LLM Information Extraction

Extracting structured data from unstructured text using large language models (LLMs) becomes challenging when target schemas are large and complex. In such cases, including the full schema in the prompt increases cost and latency, risks lost-in-the-middle performance degradation, and can exceed context length limits. We propose SchemaRAG, a retrieval-augmented generation (RAG) framework that dynamically prunes the output schema space for schema-conditioned information extraction tasks by leveraging schema metadata and few-shot examples when available. We evaluate SchemaRAG on real-world healthcare and e-commerce datasets. Our results show that SchemaRAG can achieve up to an 8.8% increase in micro-F1, a 47% reduction in latency, and a 48% reduction in token costs, demonstrating its practicality for large-schema extraction.

Earnings calls are a key source of financial information about public companies. However, extracting information from these calls is difficult. Unlike the templatic filings required by the U.S. Securities and Exchange Commission (SEC) to report a company's financial situation, earnings conference calls have no built-in labels, are unstructured, and feature conversational language. We explore this challenging domain by assessing the information captured by models trained on SEC filings and in-context learning methods. To establish a baseline, we first evaluate the generalization capabilities of SEC-trained models across established SEC datasets. To support our investigation, we introduce three novel benchmarks: (1) SEC Filings Benchmark (SECB), (2) Earnings Calls Benchmark (ECB), and ECB-A, a subset with 2,460 expert annotation groups to support our qualitative analysis. We find that encoder-based models struggle with the domain shift. Finally, we propose a system utilizing LLMs to perform open-ended extraction from unstructured call transcripts, verified by human evaluation (79.7% precision), providing a baseline for this valuable domain through the consistent tracking of emergent KPIs.

BIM models provide structured representations of building geometry, semantics, and topology, yet extracting specific information from them remains remarkably difficult. Current approaches translate natural language into structured queries by assuming a fixed data organization (static approach), which BIM heterogeneity eventually invalidates. We address this with a new paradigm, adaptive exploration, where an LLM-based agent iteratively executes code to extract information from a BIM model, discovering its structure at runtime instead of assuming it. We evaluate this approach on ifc-bench v2, an open-source BIM question-answering benchmark introduced alongside this work, comprising 1,027 tasks across 37 IFC models from 21 projects. A factorial ablation across two LLM capability levels and four augmentation strategies shows that adaptive exploration significantly outperforms static query generation across all configurations, regardless of the augmentation strategy. These results indicate that BIM heterogeneity is best addressed at the paradigm level, not by further optimizing static approaches.

Persistent AI memory is often reduced to a retrieval problem: store prior interactions as text, embed them, and ask the model to recover relevant context later. This design is useful for thematic recall, but it is mismatched to the kinds of memory that agents need in production: exact facts, current state, updates and deletions, aggregation, relations, negative queries, and explicit unknowns. These operations require memory to behave less like search and more like a system of record. This paper argues that reliable external AI memory must be schema-grounded. Schemas define what must be remembered, what may be ignored, and which values must never be inferred. We present an iterative, schema-aware write path that decomposes memory ingestion into object detection, field detection, and field-value extraction, with validation gates, local retries, and stateful prompt control. The result shifts interpretation from the read path to the write path: reads become constrained queries over verified records rather than repeated inference over retrieved prose. We evaluate this design on structured extraction and end-to-end memory benchmarks. On the extraction benchmark, the judge-in-the-loop configuration reaches 90.42% object-level accuracy and 62.67% output accuracy, above all tested frontier structured-output baselines. On our end-to-end memory benchmark, xmemory reaches 97.10% F1, compared with 80.16%-87.24% across the third-party baselines. On the application-level task, xmemory reaches 95.2% accuracy, outperforming specialised memory systems, code-generated Markdown harnesses, and customer-facing frontier-model application harnesses. The results show that, for memory workloads requiring stable facts and stateful computation, architecture matters more than retrieval scale or model strength alone.

