Relation_Extraction
-
Calibrated Typed Decisions for Entity, Relation, and Event Extraction
2026-10-12 17:05:20Yang Wang, Hanlin Xiao, Yanan Ma, Chenghao Xiao, Chenghua LinAbstract
Information extraction models often perform well on the datasets they are trained on, but transferring to new domains and annotation guidelines remains challenging. Supporting user-specified types alone does not resolve this problem. We present CalOn, a unified 0.6B-parameter encoder for entity, relation, and event extraction across datasets and schemas. The model jointly encodes text and type definitions, then directly identifies entity spans, relations between spans, and event triggers and arguments. Its extraction decisions consider the requested types together, using their combined evidence to identify relevant candidates before assigning a type. This gives all three tasks a common probabilistic formulation while keeping every extracted mention anchored to the input text. We train on diverse sources, and supplement supervised learning with a reward that encourages correct extractions and penalises incorrect ones. Across 40 benchmarks, CalOn outperforms the evaluated baselines on most benchmarks. It leads all reported relation extraction benchmarks and achieves the highest average F1 for event triggers and arguments with gold triggers. The same model also performs strongly on aspect sentiment triplet extraction and pronoun resolution through its span-pair formulation. A correction for the probability bias introduced during training improves confidence estimates for entities, relations, and event arguments after calibration, with little change in F1.
Abstract (translated)
URL
https://arxiv.org/abs/2610.17113
PDF
-
U4RASD at KnowledgeGraphEval-2026: Ontology-Constrained Encoder and LLM Systems for Arabic Relation Extraction
2026-10-08 21:41:29Ahmad Abbas, Hussein Mazeh, Chadi Abou Chakra, Aya Jouni, Mohammad Ballout, Fadi A. ZaraketAbstract
This paper details our submission to KnowledgeGraphEval 2026 Subtask 2 on directed Arabic relation extraction. We explored encoder-based and large language model approaches for predicting one of 40 relations or no_relation from an Arabic sentence and a subject-object pair. Our encoder systems use typed entity markers and separate relation-existence and relation-classification heads, while our LLM systems fine-tune Yehia and Qwen3.5 with QLoRA and ontology-constrained prediction. Our best system, an ensemble of Yehia-RE, Qwen-RE, and TypedPair, achieved a micro-F1 score of 94.06 and ranked 1st in Subtask 2. Yehia-RE (full-vocabulary) achieved 92.98, while the best encoder and Qwen-RE achieved 92.69 and 91.94 respectively. Our results highlight the importance of constrained prediction and complementary modeling approaches for Arabic relation extraction.
Abstract (translated)
URL
https://arxiv.org/abs/2610.12742
PDF
-
BioBigBird: A Sparse Attention Model for Long-Range Dependency Processing in Biomedical Text
2026-10-08 07:54:12Roshan Balaji, Pavan Kumar S, Vasudev Gupta, Sreejith N, Keerthana Sridhar, Nirav BhattAbstract
While domain-specific Large Language Models (LLMs) have encoded vast biomedical knowledge, their limited context windows often hinder a deep understanding of nuanced relationships within and across texts. To address this limitation, we introduce BioBigBird, a bidirectional language model pre-trained on extensive biomedical literature and clinical data, specifically designed to handle long-range dependencies. BioBigBird leverages a sparse attention mechanism to process sequences up to 4096 tokens, and its training incorporates a multi-stage process to mitigate noise from the large-scale pre-training corpus. We further enhance its performance by employing a multi-task learning (MTL) framework that jointly optimizes for Named Entity Recognition and Relation Extraction. Comprehensive evaluations on the BLURB benchmark reveal that our MTL-enhanced BioBigBird achieves highly competitive results against state-of-the-art models. Our work contributes an effective methodology for developing powerful, long-context language models for specialized domains, demonstrating the value of extended sequence processing for complex text analysis. Our models are publicly available at this https URL.
