled, the Interventions studied and to what they were Compared, and the Outcomes measured (the `PICO' elements). These spans are further annotated at a more granular level, e.g., individual interventions within them are marked and mapped onto a structured medical vocabulary. We acquired annotations from a diverse set of workers with varying levels of expertise and cost. We describe our data collection process and the corpus itself in detail. We then outline a set of challenging NLP tasks that would aid searching of the medical literature and the practice of evidence-based medicine.

We investigated the evolution and transformation of scientific knowledge in the early modern period, analyzing more than 350 different editions of textbooks used for teaching astronomy in European universities from the late fifteenth century to mid-seventeenth century. These historical sources constitute the Sphaera Corpus. By examining different semantic relations among individual parts of each edition on record, we built a multiplex network consisting of six layers, as well as the aggregated network built from the superposition of all the layers. The network analysis reveals the emergence of five different communities. The contribution of each layer in shaping the communities and the properties of each community are studied. The most influential books in the corpus are found by calculating the average age of all the out-going and in-coming links for each book. A small group of editions is identified as a transmitter of knowledge as they bridge past knowledge to the future through a long temporal interval. Our analysis, moreover, identifies the most disruptive books. These books introduce new knowledge that is then adopted by almost all the books published afterwards until the end of the whole period of study. The historical research on the content of the identified books, as an empirical test, finally corroborates the results of all our analyses.

In this work, we evaluate the capacity for foundation models to retrieve encyclopedic knowledge across a wide range of languages, topics, and contexts. To support this effort, we 1) produce a new dataset containing 303k factual associations in 20 different languages, 2) formulate a new counterfactual knowledge assessment, Polyglot or Not, and 3) benchmark 5 foundation models in a multilingual setting and a diverse set of 20 models in an English-only setting. We observed significant accuracy differences in models of interest, with Meta's LLaMA topping both the multilingual and English-only assessments. Error analysis reveals a significant deficiency in LLaMA's ability to retrieve facts in languages written in the Cyrillic script and gaps in its understanding of facts based on the location and gender of entailed subjects. Ultimately, we argue that the promise of utilizing foundation language models as bonafide polyglots is greatly diminished when they are tasked with retrieving information in languages other than English. Supporting code (https://github.com/daniel-furman/Polyglot-or-Not) and dataset (https://huggingface.co/datasets/Polyglot-or-Not/Fact-Completion) are openly released.

Scientific progress depends on researchers' ability to synthesize the growing body of literature. Can large language models (LMs) assist scientists in this task? We introduce OpenScholar, a specialized retrieval-augmented LM that answers scientific queries by identifying relevant passages from 45 million open-access papers and synthesizing citation-backed responses. To evaluate OpenScholar, we develop ScholarQABench, the first large-scale multi-domain benchmark for literature search, comprising 2,967 expert-written queries and 208 long-form answers across computer science, physics, neuroscience, and biomedicine. On ScholarQABench, OpenScholar-8B outperforms GPT-4o by 5% and PaperQA2 by 7% in correctness, despite being a smaller, open model. While GPT4o hallucinates citations 78 to 90% of the time, OpenScholar achieves citation accuracy on par with human experts. OpenScholar's datastore, retriever, and self-feedback inference loop also improves off-the-shelf LMs: for instance, OpenScholar-GPT4o improves GPT-4o's correctness by 12%. In human evaluations, experts preferred OpenScholar-8B and OpenScholar-GPT4o responses over expert-written ones 51% and 70% of the time, respectively, compared to GPT4o's 32%. We open-source all of our code, models, datastore, data and a public demo.

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.

Large language models (LLMs) are increasingly adopted for automating survey paper generation wang2406autosurvey, liang2025surveyx, yan2025surveyforge,su2025benchmarking,wen2025interactivesurvey. Existing approaches typically extract content from a large collection of related papers and prompt LLMs to summarize them directly. However, such methods often overlook the structural relationships among papers, resulting in generated surveys that lack a coherent taxonomy and a deeper contextual understanding of research progress. To address these shortcomings, we propose SurveyG, an LLM-based agent framework that integrates hierarchical citation graph, where nodes denote research papers and edges capture both citation dependencies and semantic relatedness between their contents, thereby embedding structural and contextual knowledge into the survey generation process. The graph is organized into three layers: Foundation, Development, and Frontier, to capture the evolution of research from seminal works to incremental advances and emerging directions. By combining horizontal search within layers and vertical depth traversal across layers, the agent produces multi-level summaries, which are consolidated into a structured survey outline. A multi-agent validation stage then ensures consistency, coverage, and factual accuracy in generating the final survey. Experiments, including evaluations by human experts and LLM-as-a-judge, demonstrate that SurveyG outperforms state-of-the-art frameworks, producing surveys that are more comprehensive and better structured to the underlying knowledge taxonomy of a field.

Scientific knowledge is growing rapidly, making it challenging to track progress and high-level conceptual links across broad disciplines. While existing tools like citation networks and search engines make it easy to access a few related papers, they fundamentally lack the flexible abstraction needed to represent the density of activity in various scientific subfields. We motivate SCIENCE HIERARCHOGRAPHY, the goal of organizing scientific literature into a high-quality hierarchical structure that allows for the categorization of scientific work across varying levels of abstraction, from very broad fields to very specific studies. Such a representation can provide insights into which fields are well-explored and which are under-explored. To achieve the goals of SCIENCE HIERARCHOGRAPHY, we develop a range of algorithms. Our primary approach combines fast embedding-based clustering with LLM-based prompting to balance the computational efficiency of embedding methods with the semantic precision offered by LLM prompting. We demonstrate that this approach offers the best trade-off between quality and speed compared to methods that heavily rely on LLM prompting, such as iterative tree construction with LLMs. To better reflect the interdisciplinary and multifaceted nature of research papers, our hierarchy captures multiple dimensions of categorization beyond simple topic labels. We evaluate the utility of our framework by assessing how effectively an LLM-based agent can locate target papers using the hierarchy. Results show that this structured approach enhances interpretability, supports trend discovery, and offers an alternative pathway for exploring scientific literature beyond traditional search methods. Code, data and demo: https://github.com/JHU-CLSP/science-hierarchography{https://github.com/JHU-CLSP/science-hierarchography}

In order to address increasing demands of real-world applications, the research for knowledge-intensive NLP (KI-NLP) should advance by capturing the challenges of a truly open-domain environment: web-scale knowledge, lack of structure, inconsistent quality and noise. To this end, we propose a new setup for evaluating existing knowledge intensive tasks in which we generalize the background corpus to a universal web snapshot. We investigate a slate of NLP tasks which rely on knowledge - either factual or common sense, and ask systems to use a subset of CCNet - the Sphere corpus - as a knowledge source. In contrast to Wikipedia, otherwise a common background corpus in KI-NLP, Sphere is orders of magnitude larger and better reflects the full diversity of knowledge on the web. Despite potential gaps in coverage, challenges of scale, lack of structure and lower quality, we find that retrieval from Sphere enables a state of the art system to match and even outperform Wikipedia-based models on several tasks. We also observe that while a dense index can outperform a sparse BM25 baseline on Wikipedia, on Sphere this is not yet possible. To facilitate further research and minimise the community's reliance on proprietary, black-box search engines, we share our indices, evaluation metrics and infrastructure.

Deep iterative chain-of-thought (CoT) reasoning enables LLMs to tackle complex tasks by progressively activating relevant pre-trained knowledge. However, it faces challenges in ensuring continual improvement and determining a stopping criterion. In this paper, we investigate whether the relevant knowledge that contributes directly to solving the given question can be activated from the initial reasoning path, thus circumventing the need for iterative refinement. Our experiments reveal that increasing the diversity of initial reasoning paths can achieve comparable or superior performance, a concept we term breadth reasoning. However, existing breadth reasoning approaches, such as self-consistency, offer limited diversity. To address this limitation, we propose a simple yet effective method that enhances reasoning breadth by integrating contextual exploration with reduced sampling randomness. Extensive experiments demonstrate that our approach significantly outperforms deep iterative reasoning. Our code is provided in https://github.com/zongqianwu/breadth.

Wikipedia relies on an extensive review process to verify that the content of each individual page is unbiased and presents a neutral point of view. Less attention has been paid to possible biases in the hyperlink structure of Wikipedia, which has a significant influence on the user's exploration process when visiting more than one page. The evaluation of hyperlink bias is challenging because it depends on the global view rather than the text of individual pages. In this paper, we focus on the influence of the interconnect topology between articles describing complementary aspects of polarizing topics. We introduce a novel measure of exposure to diverse information to quantify users' exposure to different aspects of a topic throughout an entire surfing session, rather than just one click ahead. We apply this measure to six polarizing topics (e.g., gun control and gun right), and we identify cases in which the network topology significantly limits the exposure of users to diverse information on the topic, encouraging users to remain in a knowledge bubble. Our findings demonstrate the importance of evaluating Wikipedia's network structure in addition to the extensive review of individual articles.

Multi-hop reasoning over financial disclosures is often a retrieval problem before it becomes a reasoning or generation problem: relevant facts are dispersed across sections, filings, companies, and years, and LLMs often expend excessive tokens navigating noisy context. Without precise Knowledge Graph (KG)-guided selection of relevant context, even strong reasoning models either fail to answer or consume excessive tokens, whereas KG-linked evidence enables models to focus their reasoning on composing already retrieved facts. We present FinReflectKG - MultiHop, a benchmark built on FinReflectKG, a temporally indexed financial KG that links audited triples to source chunks from S&P 100 filings (2022-2024). Mining frequent 2-3 hop subgraph patterns across sectors (via GICS taxonomy), we generate financial analyst style questions with exact supporting evidence from the KG. A two-phase pipeline first creates QA pairs via pattern-specific prompts, followed by a multi-criteria quality control evaluation to ensure QA validity. We then evaluate three controlled retrieval scenarios: (S1) precise KG-linked paths; (S2) text-only page windows centered on relevant text spans; and (S3) relevant page windows with randomizations and distractors. Across both reasoning and non-reasoning models, KG-guided precise retrieval yields substantial gains on the FinReflectKG - MultiHop QA benchmark dataset, boosting correctness scores by approximately 24 percent while reducing token utilization by approximately 84.5 percent compared to the page window setting, which reflects the traditional vector retrieval paradigm. Spanning intra-document, inter-year, and cross-company scopes, our work underscores the pivotal role of knowledge graphs in efficiently connecting evidence for multi-hop financial QA. We also release a curated subset of the benchmark (555 QA Pairs) to catalyze further research.

We study how to apply large language models to write grounded and organized long-form articles from scratch, with comparable breadth and depth to Wikipedia pages. This underexplored problem poses new challenges at the pre-writing stage, including how to research the topic and prepare an outline prior to writing. We propose STORM, a writing system for the Synthesis of Topic Outlines through Retrieval and Multi-perspective Question Asking. STORM models the pre-writing stage by (1) discovering diverse perspectives in researching the given topic, (2) simulating conversations where writers carrying different perspectives pose questions to a topic expert grounded on trusted Internet sources, (3) curating the collected information to create an outline. For evaluation, we curate FreshWiki, a dataset of recent high-quality Wikipedia articles, and formulate outline assessments to evaluate the pre-writing stage. We further gather feedback from experienced Wikipedia editors. Compared to articles generated by an outline-driven retrieval-augmented baseline, more of STORM's articles are deemed to be organized (by a 25% absolute increase) and broad in coverage (by 10%). The expert feedback also helps identify new challenges for generating grounded long articles, such as source bias transfer and over-association of unrelated facts.

Benchmarks play a crucial role in tracking the rapid advancement of large language models (LLMs) and identifying their capability boundaries. However, existing benchmarks predominantly curate questions at the question level, suffering from three fundamental limitations: vulnerability to data contamination, restriction to single-knowledge-point assessment, and reliance on costly domain expert annotation. We propose Encyclo-K, a statement-based benchmark that rethinks benchmark construction from the ground up. Our key insight is that knowledge statements, not questions, can serve as the unit of curation, and questions can then be constructed from them. We extract standalone knowledge statements from authoritative textbooks and dynamically compose them into evaluation questions through random sampling at test time. This design directly addresses all three limitations: the combinatorial space is too vast to memorize, and model rankings remain stable across dynamically generated question sets, enabling reliable periodic dataset refresh; each question aggregates 8-10 statements for comprehensive multi-knowledge assessment; annotators only verify formatting compliance without requiring domain expertise, substantially reducing annotation costs. Experiments on over 50 LLMs demonstrate that Encyclo-K poses substantial challenges with strong discriminative power. Even the top-performing OpenAI-GPT-5.1 achieves only 62.07% accuracy, and model performance displays a clear gradient distribution--reasoning models span from 16.04% to 62.07%, while chat models range from 9.71% to 50.40%. These results validate the challenges introduced by dynamic evaluation and multi-statement comprehensive understanding. These findings establish Encyclo-K as a scalable framework for dynamic evaluation of LLMs' comprehensive understanding over multiple fine-grained disciplinary knowledge statements.