Some text generation tasks, such as Attribute Value Extraction (AVE), require decoding multiple independent sequences from the same document context. While standard autoregressive decoding is slow due to its sequential nature, the independence between output sequences offers an opportunity for parallelism. We present Hyper-Parallel Decoding, a novel decoding algorithm that accelerates offline decoding by leveraging both shared memory and computation across batches. HPD enables out-of-order token generation through position ID manipulation, significantly improving efficiency. Experiments on AVE show that attribute-value pairs are conditionally independent, enabling us to parallelize value generation within each prompt. By further stacking multiple documents within a single prompt, we can decode in parallel up to 96 tokens per prompt. HPD works with all LLMs, and reduces both inference costs and total inference time by up to 13.8X without compromising output quality, potentially saving hundreds of thousands of dollars on industry AVE tasks. Although designed for attribute extraction, HPD makes no assumptions unique to the AVE domain and can in theory be applied to other scenarios with independent output structures.

Large Language Models are increasingly being deployed to extract structured data from unstructured and semi-structured sources: parsing invoices, medical records, and converting PDF documents to database entries. Yet existing benchmarks for structured output generation either focus on schema compliance alone, or evaluate value correctness within a single source domain. We introduce SOB (The Structured Output Benchmark), a multi-source benchmark spanning three source modalities: native text, images, and audio conversations. All models receive a text-normalized representation of their context regardless of source modality; this deliberate design isolates structured-output capability from raw vision or speech-processing quality, ensuring a fair, source-agnostic comparison. Our benchmark comprises 5,000 text evaluation records derived from multi-hop QA drawn from a 25,091-record full corpus, 209 image records from OCR-processed PDFs across seven document types including multi-column layouts, dense tables, scanned historical documents, small-print text, and mathematical typesetting, and 115 audio records from the AMI corpus. Each record pairs a natural-language question with a JSON schema that the model must follow and a ground-truth answer verified against the source context. We evaluate 21 frontier and open-weight models across three source domains and seven metrics. Our results reveal a consistent pattern: models achieve near-perfect schema compliance, yet the best Value Accuracy, measured by exact leaf-value match, reaches only 83.0% on text, 67.2% on images, and 23.7% on audio, where longer context makes extraction substantially harder. We release the dataset, evaluation pipeline, and all related code.

The promise of data-driven materials discovery remains constrained by the scarcity of large, high-quality, and accessible experimental datasets. Here, we introduce a generalizable large language model (LLM)-powered pipeline for automated extraction and structuring of materials data from unstructured scientific literature, using concrete materials as a representative and particularly challenging example. The pipeline exhibits robust performance across a broad range of LLMs and achieves an $F_1$ score of up to 0.98 for diverse composition--process--property attributes. Within one hour, it extracts nearly 9,000 high-quality records with over 100 attributes from a corpus screened from more than 27,000 publications, enabling the construction of the largest open laboratory database for blended cement concrete. Machine learning analyses underscore the importance of large, diverse, and information-rich datasets for enhancing both in-distribution accuracy and out-of-distribution generalization to unseen materials. The proposed pipeline is readily adaptable to other materials domains and accelerates the development of scalable data infrastructures for materials informatics.

Due to the textual and repetitive nature of many Requirements Engineering (RE) artefacts, Large Language Models (LLMs) have proven useful to automate their generation and processing. In this paper, we discuss a possible approach for automating the Goal-Oriented Requirements Engineering (GORE) process by extracting functional goals from software documentation through three phases: actor identification, high and low-level goal extraction. To implement these functionalities, we propose a chain of LLMs fed with engineered prompts. We experimented with different variants of in-context learning and measured the similarities between input data and in-context examples to better investigate their impact. Another key element is the generation-critic mechanism, implemented as a feedback loop involving two LLMs. Although the pipeline achieved 61% accuracy in low-level goal identification, the final stage, these results indicate the approach is best suited as a tool to accelerate manual extraction rather than as a full replacement. The feedback-loop mechanism with Zero-shot outperformed stand-alone Few-shot, with an ablation study suggesting that performance slightly degrades without the feedback cycle. However, we reported that the combination of the feedback mechanism with Few-shot does not deliver any advantage, possibly suggesting that the primary performance ceiling is the prompting strategy applied to the 'critic' LLM. Together with the refinement of both the quantity and quality of the Shot examples, future research will integrate Retrieval-Augmented Generation (RAG) and Chain-of-Thought (CoT) prompting to improve accuracy.