Abstract (translated)
URL
https://arxiv.org/abs/2610.11430
PDF
-
Domain-Adaptive Pretraining Enhances Water Treatment Semantic Representation for Large-Scale Structured Literature Mining
2026-09-22 11:33:41Mudi Zhai (UNSW Water Research Centre, School of Civil and Environmental Engineering, The University of New South Wales, Sydney, NSW 2052, Australia), Ruihong Qiu (School of Electrical Engineering and Computer Science, The University of Queensland, Brisbane, QLD 4072, Australia), Qingyun Zeng (Microsoft Copilot Studio AI, Redmond, WA 98052, United States, Departments of Mathematics & Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA 19104, United States), T. David Waite (UNSW Water Research Centre, School of Civil and Environmental Engineering, The University of New South Wales, Sydney, NSW 2052, Australia), Bing-Jie Ni (UNSW Water Research Centre, School of Civil and Environmental Engineering, The University of New South Wales, Sydney, NSW 2052, Australia), Haoran Duan (UNSW Water Research Centre, School of Civil and Environmental Engineering, The University of New South Wales, Sydney, NSW 2052, Australia, Department of Civil Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China)Abstract
Water treatment research is expanding rapidly, but much of the knowledge acquired from this research remains scattered across unstructured literature. The field still lacks a dedicated language model that can efficiently capture water treatment-specific domain semantics for large-scale literature mining. Here, we address this by developing WaterBERT, a domain-adapted encoder model designed for semantic representation and structured information extraction from water treatment texts. WaterBERT was developed by continual pretraining on a large-scale water treatment corpus comprising about 2.97 billion tokens. Three fine-tuned models based on WaterBERT were systematically evaluated on downstream tasks, achieving the best overall performance among general-purpose and domain-specific BERT models, with F1 scores of 90.12% for multiclass treatment process classification, 79.50% for named entity recognition, and 74.04% for relation extraction. Beyond these benchmark tasks, we further demonstrated WaterBERT's advantages for large-scale literature processing. Applied to 5,144 Environmental Science & Technology articles, WaterBERT-BERTopic identified coherent, diverse, and domain-specific research topics without predefined categories. Building on WaterBERT, we processed 693,211 abstracts at substantially lower cost than commercial LLMs while retaining competitive extraction performance to construct a structured water treatment knowledge graph. The knowledge graph was then integrated with lexical and dense retrieval to develop a Water Knowledge-Enhanced Retrieval System (WaterKERS), which achieved a relevance score of 77.7, substantially outperforming text-based retrieval baselines (54.7-64.5). Through WaterBERT, this study provides a compact and scalable semantic foundation for large-scale information processing and evidence mapping in water treatment research.
Abstract (translated)
URL
https://arxiv.org/abs/2609.26034
PDF
-
CAD-Based Relation Learning and Geometric-Symbolic Planning for Robotic Assembly
2026-09-15 14:43:25Fabian Harlacher, Christian FriedrichAbstract
Assembly Sequence Planning (ASP) remains a challenging problem due to its combinatorial nature, making exhaustive planning approaches impractical for complex industrial assemblies. Furthermore, many CAD models lack reliable semantic contact information or require extensive manual preprocessing, limiting the applicability of existing methods. This paper presents a hybrid ASP framework combining learning-based relation extraction with geometric-symbolic reasoning to generate feasible robotic disassembly sequences from imperfect CAD data. A neural network predicts semantic geometric relations from point clouds, while human-in-the-loop verification enables correction of uncertain predictions and planning failures. Extracted relations are transformed into a symbolic assembly graph, enabling a geometric-symbolic planner to efficiently compute locally valid sets of robotic manipulation primitives. A visibility-based ray-casting strategy guides the search for feasible disassembly directions without requiring an exhaustive combinatorial search, while the local solution space enables efficient sequence optimization. The framework is evaluated on an introduced assembly dataset and on the ASAP test dataset. On the ASAP test dataset, the proposed planner achieves an 85.83% planning success rate while reducing the median planning time by more than one order of magnitude across all assembly sizes and by more than a factor of 50 for assemblies with more than 30 components compared to the baseline. The results demonstrate that the proposed hybrid framework enables efficient robotic assembly sequence planning from imperfect CAD data while substantially reducing planning time. By combining learning-based feature segmentation, human-in-the-loop verification, and geometric-symbolic reasoning, the framework provides a practical foundation for scalable and adaptable robotic assembly and disassembly planning.