HAL (Hyper Articles en Ligne) is the French national publication repository, used by most higher education and research organizations for their open science policy. As a digital library, it is a rich repository of scholarly documents, but its potential for advanced research has been underutilized. We present HALvest, a unique dataset that bridges the gap between citation networks and the full text of papers submitted on HAL. We craft our dataset by filtering HAL for scholarly publications, resulting in approximately 700,000 documents, spanning 34 languages across 13 identified domains, suitable for language model training, and yielding approximately 16.5 billion tokens (with 8 billion in French and 7 billion in English, the most represented languages). We transform the metadata of each paper into a citation network, producing a directed heterogeneous graph. This graph includes uniquely identified authors on HAL, as well as all open submitted papers, and their citations. We provide a baseline for authorship attribution using the dataset, implement a range of state-of-the-art models in graph representation learning for link prediction, and discuss the usefulness of our generated knowledge graph structure.

Large language models (LLMs), while exhibiting exceptional performance, suffer from hallucinations, especially on knowledge-intensive tasks. Existing works propose to augment LLMs with individual text units retrieved from external knowledge corpora to alleviate the issue. However, in many domains, texts are interconnected (e.g., academic papers in a bibliographic graph are linked by citations and co-authorships) which form a (text-attributed) graph. The knowledge in such graphs is encoded not only in single texts/nodes but also in their associated connections. To facilitate the research of augmenting LLMs with graphs, we manually construct a Graph Reasoning Benchmark dataset called GRBench, containing 1,740 questions that can be answered with the knowledge from 10 domain graphs. Then, we propose a simple and effective framework called Graph Chain-of-thought (Graph-CoT) to augment LLMs with graphs by encouraging LLMs to reason on the graph iteratively. Each Graph-CoT iteration consists of three sub-steps: LLM reasoning, LLM-graph interaction, and graph execution. We conduct systematic experiments with three LLM backbones on GRBench, where Graph-CoT outperforms the baselines consistently. The code is available at https://github.com/PeterGriffinJin/Graph-CoT.

Scientific literature is growing exponentially, creating a critical bottleneck for researchers to efficiently synthesize knowledge. While general-purpose Large Language Models (LLMs) show potential in text processing, they often fail to capture scientific domain-specific nuances (e.g., technical jargon, methodological rigor) and struggle with complex scientific tasks, limiting their utility for interdisciplinary research. To address these gaps, this paper presents SciGPT, a domain-adapted foundation model for scientific literature understanding and ScienceBench, an open source benchmark tailored to evaluate scientific LLMs. Built on the Qwen3 architecture, SciGPT incorporates three key innovations: (1) low-cost domain distillation via a two-stage pipeline to balance performance and efficiency; (2) a Sparse Mixture-of-Experts (SMoE) attention mechanism that cuts memory consumption by 55\% for 32,000-token long-document reasoning; and (3) knowledge-aware adaptation integrating domain ontologies to bridge interdisciplinary knowledge gaps. Experimental results on ScienceBench show that SciGPT outperforms GPT-4o in core scientific tasks including sequence labeling, generation, and inference. It also exhibits strong robustness in unseen scientific tasks, validating its potential to facilitate AI-augmented scientific discovery.

Real-world information needs require access to structurally diverse knowledge sources, from unstructured text and relational tables to knowledge graphs and property graphs. Existing retrievers, however, operate over one source at a time under a fixed query language, leaving the broader landscape of available knowledge fragmented behind incompatible interfaces. A natural attempt at unification would collapse these sources into a shared space, but this erases the structural affordances (such as schemas, ontologies, compositional operators) that give each source its expressive power. Effective retrieval over diverse knowledge, therefore, requires not homogenization but an overarching layer that meets each source on its own terms. To achieve this, we present OmniRetrieval, a framework that takes any natural-language query, identifies appropriate knowledge sources, and dispatches source-native queries to their native execution engines. Across an extensive benchmark spanning 13 datasets and 309 distinct knowledge bases over text, relational, and graph-structured sources, OmniRetrieval exceeds single-source baselines, demonstrating that it can serve as a general-purpose interface to the heterogeneous sources while preserving the structural distinctions that make each source valuable.

Large-scale data sets on scholarly publications are the basis for a variety of bibliometric analyses and natural language processing (NLP) applications. Especially data sets derived from publication's full-text have recently gained attention. While several such data sets already exist, we see key shortcomings in terms of their domain and time coverage, citation network completeness, and representation of full-text content. To address these points, we propose a new version of the data set unarXive. We base our data processing pipeline and output format on two existing data sets, and improve on each of them. Our resulting data set comprises 1.9 M publications spanning multiple disciplines and 32 years. It furthermore has a more complete citation network than its predecessors and retains a richer representation of document structure as well as non-textual publication content such as mathematical notation. In addition to the data set, we provide ready-to-use training/test data for citation recommendation and IMRaD classification. All data and source code is publicly available at https://github.com/IllDepence/unarXive.

In the field of Computer Science, conference and workshop papers serve as important contributions, carrying substantial weight in research assessment processes, compared to other disciplines. However, a considerable number of these papers are not assigned a Digital Object Identifier (DOI), hence their citations are not reported in widely used citation datasets like OpenCitations and Crossref, raising limitations to citation analysis. While the Microsoft Academic Graph (MAG) previously addressed this issue by providing substantial coverage, its discontinuation has created a void in available data. BIP! NDR aims to alleviate this issue and enhance the research assessment processes within the field of Computer Science. To accomplish this, it leverages a workflow that identifies and retrieves Open Science papers lacking DOIs from the DBLP Corpus, and by performing text analysis, it extracts citation information directly from their full text. The current version of the dataset contains more than 510K citations made by approximately 60K open access Computer Science conference or workshop papers that, according to DBLP, do not have a DOI.

Retrieval from graph data is crucial for augmenting large language models (LLM) with both open-domain knowledge and private enterprise data, and it is also a key component in the recent GraphRAG system (edge et al., 2024). Despite decades of research on knowledge graphs and knowledge base question answering, leading LLM frameworks (e.g. Langchain and LlamaIndex) have only minimal support for retrieval from modern encyclopedic knowledge graphs like Wikidata. In this paper, we analyze the root cause and suggest that modern RDF knowledge graphs (e.g. Wikidata, Freebase) are less efficient for LLMs due to overly large schemas that far exceed the typical LLM context window, use of resource identifiers, overlapping relation types and lack of normalization. As a solution, we propose property graph views on top of the underlying RDF graph that can be efficiently queried by LLMs using Cypher. We instantiated this idea on Wikidata and introduced CypherBench, the first benchmark with 11 large-scale, multi-domain property graphs with 7.8 million entities and over 10,000 questions. To achieve this, we tackled several key challenges, including developing an RDF-to-property graph conversion engine, creating a systematic pipeline for text-to-Cypher task generation, and designing new evaluation metrics.

We present SciRIFF (Scientific Resource for Instruction-Following and Finetuning), a dataset of 137K instruction-following demonstrations for 54 tasks covering five essential scientific literature understanding capabilities: information extraction, summarization, question answering, claim verification, and classification. SciRIFF demonstrations are notable for their long input contexts, detailed task specifications, and complex structured outputs. While instruction-following resources are available in specific domains such as clinical medicine and chemistry, SciRIFF is the first dataset focused on extracting and synthesizing information from research literature across a wide range of scientific fields. To demonstrate the utility of SciRIFF, we develop a sample-efficient strategy to adapt a general instruction-following model for science by performing additional finetuning on a mix of general-domain and SciRIFF demonstrations. In evaluations on nine held-out scientific tasks, our model -- called SciTulu -- improves over a strong LLM baseline by 28.1% and 6.5% at the 7B and 70B scales respectively, while maintaining general instruction-following performance within 2% of the baseline. We are optimistic that SciRIFF will facilitate the development and evaluation of LLMs to help researchers navigate the ever-growing body of scientific literature. We release our dataset, model checkpoints, and data processing and evaluation code to enable further research.

Large language models (LLMs) tend to generate lexically, semantically, and stylistically homogenous texts. This poses a risk of knowledge collapse, where homogenous LLMs mediate a shrinking in the range of accessible information over time. Existing works on homogenization are limited by a focus on closed-ended multiple-choice setups or fuzzy semantic features, and do not look at trends across time and cultural contexts. To overcome this, we present a new methodology to measure epistemic diversity, i.e., variation in real-world claims in LLM outputs, which we use to perform a broad empirical study of LLM knowledge collapse. We test 27 LLMs, 155 topics covering 12 countries, and 200 prompt variations sourced from real user chats. For the topics in our study, we show that while newer models tend to generate more diverse claims, nearly all models are less epistemically diverse than a basic web search. We find that model size has a negative impact on epistemic diversity, while retrieval-augmented generation (RAG) has a positive impact, though the improvement from RAG varies by the cultural context. Finally, compared to a traditional knowledge source (Wikipedia), we find that country-specific claims reflect the English language more than the local one, highlighting a gap in epistemic representation

Statutory article retrieval (SAR), the task of retrieving statute law articles relevant to a legal question, is a promising application of legal text processing. In particular, high-quality SAR systems can improve the work efficiency of legal professionals and provide basic legal assistance to citizens in need at no cost. Unlike traditional ad-hoc information retrieval, where each document is considered a complete source of information, SAR deals with texts whose full sense depends on complementary information from the topological organization of statute law. While existing works ignore these domain-specific dependencies, we propose a novel graph-augmented dense statute retriever (G-DSR) model that incorporates the structure of legislation via a graph neural network to improve dense retrieval performance. Experimental results show that our approach outperforms strong retrieval baselines on a real-world expert-annotated SAR dataset.

We present OpenGloss, a synthetic encyclopedic dictionary and semantic knowledge graph for English that integrates lexicographic definitions, encyclopedic context, etymological histories, and semantic relationships in a unified resource. OpenGloss contains 537K senses across 150K lexemes, on par with WordNet 3.1 and Open English WordNet, while providing more than four times as many sense definitions. These lexemes include 9.1M semantic edges, 1M usage examples, 3M collocations, and 60M words of encyclopedic content. Generated through a multi-agent procedural generation pipeline with schema-validated LLM outputs and automated quality assurance, the entire resource was produced in under one week for under $1,000. This demonstrates that structured generation can create comprehensive lexical resources at cost and time scales impractical for manual curation, enabling rapid iteration as foundation models improve. The resource addresses gaps in pedagogical applications by providing integrated content -- definitions, examples, collocations, encyclopedias, etymology -- that supports both vocabulary learning and natural language processing tasks. As a synthetically generated resource, OpenGloss reflects both the capabilities and limitations of current foundation models. The dataset is publicly available on Hugging Face under CC-BY 4.0, enabling researchers and educators to build upon and adapt this resource.

Scientific literature searches are often exploratory, whereby users are not yet familiar with a particular field or concept but are interested in learning more about it. However, existing systems for scientific literature search are typically tailored to keyword-based lookup searches, limiting the possibilities for exploration. We propose NLP-KG, a feature-rich system designed to support the exploration of research literature in unfamiliar natural language processing (NLP) fields. In addition to a semantic search, NLP-KG allows users to easily find survey papers that provide a quick introduction to a field of interest. Further, a Fields of Study hierarchy graph enables users to familiarize themselves with a field and its related areas. Finally, a chat interface allows users to ask questions about unfamiliar concepts or specific articles in NLP and obtain answers grounded in knowledge retrieved from scientific publications. Our system provides users with comprehensive exploration possibilities, supporting them in investigating the relationships between different fields, understanding unfamiliar concepts in NLP, and finding relevant research literature. Demo, video, and code are available at: https://github.com/NLP-Knowledge-Graph/NLP-KG-WebApp.

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.

Large Language Models provide significant new opportunities for the generation of high-quality written works. However, their employment in the research community is inhibited by their tendency to hallucinate invalid sources and lack of direct access to a knowledge base of relevant scientific articles. In this work, we present Citegeist: An application pipeline using dynamic Retrieval Augmented Generation (RAG) on the arXiv Corpus to generate a related work section and other citation-backed outputs. For this purpose, we employ a mixture of embedding-based similarity matching, summarization, and multi-stage filtering. To adapt to the continuous growth of the document base, we also present an optimized way of incorporating new and modified papers. To enable easy utilization in the scientific community, we release both, a website (https://citegeist.org), as well as an implementation harness that works with several different LLM implementations.

Natural Language Processing (NLP) is widely used to supply summarization ability from long context to structured information. However, extracting structured knowledge from scientific text by NLP models remains a challenge because of its domain-specific nature to complex data preprocessing and the granularity of multi-layered device-level information. To address this, we introduce ByteScience, a non-profit cloud-based auto fine-tuned Large Language Model (LLM) platform, which is designed to extract structured scientific data and synthesize new scientific knowledge from vast scientific corpora. The platform capitalizes on DARWIN, an open-source, fine-tuned LLM dedicated to natural science. The platform was built on Amazon Web Services (AWS) and provides an automated, user-friendly workflow for custom model development and data extraction. The platform achieves remarkable accuracy with only a small amount of well-annotated articles. This innovative tool streamlines the transition from the science literature to structured knowledge and data and benefits the advancements in natural informatics.

In this work, we focus on the problem of retrieving relevant arguments for a query claim covering diverse aspects. State-of-the-art methods rely on explicit mappings between claims and premises, and thus are unable to utilize large available collections of premises without laborious and costly manual annotation. Their diversity approach relies on removing duplicates via clustering which does not directly ensure that the selected premises cover all aspects. This work introduces a new multi-step approach for the argument retrieval problem. Rather than relying on ground-truth assignments, our approach employs a machine learning model to capture semantic relationships between arguments. Beyond that, it aims to cover diverse facets of the query, instead of trying to identify duplicates explicitly. Our empirical evaluation demonstrates that our approach leads to a significant improvement in the argument retrieval task even though it requires less data.