Event extraction is essential for event understanding and analysis. It supports tasks such as document summarization and decision-making in emergency scenarios. However, existing event extraction approaches have limitations: (1) closed-domain algorithms are restricted to predefined event types and thus rarely generalize to unseen types and (2) open-domain event extraction algorithms, capable of handling unconstrained event types, have largely overlooked the potential of large language models (LLMs) despite their advanced abilities. Additionally, they do not explicitly model document-level contextual, structural, and semantic reasoning, which are crucial for effective event extraction but remain challenging for LLMs due to lost-in-the-middle phenomenon and attention dilution. To address these limitations, we propose multimodal open-domain event extraction, MODEE , a novel approach for open-domain event extraction that combines graph-based learning with text-based representation from LLMs to model document-level reasoning. Empirical evaluations on large datasets demonstrate that MODEE outperforms state-of-the-art open-domain event extraction approaches and can be generalized to closed-domain event extraction, where it outperforms existing algorithms.

Span-level skill extraction from job advertisements underpins candidate-job matching and labor-market analytics, yet generative large language models (LLMs) often yield malformed spans, boundary drift, and hallucinations, especially with long-tail terms and cross-domain shift. We present SRICL, an LLM-centric framework that combines semantic retrieval (SR), in-context learning (ICL), and supervised fine-tuning (SFT) with a deterministic verifier. SR pulls in-domain annotated sentences and definitions from ESCO to form format-constrained prompts that stabilize boundaries and handle coordination. SFT aligns output behavior, while the verifier enforces pairing, non-overlap, and BIO legality with minimal retries. On six public span-labeled corpora of job-ad sentences across sectors and languages, SRICL achieves substantial STRICT-F1 improvements over GPT-3.5 prompting baselines and sharply reduces invalid tags and hallucinated spans, enabling dependable sentence-level deployment in low-resource, multi-domain settings.

Protein-ligand bioactivity data published in the literature are essential for drug discovery, yet manual curation struggles to keep pace with rapidly growing literature. Automated bioactivity extraction remains challenging because it requires not only interpreting biochemical semantics distributed across text, tables, and figures, but also reconstructing chemically exact ligand structures (e.g., Markush structures). To address this bottleneck, we introduce BioMiner, a multi-modal extraction framework that explicitly separates bioactivity semantic interpretation from ligand structure construction. Within BioMiner, bioactivity semantics are inferred through direct reasoning, while chemical structures are resolved via a chemical-structure-grounded visual semantic reasoning paradigm, in which multi-modal large language models operate on chemically grounded visual representations to infer inter-structure relationships, and exact molecular construction is delegated to domain chemistry tools. For rigorous evaluation and method development, we further establish BioVista, a comprehensive benchmark comprising 16,457 bioactivity entries curated from 500 publications. BioMiner validates its extraction ability and provides a quantitative baseline, achieving an F1 score of 0.32 for bioactivity triplets. BioMiner's practical utility is demonstrated via three applications: (1) extracting 82,262 data from 11,683 papers to build a pre-training database that improves downstream models performance by 3.9%; (2) enabling a human-in-the-loop workflow that doubles the number of high-quality NLRP3 bioactivity data, helping 38.6% improvement over 28 QSAR models and identification of 16 hit candidates with novel scaffolds; and (3) accelerating protein-ligand complex bioactivity annotation, achieving a 5.59-fold speed increase and 5.75% accuracy improvement over manual workflows in PoseBusters dataset.