Abstract (translated)
URL
https://arxiv.org/abs/2609.17263
PDF
-
CMNIE: An Information Extraction Benchmark for Chinese Military News
2026-09-09 18:16:08Yan Yu, Mengna Zhu, Zhenyu Song, Hao Yang, Haiwen Chen, Mao WangAbstract
Structured extraction from Chinese military news supports intelligence analysis, decision-making, and knowledge base construction. However, existing resources provide limited support for joint informa?tion extraction in this domain, especially when events, event arguments, entities, and relations must be modeled together. We present CMNIE, an information extraction benchmark for Chinese military news. Extend?ing military-domain resources beyond document-level event annotations, CMNIE jointly annotates event triggers, event arguments, named enti?ties, and entity relations under a unified domain schema. The dataset contains 13,000 instances collected from public Chinese military news, with manual annotations for 7 event types, 10 argument roles, 7 entity types, and 8 relation types. We evaluate supervised IE models, zero-shot large language models, and fine-tuned LLM-based extraction methods on a shared test set. Experimental results show that CMNIE remains chal?lenging, especially for relation extraction and exact matching of event?argument spans; zero-shot LLMs often identify relevant semantic units but fail to match gold span boundaries exactly. CMNIE provides a stan?dardized benchmark for studying schema adherence, exact span match?ing, and joint structured extraction in specialized Chinese news.
Abstract (translated)
URL
https://arxiv.org/abs/2609.10722
PDF
-
Event Interaction in Low-Rank Bottlenecks for Temporal Relation Extraction
2026-09-06 17:03:18Wei Sun, Tingyu Qu, Jesse Davis, Marie-Francine MoensAbstract
Temporal relation extraction determines whether an event occurs before, after, or simultaneously with another event, and therefore relies on accurately modeling how the two events interact. Mainstream systems achieve this by concatenating event spans or using shallow fusion, which works well when all model parameters are trainable. However, in parameter-efficient fine-tuning, low-rank bottlenecks restrict information flow and prevent these interaction signals from passing through, leading to clear performance drops. To address this limitation, we propose a theoretically grounded architecture, Convolutional Bottleneck Interaction (CBI), which first applies lightweight depthwise convolution to enhance event representations and then uses element-wise multiplication to capture effective event-event interactions inside the bottleneck. Across five datasets and seven backbone models in the Adapter and LoRA settings, CBI provides consistent and substantial gains, up to +31.7 micro F1, while adding minimal computational cost, showing that explicit interaction inside low-rank spaces is crucial for temporal relation extraction. The code is available at this https URL.
Abstract (translated)
URL
https://arxiv.org/abs/2609.06731
PDF
-
TWIX: a Two-Stage Approach for End-To-End Named Entity Recognition and Relation Extraction
2026-09-01 07:33:21Marco Martinelli, Laura MenottiAbstract
The exponential growth of scientific publications calls for automatic Information Extraction (IE) systems to support knowledge discovery. In this context, the GutBrainIE benchmark evaluates Named Entity Recognition (NER), Named Entity Recognition and Disambiguation (NERD), and Relation Extraction (RE) systems in the gut-brain axis domain. We propose Two-stage Workflow for Information eXtraction (TWIX), an end-to-end IE pipeline featuring three interconnected modules, each leveraging a two-stage framework to solve all four GutBrainIE subtasks. Evaluation on the development and test sets shows that our method substantially outperforms the baseline by a wide margin, while also ranking first among all participant submissions across all subtasks. These results indicate that the proposed two-stage pipeline effectively improves both precision and recall in practical settings.
Abstract (translated)
URL
https://arxiv.org/abs/2609.00832
PDF
-
Automated Tree Knowledge Graph Construction using Ontology Expansion and Retrieval from Vietnamese History Textbooks
2026-09-01 05:52:50Ket Doan Nguyen, Minh N. H. NguyenAbstract
Hierarchical Knowledge graph (KG)-based retrieval augmented generation (RAG) has emerged as a powerful approach for supporting large language models with structured knowledge. However, there are primary challenges: (i) the lack of methods for automatic KG construction using ontology expansion for low-resource languages such as Vietnamese, (ii) the absence of systematic evaluation for knowledge retrieval strategies leveraging the hierarchical structures. In this paper, we propose an end-to-end pipeline for KG construction and retrieval strategies evaluation. In the KG construction, we employ a three-phase hybrid relation extraction pipeline: intra-batch deduplication via Union-Find, approximate cross-batch search, and LLM extraction with a centroid filter that reduces prompts combined with a five-step dual-LLM validator to prevent bloated ontology. A two-tier architecture consists of unmergeable structural nodes to preserve the document structure and mergeable content nodes. The retrieval evaluation consists of three graph traversal strategies: Top-Down, Horizontal, and Bottom-Up, which are evaluated on a synthetically generated benchmark of 1,210 Vietnamese queries from 109 subgraphs, categorized by five query directions. In this paper, we construct the tree knowledge graph from Vietnamese high school History textbooks (nearly 400 pages) to produce 750 nodes and 4,341 semantic edges with controlled ontology growth from 40 to 41 types. Among experimental graph traversal strategies, the Top-Down strategy with structure surpasses the vector baseline by 4.7 percentage points in NDCG@10. As a result, tree-structural information provides valuable information beyond flat cosine similarity but degrades performance when the query does not require structural context.