The volume of scientific output is creating an urgent need for automated tools to help scientists keep up with developments in their field. Semantic Scholar (S2) is an open data platform and website aimed at accelerating science by helping scholars discover and understand scientific literature. We combine public and proprietary data sources using state-of-the-art techniques for scholarly PDF content extraction and automatic knowledge graph construction to build the Semantic Scholar Academic Graph, the largest open scientific literature graph to-date, with 200M+ papers, 80M+ authors, 550M+ paper-authorship edges, and 2.4B+ citation edges. The graph includes advanced semantic features such as structurally parsed text, natural language summaries, and vector embeddings. In this paper, we describe the components of the S2 data processing pipeline and the associated APIs offered by the platform. We will update this living document to reflect changes as we add new data offerings and improve existing services.

The proposed research aims to develop an innovative semantic query processing system that enables users to obtain comprehensive information about research works produced by Computer Science (CS) researchers at the Australian National University (ANU). The system integrates Large Language Models (LLMs) with the ANU Scholarly Knowledge Graph (ASKG), a structured repository of all research-related artifacts produced at ANU in the CS field. Each artifact and its parts are represented as textual nodes stored in a Knowledge Graph (KG). To address the limitations of traditional scholarly KG construction and utilization methods, which often fail to capture fine-grained details, we propose a novel framework that integrates the Deep Document Model (DDM) for comprehensive document representation and the KG-enhanced Query Processing (KGQP) for optimized complex query handling. DDM enables a fine-grained representation of the hierarchical structure and semantic relationships within academic papers, while KGQP leverages the KG structure to improve query accuracy and efficiency with LLMs. By combining the ASKG with LLMs, our approach enhances knowledge utilization and natural language understanding capabilities. The proposed system employs an automatic LLM-SPARQL fusion to retrieve relevant facts and textual nodes from the ASKG. Initial experiments demonstrate that our framework is superior to baseline methods in terms of accuracy retrieval and query efficiency. We showcase the practical application of our framework in academic research scenarios, highlighting its potential to revolutionize scholarly knowledge management and discovery. This work empowers researchers to acquire and utilize knowledge from documents more effectively and provides a foundation for developing precise and reliable interactions with LLMs.

This tutorial serves as a comprehensive guide for understanding graph databases, focusing on the fundamentals of graph theory while showcasing practical applications across various fields. It starts by introducing foundational concepts and delves into the structure of graphs through nodes and edges, covering different types such as undirected, directed, weighted, and unweighted graphs. Key graph properties, terminologies, and essential algorithms for network analysis are outlined, including Dijkstras shortest path algorithm and methods for calculating node centrality and graph connectivity. The tutorial highlights the advantages of graph databases over traditional relational databases, particularly in efficiently managing complex, interconnected data. It examines leading graph database systems such as Neo4j, Amazon Neptune, and ArangoDB, emphasizing their unique features for handling large datasets. Practical instructions on graph operations using NetworkX and Neo4j are provided, covering node and edge creation, attribute assignment, and advanced queries with Cypher. Additionally, the tutorial explores common graph visualization techniques using tools like Plotly and Neo4j Bloom, which enhance the interpretation and usability of graph data. It also delves into community detection algorithms, including the Louvain method, which facilitates clustering in large networks. Finally, the paper concludes with recommendations for researchers interested in exploring the vast potential of graph technologies.

Retrieval-augmented generation (RAG) promises grounded question answering, yet domain settings with multiple heterogeneous knowledge bases (KBs) remain challenging. In Chinese Tibetan medicine, encyclopedia entries are often dense and easy to match, which can dominate retrieval even when classics or clinical papers provide more authoritative evidence. We study a practical setting with three KBs (encyclopedia, classics, and clinical papers) and a 500-query benchmark (cutoff K{=}5) covering both single-KB and cross-KB questions. We propose two complementary methods to improve traceability, reduce hallucinations, and enable cross-KB verification. First, DAKS performs KB routing and budgeted retrieval to mitigate density-driven bias and to prioritize authoritative sources when appropriate. Second, we use an alignment graph to guide evidence fusion and coverage-aware packing, improving cross-KB evidence coverage without relying on naive concatenation. All answers are generated by a lightweight generator, openPangu-Embedded-7B. Experiments show consistent gains in routing quality and cross-KB evidence coverage, with the full system achieving the best CrossEv@5 while maintaining strong faithfulness and citation correctness.

We propose ParaSCI, the first large-scale paraphrase dataset in the scientific field, including 33,981 paraphrase pairs from ACL (ParaSCI-ACL) and 316,063 pairs from arXiv (ParaSCI-arXiv). Digging into characteristics and common patterns of scientific papers, we construct this dataset though intra-paper and inter-paper methods, such as collecting citations to the same paper or aggregating definitions by scientific terms. To take advantage of sentences paraphrased partially, we put up PDBERT as a general paraphrase discovering method. The major advantages of paraphrases in ParaSCI lie in the prominent length and textual diversity, which is complementary to existing paraphrase datasets. ParaSCI obtains satisfactory results on human evaluation and downstream tasks, especially long paraphrase generation.

There has been a surge of interest in harnessing the reasoning capabilities of Large Language Models (LLMs) to accelerate scientific discovery. While existing approaches rely on grounding the discovery process within the relevant literature, effectiveness varies significantly with the quality and nature of the retrieved literature. We address the challenge of retrieving prior work whose concepts can inspire solutions for a given research problem, a task we define as Methodology Inspiration Retrieval (MIR). We construct a novel dataset tailored for training and evaluating retrievers on MIR, and establish baselines. To address MIR, we build the Methodology Adjacency Graph (MAG); capturing methodological lineage through citation relationships. We leverage MAG to embed an "intuitive prior" into dense retrievers for identifying patterns of methodological inspiration beyond superficial semantic similarity. This achieves significant gains of +5.4 in Recall@3 and +7.8 in Mean Average Precision (mAP) over strong baselines. Further, we adapt LLM-based re-ranking strategies to MIR, yielding additional improvements of +4.5 in Recall@3 and +4.8 in mAP. Through extensive ablation studies and qualitative analyses, we exhibit the promise of MIR in enhancing automated scientific discovery and outline avenues for advancing inspiration-driven retrieval.

We propose Encyclopedic-VQA, a large scale visual question answering (VQA) dataset featuring visual questions about detailed properties of fine-grained categories and instances. It contains 221k unique question+answer pairs each matched with (up to) 5 images, resulting in a total of 1M VQA samples. Moreover, our dataset comes with a controlled knowledge base derived from Wikipedia, marking the evidence to support each answer. Empirically, we show that our dataset poses a hard challenge for large vision+language models as they perform poorly on our dataset: PaLI [14] is state-of-the-art on OK-VQA [37], yet it only achieves 13.0% accuracy on our dataset. Moreover, we experimentally show that progress on answering our encyclopedic questions can be achieved by augmenting large models with a mechanism that retrieves relevant information from the knowledge base. An oracle experiment with perfect retrieval achieves 87.0% accuracy on the single-hop portion of our dataset, and an automatic retrieval-augmented prototype yields 48.8%. We believe that our dataset enables future research on retrieval-augmented vision+language models. It is available at https://github.com/google-research/google-research/tree/master/encyclopedic_vqa .

Evaluating long-form responses to research queries heavily relies on expert annotators, restricting attention to areas like AI where researchers can conveniently enlist colleagues. Yet, research expertise is widespread: survey articles synthesize knowledge distributed across the literature. We introduce ResearchQA, a resource for evaluating LLM systems by distilling survey articles from 75 research fields into 21K queries and 160K rubric items. Each rubric, derived jointly with queries from survey sections, lists query-specific answer evaluation criteria, i.e., citing papers, making explanations, and describing limitations. Assessments by 31 Ph.D. annotators in 8 fields indicate 96% of queries support Ph.D. information needs and 87% of rubric items should be addressed in system responses by a sentence or more. Using our rubrics, we are able to construct an automatic pairwise judge obtaining 74% agreement with expert judgments. We leverage ResearchQA to analyze competency gaps in 18 systems in over 7.6K pairwise evaluations. No parametric or retrieval-augmented system we evaluate exceeds 70% on covering rubric items, and the highest-ranking agentic system shows 75% coverage. Error analysis reveals that the highest-ranking system fully addresses less than 11% of citation rubric items, 48% of limitation items, and 49% of comparison items. We release our data to facilitate more comprehensive multi-field evaluations.

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.

We introduce Darshana Graph, a corpus of over 125,000 text records spanning classical Hindu, Buddhist, and Jain philosophical traditions, drawn from public-domain and openly licensed translations of sources including the Bhagavad Gita, Brahma Sutras, principal Upanishads, the Pali Canon, and core Jain texts. Its distinctive contribution lies in a structurally unique subset of roughly 8,500 Hindu and Jain records in which the same root verse or sutra is aligned across eighteen historical commentators representing five schools of Vedanta and other darshanas, enabling direct comparison of how independent interpretive traditions read identical source material. To our knowledge, no publicly available resource provides comparable cross-commentator alignment at this scale. We present two analyses built on this corpus. First, a transparent stylometric comparison requiring no machine learning measures argumentative style through scriptural citation density, explicit refutation rate, and sentence complexity. It finds a moderate negative correlation between citation density and refutation rate, a marked increase in refutation rate across three commentators in a related doctrinal lineage, and measurable genre-level differences within the Pali Canon itself. Second, we describe a constrained large language model pipeline that extracts typed philosophical relationships between concepts using a predefined relation vocabulary and deterministic post-hoc validation. The resulting graph surfaces cross-school disagreement patterns while also revealing important extraction limitations, including cases where an independent embedding-based analysis disagrees with the graph-derived findings. We release the full corpus, extracted relationship graph, and all source code.

This systematic review explores the application of Large Language Models (LLMs) in Combinatorial Optimization (CO). We report our findings using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. We conduct a literature search via Scopus and Google Scholar, examining over 2,000 publications. We assess publications against four inclusion and four exclusion criteria related to their language, research focus, publication year, and type. Eventually, we select 103 studies. We classify these studies into semantic categories and topics to provide a comprehensive overview of the field, including the tasks performed by LLMs, the architectures of LLMs, the existing datasets specifically designed for evaluating LLMs in CO, and the field of application. Finally, we identify future directions for leveraging LLMs in this field.

Graph self-supervised learning (SSL) is now a go-to method for pre-training graph foundation models (GFMs). There is a wide variety of knowledge patterns embedded in the graph data, such as node properties and clusters, which are crucial to learning generalized representations for GFMs. However, existing surveys of GFMs have several shortcomings: they lack comprehensiveness regarding the most recent progress, have unclear categorization of self-supervised methods, and take a limited architecture-based perspective that is restricted to only certain types of graph models. As the ultimate goal of GFMs is to learn generalized graph knowledge, we provide a comprehensive survey of self-supervised GFMs from a novel knowledge-based perspective. We propose a knowledge-based taxonomy, which categorizes self-supervised graph models by the specific graph knowledge utilized. Our taxonomy consists of microscopic (nodes, links, etc.), mesoscopic (context, clusters, etc.), and macroscopic knowledge (global structure, manifolds, etc.). It covers a total of 9 knowledge categories and more than 25 pretext tasks for pre-training GFMs, as well as various downstream task generalization strategies. Such a knowledge-based taxonomy allows us to re-examine graph models based on new architectures more clearly, such as graph language models, as well as provide more in-depth insights for constructing GFMs.

While Large Language Models (LLMs) have demonstrated proficiency in Deep Research or Wide Search, their capacity to solve highly complex questions-those requiring long-horizon planning, massive evidence gathering, and synthesis across heterogeneous sources-remains largely unexplored. We introduce Super Research, a task for complex autonomous research tasks that integrates (i) structured decomposition into a research plan, (ii) super wide retrieval for diverse perspectives, and (iii) super deep investigation to resolve uncertainties through iterative queries. To evaluate this capability, we curated a benchmark of 300 expert-written questions across diverse domains, each requiring up to 100+ retrieval steps and 1,000+ web pages to reconcile conflicting evidence. Super Research produces verifiable reports with fine-grained citations and intermediate artifacts (e.g., outlines and tables) to ensure traceable reasoning. Furthermore, we present a graph-anchored auditing protocol that evaluates Super Research along five dimensions: Coverage, Logical Consistency, Report Utility, Objectivity and Citation Health. While super-complex questions may be infrequent in standard applications, Super Research serves as a critical ceiling evaluation and stress test for LLM capabilities. A model's proficiency within Super Research acts as a powerful proxy for its general research competence; success here suggests the robustness necessary to navigate nearly any subordinate research task. Leaderboard is available at: https://cnsdqd-dyb.github.io/Super-Research-Benchmark/

The cybersecurity landscape evolves rapidly and poses threats to organizations. To enhance resilience, one needs to track the latest developments and trends in the domain. It has been demonstrated that standard bibliometrics approaches show their limits in such a fast-evolving domain. For this purpose, we use large language models (LLMs) to extract relevant knowledge entities from cybersecurity-related texts. We use a subset of arXiv preprints on cybersecurity as our data and compare different LLMs in terms of entity recognition (ER) and relevance. The results suggest that LLMs do not produce good knowledge entities that reflect the cybersecurity context, but our results show some potential for noun extractors. For this reason, we developed a noun extractor boosted with some statistical analysis to extract specific and relevant compound nouns from the domain. Later, we tested our model to identify trends in the LLM domain. We observe some limitations, but it offers promising results to monitor the evolution of emergent trends.

