LLM Information Extraction

LLM: Large Language Model

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24 papers in the last four weeks, up 243% on the four weeks before. 0.2% of all new papers.

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Latest papers 152

May 29, 2026cs.CL

Wind Turbine Maintenance Log Labelling Framework: LLM-Driven Data Correction and Enrichment via Semantic Extraction of Reliability Intelligence

As wind turbine fleets age, data-driven reliability engineering is essential to optimise their operation and maintenance for service life extension and levelised cost of energy reduction. Failure event descriptions within historical maintenance logs are a source of valuable reliability intelligence. However, they typically appear as unstructured natural language entries, rendering them inaccessible for quantitative analysis. This paper presents a novel methodology leveraging a large language model (LLM) to systematically standardise and structure maintenance logs based on their free-text descriptors. Operating on a dataset of 16,316 maintenance logs from 280 turbines monitored over nine years, the developed model-agnostic framework autonomously corrected hierarchical system codes and extracted evidence-based taxonomies of maintenance actions and failure modes. The automated pipeline successfully structured over 70% of the dataset. It resolved pervasive misclassification issues, such as isolating previously unclassified pitch system faults and restoring missing system codes, and enriched the records by applying empirical taxonomies to label specific actions taken and failure modes addressed. By using system-based log batches to construct empirical dictionaries of failure modes, observable symptoms, dominant mechanisms, and candidate causes, this approach reduces the inherent subjectivity of manual failure modes and effects analysis (FMEA). Ultimately, the methodology provides a highly scalable, cost-effective blueprint for translating large sets of qualitative field observations into quantitative reliability metrics, laying the foundation for integrated root-cause analysis across the renewable energy sector, improved FMEA, and advanced predictive maintenance.

Max Malyi, Jonathan Shek, Alasdair McDonald +1

Institute for Energy Systems, School of Engineering, The University of Edinburgh, Edinburgh, UK · 2Nadara, Lisbon, Portugal

LLM-Assisted Annotation Document Information Extraction Predictive Maintenance LLM Information Extraction

May 29, 2026cs.CY

Traceable by Design: An LLM Pipeline and Dashboard for EU Regulatory Consultation Analysis

Public consultations generate large volumes of data in the form of stakeholder submissions that are practically unfeasible to analyse manually. We present an end-to-end LLM-based pipeline and interactive dashboard for structured topic extraction from regulatory consultation submissions, demonstrated on the European Commission's Digital Fairness Act (DFA) public call for evidence as a case study. The system processes raw PDF attachments and web-form responses, extracts topic annotations, and grounds every extraction in a verbatim quote from the source text. Applied to 4,322 DFA submissions, the pipeline produced 15,368 topic annotations supported by 20,951 verbatim evidence quotes. Three principles govern the proposed design: verbatim grounding, full traceability, and transparency by design. The dashboard exposes the full extraction dataset through five analytical views, from dataset-level topic overviews to individual paragraph drill-downs, with every result traceable to its source. Beyond the predefined DFA topic categories, the pipeline generated certain stakeholder concerns, such as Age Verification, Payment Processor Censorship, and Digital Ownership, that a fixed-taxonomy approach would have missed. The pipeline is domain-generic; adapting it to a new consultation requires only a prompt update and a new dataset. A live demo is available at https://dfa-dashboard.thalesbertaglia.com/. The code and processed data are publicly available at https://github.com/thalesbertaglia/dfa-dashboard.

Thales Bertaglia, Haoyang Gui, Catalina Goanta +1

Utrecht University, The Netherlands · Maastricht University, The Netherlands

LLM-Assisted Annotation Document Information Extraction Legal Document Analysis LLM Information Extraction

May 28, 2026cs.CL

AI for Monitoring and Classifying Data Used in Research Literature

While platforms like Google Scholar and Semantic Scholar track citations for academic papers, no comparable infrastructure exists for monitoring dataset usage in research literature, leaving the landscape of data use largely opaque. Addressing this gap is critical for transparency, reproducibility, and monitoring of impact, yet progress is hindered by inconsistent citation practices, scarce labeled data, and ambiguous references to datasets in the wild. Traditional NLP approaches struggle with these challenges, motivating the shift toward more adaptive, semantically rich models. Building on prior work using LLMs for data mention detection and synthetic data for bootstrapping training, this paper presents an updated methodology for scalable dataset monitoring. We introduce a multitask GLiNER-based framework that jointly performs dataset mention extraction, relation identification, and usage-context classification. To address label scarcity, the pipeline leverages synthetic data generation to produce training examples and LLM-based revalidation to filter incorrect mentions and enforce labeling consistency, together improving reliability, coverage, and output consistency across the training pipeline. This work advances the development of open-source tools for monitoring data use in research literature, contributing to the broader goal of generalizable, unconstrained dataset citation tracking.

Rafael Macalaba, Aivin V. Solatorio

Development Data Group Office of the World Bank Group Chief Statistician The World Bank 1818 H Street N.W., Washington, 20433 District of Columbia, USA

Document Information Extraction LLM Information Extraction

May 28, 2026cs.AI

Compass: Navigating Global Marine Lead Data Integration through Expert-Guided LLM Agent

Marine lead (Pb) and its isotopes are critical tracers for ocean circulation and anthropogenic pollution, yet in-situ observations remain costly and sparse. While vast historical records exist, they lie buried within the unstructured content of academic papers, creating "data silos" inaccessible to comprehensive analysis. Manual extraction is unscalable, while general-purpose Large Language Models (LLMs) lack the necessary domain-specific knowledge, leading to hallucinations and scientifically invalid outputs. To address this, we introduce an expert-guided adaptation approach that enables LLMs to perform rigorous scientific data extraction without fine-tuning. We operationalize this approach through Compass, an LLM agent framework enhanced by a Knowledge Tree co-designed with marine scientists, which decomposes complex tasks into verifiable steps, guiding the agent's reasoning to ensure scientific validity. Deploying Compass across a corpus of over 230,000 relevant open-access papers, we successfully extract 3,751 previously unincorporated Pb records. This effort establishes the largest integrated marine Pb database to date. Beyond standard metrics, Compass demonstrates superior reliability through multi-layered validation, achieving 92% accuracy as confirmed through expert manual verification. The newly integrated data expand coverage in previously under-sampled regions such as the East China Sea and the Southern Ocean, providing an enriched data foundation for future scientific discoveries. We release an interactive visualization platform to facilitate open scientific access. Our work demonstrates that expert-guided agents can effectively bridge the gap between general-purpose LLMs and high-stakes scientific domains, enabling scalable data discovery in geosciences.