Medication reconciliation at clinical handoffs is a high-stakes, error-prone process. Large language models are increasingly proposed to assist with this task using FHIR-structured patient records, but a fundamental and largely unstudied variable is how the FHIR data is serialised before being passed to the model. We present the first systematic comparison of four FHIR serialisation strategies (Raw JSON, Markdown Table, Clinical Narrative, and Chronological Timeline) across five open-weight models (Phi-3.5-mini, Mistral-7B, BioMistral-7B, Llama-3.1-8B, Llama-3.3-70B) on a controlled benchmark of 200 synthetic patients, totalling 4,000 inference runs. We find that serialisation strategy has a large, statistically significant effect on performance for models up to 8B parameters: Clinical Narrative outperforms Raw JSON by up to 19 F1 points for Mistral-7B (r = 0.617, p < 10^{-10}). This advantage reverses at 70B, where Raw JSON achieves the best mean F1 of 0.9956. In all 20 model and strategy combinations, mean precision exceeds mean recall: omission is the dominant failure mode, with models more often missing an active medication than fabricating one, which changes how clinical safety auditing priorities should be set. Smaller models plateau at roughly 7-10 concurrent active medications, leaving polypharmacy patients, the patients most at risk from reconciliation errors, systematically underserved. BioMistral-7B, a domain-pretrained model without instruction tuning, produces zero usable output in all conditions, showing that domain pretraining alone is not sufficient for structured extraction. These results offer practical, evidence-based format recommendations for clinical LLM deployment: Clinical Narrative for models up to 8B, Raw JSON for 70B and above. The complete pipeline is reproducible on open-source tools running on an AWS g6e.xlarge instance (NVIDIA L40S, 48 GB VRAM).

Accurate extraction of structured information from Safety Data Sheets (SDS) remains challenging in industrial safety due to heterogeneous document formats and the limitations of traditional rule-based methods. This study benchmarks state-of-the-art Large Language Models (LLMs) for automated SDS data extraction, comparing text-based and multimodal processing pipelines. We systematically evaluate four models: Gemini 1.5 Pro, GPT-4o, Claude 3.7 Sonnet, and Llama 3.1-70B, across three prompting strategies: zero-shot, few-shot, and chain-of-thought. The evaluation framework assessed accuracy, latency, and cost across more than 50,000 extracted data fields. Results show that text-based extraction consistently outperforms multimodal processing across all metrics. Gemini 1.5 Pro combined with a Chain-of-Thought prompt achieved the highest accuracy (84%), outperforming GPT-4o (81%) and Claude 3.7 Sonnet (79%). However, no model surpassed the 90% accuracy threshold commonly required for reliable real-world deployment. These findings indicate that general-purpose LLMs are not yet robust enough for unsupervised industrial use, though performance suggests strong potential with task-specific fine-tuning. Future research should focus on domain-adapted training, model calibration, and the integration of Human-in-the-Loop verification to ensure safety-critical reliability.

Knowledge Graph (KG) can effectively integrate valuable information from massive data, and thus has been rapidly developed and widely used in many fields. Traditional KG construction methods rely on manual annotation, which often consumes a lot of time and manpower. And KG construction schemes based on deep learning tend to have weak generalization capabilities. With the rapid development of Pre-trained Language Models (PLM), PLM has shown great potential in the field of KG construction. This paper provides a comprehensive review of recent research advances in the field of construction of KGs using PLM. In this paper, we explain how PLM can utilize its language understanding and generation capabilities to automatically extract key information for KGs, such as entities and relations, from textual data. In addition, We also propose a new Hyper-Relarional Knowledge Graph construction framework based on lightweight Large Language Model (LLM) named LLHKG and compares it with previous methods. Under our framework, the KG construction capability of lightweight LLM is comparable to GPT3.5.