Extraction and synthesis of structured knowledge from extensive scientific literature are crucial for advancing and disseminating scientific progress. Although many existing systems facilitate literature review and digest, they struggle to process multimodal, varied, and inconsistent information within and across the literature into structured data. We introduce SciDaSynth, a novel interactive system powered by large language models (LLMs) that enables researchers to efficiently build structured knowledge bases from scientific literature at scale. The system automatically creates data tables to organize and summarize users' interested knowledge in literature via question-answering. Furthermore, it provides multi-level and multi-faceted exploration of the generated data tables, facilitating iterative validation, correction, and refinement. Our within-subjects study with researchers demonstrates the effectiveness and efficiency of SciDaSynth in constructing quality scientific knowledge bases. We further discuss the design implications for human-AI interaction tools for data extraction and structuring.

We introduce S2ORC, a large corpus of 81.1M English-language academic papers spanning many academic disciplines. The corpus consists of rich metadata, paper abstracts, resolved bibliographic references, as well as structured full text for 8.1M open access papers. Full text is annotated with automatically-detected inline mentions of citations, figures, and tables, each linked to their corresponding paper objects. In S2ORC, we aggregate papers from hundreds of academic publishers and digital archives into a unified source, and create the largest publicly-available collection of machine-readable academic text to date. We hope this resource will facilitate research and development of tools and tasks for text mining over academic text.

There has been rapid growth in biomedical literature, yet capturing the heterogeneity of the bibliographic information of these articles remains relatively understudied. Although graph mining research via heterogeneous graph neural networks has taken center stage, it remains unclear whether these approaches capture the heterogeneity of the PubMed database, a vast digital repository containing over 33 million articles. We introduce PubMed Graph Benchmark (PGB), a new benchmark dataset for evaluating heterogeneous graph embeddings for biomedical literature. The benchmark contains rich metadata including abstract, authors, citations, MeSH terms, MeSH hierarchy, and some other information. The benchmark contains three different evaluation tasks encompassing systematic reviews, node classification, and node clustering. In PGB, we aggregate the metadata associated with the biomedical articles from PubMed into a unified source and make the benchmark publicly available for any future works.

The burgeoning utilization of Large Language Models (LLMs) in scientific research necessitates advanced benchmarks capable of evaluating their understanding and application of scientific knowledge comprehensively. To address this need, we introduce the SciKnowEval benchmark, a novel framework that systematically evaluates LLMs across five progressive levels of scientific knowledge: studying extensively, inquiring earnestly, thinking profoundly, discerning clearly, and practicing assiduously. These levels aim to assess the breadth and depth of scientific knowledge in LLMs, including knowledge coverage, inquiry and exploration capabilities, reflection and reasoning abilities, ethic and safety considerations, as well as practice proficiency. Specifically, we take biology and chemistry as the two instances of SciKnowEval and construct a dataset encompassing 50K multi-level scientific problems and solutions. By leveraging this dataset, we benchmark 20 leading open-source and proprietary LLMs using zero-shot and few-shot prompting strategies. The results reveal that despite achieving state-of-the-art performance, the proprietary LLMs still have considerable room for improvement, particularly in addressing scientific computations and applications. We anticipate that SciKnowEval will establish a comprehensive standard for benchmarking LLMs in science research and discovery, and promote the development of LLMs that integrate scientific knowledge with strong safety awareness. The dataset and code are publicly available at https://github.com/hicai-zju/sciknoweval .

Scientific literature is typically dense, requiring significant background knowledge and deep comprehension for effective engagement. We introduce SciDQA, a new dataset for reading comprehension that challenges LLMs for a deep understanding of scientific articles, consisting of 2,937 QA pairs. Unlike other scientific QA datasets, SciDQA sources questions from peer reviews by domain experts and answers by paper authors, ensuring a thorough examination of the literature. We enhance the dataset's quality through a process that carefully filters out lower quality questions, decontextualizes the content, tracks the source document across different versions, and incorporates a bibliography for multi-document question-answering. Questions in SciDQA necessitate reasoning across figures, tables, equations, appendices, and supplementary materials, and require multi-document reasoning. We evaluate several open-source and proprietary LLMs across various configurations to explore their capabilities in generating relevant and factual responses. Our comprehensive evaluation, based on metrics for surface-level similarity and LLM judgements, highlights notable performance discrepancies. SciDQA represents a rigorously curated, naturally derived scientific QA dataset, designed to facilitate research on complex scientific text understanding.

We introduce a novel graph-based Retrieval-Augmented Generation (RAG) framework specifically designed for the medical domain, called MedGraphRAG, aimed at enhancing Large Language Model (LLM) capabilities and generating evidence-based results, thereby improving safety and reliability when handling private medical data. Our comprehensive pipeline begins with a hybrid static-semantic approach to document chunking, significantly improving context capture over traditional methods. Extracted entities are used to create a three-tier hierarchical graph structure, linking entities to foundational medical knowledge sourced from medical papers and dictionaries. These entities are then interconnected to form meta-graphs, which are merged based on semantic similarities to develop a comprehensive global graph. This structure supports precise information retrieval and response generation. The retrieval process employs a U-retrieve method to balance global awareness and indexing efficiency of the LLM. Our approach is validated through a comprehensive ablation study comparing various methods for document chunking, graph construction, and information retrieval. The results not only demonstrate that our hierarchical graph construction method consistently outperforms state-of-the-art models on multiple medical Q\&A benchmarks, but also confirms that the responses generated include source documentation, significantly enhancing the reliability of medical LLMs in practical applications. Code will be at: https://github.com/MedicineToken/Medical-Graph-RAG/tree/main

Aspect-based summarization is the task of generating focused summaries based on specific points of interest. Such summaries aid efficient analysis of text, such as quickly understanding reviews or opinions from different angles. However, due to large differences in the type of aspects for different domains (e.g., sentiment, product features), the development of previous models has tended to be domain-specific. In this paper, we propose WikiAsp, a large-scale dataset for multi-domain aspect-based summarization that attempts to spur research in the direction of open-domain aspect-based summarization. Specifically, we build the dataset using Wikipedia articles from 20 different domains, using the section titles and boundaries of each article as a proxy for aspect annotation. We propose several straightforward baseline models for this task and conduct experiments on the dataset. Results highlight key challenges that existing summarization models face in this setting, such as proper pronoun handling of quoted sources and consistent explanation of time-sensitive events.

Large Language Models (LLMs) have achieved remarkable success in natural language processing through strong semantic understanding and generation. However, their black-box nature limits structured and multi-hop reasoning. In contrast, Text-Attributed Graphs (TAGs) provide explicit relational structures enriched with textual context, yet often lack semantic depth. Recent research shows that combining LLMs and TAGs yields complementary benefits: enhancing TAG representation learning and improving the reasoning and interpretability of LLMs. This survey provides the first systematic review of LLM--TAG integration from an orchestration perspective. We introduce a novel taxonomy covering two fundamental directions: LLM for TAG, where LLMs enrich graph-based tasks, and TAG for LLM, where structured graphs improve LLM reasoning. We categorize orchestration strategies into sequential, parallel, and multi-module frameworks, and discuss advances in TAG-specific pretraining, prompting, and parameter-efficient fine-tuning. Beyond methodology, we summarize empirical insights, curate available datasets, and highlight diverse applications across recommendation systems, biomedical analysis, and knowledge-intensive question answering. Finally, we outline open challenges and promising research directions, aiming to guide future work at the intersection of language and graph learning.

For centuries, researchers have sought out ways to connect disparate areas of knowledge. While early scholars (Galileo, da Vinci, etc.) were experts across fields, specialization has taken hold later. With the advent of Artificial Intelligence, we can now explore relationships across areas (e.g., mechanics-biology) or disparate domains (e.g., failure mechanics-art). To achieve this, we use a fine-tuned Large Language Model (LLM), here for a subset of knowledge in multiscale materials failure. The approach includes the use of a general-purpose LLM to distill question-answer pairs from raw sources followed by LLM fine-tuning. The resulting MechGPT LLM foundation model is used in a series of computational experiments to explore its capacity for knowledge retrieval, various language tasks, hypothesis generation, and connecting knowledge across disparate areas. While the model has some ability to recall knowledge from training, we find that LLMs are particularly useful to extract structural insights through Ontological Knowledge Graphs. These interpretable graph structures provide explanatory insights, frameworks for new research questions, and visual representations of knowledge that also can be used in retrieval-augmented generation. Three versions of MechGPT are discussed, featuring different sizes from 13 billion to 70 billion parameters, and reaching context lengths of more than 10,000 tokens. This provides ample capacity for sophisticated retrieval augmented strategies, as well as agent-based modeling where multiple LLMs interact collaboratively and/or adversarially, the incorporation of new data from the literature or web searches, as well as multimodality.

Large language models have demonstrated remarkable potential in various tasks, however, there remains a significant scarcity of open-source models and data for specific domains. Previous works have primarily focused on manually specifying resources and collecting high-quality data on specific domains, which significantly consume time and effort. To address this limitation, we propose an efficient data collection method~Query of CC based on large language models. This method bootstraps seed information through a large language model and retrieves related data from public corpora. It not only collects knowledge-related data for specific domains but unearths the data with potential reasoning procedures. Through the application of this method, we have curated a high-quality dataset called~Knowledge Pile, encompassing four major domains, including stem and humanities sciences, among others. Experimental results demonstrate that~Knowledge Pile significantly improves the performance of large language models in mathematical and knowledge-related reasoning ability tests. To facilitate academic sharing, we open-source our dataset and code, providing valuable support to the academic community.

Half a billion citation edges extracted from 100.7 million Ukrainian court decisions reveal that judicial citation structure encodes legal domain boundaries without supervision and predicts future legislative importance with near-perfect accuracy. We construct the first large-scale citation graph from the complete EDRSR registry (99.5 million full texts, 1.1 TB), extracting 502 million citation links across six types via regex on commodity hardware in approximately 5 hours, with precision of 1.00 on a 200-decision validation sample (95% Wilson CI: [0.982, 1.000]). Three principal findings emerge. (1) The degree distribution follows a power law (alpha = 1.57 +/- 0.008), placing the Ukrainian court network near the EU Court of Justice and below the US Supreme Court, with hub articles cited by millions of decisions. (2) Louvain community detection on the co-citation projection recovers legal domain boundaries (civil, criminal, administrative, commercial) with modularity Q = 0.44-0.55 and temporal stability (NMI = 0.83-0.86 across periods), constituting an automatically constructed legal ontology grounded in judicial practice. (3) Citation features predict top-1000 articles with AUC = 0.9984, substantially outperforming a naive frequency baseline (P@1000 = 0.655); temporal dynamics detect legislative regime changes as phase transitions and the 2022 invasion as a citation entropy spike (H: 11.02 -> 13.49) with emergent wartime legislation nodes. The citation-derived ontology is operationalized as the domain layer of a workflow memory system for LLM-assisted legal analysis, connecting to the ontology-controlled paradigm. The extraction pipeline, analysis code, and aggregated statistics are released as open data.

Understanding the creation, evolution, and dissemination of scientific knowledge is crucial for bridging diverse subject areas and addressing complex global challenges such as pandemics, climate change, and ethical AI. Scientometrics, the quantitative and qualitative study of scientific literature, provides valuable insights into these processes. We introduce Scito2M, a longitudinal scientometric dataset with over two million academic publications, providing comprehensive contents information and citation graphs to support cross-disciplinary analyses. Using Scito2M, we conduct a temporal study spanning over 30 years to explore key questions in scientometrics: the evolution of academic terminology, citation patterns, and interdisciplinary knowledge exchange. Our findings reveal critical insights, such as disparities in epistemic cultures, knowledge production modes, and citation practices. For example, rapidly developing, application-driven fields like LLMs exhibit significantly shorter citation age (2.48 years) compared to traditional theoretical disciplines like oral history (9.71 years).

Deploying Large Language Models (LLMs) for regulatory compliance demands rigorous traceability via comprehensive citations across multi-tiered authority structures. Unlike traditional multi-hop or legal QA, this task requires structured procedural lookups and evidence-set closure rather than entity resolution or case-law reasoning. Existing RAG systems struggle here due to flattened citation edges, fragmented retrieval expansions, and fragile post-hoc attribution. We formalize Regulatory Compliance QA with RegOps-Bench, a novel benchmark featuring an Operational Knowledge Graph derived from complex national R\&D regulations. To address these bottlenecks, we propose RefWalk, a unified framework driven by a shared topic anchor. RefWalk traverses cross-document citations, fuses multi-view candidates via max-based aggregation, and enforces per-rule attribution to explicitly map claims to sources. We establish a strong baseline with substantial improvements in retrieval recall and citation accuracy. Finally, a contrastive evaluation on a U.S. health compliance dataset (HIPAA) reveals that existing systems exhibit saturation on flat-structure rules, underscoring the need for RegOps-Bench. Our code is available at https://github.com/yeongjoonJu/RefWalk.