Yiming Liu, Bin Lu, Meng Jin +6

AI Agents for Scientific Discovery Document Information Extraction LLM Information Extraction

May 27, 2026cs.AI

From Learning Resources to Competencies: LLM-Based Tagging with Evidence and Graph Constraints

Linking learning resources to a structured competency framework is key to enabling competency-based search and curriculum analytics in Learning Management Systems (LMS). However, manual tagging is labor-intensive, and fully automatic methods often lack transparency. In this paper, we present an end-to-end alignment pipeline that uses a large language model (LLM) as a constrained, evidence-producing tagger. LMS resources -both instructional content and assessments -are first segmented into meaningful pedagogical fragments. For each fragment, a small set of candidate competencies is retrieved from structured competency profiles enriched with graph-based context. The LLM then selects the most relevant competencies from this set and provides supporting evidence spans from the fragment text. These predictions are refined using the structure of the competency graph and aggregated at the resource level. We evaluate our approach on a dataset built from the Computer Science department's competency referential at the Université de Technologie de Compiègne (UTC), covering 22 competencies across multiple course materials. Our LLM+BM25+Graph (LBG) pipeline achieves strong results, with a micro-F1 of 0.57 and macro-F1 of 0.50 at the fragment level, 0.51 macro-F1 at the resource level, and an MRR of 0.82outperforming zero-shot and few-shot LLM variants, retrieval/similarity baselines, and supervised classifiers -while also producing more mechanically traceable evidence spans to support human auditing and educational analysis.

Ngoc Luyen Le, Marie-Hélène Abel, Bertrand Laforge

Gamaizer, 93340 Le Raincy, France · Université de technologie de Compiègne, CNRS, Heudiasyc (Heuristics and Diagnosis of Complex Systems), CS 60319 - 60203 Compiègne Cedex, France · Sorbonne Université, CNRS UMR 7585, LPMHE (Laboratoire de Physique Nucléaire et des Hautes Énergies), 75252 Paris cedex 05, France

LLM-Assisted Annotation LLM Information Extraction

May 27, 2026cs.CL

PrionNER: A Named Entity Recognition Dataset for Prion Disease Biomedical Literature

Prion diseases are rare, rapidly progressive, and fatal neurodegenerative disorders that remain difficult to diagnose, particularly in their early stages because of nonspecific clinical presentations. However, to our knowledge, there is no publicly available prion-disease-focused dataset designed to capture a broad range of clinically relevant entities from the biomedical literature. We introduce PrionNER, a manually annotated named entity recognition dataset for prion disease clinical information in PubMed abstracts. The current release comprises 317 abstracts, 2,943 sentences, and 6,955 text-bound entity annotations spanning 15 coarse-grained and 31 fine-grained clinically oriented entity types covering diseases, symptoms, diagnostics, findings, anatomy, treatments, and temporal and statistical evidence. Inter-annotator agreement reaches 81.78 exact-match F1, indicating strong annotation consistency. We benchmark supervised BERT baselines, W2NER, and zero-shot extractors on PrionNER. W2NER is the strongest supervised model, and Gemma-4-31B is the strongest zero-shot model, but the benchmark remains challenging, especially for structurally complex mentions and fine-grained clinically adjacent label distinctions. PrionNER provides a clinically grounded benchmark for prion-disease information extraction and supports research on rare-disease biomedical NLP under low-resource, fine-grained, and non-flat extraction conditions. The dataset, annotation guidelines, and evaluation scripts are available at https://github.com/daotuanan/PrionNER/.

An Dao, Nhan Ly, Thao Tran +2

The University of Tokyo, Tokyo, Japan · Medical Doctor, Independent Researcher · Center for Language AI Research, Tohoku University, Sendai, Japan +2

Named Entity Recognition Healthcare Clinical Information Extraction LLM Information Extraction

May 27, 2026cs.SI

Snippet-Driven Supply Chain Discovery with LLMs: Scaling Visibility in China

Financial and economic research often relies on structured supply-chain disclosures and commercial databases. In China, supplier--customer disclosure is typically limited to major partners of listed firms, leaving unlisted firms and long-tail inter-firm links poorly captured in structured data. Public web evidence can partly complement this gap through corporate, government, and trade-media disclosures; however, full-text web mining at scale is costly because pages are often inaccessible or expensive to process with large language models (LLMs). We propose a snippet-driven method for constructing a supply chain knowledge graph (SCKG), with firms as nodes and inter-firm relationships as edges. Web search snippets are query-biased summaries returned with search results. We use them as a scalable first-pass evidence layer for LLM-based relationship extraction. We evaluate the pipeline in terms of extraction efficiency and coverage. For extraction efficiency, exhaustive full-text chunking discovers 19.8

\times

more unique relationships than snippets, but requires 251.2

\times

more input tokens and yields higher redundancy. For coverage, we use 130,685 Chinese firms as search seeds, covering Shanghai/Shenzhen-listed firms and large unlisted firms as of 2024. In the listed-firm subset, the resulting SCKG covers 7.2

\times

more firms and 9.3

\times

more relationships than the CSMAR disclosure-based benchmark, while revealing heavy-tailed degree patterns. Retained provenance metadata make the SCKG an auditable complement to disclosure-based databases.