Indistinguishability properties such as differential privacy bounds or low empirically measured membership inference are widely treated as proxies to show a model is sufficiently protected against broader memorization risks. However, we show that indistinguishability properties are neither sufficient nor necessary for preventing data extraction in LLM APIs. We formalize a privacy-game separation between extraction and indistinguishability-based privacy, showing that indistinguishability and inextractability are incomparable: upper-bounding distinguishability does not upper-bound extractability. To address this gap, we introduce $(l, b)$-inextractability as a definition that requires at least $2^b$ expected queries for any black-box adversary to induce the LLM API to emit a protected $l$-gram substring. We instantiate this via a worst-case extraction game and derive a rank-based extraction risk upper bound for targeted exact extraction, as well as extensions to cover untargeted and approximate extraction. The resulting estimator captures the extraction risk over multiple attack trials and prefix adaptations. We show that it can provide a tight and efficient estimation for standard greedy extraction and an upper bound on the probabilistic extraction risk given any decoding configuration. We empirically evaluate extractability across different models, clarifying its connection to distinguishability, demonstrating its advantage over existing extraction risk estimators, and providing actionable mitigation guidelines across model training, API access, and decoding configurations in LLM API deployment. Our code is publicly available at: https://github.com/Emory-AIMS/Inextractability.

Segment-level disclosures are a central component of financial reporting, providing insight into firms' internal organization and the allocation of economic activities across operating units. However, segment information is often presented in both qualitative and quantitative forms, dispersed across tables and narrative sections of Form 10-K filings. Empirical research relying on structured databases faces both completeness and comparability challenges, as some firm-year observations may be missing, nested segment disclosures are not captured, and support for longitudinal and cross-firm comparability is limited. This study develops a large language model-based framework to extract segment disclosures directly from Form 10-K filings and to preserve both reportable and nested segment information. We further design a retrieval augmented system that incorporates information across multiple filings to support comparability. We use two representative settings to demonstrate its application: longitudinal analysis within a firm to interpret segment changes over time, and cross firm alignment of geographic segments across firms with different reporting structures. The results indicate that the artifact accurately extracts segment-level information and effectively addresses questions that require cross-period knowledge, demonstrating the potential of LLM-based approaches to enhance the measurement and interpretation of segment disclosures.

Extracting clinically relevant information from unstructured medical narratives such as admission notes, discharge summaries, and emergency case histories remains a challenge in clinical natural language processing (NLP). Medical Entity Recognition (MER) identifies meaningful concepts embedded in these records. Recent advancements in large language models (LLMs) have shown competitive MER performance; however, evaluations often focus on general entity types, offering limited utility for real-world clinical needs requiring finer-grained extraction. To address this gap, we rigorously evaluated the open-source LLaMA3 model for fine-grained medical entity recognition across 18 clinically detailed categories. To optimize performance, we employed three learning paradigms: zero-shot, few-shot, and fine-tuning with Low-Rank Adaptation (LoRA). To further enhance few-shot learning, we introduced two example selection methods based on token- and sentence-level embedding similarity, utilizing a pre-trained BioBERT model. Unlike prior work assessing zero-shot and few-shot performance on proprietary models (e.g., GPT-4) or fine-tuning different architectures, we ensured methodological consistency by applying all strategies to a unified LLaMA3 backbone, enabling fair comparison across learning settings. Our results showed that fine-tuned LLaMA3 surpasses zero-shot and few-shot approaches by 63.11% and 35.63%, respectivel respectively, achieving an F1 score of 81.24% in granular medical entity extraction.