Cybersecurity literature reviews require a reproducible denominator: the set of papers that a protocol includes before screening and synthesis begin. Today, that denominator is often reconstructed from publisher portals, bibliographic indices, and scholarly application programming interfaces (APIs) whose coverage, formats, and query semantics change over time. This paper presents TopVenues, an open-source system that materializes corpus construction as a versioned research artifact. TopVenues declares a venue and year scope, uses DBLP Computer Science Bibliography (DBLP) as the metadata spine, enriches records with abstracts and BibTeX entries via open scholarly APIs and publisher-specific extractors, and stores the results in a monotonic SQLite snapshot, accessible via a command-line interface (CLI), a web interface, and export paths for review workflows. The May 2026 snapshot contains 9,925 papers from 11 cybersecurity sources over 2017 to 2026, with 99.86% abstract coverage and 99.99% BibTeX coverage; keyword search over the full corpus completes in under 31 ms, and a 250-test suite validates the data-integrity invariants. The fixed denominator also enables repeatable measurement: 29.2% of 2024 to 2025 papers from the four top-ranked security conferences in our scope appear as arXiv preprints, with a median of five months before publication, and a prior-author-track-record filter yields a 16.5x precision gain at 90% recall for triaging preprints that later appear in the same venue set. TopVenues links corpus construction to auditable cybersecurity measurement by making the corpus itself executable, inspectable, and citable. The artifact is available at https://github.com/sidneibarbieri/topVenues.

We present a new kind of question answering dataset, OpenBookQA, modeled after open book exams for assessing human understanding of a subject. The open book that comes with our questions is a set of 1329 elementary level science facts. Roughly 6000 questions probe an understanding of these facts and their application to novel situations. This requires combining an open book fact (e.g., metals conduct electricity) with broad common knowledge (e.g., a suit of armor is made of metal) obtained from other sources. While existing QA datasets over documents or knowledge bases, being generally self-contained, focus on linguistic understanding, OpenBookQA probes a deeper understanding of both the topic---in the context of common knowledge---and the language it is expressed in. Human performance on OpenBookQA is close to 92%, but many state-of-the-art pre-trained QA methods perform surprisingly poorly, worse than several simple neural baselines we develop. Our oracle experiments designed to circumvent the knowledge retrieval bottleneck demonstrate the value of both the open book and additional facts. We leave it as a challenge to solve the retrieval problem in this multi-hop setting and to close the large gap to human performance.

The scientific literature's exponential growth makes it increasingly challenging to navigate and synthesize knowledge across disciplines. Large language models (LLMs) are powerful tools for understanding scientific text, but they fail to capture detailed relationships across large bodies of work. Unstructured approaches, like retrieval augmented generation, can sift through such corpora to recall relevant facts; however, when millions of facts influence the answer, unstructured approaches become cost prohibitive. Structured representations offer a natural complement -- enabling systematic analysis across the whole corpus. Recent work enhances LLMs with unstructured or semistructured representations of scientific concepts; to complement this, we try extracting structured representations using LLMs. By combining LLMs' semantic understanding with a schema of scientific concepts, we prototype a system that answers precise questions about the literature as a whole. Our schema applies across scientific fields and we extract concepts from it using only 20 manually annotated abstracts. To demonstrate the system, we extract concepts from 30,000 papers on arXiv spanning astrophysics, fluid dynamics, and evolutionary biology. The resulting database highlights emerging trends and, by visualizing the knowledge graph, offers new ways to explore the ever-growing landscape of scientific knowledge. Demo: abby101/surveyor-0 on HF Spaces. Code: https://github.com/chiral-carbon/kg-for-science.

Effective scientific communication depends on accurate citations that validate sources and guide readers to supporting evidence. Yet academic literature faces mounting challenges: semantic citation errors that misrepresent sources, AI-generated hallucinated references, and traditional citation formats that point to entire papers without indicating which sections substantiate specific claims. We introduce SemanticCite, an AI-powered system that verifies citation accuracy through full-text source analysis while providing rich contextual information via detailed reasoning and relevant text snippets. Our approach combines multiple retrieval methods with a four-class classification system (Supported, Partially Supported, Unsupported, Uncertain) that captures nuanced claim-source relationships and enables appropriate remedial actions for different error types. Our experiments show that fine-tuned lightweight language models achieve performance comparable to large commercial systems with significantly lower computational requirements, making large-scale citation verification practically feasible. The system provides transparent, evidence-based explanations that support user understanding and trust. We contribute a comprehensive dataset of over 1,000 citations with detailed alignments, functional classifications, semantic annotations, and bibliometric metadata across eight disciplines, alongside fine-tuned models and the complete verification framework as open-source software. SemanticCite addresses critical challenges in research integrity through scalable citation verification, streamlined peer review, and quality control for AI-generated content, providing an open-source foundation for maintaining citation accuracy at scale.

The rapid expansion of medical literature presents growing challenges for structuring and integrating domain knowledge at scale. Knowledge Graphs (KGs) offer a promising solution by enabling efficient retrieval, automated reasoning, and knowledge discovery. However, current KG construction methods often rely on supervised pipelines with limited generalizability or naively aggregate outputs from Large Language Models (LLMs), treating biomedical corpora as static and ignoring the temporal dynamics and contextual uncertainty of evolving knowledge. To address these limitations, we introduce MedKGent, a LLM agent framework for constructing temporally evolving medical KGs. Leveraging over 10 million PubMed abstracts published between 1975 and 2023, we simulate the emergence of biomedical knowledge via a fine-grained daily time series. MedKGent incrementally builds the KG in a day-by-day manner using two specialized agents powered by the Qwen2.5-32B-Instruct model. The Extractor Agent identifies knowledge triples and assigns confidence scores via sampling-based estimation, which are used to filter low-confidence extractions and inform downstream processing. The Constructor Agent incrementally integrates the retained triples into a temporally evolving graph, guided by confidence scores and timestamps to reinforce recurring knowledge and resolve conflicts. The resulting KG contains 156,275 entities and 2,971,384 relational triples. Quality assessments by two SOTA LLMs and three domain experts demonstrate an accuracy approaching 90%, with strong inter-rater agreement. To evaluate downstream utility, we conduct RAG across seven medical question answering benchmarks using five leading LLMs, consistently observing significant improvements over non-augmented baselines. Case studies further demonstrate the KG's value in literature-based drug repurposing via confidence-aware causal inference.

Scientific discovery is a cumulative process and requires new ideas to be situated within an ever-expanding landscape of existing knowledge. An emerging and critical challenge is how to identify conceptually relevant prior work from rapidly growing literature, and assess how a new idea differentiates from existing research. Current embedding approaches typically conflate distinct conceptual aspects into single representations and cannot support fine-grained literature retrieval; meanwhile, LLM-based evaluators are subject to sycophancy biases, failing to provide discriminative novelty assessment. To tackle these challenges, we introduce the Ideation Space, a structured representation that decomposes scientific knowledge into three distinct dimensions, i.e., research problem, methodology, and core findings, each learned through contrastive training. This framework enables principled measurement of conceptual distance between ideas, and modeling of ideation transitions that capture the logical connections within a proposed idea. Building upon this representation, we propose a Hierarchical Sub-Space Retrieval framework for efficient, targeted literature retrieval, and a Decomposed Novelty Assessment algorithm that identifies which aspects of an idea are novel. Extensive experiments demonstrate substantial improvements, where our approach achieves Recall@30 of 0.329 (16.7% over baselines), our ideation transition retrieval reaches Hit Rate@30 of 0.643, and novelty assessment attains 0.37 correlation with expert judgments. In summary, our work provides a promising paradigm for future research on accelerating and evaluating scientific discovery.

We present a detailed replication study of the BASS framework, an abstractive summarization system based on the notion of Unified Semantic Graphs. Our investigation includes challenges in replicating key components and an ablation study to systematically isolate error sources rooted in replicating novel components. Our findings reveal discrepancies in performance compared to the original work. We highlight the significance of paying careful attention even to reasonably omitted details for replicating advanced frameworks like BASS, and emphasize key practices for writing replicable papers.

We present a scientific reasoning foundation model that aligns natural language with heterogeneous scientific representations. The model is pretrained on a 206B-token corpus spanning scientific text, pure sequences, and sequence-text pairs, then aligned via SFT on 40M instructions, annealed cold-start bootstrapping to elicit long-form chain-of-thought, and reinforcement learning with task-specific reward shaping, which instills deliberate scientific reasoning. It supports four capability families, covering up to 103 tasks across workflows: (i) faithful translation between text and scientific formats, (ii) text/knowledge extraction, (iii) property prediction, (iv) property classification, (v) unconditional and conditional sequence generation and design. Compared with specialist systems, our approach broadens instruction coverage, improves cross-domain generalization, and enhances fidelity. We detail data curation and training and show that cross-discipline learning strengthens transfer and downstream reliability. The model, instruct tuning datasets and the evaluation code are open-sourced at https://huggingface.co/SciReason and https://github.com/open-sciencelab/SciReason.

It is desirable to coarsely classify short scientific texts, such as grant or publication abstracts, for strategic insight or research portfolio management. These texts efficiently transmit dense information to experts possessing a rich body of knowledge to aid interpretation. Yet this task is remarkably difficult to automate because of brevity and the absence of context. To address this gap, we have developed a novel approach to generate and appropriately assign coarse domain-specific labels. We show that a Large Language Model (LLM) can provide metadata essential to the task, in a process akin to the augmentation of supplemental knowledge representing human intuition, and propose a workflow. As a pilot study, we use a corpus of award abstracts from the National Aeronautics and Space Administration (NASA). We develop new assessment tools in concert with established performance metrics.

We propose a novel framework that leverages LLMs for full causal graph discovery. While previous LLM-based methods have used a pairwise query approach, this requires a quadratic number of queries which quickly becomes impractical for larger causal graphs. In contrast, the proposed framework uses a breadth-first search (BFS) approach which allows it to use only a linear number of queries. We also show that the proposed method can easily incorporate observational data when available, to improve performance. In addition to being more time and data-efficient, the proposed framework achieves state-of-the-art results on real-world causal graphs of varying sizes. The results demonstrate the effectiveness and efficiency of the proposed method in discovering causal relationships, showcasing its potential for broad applicability in causal graph discovery tasks across different domains.

Many disciplines pose natural-language research questions over large document collections whose answers typically require structured evidence, traditionally obtained by manually designing an annotation schema and exhaustively labeling the corpus, a slow and error-prone process. We introduce ScheMatiQ, which leverages calls to a backbone LLM to take a question and a corpus to produce a schema and a grounded database, with a web interface that lets steer and revise the extraction. In collaboration with domain experts, we show that ScheMatiQ yields outputs that support real-world analysis in law and computational biology. We release ScheMatiQ as open source with a public web interface, and invite experts across disciplines to use it with their own data. All resources, including the website, source code, and demonstration video, are available at: www.ScheMatiQ-ai.com

Existing KBQA methods have traditionally relied on multi-stage methodologies, involving tasks such as entity linking, subgraph retrieval and query structure generation. However, multi-stage approaches are dependent on the accuracy of preceding steps, leading to cascading errors and increased inference time. Although a few studies have explored the use of end-to-end models, they often suffer from lower accuracy and generate inoperative query that is not supported by the underlying data. Furthermore, most prior approaches are limited to the static training data, potentially overlooking the evolving nature of knowledge bases over time. To address these challenges, we present a novel end-to-end natural language to SPARQL framework, SPARKLE. Notably SPARKLE leverages the structure of knowledge base directly during the decoding, effectively integrating knowledge into the query generation. Our study reveals that simply referencing knowledge base during inference significantly reduces the occurrence of inexecutable query generations. SPARKLE achieves new state-of-the-art results on SimpleQuestions-Wiki and highest F1 score on LCQuAD 1.0 (among models not using gold entities), while getting slightly lower result on the WebQSP dataset. Finally, we demonstrate SPARKLE's fast inference speed and its ability to adapt when the knowledge base differs between the training and inference stages.

High-quality medical systematic reviews require comprehensive literature searches to ensure the recommendations and outcomes are sufficiently reliable. Indeed, searching for relevant medical literature is a key phase in constructing systematic reviews and often involves domain (medical researchers) and search (information specialists) experts in developing the search queries. Queries in this context are highly complex, based on Boolean logic, include free-text terms and index terms from standardised terminologies (e.g., MeSH), and are difficult and time-consuming to build. The use of MeSH terms, in particular, has been shown to improve the quality of the search results. However, identifying the correct MeSH terms to include in a query is difficult: information experts are often unfamiliar with the MeSH database and unsure about the appropriateness of MeSH terms for a query. Naturally, the full value of the MeSH terminology is often not fully exploited. This paper investigates methods to suggest MeSH terms based on an initial Boolean query that includes only free-text terms. These methods promise to automatically identify highly effective MeSH terms for inclusion in a systematic review query. Our study contributes an empirical evaluation of several MeSH term suggestion methods. We perform an extensive analysis of the retrieval, ranking, and refinement of MeSH term suggestions for each method and how these suggestions impact the effectiveness of Boolean queries.

Understanding the changing structure of science over time is essential to elucidating how science evolves. We develop diachronic embeddings of scholarly periodicals to quantify "semantic changes" of periodicals across decades, allowing us to track the evolution of research topics and identify rapidly developing fields. By mapping periodicals within a physical-life-health triangle, we reveal an evolving interdisciplinary science landscape, finding an overall trend toward specialization for most periodicals but increasing interdisciplinarity for bioscience periodicals. Analyzing a periodical's trajectory within this triangle over time allows us to visualize how its research focus shifts. Furthermore, by monitoring the formation of local clusters of periodicals, we can identify emerging research topics such as AIDS research and nanotechnology in the 1980s. Our work offers novel quantification in the science of science and provides a quantitative lens to examine the evolution of science, which may facilitate future investigations into the emergence and development of research fields.