Hiroto Fukada, Takayuki Mizuno

Graduate Institute for Advanced Studies (SOKENDAI) · National Institute of Informatics · Tokyo, Japan

Relation Extraction KG Construction LLM Information Extraction Supply Chain Management Knowledge Graphs

May 26, 2026cs.AI

LELA: An End-to-end LLM-based Entity Linking Framework with Zero-shot Domain Adaptation

Entity linking is a key component of many downstream NLP systems, yet existing approaches are often tied to the specific target knowledge bases and domains, limiting their real world application. In this paper, we extend LELA, a modular and domain-agnostic LLM-based entity disambiguation method, into a practical Python library that integrates zero-shot Named Entity Recognition (NER) -thereby providing a complete end-toend pipeline for entity-linking in real-world usage. We provide experimental results validating LELA's performance and robustness across diverse entity linking settings. In our demo, users can play with the system on their own input texts.

Samy Haffoudhi, Nikola Dobričić, Fabian Suchanek +1

IP Paris, LTCI, DIG · T´el´ecom Paris, Institut Polytechnique de Paris · IP Paris +1

LLM Information Extraction Entity Linking

May 26, 2026cs.DL

Can LLMs extract scientific consensus? A case study in high-temperature superconductivity

Scientific knowledge is increasingly dispersed across vast and heterogeneous scientific literature, where important claims are often implicit, evolving, and internally debated. While large language models (LLMs) have shown impressive performance in information extraction and summarization, their ability to recover latent scientific consensus remains unclear. Here, we investigate this problem in the context of high-temperature superconductivity (HTS), a long-standing and highly debated topic in condensed matter physics, as a challenging testbed. Using near 18,000 highly-cited publications over the past seven decades, we construct a structured knowledge graph linking competing superconducting mechanisms, material families, evidential modalities, and citation relations. We find that LLM-extracted representations recover coherent and physically interpretable structures, including family-dependent mechanism profiles, evidence-specific correlations, and citation-mediated temporal evolution of scientific beliefs. Ablation studies on LLM further show that the global structure remains robust across prompting, decoding, and model variations. Our results suggest that LLMs can indeed serve as scalable tools for deciphering scientific knowledge in domains characterized by competing interpretations and evolving knowledge.

Mouyang Cheng, Wenhao He, Zhuotao Jin +9

Center for Computational Science and Engineering, MIT, Cambridge, MA 02139, USA. · Department of Materials Science and Engineering, MIT, Cambridge, MA 02139, USA. · Department of Physics, MIT, Cambridge, MA 02139, USA. +5

LLM Information Extraction

May 24, 2026cs.AI

Privacy-Preserving Local Language Models for Longitudinal Data Retrieval in Chronic Dermatologic Disease: Implementation in Pemphigus Patients

Chronic dermatologic diseases such as pemphigus require long-term follow-up, generating extensive longitudinal clinical documentation that is difficult to review comprehensively during routine visits and increasing clinician workload as well as the risk of missing critical historical information. We evaluated whether a locally deployed, privacy-preserving small language model (SLM) could retrieve structured clinical features and generate longitudinal summaries from long-term dermatology follow-up records. In this retrospective case series, thirty pemphigus patients contributed 541 visit notes that were aggregated into full longitudinal records (89,336 words); 56 clinically relevant features were annotated by two expert dermatologists. The locally deployed SLM (Qwen3 4B Thinking 2507) was queried with each complete record to retrieve 56 features and generate one final report summaries. Across 1,680 feature retrieval tasks, mean accuracy was 82.25%. Dermatologists' ratings of AI-generated summaries were high for overall quality (8.23-8.47), clinical accuracy (7.93-8.20), and usefulness (8.47-8.50), with no significant inter-evaluator differences and an overall preference for AI summaries in 53.3% of evaluations. These findings suggest that privacy-preserving, locally deployed SLMs can outperform medical experts and reliably generate clinically meaningful longitudinal summaries. SLMs may support clinical decision-making when integrated with appropriate oversight.

Abdurrahim Yilmaz, Ayşe Esra Koku Aksu, Duygu Yamen +5

Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London · Department of Dermatology and Venereology, Istanbul Research and Training Hospital · Department of Dermatology and Venereology, Istanbul Medeniyet University +1

Privacy-Preserving Language Models Healthcare Text Summarization LLM Information Extraction Longitudinal EHR Modeling Clinical Language Model Evaluation

May 22, 2026cs.AI

EPPC-OASIS: Ontology-Aware Adaptation and Structured Inference Refinement for Electronic Patient-Provider Communication Mining in Secure Messages

Secure patient-provider messages contain clinically important communication behaviors that are difficult to characterize manually at scale. The Electronic Patient-Provider Communication (EPPC) framework provides an ontology for coding these behaviors, but automated extraction remains challenging because predictions must preserve fine-grained code/sub-code structure while grounding annotations in message text. We developed EPPC-OASIS, an ontology-aware adaptation approach for structured EPPC extraction, and combined it with deployable inference-refinement procedures designed to improve the coherence of final annotations. EPPC-OASIS augments supervised fine-tuning with a Wasserstein alignment objective that encourages alignment between model representation neighborhoods and EPPC ontology-derived neighborhoods, while inference refinement uses verification, self-consistency, hybrid correction, and selection or ensembling to address residual prediction errors. We evaluated the framework on a de-identified corpus of secure patient-provider messages against prompting, supervised fine-tuning, preference-based, and robustness-oriented baselines across multiple open-weight language models. Across model families, the best deployable pipeline achieved 77.13% Code+Sub-code F1 and 63.83% Triplet F1, corresponding to modest but consistent absolute gains of +1.39 and +2.12 F1 points over the strongest supervised fine-tuning baseline. These results suggest that ontology-aware adaptation with structured inference refinement can support scalable retrospective EPPC mining, although external validation is needed before operational use.

