Search arXiv⌕ Search
Home/Archive/arXiv

arXiv · 2504.00748

IHC-LLMiner: Automated extraction of tumour immunohistochemical profiles from PubMed abstracts using large language models

Yunsoo Kim·Michal W. S. Ong·Daniel W. Rogalsky·Manuel Rodriguez-Justo·Honghan Wu·Adam P. Levine
View original source ↗Read source document ↗Export metadata ↓

Abstract

Immunohistochemistry (IHC) is essential in diagnostic pathology and biomedical research, offering critical insights into protein expression and tumour biology. This study presents an automated pipeline, IHC-LLMiner, for extracting IHC-tumour profiles from PubMed abstracts, leveraging advanced biomedical text mining. There are two subtasks: abstract classification (include/exclude as relevant) and IHC-tumour profile extraction on relevant included abstracts. The best-performing model, "Gemma-2 finetuned", achieved 91.5% accuracy and an F1 score of 91.4, outperforming GPT4-O by 9.5% accuracy with 5.9 times faster inference time. From an initial dataset of 107,759 abstracts identified for 50 immunohistochemical markers, the classification task identified 30,481 relevant abstracts (Include) using the Gemma-2 finetuned model. For IHC-tumour profile extraction, the Gemma-2 finetuned model achieved the best performance with 63.3% Correct outputs. Extracted IHC-tumour profiles (tumour types and markers) were normalised to Unified Medical Language System (UMLS) concepts to ensure consistency and facilitate IHC-tumour profile landscape analysis. The extracted IHC-tumour profiles demonstrated excellent concordance with available online summary data and provided considerable added value in terms of both missing IHC-tumour profiles and quantitative assessments. Our proposed LLM based pipeline provides a practical solution for large-scale IHC-tumour profile data mining, enhancing the accessibility and utility of such data for research and clinical applications as well as enabling the generation of quantitative and structured data to support cancer-specific knowledge base development. Models and training datasets are available at https://github.com/knowlab/IHC-LLMiner.

Explore related subjects

cs.CL

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Yunsoo Kim, Michal W. S. Ong, Daniel W. Rogalsky, Manuel Rodriguez-Justo, Honghan Wu, Adam P. Levine. 2025-04-01. IHC-LLMiner: Automated extraction of tumour immunohistochemical profiles from PubMed abstracts using large language models. https://arxiv.org/abs/2504.00748

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

What is the Role of Small Models in the LLM Era: A Survey

Large Language Models (LLMs) have demonstrated remarkable capabilities in various reasoning tasks, which leads to the development of increasingly large models. However, scaling up model sizes results in significantly higher computational costs and energy consumption, which makes these models impractical for academic researchers and businesses with limited resources. At the same time, Small Models (SMs) are frequently used in practical settings, although their significance is currently underestimated. This raises important questions about the role of small models in the era of LLMs, a topic that has received limited attention in prior surveys. In this work, we systematically examine the relationship between LLMs and SMs from two key perspectives: Collaboration and Competition (or Complementarity). We hope this survey provides valuable insights for practitioners, fostering a deeper understanding of the contribution of small models and promoting more efficient use of computational resources.

cs.CL↗
arXiv2026

SG-FSM: A Self-Guiding Zero-Shot Prompting Paradigm for Multi-Hop Question Answering Based on Finite State Machine

Large Language Models with chain-of-thought prompting, such as OpenAI-o1, have shown impressive capabilities in natural language inference tasks. However, Multi-hop Question Answering (MHQA) remains challenging for many existing models due to issues like hallucination, error propagation, and limited context length. To address these challenges and enhance LLMs' performance on MHQA, we propose the Self-Guiding prompting Finite State Machine (SG-FSM), designed to strengthen multi-hop reasoning abilities. Unlike traditional chain-of-thought methods, SG-FSM tackles MHQA by iteratively breaking down complex questions into sub-questions, correcting itself to improve accuracy. It processes one sub-question at a time, dynamically deciding the next step based on the current context and results, functioning much like an automaton. Experiments across various benchmarks demonstrate the effectiveness of our approach, outperforming strong baselines on challenging datasets such as Musique. SG-FSM reduces hallucination, enabling recovery of the correct final answer despite intermediate errors. It also improves adherence to specified output formats, simplifying evaluation significantly.

cs.CL↗
arXiv2026

A Course Intelligence Platform for Higher Education: Lessons from AI-Assisted Course Evaluation

The rapid adoption of generative AI has created new opportunities for teaching, learning, and quality assurance. Existing applications, however, remain largely student-facing, with comparatively limited attention to institution-level needs. This paper presents a course intelligence platform deployed across more than 100 universities and serving over 10,000 instructors in China. By linking competency requirements, knowledge structures, teaching activities, and assessment evidence, it establishes a shared foundation for knowledge organization, instructional design, learning assessment, and quality evaluation. The course evaluation module is examined as a representative institution-facing application of the platform, which integrates national evaluation standards, structured educational evidence, customized prompting strategies, and domain-adapted LLMs to generate quantitative scores and qualitative feedback. A case study involving 100 authentic university courses is conducted to evaluate its alignment with expert judgments and the interpretability of its outputs. Statistical analyses show substantial agreement between AI-generated assessments and expert ratings, while qualitative results highlight the credibility of the feedback. The findings further suggest that AI-assisted evaluation requires not only capable models but also structured domain knowledge and transparent criteria. In this context, human ratings should be treated as an informative reference rather than an error-free gold standard, and the objective is to achieve consistent, interpretable, and defensible judgments instead of merely replicating expert scores.

cs.CL↗