Abstract (translated)
URL
https://arxiv.org/abs/2609.00763
PDF
-
Configurable Semantic Chunking for Biomedical Information Extraction in Retrieval-Augmented Generation
2026-08-31 17:44:54Riya Ahuja (Institute of Data Science in Biomedicine, TU Braunschweig, Braunschweig, Germany, Braunschweig Integrated Centre of Systems Biology, TU Braunschweig, Braunschweig, Germany), Tim Kacprowski (Institute of Data Science in Biomedicine, TU Braunschweig, Braunschweig, Germany, Braunschweig Integrated Centre of Systems Biology, TU Braunschweig, Braunschweig, Germany), Roya Shiasi Sardoabi (Institute of Data Science in Biomedicine, TU Braunschweig, Braunschweig, Germany, Braunschweig Integrated Centre of Systems Biology, TU Braunschweig, Braunschweig, Germany)Abstract
BioMedRAG introduced retrieval-augmented generation with a learned chunk scorer for biomedical information extraction. However, it relies on fixed-size chunking which can fragment semantic evidence. We propose a configurable semantic chunking framework that addresses this limitation by combining entity-preserving windows, trigger-centered chunking, proposition-first extraction, tiered trigger prioritization, and hierarchical relation resolution. The framework integrates with BioMedRAG by replacing only the chunk construction stage while preserving the embedding model, learned chunk scorer, generator, and evaluation protocol. We evaluate the framework on biomedical relation extraction benchmarks (GM-CIHT, DDI, ChemProt) and adverse event classification (ADE). On GM-CIHT, the full hybrid configuration achieves 82.6% F1, improving over the fixed-size baseline (74.2% F1) by 8.4 points under our experimental setup. Cross-dataset analysis shows that semantic chunking improves extraction datasets with explicit relation cues, such as GM-CIHT and DDI, while fixed chunking remains competitive or stronger for dense biochemical extraction and binary classification settings such as ChemProt and ADE. By externalizing chunking logic into configuration files, the framework provides an interpretable and adaptable alternative to rigid fixed-size chunking for biomedical RAG pipelines.
Abstract (translated)
URL
https://arxiv.org/abs/2608.31139
PDF
-
MiNER: Fine-Tuned Biomedical Natural Language Processing for Malaria Disease Entity Recognition in Clinical Texts
2026-08-31 06:54:27V. S. Anoop, Devika NAbstract
Malaria remains a significant global health burden, necessitating continuous research efforts to understand its complex molecular mechanisms, epidemiology, and potential therapeutic interventions. Extracting essential biomedical information from the vast and constantly growing malaria literature is a challenging task that demands innovative approaches. Recently, pre-trained language models have revolutionized natural language processing tasks, demonstrating remarkable capabilities in various domains. This paper proposes a fine-tuned pre-trained biomedical language model for biomedical information extraction from scientific literature on malaria disease. The proposed methodology selects and preprocesses a large corpus of scientific articles on malaria, and then annotates them with entities of clinical significance. It then leverages BioBERT, a state-of-the-art pre-trained language model, to encode the textual data into context-aware representations. We fine-tune the model using domain-specific annotations and supervised learning to enhance its ability to extract relevant biomedical named entities. Extensive experiments and comparisons with different encoding and machine learning algorithms show that the proposed approach significantly outperforms them in precision, recall, and accuracy. We also publish our human-labeled dataset for entity and relation extraction to enable other health informatics researchers to train advanced models for malaria information extraction.