Samah Fodeh, Sreeraj Ramachandran, Elyas Irankhah +7

Yale University, New Haven, CT, USA · Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland Clinic, Cleveland, OH, USA · Medical Oncology, Yale School of Medicine, New Haven, CT, USA

Clinical Information Extraction LLM Information Extraction

May 21, 2026cs.CL

Comparing LLM and Fine-Tuned Model Performance on NVDRS Circumstance Extraction with Varying Prompt Complexity

Suicide is a leading cause of death in the United States, and understanding the circumstances that precede it requires extracting structured information from death investigation narratives. Many of these circumstances require semantic inference beyond simple keyword matching. We develop a ``Complexity Score'' algorithm that analyzes coding manual structure to predict when detailed prompts with full coding guidelines improve over name-only prompts. We then construct a hybrid approach that selects prompt strategy per circumstance. We evaluate large language models (LLMs) against fine-tuned RoBERTa on 25 inferentially complex circumstances from the National Violent Death Reporting System (NVDRS). We found that LLMs substantially outperform on low-prevalence circumstances where training data is insufficient. We further demonstrate that our framework generalizes across frontier LLMs, with GPT-5.2, Gemini 2.5 Pro and Llama-3 70B showing consistent performance patterns. These findings support a hybrid architecture where LLMs handle rare, inferentially complex circumstances while fine-tuned models handle common ones.

Geoffrey Martin, Xuan Zhong Feng, Yifan Peng

Department of Population Health Sciences, Weill Cornell Medicine, New York, USA · Systems Engineering, Cornell University, New York, USA

LLM Prompting LLM Information Extraction

May 15, 2026cs.AI

GRID: Graph Representation of Intelligence Data for Security Text Knowledge Graph Construction

Security knowledge graphs can provide computable external memory for security agents, but constructing them from long-form cyber threat intelligence (CTI) remains difficult: LLMs often lack grounded security-domain knowledge, and end-to-end document-to-graph training is hard to supervise with cheap, stable rewards. We present GRID (Graph Representation of Intelligence Data), an end-to-end framework for security text knowledge graph construction. GRID first builds security-domain supervision from CTI articles by creating traceable article-graph alignments through graph extraction and knowledge-graph-conditioned text revision. It then turns document-to-graph learning into a scripted task bank combining four-option multi-select questions with triple-level regex matching targets, yielding more stable task-specific rewards than repeatedly scoring full graph outputs with an LLM judge. Using this supervision pipeline, we train two Qwen3-4B-Instruct-2507-based 4B extractors: a primary Task-bank Reward model and a secondary End2End Reward model with LLM-as-judge precision/recall rewards. On 249 CTI articles from GRID, CASIE, CTINexus, MalKG, and SecureNLP, the Task-bank Reward model with the ontology-guided GRID extraction pipeline reaches 84.62% source-averaged precision, 64.91% source-averaged recall, and 68.53% Avg F1, achieving the best source-averaged recall and near-top Avg F1 with lower token usage and deployment cost. The End2End Reward model reaches 76.91% precision, 53.85% recall, and 58.06% Avg F1. Further analyses show that task-bank rewards can be built once offline and reused across later post-training runs, outperforming online End2End LLM-as-judge reward and weaker alternatives such as Choice-only Reward and End2End SFT without RL.

Liangyi Huang, Zichen Liu, Fei Shao +5

Arizona State University · Case Western Reserve University · University of Notre Dame +2

KG Construction Cyber Threat Intelligence LLMs for Cybersecurity LLM Information Extraction Reinforcement Learning with Verifiable Rewards

May 14, 2026cs.CL

Retrieval-Augmented Large Language Models for Schema-Constrained Clinical Information Extraction

Conversational nurse-patient transcripts contain actionable observations, but converting these transcripts into structured representations at scale remains challenging. Documentation burden is substantial, with prior studies showing clinicians spend large portions of their workday on documentation and related desk work rather than direct patient care. MEDIQA-SYNUR focuses on observation extraction from conversational nurse-patient transcripts, requiring systems to normalize these narratives into a predefined schema with value-type constraints. We propose a modular retrieval-augmented generation (RAG) pipeline that uses the training set as an exemplar corpus, combines schema-constrained prompting (full schema vs. pruned candidate schema), deterministic schema-based postprocessing, and a second-pass audit, with two LLM backbones: Llama-4-Scout-17B-16E-Instruct and GPT-5.2 with corresponding embedding models for RAG. Our best configuration uses GPT-5.2 with full schema, RAG, and a second-pass auditing, achieving 80.36% F1 score. Overall, our results show that RAG consistently improves performance, while the optimal degree of schema constraint depends on the model, and second-pass auditing yields modest additional gains by correcting residual schema-adherence errors.

A H M Rezaul Karim, Ozlem Uzuner

George Mason University, VA, USA

Retrieval-Augmented Generation Healthcare Clinical Information Extraction LLM Information Extraction Text Generation

May 13, 2026cs.CL

An LLM-Based System for Argument Mining

Arguments are a fundamental aspect of human reasoning, in which claims are supported, challenged, and weighed against one another. We present an end-to-end large language model (LLM)-based system for reconstructing arguments from natural language text into abstract argument graphs. The system follows a multi-stage pipeline that progressively identifies argumentative components, selects relevant elements, and uncovers their logical relations. These elements are represented as directed acyclic graphs consisting of two component types (premises and conclusions) and three relation types (support, attack, and undercut). We conduct two complementary experiments to evaluate the system. First, we perform a manual evaluation on arguments drawn from an argumentation theory textbook to assess the system's ability to recover argumentative structure. Second, we conduct a quantitative evaluation on benchmark datasets, allowing comparison with prior work by mapping our outputs to established annotation schemes. Results show that the system can adequately recover argumentative structures and, when adapted to different annotation schemes, achieve reasonable performance across benchmark datasets. These findings highlight the potential of LLM-based pipelines for scalable argument mining.