Within the past few decades we have witnessed digital revolution, which moved scholarly communication to electronic media and also resulted in a substantial increase in its volume. Nowadays keeping track with the latest scientific achievements poses a major challenge for the researchers. Scientific information overload is a severe problem that slows down scholarly communication and knowledge propagation across the academia. Modern research infrastructures facilitate studying scientific literature by providing intelligent search tools, proposing similar and related documents, visualizing citation and author networks, assessing the quality and impact of the articles, and so on. In order to provide such high quality services the system requires the access not only to the text content of stored documents, but also to their machine-readable metadata. Since in practice good quality metadata is not always available, there is a strong demand for a reliable automatic method of extracting machine-readable metadata directly from source documents. This research addresses these problems by proposing an automatic, accurate and flexible algorithm for extracting wide range of metadata directly from scientific articles in born-digital form. Extracted information includes basic document metadata, structured full text and bibliography section. Designed as a universal solution, proposed algorithm is able to handle a vast variety of publication layouts with high precision and thus is well-suited for analyzing heterogeneous document collections. This was achieved by employing supervised and unsupervised machine-learning algorithms trained on large, diverse datasets. The evaluation we conducted showed good performance of proposed metadata extraction algorithm. The comparison with other similar solutions also proved our algorithm performs better than competition for most metadata types.

The exponential growth of scientific literature requires effective management and extraction of valuable insights. While existing scientific search engines excel at delivering search results based on relational databases, they often neglect the analysis of collaborations between scientific entities and the evolution of ideas, as well as the in-depth analysis of content within scientific publications. The representation of heterogeneous graphs and the effective measurement, analysis, and mining of such graphs pose significant challenges. To address these challenges, we present AceMap, an academic system designed for knowledge discovery through academic graph. We present advanced database construction techniques to build the comprehensive AceMap database with large-scale academic entities that contain rich visual, textual, and numerical information. AceMap also employs innovative visualization, quantification, and analysis methods to explore associations and logical relationships among academic entities. AceMap introduces large-scale academic network visualization techniques centered on nebular graphs, providing a comprehensive view of academic networks from multiple perspectives. In addition, AceMap proposes a unified metric based on structural entropy to quantitatively measure the knowledge content of different academic entities. Moreover, AceMap provides advanced analysis capabilities, including tracing the evolution of academic ideas through citation relationships and concept co-occurrence, and generating concise summaries informed by this evolutionary process. In addition, AceMap uses machine reading methods to generate potential new ideas at the intersection of different fields. Exploring the integration of large language models and knowledge graphs is a promising direction for future research in idea evolution. Please visit https://www.acemap.info for further exploration.

Large language models (LLMs) have demonstrated remarkable capabilities in a wide range of tasks, yet their application to specialized domains remains challenging due to the need for deep expertise. Retrieval-augmented generation (RAG) has emerged as a promising solution to customize LLMs for professional fields by seamlessly integrating external knowledge bases, enabling real-time access to domain-specific expertise during inference. Despite its potential, traditional RAG systems, based on flat text retrieval, face three critical challenges: (i) complex query understanding in professional contexts, (ii) difficulties in knowledge integration across distributed sources, and (iii) system efficiency bottlenecks at scale. This survey presents a systematic analysis of Graph-based Retrieval-Augmented Generation (GraphRAG), a new paradigm that revolutionizes domain-specific LLM applications. GraphRAG addresses traditional RAG limitations through three key innovations: (i) graph-structured knowledge representation that explicitly captures entity relationships and domain hierarchies, (ii) efficient graph-based retrieval techniques that enable context-preserving knowledge retrieval with multihop reasoning ability, and (iii) structure-aware knowledge integration algorithms that leverage retrieved knowledge for accurate and logical coherent generation of LLMs. In this survey, we systematically analyze the technical foundations of GraphRAG and examine current implementations across various professional domains, identifying key technical challenges and promising research directions. All the related resources of GraphRAG, including research papers, open-source data, and projects, are collected for the community in blue{https://github.com/DEEP-PolyU/Awesome-GraphRAG}.

AI answer engines increasingly mediate access to domain knowledge by generating responses and citing web sources. We introduce GEO-16, a 16 pillar auditing framework that converts on page quality signals into banded pillar scores and a normalized GEO score G that ranges from 0 to 1. Using 70 product intent prompts, we collected 1,702 citations across three engines (Brave Summary, Google AI Overviews, and Perplexity) and audited 1,100 unique URLs. In our corpus, the engines differed in the GEO quality of the pages they cited, and pillars related to Metadata and Freshness, Semantic HTML, and Structured Data showed the strongest associations with citation. Logistic models with domain clustered standard errors indicate that overall page quality is a strong predictor of citation, and simple operating points (for example, G at least 0.70 combined with at least 12 pillar hits) align with substantially higher citation rates in our data. We report per engine contrasts, vertical effects, threshold analysis, and diagnostics, then translate findings into a practical playbook for publishers. The study is observational and focuses on English language B2B SaaS pages; we discuss limitations, threats to validity, and reproducibility considerations.

Scientific inquiry requires systems-level reasoning that integrates heterogeneous experimental data, cross-domain knowledge, and mechanistic evidence into coherent explanations. While Large Language Models (LLMs) offer inferential capabilities, they often depend on retrieval-augmented contexts that lack structural depth. Traditional Knowledge Graphs (KGs) attempt to bridge this gap, yet their pairwise constraints fail to capture the irreducible higher-order interactions that govern emergent physical behavior. To address this, we introduce a methodology for constructing hypergraph-based knowledge representations that faithfully encode multi-entity relationships. Applied to a corpus of ~1,100 manuscripts on biocomposite scaffolds, our framework constructs a global hypergraph of 161,172 nodes and 320,201 hyperedges, revealing a scale-free topology (power law exponent ~1.23) organized around highly connected conceptual hubs. This representation prevents the combinatorial explosion typical of pairwise expansions and explicitly preserves the co-occurrence context of scientific formulations. We further demonstrate that equipping agentic systems with hypergraph traversal tools, specifically using node-intersection constraints, enables them to bridge semantically distant concepts. By exploiting these higher-order pathways, the system successfully generates grounded mechanistic hypotheses for novel composite materials, such as linking cerium oxide to PCL scaffolds via chitosan intermediates. This work establishes a "teacherless" agentic reasoning system where hypergraph topology acts as a verifiable guardrail, accelerating scientific discovery by uncovering relationships obscured by traditional graph methods.

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.

Scientific research involves complex information-seeking and reasoning workflows across heterogeneous sources. However, existing benchmarks primarily emphasize general-domain retrieval or static scientific question answering, and therefore fail to assess key capabilities required in realistic scientific research workflows. We introduce SciExplore, a benchmark designed to evaluate scientific information-seeking and reasoning capabilities of LLMs and agents. SciExplore comprises four task types covering 103 expert-curated tasks across more than ten scientific disciplines: scientific database navigation, ambiguous literature retrieval, missing reference completion, and cross-source structured knowledge synthesis, which probe progressively higher-level abilities from entity-level reasoning and document-level identification to evidence-level grounding and domain-level synthesis. We evaluate over ten state-of-the-art LLMs and autonomous agents on SciExplore, revealing substantial performance gaps with performance degrading sharply as task complexity increases and extremely low accuracy on the most challenging structured synthesis tasks. These results highlight significant limitations of current models and agents in realistic scientific information-seeking scenarios.

Citations are the bedrock of scientific authority, yet their integrity is compromised by widespread miscitations: ranging from nuanced distortions to fabricated references. Systematic citation verification is currently unfeasible; manual review cannot scale to modern publishing volumes, while existing automated tools are restricted by abstract-only analysis or small-scale, domain-specific datasets in part due to the "paywall barrier" of full-text access. We introduce BibAgent, a scalable, end-to-end agentic framework for automated citation verification. BibAgent integrates retrieval, reasoning, and adaptive evidence aggregation, applying distinct strategies for accessible and paywalled sources. For paywalled references, it leverages a novel Evidence Committee mechanism that infers citation validity via downstream citation consensus. To support systematic evaluation, we contribute a 5-category Miscitation Taxonomy and MisciteBench, a massive cross-disciplinary benchmark comprising 6,350 miscitation samples spanning 254 fields. Our results demonstrate that BibAgent outperforms state-of-the-art Large Language Model (LLM) baselines in citation verification accuracy and interpretability, providing scalable, transparent detection of citation misalignments across the scientific literature.

Biomedical research is growing at such an exponential pace that scientists, researchers, and practitioners are no more able to cope with the amount of published literature in the domain. The knowledge presented in the literature needs to be systematized in such a way that claims and hypotheses can be easily found, accessed, and validated. Knowledge graphs can provide such a framework for semantic knowledge representation from literature. However, in order to build a knowledge graph, it is necessary to extract knowledge as relationships between biomedical entities and normalize both entities and relationship types. In this paper, we present and compare few rule-based and machine learning-based (Naive Bayes, Random Forests as examples of traditional machine learning methods and DistilBERT, PubMedBERT, T5 and SciFive-based models as examples of modern deep learning transformers) methods for scalable relationship extraction from biomedical literature, and for the integration into the knowledge graphs. We examine how resilient are these various methods to unbalanced and fairly small datasets. Our experiments show that transformer-based models handle well both small (due to pre-training on a large dataset) and unbalanced datasets. The best performing model was the PubMedBERT-based model fine-tuned on balanced data, with a reported F1-score of 0.92. DistilBERT-based model followed with F1-score of 0.89, performing faster and with lower resource requirements. BERT-based models performed better then T5-based generative models.

In this paper, we champion the use of structured and semantic content representation of discourse-based scholarly communication, inspired by tools like Wikipedia infoboxes or structured Amazon product descriptions. These representations provide users with a concise overview, aiding scientists in navigating the dense academic landscape. Our novel automated approach leverages the robust text generation capabilities of LLMs to produce structured scholarly contribution summaries, offering both a practical solution and insights into LLMs' emergent abilities. For LLMs, the prime focus is on improving their general intelligence as conversational agents. We argue that these models can also be applied effectively in information extraction (IE), specifically in complex IE tasks within terse domains like Science. This paradigm shift replaces the traditional modular, pipelined machine learning approach with a simpler objective expressed through instructions. Our results show that finetuned FLAN-T5 with 1000x fewer parameters than the state-of-the-art GPT-davinci is competitive for the task.

In pace with developments in the research field of artificial intelligence, knowledge graphs (KGs) have attracted a surge of interest from both academia and industry. As a representation of semantic relations between entities, KGs have proven to be particularly relevant for natural language processing (NLP), experiencing a rapid spread and wide adoption within recent years. Given the increasing amount of research work in this area, several KG-related approaches have been surveyed in the NLP research community. However, a comprehensive study that categorizes established topics and reviews the maturity of individual research streams remains absent to this day. Contributing to closing this gap, we systematically analyzed 507 papers from the literature on KGs in NLP. Our survey encompasses a multifaceted review of tasks, research types, and contributions. As a result, we present a structured overview of the research landscape, provide a taxonomy of tasks, summarize our findings, and highlight directions for future work.

Knowledge Graph-to-Text (G2T) generation involves verbalizing structured knowledge graphs into natural language text. Recent advancements in Pretrained Language Models (PLMs) have improved G2T performance, but their effectiveness depends on datasets with precise graph-text alignment. However, the scarcity of high-quality, general-domain G2T generation datasets restricts progress in the general-domain G2T generation research. To address this issue, we introduce Wikipedia Ontology-Free Graph-text dataset (WikiOFGraph), a new large-scale G2T dataset generated using a novel method that leverages Large Language Model (LLM) and Data-QuestEval. Our new dataset, which contains 5.85M general-domain graph-text pairs, offers high graph-text consistency without relying on external ontologies. Experimental results demonstrate that PLM fine-tuned on WikiOFGraph outperforms those trained on other datasets across various evaluation metrics. Our method proves to be a scalable and effective solution for generating high-quality G2T data, significantly advancing the field of G2T generation.

The surge in scientific publications challenges traditional review methods, demanding tools that integrate structured metadata with full-text analysis. Hybrid Retrieval Augmented Generation (RAG) systems, combining graph queries with vector search offer promise but are typically static, rely on proprietary tools, and lack uncertainty estimates. We present an agentic approach that encapsulates the hybrid RAG pipeline within an autonomous agent capable of (1) dynamically selecting between GraphRAG and VectorRAG for each query, (2) adapting instruction-tuned generation in real time to researcher needs, and (3) quantifying uncertainty during inference. This dynamic orchestration improves relevance, reduces hallucinations, and promotes reproducibility. Our pipeline ingests bibliometric open-access data from PubMed, arXiv, and Google Scholar APIs, builds a Neo4j citation-based knowledge graph (KG), and embeds full-text PDFs into a FAISS vector store (VS) using the all-MiniLM-L6-v2 model. A Llama-3.3-70B agent selects GraphRAG (translating queries to Cypher for KG) or VectorRAG (combining sparse and dense retrieval with re-ranking). Instruction tuning refines domain-specific generation, and bootstrapped evaluation yields standard deviation for evaluation metrics. On synthetic benchmarks mimicking real-world queries, the Instruction-Tuned Agent with Direct Preference Optimization (DPO) outperforms the baseline, achieving a gain of 0.63 in VS Context Recall and a 0.56 gain in overall Context Precision. Additional gains include 0.24 in VS Faithfulness, 0.12 in both VS Precision and KG Answer Relevance, 0.11 in overall Faithfulness score, 0.05 in KG Context Recall, and 0.04 in both VS Answer Relevance and overall Precision. These results highlight the system's improved reasoning over heterogeneous sources and establish a scalable framework for autonomous, agentic scientific discovery.