The interpretation of implicit meanings is an integral aspect of human communication. However, this framework may not transfer to interactions with Large Language Models (LLMs). To investigate this, we introduce the task of Implicit Information Extraction (IIE) and propose an LLM-based IIE pipeline that builds a structured knowledge graph from a context sentence by extracting relational triplets, validating implicit inferences, and analyzing temporal relations. We evaluate two LLMs against crowdsourced human judgments on two datasets. We find that humans agree with most model triplets yet consistently propose many additions, indicating limited coverage in current LLM-based IIE. Moreover, in our experiments, models appear to be more conservative about implicit inferences than humans in socially rich contexts, whereas humans become more conservative in shorter, fact-oriented contexts. Our code is available at https://github.com/Antonio-Dee/IIE_from_LLM.

Personal Knowledge Graphs (PKGs) offer a privacy-preserving framework for modeling user preferences, yet constructing them from unstructured, decentralized conversational data remains a challenge. This paper bridges the gap between conversational "strings" and semantic "things" by presenting a reproducible pipeline for extracting structured user-preference triples using lightweight Large Language Models. We evaluate Qwen- and Gemma-based models on their ability to extract RDF-compliant triples linked to Wikidata identifiers from conversational data for PKG construction. Our evaluation assesses both the semantic extraction fidelity and the utility of the resulting graphs in a downstream recommendation task. We found that certain models performed well and had proportionally high downstream performance relative to their triple extraction performance.

The accurate extraction of scientific measurements from literature is a critical yet challenging task in AI4Science, enabling large-scale analysis and integration of quantitative research findings. However, Large Language Models (LLMs) frequently exhibit severe hallucinations, which significantly undermine the reliability of automated scientific document understanding systems. To address this problem, we propose MeasHalu, a novel framework for mitigating scientific measurement hallucinations through enhanced reasoning and targeted optimization. We first present a fine-grained taxonomy of measurement-specific hallucinations, categorizing errors across quantities, units, modifiers, and relations. Our approach incorporates a two-stage reasoning-aware fine-tuning strategy using augmented scientific data and process-based supervision. Furthermore, we introduce a progressive reward curriculum designed to penalize specific hallucination types, significantly improving extraction faithfulness. Experimental results demonstrate that MeasHalu substantially reduces hallucination rates and improves overall accuracy on the MeasEval benchmark. This work provides a targeted solution to a key bottleneck in automated scientific knowledge extraction, facilitating more trustworthy and scalable machine-assisted scientific literature analysis.

Urgent blood donation seeking posts and messages on social media often go unnoticed due to the overwhelming volume of daily communications. Traditional app-based systems, reliant on manual input, struggle to reach users in low-resource settings, delaying critical responses. To address this, we introduce the Cognitive Blood Request System (CBRS), a multi-platform framework that efficiently filters and parses blood donation requests from social media streams using a cost-efficient dual-layered architecture. To do so, we curate a novel dataset of 11K parsed blood donation request messages in Bengali, English, and transliterated Bengali, capturing the linguistic diversity of real social media communications. The inclusion of adversarial negatives further enhances the robustness of our model. CBRS achieves an impressive 99% accuracy and precision in filtering, surpassing benchmark methods. In the parsing task, our LoRA finetuned Llama-3.2-3B model achieves 92% zero-shot accuracy, surpassing the base model by 41.54% and exceeding the few-shot performance of GPT-4o-mini, Gemini-2.0-Flash, and other LLMs, while resulting in a 35X reduction in input token usage. This work lays a robust foundation for scalable, inclusive information extraction in time-sensitive, object-focused tasks. Our code, dataset, and trained models are publicly available at https://github.com/aaniksahaa/CBRS.

