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Playing Along: Learning a Double-Agent Defender for Belief Steering via Theory of Mind RPA-Check: A Multi-Stage Automated Framework for Evaluating Dynamic LLM-based Role-Playing Agents A Triadic Suffix Tokenization Scheme for Numerical Reasoning Hidden Measurement Error in LLM Pipelines Distorts Annotation, Evaluation, and Benchmarking Synthius-Mem: Brain-Inspired Hallucination-Resistant Persona Memory Achieving 94.4% Memory Accuracy and 99.6% Adversarial Robustness on LoCoMo Time is Not a Label: Continuous Phase Rotation for Temporal Knowledge Graphs and Agentic Memory NovBench: Evaluating Large Language Models on Academic Paper Novelty Assessment Policy Split: Incentivizing Dual-Mode Exploration in LLM Reinforcement with Dual-Mode Entropy Regularization METER: Evaluating Multi-Level Contextual Causal Reasoning in Large Language Models Think Before you Write: QA-Guided Reasoning for Character Descriptions in Books METRO: Towards Strategy Induction from Expert Dialogue Transcripts for Non-collaborative Dialogues Retrieval as Generation: A Unified Framework with Self-Triggered Information Planning Do LLMs Know Tool Irrelevance? Demystifying Structural Alignment Bias in Tool Invocations Enhancing Multimodal Large Language Models for Ancient Chinese Character Evolution Analysis via Glyph-Driven Fine-Tuning Polyglot Teachers: Evaluating Language Models for Multilingual Synthetic Data Generation Exploring Knowledge Conflicts for Faithful LLM Reasoning: Benchmark and Method CocoaBench: Evaluating Unified Digital Agents in the Wild MathAgent: Adversarial Evolution of Constraint Graphs for Mathematical Reasoning Data Synthesis Evaluating Memory Capability in Continuous Lifelog Scenario How Robust Are Large Language Models for Clinical Numeracy? An Empirical Study on Numerical Reasoning Abilities in Clinical Contexts Efficient Training for Cross-lingual Speech Language Models Shared Emotion Geometry Across Small Language Models: A Cross-Architecture Study of Representation, Behavior, and Methodological Confounds A Systematic Analysis of the Impact of Persona Steering on LLM Capabilities Uncertainty-Aware Web-Conditioned Scientific Fact-Checking When Valid Signals Fail: Regime Boundaries Between LLM Features and RL Trading Policies When Verification Fails: How Compositionally Infeasible Claims Escape Rejection Mem$^2$Evolve: Towards Self-Evolving Agents via Co-Evolutionary Capability Expansion and Experience Distillation AOP-Smart: A RAG-Enhanced Large Language Model Framework for Adverse Outcome Pathway Analysis OccuBench: Evaluating AI Agents on Real-World Professional Tasks via Language Environment Simulation Advancing Polish Language Modeling through Tokenizer Optimization in the Bielik v3 7B and 11B Series
Leveraging large language models for structured informati...
Jeya Balaji Balasubramanian, Daniel Adams, Ioannis Roxanis, Amy · 2025-02-15 · via cs.CL updates on arXiv.org

Background: Structured information extraction from unstructured histopathology reports facilitates data accessibility for clinical research. Manual extraction by experts is time-consuming and expensive, limiting scalability. Large language models (LLMs) offer efficient automated extraction through zero-shot prompting, requiring only natural language instructions without labeled data or training. We evaluate LLMs' accuracy in extracting structured information from breast cancer histopathology reports, compared to manual extraction by a trained human annotator. Methods: We developed the Medical Report Information Extractor, a web application leveraging LLMs for automated extraction. We developed a gold standard extraction dataset to evaluate the human annotator alongside five LLMs including GPT-4o, a leading proprietary model, and the Llama 3 model family, which allows self-hosting for data privacy. Our assessment involved 111 histopathology reports from the Breast Cancer Now (BCN) Generations Study, extracting 51 pathology features specified in the study's data dictionary. Results: Evaluation against the gold standard dataset showed that both Llama 3.1 405B (94.7% accuracy) and GPT-4o (96.1%) achieved extraction accuracy comparable to the human annotator (95.4%; p = 0.146 and p = 0.106, respectively). While Llama 3.1 70B (91.6%) performed below human accuracy (p <0.001), its reduced computational requirements make it a viable option for self-hosting. Conclusion: We developed an open-source tool for structured information extraction that can be customized by non-programmers using natural language. Its modular design enables reuse for various extraction tasks, producing standardized, structured data from unstructured text reports to facilitate analytics through improved accessibility and interoperability.