Paulo Pirozelli, Victor Hugo Nascimento Rocha, Fabio G. Cozman +1

Universidade de S˜ao Paulo · Center for Artificial Intelligence (C4AI) · Instituto Mau´a de Tecnologia +1

Argument Mining Computational Argumentation LLM Information Extraction

May 12, 2026cs.CR

Reconstruction of Personally Identifiable Information from Supervised Finetuned Models

Supervised Finetuning (SFT) has become one of the primary methods for adapting a large language model (LLM) with extensive pre-trained knowledge to domain-specific, instruction-following tasks. SFT datasets, composed of instruction-response pairs, often include user-provided information that may contain sensitive data such as personally identifiable information (PII), raising privacy concerns. This paper studies the problem of PII reconstruction from SFT models for the first time. We construct multi-turn, user-centric Q&A datasets in sensitive domains, specifically medical and legal settings, that incorporate PII to enable realistic evaluation of leakage. Using these datasets, we evaluate the extent to which an adversary, with varying levels of knowledge about the fine-tuning dataset, can infer sensitive information about individuals whose data was used during SFT. In the reconstruction setting, we propose COVA, a novel decoding algorithm to reconstruct PII under prefix-based attacks, consistently outperforming existing extraction methods. Our results show that even partial attacker knowledge can significantly improve reconstruction success, while leakage varies substantially across PII types.

Sae Furukawa, Alina Oprea

Northeastern University Boston, Massachusetts, USA

Supervised Fine-Tuning Privacy Leakage in Language Models LLM Information Extraction

May 12, 2026cs.CL

Large Language Models for Causal Relations Extraction in Social Media: A Validation Framework for Disaster Intelligence

During disasters, extracting causal relations from social media can strengthen situational awareness by identifying factors linked to casualties, physical damage, infrastructure disruption, and cascading impacts. However, disaster-related posts are often informal, fragmented, and context-dependent, and they may describe personal experiences rather than explicit causal relations. In this work, we examine whether Large Language Models (LLMs) can effectively extract causal relations from disaster-related social media posts. To this end, we (1) propose an expert-grounded evaluation framework that compares LLM-generated causal graphs with reference graphs derived from disaster-specific reports and (2) assess whether the extracted relations are supported by post-event evidence or instead reflect model priors. Our findings highlight both the potential and risks of using LLMs for causal relation extraction in disaster decision-support systems.

Ujun Jeong, Saketh Vishnubhatla, Bohan Jiang +3

Arizona State University, Tempe, Arizona, USA · DEVCOM Army Research Laboratory, Adelphi, Maryland, USA

Relation Extraction LLM Evaluation LLM Information Extraction

May 11, 2026q-bio.QM

Beyond Manual Curation: Augmenting Targeted Protein Degradation Databases via Agentic Literature Extraction Workflows

Predictive models in biomedicine depend on structured assay data locked in the text, tables, and supplements of primary publications. This bottleneck is especially acute in targeted protein degradation (TPD), where each assay record must combine compound identity, degradation target, recruiter, assay context, and endpoint values reported across sections, tables, and supplementary files. Inconsistent compound identifiers and incomplete or implicit assay context further demand domain-specific logic that generic LLM pipelines do not provide. Existing molecular glue and PROTAC databases are manually curated and often lack the experimental context required for downstream modeling. We formulate TPD database extraction as a domain-specific curation task and present an expert-in-the-loop LLM workflow, evaluated through a triangular comparison among LLM predictions, standardized baseline records, and expert-annotated ground truth. A lightweight cross-validated prompt-refinement module adapts extraction instructions from scarce expert annotations. With only seven annotated molecular glue publications, the workflow achieved record-level

F_1 = 0.98

and transferred to PROTACs by terminology substitution alone, maintaining record-level

F_1 > 0.93

. Applied at scale, it expanded molecular glue and PROTAC databases by 81% and 92% records, respectively, with 92% and 82.5% of newly recovered records validated as correct upon expert review. The workflow also recovered kinetic and assay-context information essential for cross-study potency comparison and condition-aware degradation modeling. We release the workflow, prompts, evaluation code, and extracted datasets as resources for TPD data curation and AI-assisted scientific curation more broadly.

Yaochen Rao, Farzaneh Jalalypour, N. M. Anoop Krishnan +1

Department of Computer Science and Engineering, Chalmers University of Technology and University of Gothenburg, Gothenburg, SE · Yardi School of Artificial Intelligence, Indian Institute of Technology Delhi, New Delhi, IN

Training Data Curation Document Information Extraction LLM Information Extraction

May 8, 2026cs.CL

Uncertainty-Aware Structured Data Extraction from Full CMR Reports via Distilled LLMs

Converting free-text cardiac magnetic resonance (CMR) reports into auditable structured data remains a bottleneck for cohort assembly, longitudinal curation, and clinical decision support. We present CMR-EXTR, a lightweight framework that converts free-text CMR reports into structured data and assigns per-field confidence for quality control. A teacher-student distillation pipeline enables fully offline inference while limiting manual annotation. Uncertainty integrates three complementary principles -- distribution plausibility, sampling stability, and cross-field consistency -- to triage human review. Experiments show that CMR-EXTR achieves 99.65% variable-level accuracy, demonstrating both reliable extraction and informative confidence scores. To our knowledge, this is the first CMR-specific extraction system with integrated confidence estimation. The code is available at https://github.com/yuyi1005/CMR-EXTR.