The development of vision-language models (VLMs) is driven by large-scale and diverse multimodal datasets. However, progress toward generalist biomedical VLMs is limited by the lack of annotated, publicly accessible datasets across biology and medicine. Existing efforts are restricted to narrow domains, missing the full diversity of biomedical knowledge encoded in scientific literature. To address this gap, we introduce BIOMEDICA, a scalable, open-source framework to extract, annotate, and serialize the entirety of the PubMed Central Open Access subset into an easy-to-use, publicly accessible dataset.Our framework produces a comprehensive archive with over 24 million unique image-text pairs from over 6 million articles. Metadata and expert-guided annotations are also provided. We demonstrate the utility and accessibility of our resource by releasing BMCA-CLIP, a suite of CLIP-style models continuously pre-trained on the BIOMEDICA dataset via streaming, eliminating the need to download 27 TB of data locally.On average, our models achieve state-of-the-art performance across 40 tasks - spanning pathology, radiology, ophthalmology, dermatology, surgery, molecular biology, parasitology, and cell biology - excelling in zero-shot classification with a 6.56% average improvement (as high as 29.8% and 17.5% in dermatology and ophthalmology, respectively), and stronger image-text retrieval, all while using 10x less compute. To foster reproducibility and collaboration, we release our codebase and dataset for the broader research community.

With the rapid growth of Web-based academic publications, more and more papers are being published annually, making it increasingly difficult to find relevant prior work. Citation prediction aims to automatically suggest appropriate references, helping scholars navigate the expanding scientific literature. Here we present CiteRAG, the first comprehensive retrieval-augmented generation (RAG)-integrated benchmark for evaluating large language models on academic citation prediction, featuring a multi-level retrieval strategy, specialized retrievers, and generators. Our benchmark makes four core contributions: (1) We establish two instances of the citation prediction task with different granularity. Task 1 focuses on coarse-grained list-specific citation prediction, while Task 2 targets fine-grained position-specific citation prediction. To enhance these two tasks, we build a dataset containing 7,267 instances for Task 1 and 8,541 instances for Task 2, enabling comprehensive evaluation of both retrieval and generation. (2) We construct a three-level large-scale corpus with 554k papers spanning many major subfields, using an incremental pipeline. (3) We propose a multi-level hybrid RAG approach for citation prediction, fine-tuning embedding models with contrastive learning to capture complex citation relationships, paired with specialized generation models. (4) We conduct extensive experiments across state-of-the-art language models, including closed-source APIs, open-source models, and our fine-tuned generators, demonstrating the effectiveness of our framework. Our open-source toolkit enables reproducible evaluation and focuses on academic literature, providing the first comprehensive evaluation framework for citation prediction and serving as a methodological template for other scientific domains. Our source code and data are released at https://github.com/LQgdwind/CiteRAG.

Information retrieval methods often rely on a single embedding model trained on large, general-domain datasets like MSMARCO. While this approach can produce a retriever with reasonable overall performance, models trained on domain-specific data often yield better results within their respective domains. While prior work in information retrieval has tackled this through multi-task training, the topic of combining multiple domain-specific expert retrievers remains unexplored, despite its popularity in language model generation. In this work, we introduce RouterRetriever, a retrieval model that leverages multiple domain-specific experts along with a routing mechanism to select the most appropriate expert for each query. It is lightweight and allows easy addition or removal of experts without additional training. Evaluation on the BEIR benchmark demonstrates that RouterRetriever outperforms both MSMARCO-trained (+2.1 absolute nDCG@10) and multi-task trained (+3.2) models. This is achieved by employing our routing mechanism, which surpasses other routing techniques (+1.8 on average) commonly used in language modeling. Furthermore, the benefit generalizes well to other datasets, even in the absence of a specific expert on the dataset. To our knowledge, RouterRetriever is the first work to demonstrate the advantages of using multiple domain-specific expert embedding models with effective routing over a single, general-purpose embedding model in retrieval tasks.

Standard Retrieval-Augmented Generation (RAG) relies on chunk-based retrieval, whereas GraphRAG advances this approach by graph-based knowledge representation. However, existing graph-based RAG approaches are constrained by binary relations, as each edge in an ordinary graph connects only two entities, limiting their ability to represent the n-ary relations (n >= 2) in real-world knowledge. In this work, we propose HyperGraphRAG, a novel hypergraph-based RAG method that represents n-ary relational facts via hyperedges, and consists of knowledge hypergraph construction, retrieval, and generation. Experiments across medicine, agriculture, computer science, and law demonstrate that HyperGraphRAG outperforms both standard RAG and previous graph-based RAG methods in answer accuracy, retrieval efficiency, and generation quality.

Question answering over Scholarly Knowledge Graphs (SKGs) remains a challenging task due to the complexity of scholarly content and the intricate structure of these graphs. Large Language Model (LLM) approaches could be used to translate natural language questions (NLQs) into SPARQL queries; however, these LLM-based approaches struggle with SPARQL query generation due to limited exposure to SKG-specific content and the underlying schema. We identified two main types of errors in the LLM-generated SPARQL queries: (i) structural inconsistencies, such as missing or redundant triples in the queries, and (ii) semantic inaccuracies, where incorrect entities or properties are shown in the queries despite a correct query structure. To address these issues, we propose FIRESPARQL, a modular framework that supports fine-tuned LLMs as a core component, with optional context provided via retrieval-augmented generation (RAG) and a SPARQL query correction layer. We evaluate the framework on the SciQA Benchmark using various configurations (zero-shot, zero-shot with RAG, one-shot, fine-tuning, and fine-tuning with RAG) and compare the performance with baseline and state-of-the-art approaches. We measure query accuracy using BLEU and ROUGE metrics, and query result accuracy using relaxed exact match(RelaxedEM), with respect to the gold standards containing the NLQs, SPARQL queries, and the results of the queries. Experimental results demonstrate that fine-tuning achieves the highest overall performance, reaching 0.90 ROUGE-L for query accuracy and 0.85 RelaxedEM for result accuracy on the test set.

Extensive efforts in the past have been directed toward the development of summarization datasets. However, a predominant number of these resources have been (semi)-automatically generated, typically through web data crawling, resulting in subpar resources for training and evaluating summarization systems, a quality compromise that is arguably due to the substantial costs associated with generating ground-truth summaries, particularly for diverse languages and specialized domains. To address this issue, we present ACLSum, a novel summarization dataset carefully crafted and evaluated by domain experts. In contrast to previous datasets, ACLSum facilitates multi-aspect summarization of scientific papers, covering challenges, approaches, and outcomes in depth. Through extensive experiments, we evaluate the quality of our resource and the performance of models based on pretrained language models and state-of-the-art large language models (LLMs). Additionally, we explore the effectiveness of extractive versus abstractive summarization within the scholarly domain on the basis of automatically discovered aspects. Our results corroborate previous findings in the general domain and indicate the general superiority of end-to-end aspect-based summarization. Our data is released at https://github.com/sobamchan/aclsum.

Integrating information from different reference data sources is a major challenge for Retrieval-Augmented Generation (RAG) systems because each knowledge source adopts a unique data structure and follows different conventions. Retrieving from multiple knowledge sources with one fixed strategy usually leads to under-exploitation of information. To mitigate this drawback, inspired by Mix-of-Expert, we introduce Mix-of-Granularity (MoG), a method that dynamically determines the optimal granularity of a knowledge database based on input queries using a router. The router is efficiently trained with a newly proposed loss function employing soft labels. We further extend MoG to Mix-of-Granularity-Graph (MoGG), where reference documents are pre-processed into graphs, enabling the retrieval of relevant information from distantly situated chunks. Extensive experiments demonstrate that both MoG and MoGG effectively predict optimal granularity levels, significantly enhancing the performance of the RAG system in downstream tasks. The code of both MoG and MoGG will be made public.

We explore local vs. global evolution of knowledge systems through the framework of socio-epistemic networks (SEN), applying two complementary methods to a corpus of scientific texts. The framework comprises three interconnected layers-social, semiotic (material), and semantic-proposing a multilayered approach to understanding structural developments of knowledge. To analyse diachronic changes on the semantic layer, we first use information-theoretic measures based on relative entropy to detect semantic shifts, assess their significance, and identify key driving features. Second, variations in document embedding densities reveal changes in semantic neighbourhoods, tracking how concentration of similar documents increase, remain stable, or disperse. This enables us to trace document trajectories based on content (topics) or metadata (authorship, institution). Case studies of Joseph Silk and Hans-J\"urgen Treder illustrate how individual scholar's work aligns with broader disciplinary shifts in general relativity and gravitation research, demonstrating the applications, limitations, and further potential of this approach.

Recent advances in Retrieval-Augmented Generation (RAG) have shifted from simple vector similarity to structure-aware approaches like HippoRAG, which leverage Knowledge Graphs (KGs) and Personalized PageRank (PPR) to capture multi-hop dependencies. However, these methods suffer from a "Static Graph Fallacy": they rely on fixed transition probabilities determined during indexing. This rigidity ignores the query-dependent nature of edge relevance, causing semantic drift where random walks are diverted into high-degree "hub" nodes before reaching critical downstream evidence. Consequently, models often achieve high partial recall but fail to retrieve the complete evidence chain required for multi-hop queries. To address this, we propose CatRAG, Context-Aware Traversal for robust RAG, a framework that builds on the HippoRAG 2 architecture and transforms the static KG into a query-adaptive navigation structure. We introduce a multi-faceted framework to steer the random walk: (1) Symbolic Anchoring, which injects weak entity constraints to regularize the random walk; (2) Query-Aware Dynamic Edge Weighting, which dynamically modulates graph structure, to prune irrelevant paths while amplifying those aligned with the query's intent; and (3) Key-Fact Passage Weight Enhancement, a cost-efficient bias that structurally anchors the random walk to likely evidence. Experiments across four multi-hop benchmarks demonstrate that CatRAG consistently outperforms state of the art baselines. Our analysis reveals that while standard Recall metrics show modest gains, CatRAG achieves substantial improvements in reasoning completeness, the capacity to recover the entire evidence path without gaps. These results reveal that our approach effectively bridges the gap between retrieving partial context and enabling fully grounded reasoning. Resources are available at https://github.com/kwunhang/CatRAG.

Large language models (LLMs) have significantly advanced the field of natural language processing (NLP), providing a highly useful, task-agnostic foundation for a wide range of applications. However, directly applying LLMs to solve sophisticated problems in specific domains meets many hurdles, caused by the heterogeneity of domain data, the sophistication of domain knowledge, the uniqueness of domain objectives, and the diversity of the constraints (e.g., various social norms, cultural conformity, religious beliefs, and ethical standards in the domain applications). Domain specification techniques are key to make large language models disruptive in many applications. Specifically, to solve these hurdles, there has been a notable increase in research and practices conducted in recent years on the domain specialization of LLMs. This emerging field of study, with its substantial potential for impact, necessitates a comprehensive and systematic review to better summarize and guide ongoing work in this area. In this article, we present a comprehensive survey on domain specification techniques for large language models, an emerging direction critical for large language model applications. First, we propose a systematic taxonomy that categorizes the LLM domain-specialization techniques based on the accessibility to LLMs and summarizes the framework for all the subcategories as well as their relations and differences to each other. Second, we present an extensive taxonomy of critical application domains that can benefit dramatically from specialized LLMs, discussing their practical significance and open challenges. Last, we offer our insights into the current research status and future trends in this area.

Large language models (LLMs) are capable of generating coherent summaries from very long contexts given a user query. Extracting and properly citing evidence spans could help improve the transparency and reliability of these summaries. At the same time, LLMs suffer from positional biases in terms of which information they understand and attend to, which could affect evidence citation. Whereas previous work has focused on evidence citation with predefined levels of granularity (e.g. sentence, paragraph, document, etc.), we propose the task of long-context query focused summarization with unstructured evidence citation. We show how existing systems struggle to generate and properly cite unstructured evidence from their context, and that evidence tends to be "lost-in-the-middle". To help mitigate this, we create the Summaries with Unstructured Evidence Text dataset (SUnsET), a synthetic dataset generated using a novel domain-agnostic pipeline which can be used as supervision to adapt LLMs to this task. We demonstrate across 5 LLMs of different sizes and 4 datasets with varying document types and lengths that LLMs adapted with SUnsET data generate more relevant and factually consistent evidence than their base models, extract evidence from more diverse locations in their context, and can generate more relevant and consistent summaries.