Abstract (translated)
URL
https://arxiv.org/abs/2609.00073
PDF
-
Ontology-Driven Structural Regularization for Document-Level Relation Extraction
2026-08-21 08:22:42Laura Menotti, Stefano Marchesin, Gianmaria SilvelloAbstract
Document-Level Relation Extraction (DocRE) relies heavily on costly manually annotated datasets, while large distant supervision resources such as DocRED distant remain underexploited due to noise. We show that a critical yet overlooked source of noise lies in structural inconsistencies within relational triples, including violations of ontology constraints and logical contradictions. We introduce an ontology-driven framework to quantify and enforce structural consistency in DocRE datasets. Our analysis reveals substantial structural noise in DocRED distant and demonstrates that such inconsistencies propagate to model predictions. Enforcing structural well-formedness during training significantly reduces logical contradictions and consistently improves generalization performance. These findings establish structural consistency as a missing axis of supervision in DocRE and highlight structural regularization as an effective strategy for leveraging distant data at scale.
Abstract (translated)
URL
https://arxiv.org/abs/2608.20856
PDF
-
ViTOED: A Dataset for Target-Oriented Emotion Detection on Vietnamese Social Media Texts
2026-08-13 03:35:14Chanh Vo, Son T. Luu, Ngan Luu-Thuy NguyenAbstract
This paper introduces ViTOED, a novel dataset for target-oriented emotion detection in Vietnamese social media texts. The ViTOED comprises 10,985 user comments and 21,244 manually annotated opinion quadruples (source, target, expression, polarity) that follow strict guidelines. The dataset reveals Vietnamese-specific phenomena, such as implicit sources and targets and vocabulary ambiguities, enabling deeper analysis of user emotions toward entities. We propose a baseline using structured sentiment graphs and evaluate various Vietnamese pre-trained language models. The empirical results highlight challenges in span detection and relation extraction and indicate substantial room for model improvement in Vietnamese Target-Oriented Emotion Detection tasks.
Abstract (translated)
URL
https://arxiv.org/abs/2608.12776
PDF
-
Integrated Multimodal AI System for Retrieval-Augmented Reasoning, Object Sensing, and Damage Analysis
2026-08-09 21:53:37Kalelo Dukuray, Israel Pina, Evan Perez, Erika Ardiles-Cruz, Jie WeiAbstract
This work presents a unified multimodal AI system for damage assessment that integrates retrieval-augmented generation (RAG) models, thermal spectrum perception, vision foundation model pipelines, and exploratory wireless signal sensing. A RAG component is developed to ground a locally hosted language model in project-specific documentation, including specialized damage level classification criteria to mitigate hallucinations during inference. Controlled comparisons against static few-shot prompting demonstrate that dynamic retrieval improves grounding and factual consistency. We further compare vector-based RAG with a knowledge graph variant constructed via entity-relation extraction, and show that graph-based retrieval produces stronger responses for damage assessment queries requiring cross-document reasoning, motivating hybrid dense, sparse, and graph-aware retrieval. To address limitations of EO imagery under adverse lighting and weather conditions, infrared (IR)/thermal sensing is employed for object detection and segmentation. Our detectors generate candidate detections, yielding improved segmentation of a broad array of objects. Paired IR versus visible spectrum tracking experiments reveal failure modes, motivating multimodal fusion for robust object detection and damage analysis. Vision foundation and vision-language models are leveraged to generate synthetic damage imagery and classify damage severity with high accuracy, supporting training and validation of downstream damage assessment models. Finally, exploratory Wireless-based sensing demonstrates potential to detect presence, motion, and post-event environmental changes where EO and IR sensing are ineffective.
Abstract (translated)
URL
https://arxiv.org/abs/2608.08935
PDF
-
A Grounded and Decomposed Framework for Relation-Level Hallucination Evaluation in Abstractive Summarization
2026-08-08 15:16:51Praveen Kumar Katwe, Rakesh Chandra Balabantaray, Kali Prasad Vittala, Naman KabadiAbstract
Abstractive text summarization systems frequently generate fluent yet unfaithful summaries by fabricating or distorting relationships between entities and events. Such relation-level hallucinations undermine the reliability of generated summaries, particularly in high-stakes domains. In this work, we present a refined and grounded framework for evaluating relation hallucination in abstractive summarization. We present the empirical Relation Hallucination Index (RHI) by introducing a dependency-aware relation extraction algorithm that incorporates lemmatization-based normalization, named entity grounded subject resolution, passive agent recovery, negation-aware verb modeling, reporting verb filtering, nominal relation fallback, clausal propagation, and systematic deduplication. These enhancements improve the structural fidelity of extracted relation triples and reduce spurious matches during evaluation. In addition, we introduce a normalized formulation of RHI to ensure scale-invariant comparison between datasets and models. The revised metric decomposes hallucination into interpretable components, aggregates relation hallucination metric into a normalized relation faithfulness score. Extensive evaluation across multiple state-of-the-art summarization models demonstrates that the grounded extraction process yields more stable and discriminative hallucination measurements. The proposed framework advances automated relation-level faithfulness evaluation and supports coherence-aware, hallucination-sensitive model analysis.