Yi Yu, Parker Martin, Zhenyu Bu +5

†The Ohio State University · ‡NetMind.AI

Clinical Information Extraction LLM Information Extraction LLM Uncertainty Estimation Structured Output Generation Cardiac MRI

May 8, 2026cs.CL

TCMIIES: A Browser-Based LLM-Powered Intelligent Information Extraction System for Academic Literature

The exponential growth of academic publications has created an urgent need for automated tools capable of extracting structured knowledge from unstructured scientific texts. While large language models (LLMs) have demonstrated remarkable capabilities in natural language understanding and information extraction, existing solutions often require specialized infrastructure, programming expertise, or fine-tuned domain-specific models that create barriers for researchers in specialized fields. This paper presents TCMIIES, a browser-based, zero-installation platform that leverages commercial LLM APIs to perform structured information extraction from academic literature. The system employs a novel schema-guided prompting framework with automatic system prompt generation, enabling researchers to define custom extraction schemas through an intuitive graphical interface without any programming. TCMIIES features a pure front-end architecture that ensures data privacy by processing all information locally in the browser, supports five major LLM providers, implements concurrent batch processing with automatic retry mechanisms, and provides intelligent field mapping for Chinese academic databases including CNKI and Wanfang. We demonstrate the system's effectiveness through comprehensive evaluation across multiple extraction scenarios in Traditional Chinese Medicine research, achieving structured output compliance rates exceeding 94% and information extraction accuracy comparable to domain-expert annotation. The system represents a practical, accessible solution that bridges the gap between advanced LLM capabilities and domain-specific academic information extraction needs, particularly for researchers in specialized fields who require flexible, privacy-preserving, and cost-effective extraction tools.

Hanqing Zhao

Hebei University, College of Traditional Chinese Medicine Baoding, Hebei 071002, China

Document Information Extraction LLM Information Extraction

May 8, 2026cs.CL

The Text Uncanny Valley: Non-Monotonic Performance Degradation in LLM Information Retrieval

Existing Large Language Model (LLM) benchmarks primarily focus on syntactically correct inputs, leaving a significant gap in evaluation on imperfect text. In this work, we study how word-boundary corruption affects how LLMs detect targeted information. By inserting whitespace characters within words to break them into fragments, LLMs' detection accuracy follows a U-shaped curve with the increase in insertion rate. We refer to this curve as the Text Uncanny Valley. To explain such observation, we propose a mode transition hypothesis: LLMs operate in a word-level mode for near-normal text and a character-level mode for heavily fragmented text, with the valley marking the disordered transition where neither mode is effective. Four experiments and one analysis are consistent with this account: in-context learning fails to rescue valley-bottom performance; regularizing the perturbation substantially reduces the U-shape; a math reasoning task replicates the U-shape for Gemini 3.0 Flash but not for stronger models, suggesting the effect is attenuated when tasks rely less on exact lexical alignment; and tokenization entropy peaks before the F1 minimum, consistent with a regime-conflict interpretation. These findings reveal a failure mode invisible to clean-text benchmarks yet directly relevant to any deployment scenario involving noisy or uncurated text inputs.

Zekai Tong, Ruiyao Xu, Aryan Shrivastava +2

University of Chicago · 2Northwestern University

LLM Evaluation LLM Reliability LLM Information Extraction Language Model Robustness

May 7, 2026cs.LG

Self-Driving Datasets: From 20 Million Papers to Nuanced Biomedical Knowledge at Scale

Manually curated biomedical repositories -- spanning bioactivity, genomics, and chemistry -- are expensive to maintain, lag behind primary literature, and discard experimental context, obscuring nuances needed to assess data correctness and coverage. We show that PubMed itself can be autonomously and cost-effectively turned into structured datasets that are larger, more nuanced, and more accurate than the curated databases they replace. We present three coupled contributions: (1) an LLM-based entity-tagging pipeline, grounded in nine biomedical ontologies, that tags 4.5B entities across 19 categories in a 22.5M-paper, 2.5T-token PubMed corpus; (2) hybrid sparse-dense retrieval supporting entity-filtered semantic queries over the tagged corpus; and (3) Starling, a multi-agent deep research system that, given only a natural-language task description, designs precision- and recall-targeted retrieval filters, induces an extraction schema, and emits structured records with nuance-rich fields and supporting passages. Across six tasks -- blood-brain barrier permeability, oral bioavailability, acute toxicity (LD50), gene-disease associations, protein subcellular localization, and chemical reactions -- Starling produces ~6.3M records (91K-3M per task); several are, to our knowledge, the largest public datasets for their property. Frontier-model rejection of our extractions is 0.6-7.7% across tasks, far below error rates we measure on widely used curated counterparts (e.g., 16.5% on BBB_Martins, 7.3% on Bioavailability_Ma). Beyond scale and accuracy, the supporting passages carry nuance tabular databases discard -- e.g., oral bioavailability may depend on fed vs. fasted state. Together, the corpus, retrieval, and agent establish a foundation for AI-driven therapeutic design. Code and datasets: https://github.com/starling-labs/starling.

Haydn Jones, Yimeng Zeng, Alden Rose +11

Department of Computer and Information Science, University of Pennsylvania · Department of Genetics, University of Pennsylvania · 3Departments of Bioengineering and Chemical and Biomolecular Engineering,2026 University of Pennsylvania

AI Agents for Scientific Discovery LLM Information Extraction Biomedical IR

May 7, 2026cs.AI

Addressing Labelled Data Scarcity: Taxonomy-Agnostic Annotation of PII Values in HTTP Traffic using LLMs

Automated privacy audits of web and mobile applications often analyse outbound HTTP traffic to detect Personally Identifiable Information (PII) leakage. However, existing learning-based detectors typically depend on scarce, manually labelled traffic and are tightly coupled to fixed label taxonomies, limiting transferability across domains and evolving definitions of PII. This paper investigates whether Large Language Models (LLMs) can support taxonomy-agnostic annotation of explicitly transmitted PII values in HTTP message bodies when the taxonomy is provided at runtime. We introduce a multi-stage LLM-based pipeline that combines deterministic pre-processing with label-level classification, targeted instance-level value annotation, and output validation. To enable controlled evaluation and exemplar-based prompting without relying on sensitive real-user captures, we further propose an LLM-based generator for synthetic HTTP traffic with manually validated, taxonomy-derived PII annotations. We evaluate the approach across three taxonomies spanning different PII domains and granularity levels. Results show that the pipeline accurately detects PII types and extracts corresponding values for concrete PII taxonomies. Overall, our findings position LLMs as a promising foundation for flexible, taxonomy-agnostic traffic annotation and for creating labelled data under evolving privacy taxonomies.