The rapid acceleration of scientific publishing has created substantial challenges for researchers attempting to discover, contextualize, and interpret relevant literature. Traditional keyword-based search systems provide limited semantic understanding, while existing AI-driven tools typically focus on isolated tasks such as retrieval, clustering, or bibliometric visualization. This paper presents an integrated system for scientific literature exploration that combines large-scale data acquisition, hybrid retrieval, semantic topic modeling, and heterogeneous knowledge graph construction. The system builds a comprehensive corpus by merging full-text data from arXiv with structured metadata from OpenAlex. A hybrid retrieval architecture fuses BM25 lexical search with embedding-based semantic search using Reciprocal Rank Fusion. Topic modeling is performed on retrieved results using BERTopic or non-negative matrix factorization depending on computational resources. A knowledge graph unifies papers, authors, institutions, countries, and extracted topics into an interpretable structure. The system provides a multi-layered exploration environment that reveals not only relevant publications but also the conceptual and relational landscape surrounding a query. Evaluation across multiple queries demonstrates improvements in retrieval relevance, topic coherence, and interpretability. The proposed framework contributes an extensible foundation for AI-assisted scientific discovery.

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.

Prior work on Data-To-Text Generation, the task of converting knowledge graph (KG) triples into natural text, focused on domain-specific benchmark datasets. In this paper, however, we verbalize the entire English Wikidata KG, and discuss the unique challenges associated with a broad, open-domain, large-scale verbalization. We further show that verbalizing a comprehensive, encyclopedic KG like Wikidata can be used to integrate structured KGs and natural language corpora. In contrast to the many architectures that have been developed to integrate these two sources, our approach converts the KG into natural text, allowing it to be seamlessly integrated into existing language models. It carries the further advantages of improved factual accuracy and reduced toxicity in the resulting language model. We evaluate this approach by augmenting the retrieval corpus in a retrieval language model and showing significant improvements on the knowledge intensive tasks of open domain QA and the LAMA knowledge probe.

Knowledge base population seeks to expand knowledge graphs with facts that are typically extracted from a text corpus. Recently, language models pretrained on large corpora have been shown to contain factual knowledge that can be retrieved using cloze-style strategies. Such approach enables zero-shot recall of facts, showing competitive results in object prediction compared to supervised baselines. However, prompt-based fact retrieval can be brittle and heavily depend on the prompts and context used, which may produce results that are unintended or hallucinatory.We propose to use textual entailment to validate facts extracted from language models through cloze statements. Our results show that triple validation based on textual entailment improves language model predictions in different training regimes. Furthermore, we show that entailment-based triple validation is also effective to validate candidate facts extracted from other sources including existing knowledge graphs and text passages where named entities are recognized.

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.

Mixture of Experts (MoEs) plays an important role in the development of more efficient and effective large language models (LLMs). Due to the enormous resource requirements, studying large scale MoE algorithms remain in-accessible to many researchers. This work develops LibMoE, a comprehensive and modular framework to streamline the research, training, and evaluation of MoE algorithms. Built upon three core principles: (i) modular design, (ii) efficient training; (iii) comprehensive evaluation, LibMoE brings MoE in LLMs more accessible to a wide range of researchers by standardizing the training and evaluation pipelines. Using LibMoE, we extensively benchmarked five state-of-the-art MoE algorithms over three different LLMs and 11 datasets under the zero-shot setting. The results show that despite the unique characteristics, all MoE algorithms perform roughly similar when averaged across a wide range of tasks. With the modular design and extensive evaluation, we believe LibMoE will be invaluable for researchers to make meaningful progress towards the next generation of MoE and LLMs. Project page: https://fsoft-aic.github.io/fsoft-LibMoE.github.io.

This paper presents a hybrid framework for literature reviews that augments traditional bibliometric methods with large language models (LLMs). By fine-tuning open-source LLMs, our approach enables scalable extraction of qualitative insights from large volumes of research content, enhancing both the breadth and depth of knowledge synthesis. To improve annotation efficiency and consistency, we introduce an error-focused validation process in which LLMs generate initial labels and human reviewers correct misclassifications. Applying this framework to over 20000 scientific articles about human migration, we demonstrate that a domain-adapted LLM can serve as a "specialist" model - capable of accurately selecting relevant studies, detecting emerging trends, and identifying critical research gaps. Notably, the LLM-assisted review reveals a growing scholarly interest in climate-induced migration. However, existing literature disproportionately centers on a narrow set of environmental hazards (e.g., floods, droughts, sea-level rise, and land degradation), while overlooking others that more directly affect human health and well-being, such as air and water pollution or infectious diseases. This imbalance highlights the need for more comprehensive research that goes beyond physical environmental changes to examine their ecological and societal consequences, particularly in shaping migration as an adaptive response. Overall, our proposed framework demonstrates the potential of fine-tuned LLMs to conduct more efficient, consistent, and insightful literature reviews across disciplines, ultimately accelerating knowledge synthesis and scientific discovery.

We present Spacerini, a modular framework for seamless building and deployment of interactive search applications, designed to facilitate the qualitative analysis of large scale research datasets. Spacerini integrates features from both the Pyserini toolkit and the Hugging Face ecosystem to ease the indexing text collections and deploy them as search engines for ad-hoc exploration and to make the retrieval of relevant data points quick and efficient. The user-friendly interface enables searching through massive datasets in a no-code fashion, making Spacerini broadly accessible to anyone looking to qualitatively audit their text collections. This is useful both to IR~researchers aiming to demonstrate the capabilities of their indexes in a simple and interactive way, and to NLP~researchers looking to better understand and audit the failure modes of large language models. The framework is open source and available on GitHub: https://github.com/castorini/hf-spacerini, and includes utilities to load, pre-process, index, and deploy local and web search applications. A portfolio of applications created with Spacerini for a multitude of use cases can be found by visiting https://hf.co/spacerini.

We wish to measure the information coverage of an ad hoc retrieval algorithm, that is, how much of the range of available relevant information is covered by the search results. Information coverage is a central aspect for retrieval, especially when the retrieval system is integrated with generative models in a retrieval-augmented generation (RAG) system. The classic metrics for ad hoc retrieval, precision and recall, reward a system as more and more relevant documents are retrieved. However, since relevance in ad hoc test collections is defined for a document without any relation to other documents that might contain the same information, high recall is sufficient but not necessary to ensure coverage. The same is true for other metrics such as rank-biased precision (RBP), normalized discounted cumulative gain (nDCG), and mean average precision (MAP). Test collections developed around the notion of diversity ranking in web search incorporate multiple aspects that support a concept of coverage in the web domain. In this work, we construct a suite of collections for evaluating information coverage from existing collections. This suite offers researchers a unified testbed spanning multiple genres and tasks. All topics, nuggets, relevance labels, and baseline rankings are released on Hugging Face Datasets, along with instructions for accessing the publicly available document collections.

Wikipedia plays a key role in shaping public understanding of science, and its openly accessible revision history is a unique record of how scientific knowledge evolves over time. Yet scientifically meaningful revisions are obscured by the sheer volume of routine edits, leaving each article's scientific history hidden. We present WikiSTAR (Scientific Tracking of Article Revisions), an interactive system for exploring scientifically meaningful changes across an article's revision history. Using an LLM classifier with an expert-designed multi-label taxonomy, WikiSTAR first tags edit types such as the addition of technical terms, new research findings, and changes in scientific narrative. Then, through interactive views, an article's full revision history can be traced at any granularity - from aggregate trends that reveal when and in which sections scientific content was added or refined, down to individual edits - showing how scientific knowledge develops at a scale previously impossible. In a user study, experts from three domains found that WikiSTAR surfaced new patterns and research questions and enabled previously impractical analyses. We release our system, code and a human-annotated benchmark.

Experts advising decision-makers are likely to display expertise which varies as a function of the problem instance. In practice, this may lead to sub-optimal or discriminatory decisions against minority cases. In this work we model such changes in depth and breadth of knowledge as a partitioning of the problem space into regions of differing expertise. We provide here new algorithms that explicitly consider and adapt to the relationship between problem instances and experts' knowledge. We first propose and highlight the drawbacks of a naive approach based on nearest neighbor queries. To address these drawbacks we then introduce a novel algorithm - expertise trees - that constructs decision trees enabling the learner to select appropriate models. We provide theoretical insights and empirically validate the improved performance of our novel approach on a range of problems for which existing methods proved to be inadequate.

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.

Statutory article retrieval is the task of automatically retrieving law articles relevant to a legal question. While recent advances in natural language processing have sparked considerable interest in many legal tasks, statutory article retrieval remains primarily untouched due to the scarcity of large-scale and high-quality annotated datasets. To address this bottleneck, we introduce the Belgian Statutory Article Retrieval Dataset (BSARD), which consists of 1,100+ French native legal questions labeled by experienced jurists with relevant articles from a corpus of 22,600+ Belgian law articles. Using BSARD, we benchmark several state-of-the-art retrieval approaches, including lexical and dense architectures, both in zero-shot and supervised setups. We find that fine-tuned dense retrieval models significantly outperform other systems. Our best performing baseline achieves 74.8% R@100, which is promising for the feasibility of the task and indicates there is still room for improvement. By the specificity of the domain and addressed task, BSARD presents a unique challenge problem for future research on legal information retrieval. Our dataset and source code are publicly available.

Large Language Models (LLMs) exhibit strong reasoning capabilities in complex tasks. However, they still struggle with hallucinations and factual errors in knowledge-intensive scenarios like knowledge graph question answering (KGQA). We attribute this to the semantic gap between structured knowledge graphs (KGs) and unstructured queries, caused by inherent differences in their focuses and structures. Existing methods usually employ resource-intensive, non-scalable workflows reasoning on vanilla KGs, but overlook this gap. To address this challenge, we propose a flexible framework, Enrich-on-Graph (EoG), which leverages LLMs' prior knowledge to enrich KGs, bridge the semantic gap between graphs and queries. EoG enables efficient evidence extraction from KGs for precise and robust reasoning, while ensuring low computational costs, scalability, and adaptability across different methods. Furthermore, we propose three graph quality evaluation metrics to analyze query-graph alignment in KGQA task, supported by theoretical validation of our optimization objectives. Extensive experiments on two KGQA benchmark datasets indicate that EoG can effectively generate high-quality KGs and achieve the state-of-the-art performance. Our code and data are available at https://github.com/zjukg/Enrich-on-Graph.

Recent GraphRAG methods integrate graph structures into text indexing and retrieval, using knowledge graph triples to connect text chunks, thereby improving retrieval coverage and precision. However, we observe that treating text chunks as the basic unit of knowledge representation rigidly groups multiple atomic facts together, limiting the flexibility and adaptability needed to support diverse retrieval scenarios. Additionally, triple-based entity linking is sensitive to relation-extraction errors, which can lead to missing or incorrect reasoning paths and ultimately hurt retrieval accuracy. To address these issues, we propose the Atom-Entity Graph, a more precise and reliable architecture for knowledge representation and indexing. In our approach, knowledge is stored as knowledge atoms, namely individual, self-contained units of factual information, rather than coarse-grained text chunks. This allows knowledge elements to be flexibly reassembled without mutual interference, thereby enabling seamless alignment with diverse query perspectives. Edges between entities simply indicate whether a relationship exists. By combining personalized PageRank with relevance-based filtering, we maintain accurate entity connections and improve the reliability of reasoning. Theoretical analysis and experiments on five public benchmarks show that the proposed AtomicRAG algorithm outperforms strong RAG baselines in retrieval accuracy and reasoning robustness. Code: https://github.com/7HHHHH/AtomicRAG.

Literature-Based Discovery (LBD) aims to discover new scientific knowledge by mining papers and generating hypotheses. Standard LBD is limited to predicting pairwise relations between discrete concepts (e.g., drug-disease links), and ignores critical contexts like experimental settings (e.g., a specific patient population where a drug is evaluated) and background motivations (e.g., to find drugs without specific side effects). We address these limitations with a novel formulation of contextualized-LBD (C-LBD): generating scientific hypotheses in natural language, while grounding them in a context that controls the hypothesis search space. We present a modeling framework using retrieval of ``inspirations'' from past scientific papers. Our evaluations reveal that GPT-4 tends to generate ideas with overall low technical depth and novelty, while our inspiration prompting approaches partially mitigate this issue. Our work represents a first step toward building language models that generate new ideas derived from scientific literature.

Mathematical knowledge is organized around statements and their dependencies, but this structure is exposed unevenly: informal papers cite mostly at the document level, while formal libraries record fine-grained dependencies over a much smaller body of mathematics. We introduce TheoremGraph, a unified statement-level dependency graph spanning both informal and formal mathematics. On the informal side, we parse 11.7M theorem-like environments from mathematics arXiv and recover 18.3M candidate directed dependencies, each labeled by the extractor that proposed it so downstream users can trade coverage for precision. On the formal side, we release LeanGraph, a Lean 4 elaborator-level extractor producing 388,105 declaration nodes and 11.3M typed edges across 25 Lean projects. We bridge the two graphs by embedding generated natural-language slogans into a shared semantic space, linking related statements across papers and across the informal/formal divide; an LLM judge affirms 47,952 such matches above a 0.8 cosine floor, with the judge-acceptance rate rising from 48% across the floor to 87% in the >=0.9 tier. On formal concept retrieval, our name-and-signature representation with graph expansion comes within 0.5pp of LeanSearch v2's reranked Recall@10 (0.775 vs. 0.780) without an LM reranker. We release the dataset, extractors, HTTP API, and MCP interface as infrastructure for mathematical search, attribution, and retrieval-augmented reasoning, available at theoremsearch.com and huggingface.co/datasets/uw-math-ai/theorem-matching.