Abstract (translated)
URL
https://arxiv.org/abs/2608.08180
PDF
-
UG-UMRE: Uncertainty-Guided Modality Augmentation and Distributional Calibration for Unified Multimodal Relation Extraction
2026-08-05 15:18:16Bo Kong, Liruiz Jia, Yi Liang, Chao Liu, Dongfang Han, Tianwei Yan, Yuan Liu, Shengquan LiuAbstract
Unified Multimodal Relation Extraction (UMRE) aims to identify intra-modal and cross-modal relations between textual entities and visual objects. However, existing UMRE studies still encounter two critical issues: ignoring inherent aleatoric uncertainty causes noise propagation, and deep-seated heterogeneity between distinct modal distributions hinders alignment. To address these issues, we propose the Uncertainty-Guided UMRE Network (UG-UMRE). Specifically, we design an Uncertainty-Driven Unimodal Augmentation (UDUA) module, which models features as Gaussian distributions based on the Variational Information Bottleneck. By incorporating an uncertainty-aware self-supervised contrastive learning mechanism, UDUA effectively filters out noise while maintaining semantic consistency. Furthermore, we introduce the Joint Aleatoric Uncertainty Alignment (JAUA) module as a global semantic pre-calibration mechanism. JAUA leverages probabilistic distribution consistency to construct a shared latent space, eliminating the distributional gap by synchronizing cross-modal statistical properties, thereby laying a robust foundation for fine-grained interaction. Experiments on three benchmark datasets (UMRE, MORE, and MNRE) demonstrate that UG-UMRE achieves state-of-the-art performance. Further analysis validates the pluggable and effective performance of the proposed UDUA and JAUA modules.
Abstract (translated)
URL
https://arxiv.org/abs/2608.04949
PDF
-
ANCHOR-RE: An Agentic Neuro-Symbolic Framework for Grounded Biomedical Relation Extraction
2026-08-04 05:36:19Shufan Ming, Yikun Han, Gibong Hong, Rui Zhang, Halil KilicogluAbstract
Biomedical relation extraction (BioRE) extracts structured knowledge from biomedical literature for applications such as knowledge base construction and hypothesis generation. Traditional symbolic systems such as SemRep provide high precision but limited recall, while large language models (LLMs) offer stronger contextual reasoning but remain prone to false-positive predictions. We developed ANCHOR-RE, a framework that integrates ontology-guided reasoning, external knowledge grounding, and data-driven verification rules into LLM inference. We evaluated it on three BioRE benchmarks (SemRepGS, DDI, and ChemProt) using both proprietary and open-weight LLMs. To assess generalizability beyond benchmark datasets while reducing potential evaluation bias from LLM pretraining contamination, we conducted a temporal evaluation using 100 biomedical articles published in 2026. With the proprietary backbone, ANCHOR-RE outperformed direct LLM prompting, improving micro-F1 from 0.654 to 0.676 on SemRepGS, from 0.769 to 0.872 on DDI, and from 0.939 to 0.941 on ChemProt. On DDI and ChemProt, it also outperformed previously reported inference-only methods and approached fine-tuned or instruction-tuned systems without parameter updates. Similar performance gains observed with open-weight LLMs indicate that the benefits were not limited to the proprietary backbone. On the post-cutoff set, manual assessment of 500 randomly sampled predictions yielded a precision of 69%, maintaining consistent precision on previously unseen biomedical literature. Neuro-symbolic reasoning can improve the reliability of LLM-based BioRE without fine-tuning. Results across multiple benchmarks, model families, and post-cutoff literature support ANCHOR-RE as a practical training-free approach to biomedical literature mining.