Large language models (LLMs) have advanced information extraction (IE) by enabling zero-shot and few-shot named entity recognition (NER), yet their generative outputs still show persistent and systematic errors. Despite progress through instruction fine-tuning, zero-shot NER still lags far behind supervised systems. These recurring errors mirror inconsistencies observed in early-stage human annotation processes that resolve disagreements through pilot annotation. Motivated by this analogy, we introduce DiZiNER (Disagreement-guided Instruction Refinement via Pilot Annotation Simulation for Zero-shot Named Entity Recognition), a framework that simulates the pilot annotation process, employing LLMs to act as both annotators and supervisors. Multiple heterogeneous LLMs annotate shared texts, and a supervisor model analyzes inter-model disagreements to refine task instructions. Across 18 benchmarks, DiZiNER achieves zero-shot SOTA results on 14 datasets, improving prior bests by +8.0 F1 and reducing the zero-shot to supervised gap by over +11 points. It also consistently outperforms its supervisor, GPT-5 mini, indicating that improvements stem from disagreement-guided instruction refinement rather than model capacity. Pairwise agreement between models shows a strong correlation with NER performance, further supporting this finding.

Information Extraction aims to distill structured, decision-relevant information from unstructured text, serving as a foundation for downstream understanding and reasoning. However, it is traditionally treated merely as a terminal objective: once extracted, the resulting structure is often consumed in isolation rather than maintained and reused during multi-step inference. Moving beyond this, we propose \textit{IE-as-Cache}, a framework that repurposes IE as a cognitive cache to enhance agentic reasoning. Drawing inspiration from hierarchical computer memory, our approach combines query-driven extraction with cache-aware reasoning to dynamically maintain compact intermediate information and filter noise. Experiments on challenging benchmarks across diverse LLMs demonstrate significant improvements in reasoning accuracy, indicating that IE can be effectively repurposed as a reusable cognitive resource and offering a promising direction for future research on downstream uses of IE.

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

Scientific discovery is slowed by fragmented literature that requires excessive human effort to gather, analyze, and understand. AI tools, including autonomous summarization and question answering, have been developed to aid in understanding scientific literature. However, these tools lack the structured, multi-step approach necessary for extracting deep insights from scientific literature. Large Language Models (LLMs) offer new possibilities for literature analysis, but remain unreliable due to hallucinations and incomplete extraction. We introduce Elhuyar, a multi-agent, human-in-the-loop system that integrates LLMs, structured AI, and human scientists to extract, analyze, and iteratively refine insights from scientific literature. The framework distributes tasks among specialized agents for filtering papers, extracting data, fitting models, and summarizing findings, with human oversight ensuring reliability. The system generates structured reports with extracted data, visualizations, model equations, and text summaries, enabling deeper inquiry through iterative refinement. Deployed in materials science, it analyzed literature on tungsten under helium-ion irradiation, showing experimentally correlated exponential helium bubble growth with irradiation dose and temperature, offering insight for plasma-facing materials (PFMs) in fusion reactors. This demonstrates how AI-assisted literature review can uncover scientific patterns and accelerate discovery.

Maritime distress communications transmitted over very high frequency (VHF) radio are safety-critical voice messages used to report emergencies at sea. Under the Global Maritime Distress and Safety System (GMDSS), such messages follow standardized procedures and are expected to convey essential details, including vessel identity, position, nature of the distress, and required assistance. In practice, however, automatic analysis remains difficult because distress messages are often brief, noisy, and produced under stress, may deviate from the prescribed format, and are further degraded by automatic speech recognition (ASR) errors caused by channel noise and speaker stress. This paper presents SeaAlert, a controlled experimental framework for evaluating robust analysis of maritime distress communications using transformer-based severity classification and LLM-based structured extraction. To address the scarcity of labeled real-world data, we develop a synthetic data generation pipeline in which an LLM produces diverse maritime messages, including challenging variants in which standard distress codewords are omitted or replaced with less explicit expressions. The generated utterances are synthesized into speech, degraded with simulated VHF noise, and transcribed by an ASR system to obtain controlled noise-degraded transcripts. The resulting evaluation shows that transformer-based classification degrades more gracefully than lexical baselines under ASR noise and codeword masking, while LLM-based extraction is more effective than Regex-based extraction for noisy structured fields.