Thomas Cory, Axel Küpper

Technische Universität Berlin

Privacy Auditing LLM-Assisted Annotation LLM Information Extraction PII Detection

May 7, 2026cs.AI

Systematic Evaluation of Large Language Models for Post-Discharge Clinical Action Extraction

The work in this paper evaluates zero-shot and few-shot large language models (LLMs) for safety-critical clinical action extraction using the CLIP discharge-note dataset, with particular emphasis on transitions of care and post-discharge patient safety. To manage the complexity of clinical documentation, we introduce a two-stage extraction framework that decomposes discharge notes, that are written in narrative form, into fine-grained, explicitly actionable clinical tasks through a staged prompting strategy. Our contributions include a systematic assessment of generative LLMs for clinical action extraction, a detailed comparison between general-purpose LLMs and task-specific supervised BERT-based models, and an analysis of annotation inconsistencies across different action categories. We show that contemporary LLMs achieve performance comparable to or exceeding supervised models on binary actionability detection, while supervised baselines retain a meaningful advantage on fine-grained multi-label category classification, despite the absence of task-specific fine-tuning and under strict data-privacy constraints. Qualitative error analysis reveals that many failures stem from misalignment between model reasoning and dataset annotation conventions, particularly in cases involving implicit clinical actions and rigid structural labeling rules. These results indicate that reported performance reflects model limitations due to lack of clinical reasoning, that is not captured by plain annotations. Labels without rationales make it impossible to distinguish clinical reasoning failures from annotation convention mismatches. Advancing clinical NLP requires reasoning-annotated datasets that document why specific spans are actionable, not merely which spans were labeled, enabling proper evaluation of model clinical understanding.

Shivali Dalmia, Ananya Mantravadi, Prasanna Desikan

Centific AI Research · Centific Global Solutions, Inc.

Document Information Extraction Clinical Information Extraction LLM Information Extraction Clinical Language Model Evaluation

May 7, 2026cs.CL

IRC-Bench: Recognizing Entities from Contextual Cues in First-Person Reminiscences

When people recount personal memories, they often refer to people, places, and events indirectly, relying on con-textual cues rather than explicit names. Such implicit references are central to reminiscence narratives: first-person accounts of lived experience used in therapeutic, archival, and social settings. They pose a difficult computational problem because the intended entity must be inferred from dispersed narrative evidence rather than from a local mention. We introduce IRC-Bench, the Implicit Reminiscence Context Benchmark, for evaluating implicit entity recognition in reminiscence transcripts. The benchmark targets non-locality: entity-identifying cues are distributed across multiple, non-contiguous clauses, unlike named entity recognition, entity linking, or coreference resolution. IRC-Bench comprises 25,136 samples constructed from 12,337 Wikidata-linked entities across 1,994 transcripts spanning 11 thematic domains. Each sample pairs an Entity-Grounded Narrative, in which the target entity is ex-plicitly mentioned, with an Entity-Elided Narrative, in which direct mentions are removed. We evaluate 19 config-urations across LLM generation, dense retrieval, RAG, and fine-tuning. QLoRA-adapted Llama 3.1 8B performs best in the open-world setting (38.94% exact match; 51.59% Jaccard), while fine-tuned DPR leads closed-world retrieval (35.38% Hit@1; 71.49% Hit@10). We release IRC-Bench with data, code, and evaluation tools.

Yehudit Aperstein, Eden Moran, Alexander Apartsin

Intelligent Systems, Afeka Academic College of Engineering, Tel Aviv, Israel · School of Computer Science, Faculty of Sciences, Holon Institute of Technology, Holon, Israel

LLM Information Extraction

May 7, 2026cs.DL

Vidya: An AI-Driven Modular Pipeline for Archival Automation and Semantic Metadata Enrichment

The large-scale digitization of historical archives has created a paradox: "dark data"-digital objects lacking metadata for retrieval. Manual archival description is slow and expensive, limiting discovery and reuse. We propose Vidya, a modular pipeline that orchestrates Large Language Models (LLMs) and FOSS tools to automate semantic enrichment and archival ingestion at scale. Vidya constrains generations using YAML-defined ontologies and Pydantic validation, producing deterministic, structured JSON outputs from probabilistic models. Developed at Laboratory for Digital Humanities and Innovation (LAMUHDI) of the State University of Ponta Grossa (UEPG), Vidya applies Maker principles and open-source practices to enable low-cost deployment in memory institutions using modest hardware. We compare LLM performance and present a cost-benefit analysis showing major gains, reducing processing time from decades to days while complying with NOBRADE and ISAD(G).