Abstract (translated)
URL
https://arxiv.org/abs/2608.03154
PDF
-
CONSISTRE: A Unified Consistency-Aware Framework for Document-Level Relation Extraction with Large Language Models
2026-07-27 11:56:29Mingxuan SunAbstract
Document-level relation extraction (DocRE) aims to extract relations among multiple entities across extended contexts while maintaining consistency across predicted triples. Although large language models (LLMs) show remarkable reasoning capabilities in information extraction, their predictions are typically generated independently for each candidate triple and may violate fundamental relational constraints such as transitivity, symmetry, and functional uniqueness, leading to contradictory and unreliable outputs. We propose CONSISTRE, a unified consistency-aware framework for DocRE that addresses this limitation through two complementary tracks. The first operates at inference time for black-box LLMs, combining constraint-aware prompting, constraint-based verification, and iterative self-reflection to refine predictions without task-specific fine-tuning. The second injects consistency knowledge into smaller open-source models via a knowledge distillation and reinforcement learning pipeline: reasoning traces from a powerful teacher are distilled into a student via supervised fine-tuning, followed by GRPO alignment using a composite reward that jointly optimizes extraction performance and relational consistency. Together, the two tracks cover both API-accessible and locally deployable scenarios under a unified consistency formulation. Experiments on DocRED show that both tracks outperform their baselines, with the inference-time track achieving competitive F1 using off-the-shelf black-box LLMs and the training-time track substantially narrowing the gap between 7--8B open-source models and state-of-the-art proprietary LLMs at a fraction of their inference cost. Ablation studies confirm that explicit consistency modeling mitigates relational contradictions and enhances the reliability of LLM-based DocRE across both deployment paradigms.
Abstract (translated)
URL
https://arxiv.org/abs/2607.24312
PDF
-
LA-RL: Label-Aware Self-Reflection for Reinforcement Learning in Information Extraction
2026-07-26 02:35:47Xiao You, Tianwei Yan, Zixu Shan, Longyu Du, Shan ZhaoAbstract
Large language models show strong promise for information extraction (IE), but existing reflection-based correction methods are often misaligned with structured extraction outputs. Free-form self-reflection can flag an error, yet it rarely identifies whether the failure is a missing span, wrong label, boundary mismatch, invalid relation type, or reversed argument order. We introduce LA-RL (Label-Aware Reflective Reinforcement Learning), an outcome-supervised framework that guides IE self-correction with task-grounded diagnostic labels. A single backbone first predicts an extraction, diagnoses task-specific error labels, and then revises its output conditioned on the diagnosis. Training starts from diagnostic data labeled by an annotation model for cold-start supervised fine-tuning and proceeds through two GRPO stages that reward final extraction quality, format validity, and first-pass correctness, without a process reward model. Experiments on named entity recognition, relation extraction, and event extraction show consistent same-backbone gains over SFT, including 6.83 average F1 on SciER relation extraction, about 20 F1 on out-of-distribution relation extraction, and 14.80 trigger F1 plus 17.50 argument F1 on DuEE1.0. Ablations show that reflection structure is task-sensitive: stronger constraints benefit relation extraction, whereas named entity recognition needs less restrictive correction under domain shift.
Abstract (translated)
URL
https://arxiv.org/abs/2607.23420
PDF
-
Fine-Tuning Models for Biomedical Relation Extraction
2026-07-23 06:21:58Claudiu Creanga, Liviu P. Dinu, Daniela GifuAbstract
Next-Generation Sequencing has revolutionized the study of genetic mutations, enabling large-scale investigations into their roles in disease development. However, extracting meaningful insights from the vast amount of biomedical literature remains a complex challenge that cannot be addressed manually. In this paper, we present pre-trained models (PTMs) for the automatic extraction of relations from biomedical text, specifically targeting the variant-phenotype domain. Our evaluation on the SNPPhenA corpus demonstrates that fine-tuning small BERT-based models, particularly DeBERTa, yields strong performance, approaching the current state-of-the-art (SOTA). Additionally, our results indicate that carefully fine-tuning Google's Gemini Pro 1.0 outperforms the existing SOTA for both sentence-level tasks (where the model processes only the target sentence) and abstract-level tasks (where the model processes the entire abstract).
Abstract (translated)
URL
https://arxiv.org/abs/2609.20169
PDF
