cs.CVMar 9, 2026

PathoScribe: Transforming Pathology Data into a Living Library with a Unified LLM-Driven Framework for Semantic Retrieval and Clinical Integration

Authors: Abdul Rehman Akbar, Samuel Wales-McGrath, Alejadro Levya, Lina Gokhale, Rajendra Singh, Wei Chen, Anil Parwani, Muhammad Khalid Khan Niazi

Organizations: Department of Pathology, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA · Department of Pathology and Laboratory Medicine, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA, USA · PathPresenter

Read PDF
Ask AI
Cite

Copy citation

DOINot available for this paper

Abstract

Pathology underpins modern diagnosis and cancer care, yet its most valuable asset, the accumulated experience encoded in millions of narrative reports, remains largely inaccessible. Although institutions are rapidly digitizing pathology workflows, storing data without effective mechanisms for retrieval and reasoning risks transforming archives into a passive data repository, where institutional knowledge exists but cannot meaningfully inform patient care. True progress requires not only digitization, but the ability for pathologists to interrogate prior similar cases in real time while evaluating a new diagnostic dilemma. We present PathoScribe, a unified retrieval-augmented large language model (LLM) framework designed to transform static pathology archives into a searchable, reasoning-enabled living library. PathoScribe enables natural language case exploration, automated cohort construction, clinical question answering, immunohistochemistry (IHC) panel recommendation, and prompt-controlled report transformation within a single architecture. Evaluated on 70,000 multi-institutional surgical pathology reports, PathoScribe achieved perfect Recall@10 for natural language case retrieval and demonstrated high-quality retrieval-grounded reasoning (mean reviewer score 4.56/5). Critically, the system operationalized automated cohort construction from free-text eligibility criteria, assembling research-ready cohorts in minutes (mean 9.2 minutes) with 91.3% agreement to human reviewers and no eligible cases incorrectly excluded, representing orders-of-magnitude reductions in time and cost compared to traditional manual chart review. This work establishes a scalable foundation for converting digital pathology archives from passive storage systems into active clinical intelligence platforms.

More in this topic

Biomedical IR

Biomedical information retrieval finds and ranks relevant evidence in scientific literature, clinical records, databases, and biomedical knowledge resources.

See all 43 papers

Explore similar work

CardsList
Feb 11, 2025

Histopathology Multi-modal Embedding for Pathology Composed Retrieval

To overcome the black-box nature of predictive AI and the hallucination risks of generative models, retrieval-based models offer an interpretable, evidence-based paradigm for pathology clinical workflow. However, real-world clinical queries are inherently interleaved (e.g., pathology images and text). Current dual-encoders suffer from an Architectural Mismatch, lacking the mechanism to fuse such composed queries. To address this, we formalize the task of Pathology Composed Retrieval (PCR). While Multimodal Large Language Models (MLLMs) offer deep-fusion capabilities, directly applying them exposes a Task Mismatch and a Domain Mismatch. To resolve these challenges, we propose HOMIE, a model-agnostic adaptation framework that transforms any generative MLLM into a specialized pathology retrieval expert. Evaluated on our newly introduced PCR Benchmark, a lightweight 2B-parameter HOMIE variant substantially outperforms existing paradigms, surpassing specialized 7B pathology MLLMs and dual-encoders by large margins on composed retrieval, while maintaining strong performance on traditional simple retrieval. The project page is available at https://qfchou.github.io/HOMIE_page/.

Qifeng Zhou, Wenliang Zhong, Thao M. Dang +4

The University of Texas at Arlington, Arlington TX 76010, USA

Computational PathologyHealthcareMultimodal Large Language ModelsMultimodal Foundation ModelsComposed Image Retrieval
AskPDF
Feb 28, 2026

Act Like a Pathologist: Tissue-Aware Whole Slide Image Reasoning

Computational pathology has advanced rapidly in recent years, driven by domain-specific image encoders and growing interest in using vision-language models to answer natural-language questions about diseases. Yet, the core problem behind pathology question-answering remains unsolved, considering that a gigapixel slide contains far more information than necessary for a given question. Pathologists naturally navigate tissue and morphology complexity by scanning broadly, and zooming in selectively according to the clinical questions. Current models, in contrast, rely on uniform patch sampling or broad attention maps, often attending equally to irrelevant regions while overlooking key visual evidence. In this work, we try to bring models closer to how humans actually examine slides. We propose a question-guided, tissue-aware, and coarse-to-fine retrieval framework, HistoSelect, that consists of two key components: a group sampler that identifies question-relevant tissue regions, followed by a patch selector that retrieves the most informative patches within those regions. By selecting only the most informative patches, our method becomes significantly more efficient: reducing visual token usage by 70% on average, while improving accuracy across three pathology QA tasks. Evaluated on 356,000 question-answer pairs, our approach outperforms existing methods and produces answers grounded in interpretable, pathologist-consistent regions. Our results suggest that bringing human-like search and attention patterns into WSI reasoning is a promising direction for building practical and reliable pathology VLMs. Code is available at https://github.com/winston52/HistoSelect.

Wentao Huang, Weimin Lyu, Peiliang Lou +8

Stony Brook University, NY, USA · Mayo Clinic, MN, USA · Harvard Medical School, MA, USA +1

Pathology VQAMedical VQAMedical VLMsWhole-Slide Image Analysis
AskPDF
Jun 18, 2026

Prompt, Plan, Extract: Zero-Shot Agentic LLMs Workflows for Lung Pathology Extraction from Clinical Narratives

Information extraction from pathology reports is essential for cancer staging, tumor registry population. Yet key data remains embedded in narrative reports, making manual extraction labor-intensive and error-prone. Traditional supervised Natural Language Processing pipelines address this through fully supervised Named Entity Recognition and Relation Extraction, but require expensive manual annotation and suffer cascading failures when upstream entities are missed. In this study, we developed a zero-shot, agentic workflow, and evaluated five open-source generative Large Language Models (LLMs) to populate 13 College of American Pathologists synoptic fields from lung resection pathology reports. We compared them against a state-of-the-art supervised GatorTron NER-RE baseline using a novel, registry-aligned evaluation framework. The baseline achieved Micro-F1of 0.960, while the best zero-shot model (GPT-OSS-20B) achieved Micro-F1 of 0.893 (recall: 0.949), accurately extracting complex relations like Pathologic Stage without task-specific training. These results suggest that open-source, zero-shot agentic LLMs show great potential as a low-cost solution for extracting lung pathology information.

Aman Pathak, Cheng Peng, Mengxian Lyu +8

Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL, USA · Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, College of Medicine, University of Florida, Gainesville, FL, USA · College of Nursing, Florida State University, Tallahassee, FL, USA

Computational PathologyZero-Shot LearningClinical Information ExtractionLLM Information ExtractionOncology
AskPDF