Cloter Migliorini Filho, Julia Graciela Machado, Edson Armando Silva +1

1Museu Campos Gerais - Universidade Estadual de Ponta Grossa - UEPG · 2Universidade Tecnol´ogica Federal do Paran´a - UTFPR

LLM-Assisted Annotation LLM Information Extraction Historical Document Processing

May 7, 2026cs.CL

From Articles to Premises: Building PrimeFacts, an Extraction Methodology and Resource for Fact-Checking Evidence

Fact-checking articles encode rich supporting evidence and reasoning, yet this evidence remains largely inaccessible to automated verification systems due to unstructured presentation. We introduce PrimeFacts, a methodology and resource for extracting fine-grained evidence from full fact-checking articles. We compile 13,106 PolitiFact articles with claims, verdicts, and all referenced sources, and we identify 49,718 in-article hyperlinks as natural anchors to pinpoint key evidence. Our framework leverages large language models (LLMs) to rewrite these anchor sentences into stand-alone, context-independent premises and investigates the extraction of additional implicit evidence. In evaluations on cross-article evidence retrieval and claim verification, the extracted premises substantially improve performance. Decontextualized evidence yields higher retrievability, achieving up to a 30 percent relative gain in Mean Reciprocal Rank over verbatim sentences, and using the evidence for verdict prediction raises Macro-F1 by 10-20 points over the baseline. These gains are consistent across different verdict granularities (2-class vs. 5-class) and model architectures. A qualitative analysis indicates that the decontextualized premises remain faithful to the original sources. Our work highlights the promise of reusing fact-checkers' evidence for automation and provides a large-scale resource of structured evidence from real-world fact-checks.

Premtim Sahitaj, Jawan Kolanowski, Ariana Sahitaj +7

Technische Universität Berlin, Quality and Usability Lab, Berlin, Germany · Deutsches Forschungszentrum für Künstliche Intelligenz (DFKI), Berlin, Germany · Harz University of Applied Sciences, Wernigerode, Germany +1

Automated Fact-Checking LLM Information Extraction Evidence Retrieval

May 7, 2026cs.CL

A Few Good Clauses: Comparing LLMs vs Domain-Trained Small Language Models on Structured Contract Extraction

This paper evaluates whether a domain trained Small Language Model (SLM) can outperform frontier Large Language Models on structured contract extraction at radically lower cost. We test Olava Extract, a self hosted legal domain Mixture of Experts model, against five frontier models. Olava Extract achieved the strongest aggregate performance in the study, with a macro F1 of 0.812 and a micro F1 of 0.842, while reducing inference cost by 78% to 97% compared with the frontier models tested. It also achieved the highest precision scores, producing fewer hallucinated and unsupported extractions, an important distinction in legal workflows where hallucinations create operational risk and downstream review burden. The findings shows that high performing, human comparable legal AI no longer requires the largest externally hosted models. More broadly, they challenge the assumption that commercially valuable enterprise AI capability must remain tied to ever larger models, massive infrastructure expenditure, and centrally hosted providers.

Nicole Lincoln, Nick Whitehouse, Jaron Mar +1

Onit AI Labs, Onit Inc., New Zealand

Legal NLP Mixture-of-Experts Language Models Document Information Extraction Small Language Models LLM Information Extraction Efficient Language Model Inference

May 6, 2026cs.AI

Spatial Priming Outperforms Semantic Prompting: A Grid-Based Approach to Improving LLM Accuracy on Chart Data Extraction

The automated extraction of data from scientific charts is a critical task for large-scale literature analysis. While multimodal Large Language Models (LLMs) show promise, their accuracy on non-standardized charts remains a challenge. This raises a key research question: what is the most effective strategy to improve model performance (high-level semantic priming) or low-level spatial priming? This paper presents a comparative investigation into these two distinct strategies. We describe our exploratory experiments with semantic methods, such as a two-stage metadata-first framework and Chain-of-Thought, which failed to produce a statistically significant improvement. In contrast, we present a simple but highly effective spatial priming method: overlaying a coordinate grid onto the chart image before analysis. Our quantitative experiment on a synthetic dataset demonstrates that this grid-based approach provides a statistically significant reduction in data extraction error (SMAPE reduced from 25.5% to 19.5%, p < 0.05) compared to a baseline. We conclude that for the current generation of multimodal models, providing explicit spatial context is a more effective and reliable strategy than high-level semantic guidance for this class of tasks.

Andrei Lazarev, Dmitrii Sedov, Alexander Galkin

Department of Control and Applied Mathematics Moscow Institute of Physics and Technology Moscow, Russia · Moscow Institute of Physics and Technology Moscow, Russia · Institute of Computer Science Lipetsk State Technical University Lipetsk, Russia

LLM Prompting Document Information Extraction Multimodal Large Language Models Chart Data Extraction LLM Information Extraction

May 5, 2026cs.CL

SAM-NER: Semantic Archetype Mediation for Zero-Shot Named Entity Recognition

Zero-shot Named Entity Recognition (ZS-NER) remains brittle under domain and schema shifts, where unseen label definitions often misalign with a large language model's (LLM's) intrinsic semantic organization. As a result, directly mapping entity mentions to fine-grained target labels can induce systematic semantic drift, especially when target schemas are novel or semantically overlapping. We propose \textbf{SAM-NER}, a three-stage framework based on \emph{Semantic Archetype Mediation} that stabilizes cross-domain transfer through an intermediate, domain-invariant archetype space. SAM-NER: (i) performs \emph{Entity Discovery} via cooperative extraction and consensus-based denoising to obtain high-coverage, high-fidelity entity spans; (ii) conducts \emph{Abstract Mediation} by projecting entities into a compact set of universal semantic archetypes distilled from high-level ontological abstractions; and (iii) applies \emph{Semantic Calibration} to resolve archetype-level predictions into target-domain types through constrained, definition-aligned inference with a frozen LLM. Experiments on the CrossNER benchmark show that SAM-NER consistently outperforms strong prior ZS-NER baselines in cross-domain settings. Our implementation will be open-sourced at https://github.com/DMIRLAB-Group/SAM-NER.

Ruichu Cai, Juntao Gan, Miao Mai +2

School of Computer Science, Guangdong University of Technology · Peng Cheng Laboratory · Nanfang Media Group(Nanfang Daily) +1

Named Entity Recognition Cross-Domain Transfer Learning LLM Information Extraction