Accurate extraction of Alzheimer's Disease and Related Dementias (ADRD) phenotypes from electronic health records (EHR) is critical for early-stage detection and disease staging. However, this information is usually embedded in unstructured textual data rather than tabular data, making it difficult to be extracted accurately. We therefore propose LLM-MINE, a Large Language Model-based phenotype mining framework for automatic extraction of ADRD phenotypes from clinical notes. Using two expert-defined phenotype lists, we evaluate the extracted phenotypes by examining their statistical significance across cohorts and their utility for unsupervised disease staging. Chi-square analyses confirm statistically significant phenotype differences across cohorts, with memory impairment being the strongest discriminator. Few-shot prompting with the combined phenotype lists achieves the best clustering performance (ARI=0.290, NMI=0.232), substantially outperforming biomedical NER and dictionary-based baselines. Our results demonstrate that LLM-based phenotype extraction is a promising tool for discovering clinically meaningful ADRD signals from unstructured notes.

Document-level Information Extraction (DocIE) aims to produce an output template with the entities, relations, and events of interest occurring in the given document. Standard practices include prompting decoder-only LLMs using greedy decoding to avoid output variability. Rather than treating this variability as a limitation, we show that sampling can produce substantially better solutions than greedy decoding, especially when using reasoning models. We thus propose ThinkTwice, a sampling and selection framework in which the LLM generates multiple candidate templates for a given document, and a selection module chooses the most suitable one. We introduce both an unsupervised method that exploits agreement across generated outputs, and a supervised selection method using reward models trained on labeled DocIE data. To address the scarcity of golden reasoning trajectories for DocIE, we propose a rejection-sampling-based method to generate silver training data that pairs output templates with reasoning traces. Our experiments show the validity of unsupervised and supervised ThinkTwice, consistently outperforming greedy baselines and the supervised state-of-the-art.

Large language models (LLMs) are increasingly used for text analysis tasks, such as named entity recognition or error detection. Unlike encoder-based models, however, generative architectures lack an explicit mechanism to refer to specific parts of their input. This leads to a variety of ad-hoc prompting strategies for span labeling, often with inconsistent results. In this paper, we categorize these strategies into three families: tagging the input text, indexing numerical positions of spans, and matching span content. To address the limitations of content matching, we introduce LogitMatch, a new constrained decoding method that forces the model's output to align with valid input spans. We evaluate all methods across four diverse tasks. We find that while tagging remains a robust baseline, LogitMatch improves upon competitive matching-based methods by eliminating span matching issues and outperforms other strategies in some setups.

Wide access to advanced experimental methods in materials science has given rise to an abundance of procedural knowledge, which is scattered across decades of scientific literature and recorded in unstructured formats that are challenging to analyze systematically. In this work, we present LeMat-Synth Parser, a modular, open-source, and multi-modal extraction toolbox that utilizes large language models (LLMs) and vision language models (VLMs) to automatically structure synthesis protocols and performance metrics extracted from both text and figures of publications. Applying LeMat-Synth Parser to 81K open-access publications, we curate LeMat-Synth, an extensive dataset of 58K synthesis procedures and to our knowledge the largest and most diverse structured inorganic materials synthesis dataset to date, covering 35 synthesis methods and 16 material classes based on a domain-specific ontology. We validate extraction quality against annotations by domain experts and a scalable LLM-as-a-judge framework, and benchmark a suite of models to identify optimal configurations and characterize cross-model biases. To demonstrate the extensibility of LeMat-Synth Parser, we apply it to two distinct domains. First, we link synthesis protocols and catalyst identity to thermocatalytic performance across a corpus of ammonia-decomposition publications. Second, we cross-validate text- and figure-reported critical transition temperatures across 1,384 superconductivity papers, then use the validated pipeline to recover the critical transition temperature for every composition in a sample series. We release LeMat-Synth Parser and the LeMat-Synth dataset openly on GitHub and Hugging Face