# AutoPCR: Automated Phenotype Concept Recognition by Prompting

arXiv: https://arxiv.org/abs/2507.19315 · HTML: https://mlsanity.com/paper/2507.19315/

## Key facts

- Cited by 10 papers in the map (data through 14 Oct 2026).
- Builds on 22 of its 63 references that are in the map.
- First posted on arXiv 25 Jul 2025.

## Builds on (most cited first, 22 of 22)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [The Llama 3 Herd of Models](https://mlsanity.com/paper/2407.21783/) (2024)
- [Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks](https://mlsanity.com/paper/2005.11401/) (2020)
- [Qwen3 Technical Report](https://mlsanity.com/paper/2505.09388/) (2025)
- [QLoRA: Efficient Finetuning of Quantized LLMs](https://mlsanity.com/paper/2305.14314/) (2023)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [Enriching Word Vectors with Subword Information](https://mlsanity.com/paper/1607.04606/) (2016)
- [Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing](https://mlsanity.com/paper/2007.15779/) (2020)
- [Publicly Available Clinical BERT Embeddings](https://mlsanity.com/paper/1904.03323/) (2019)
- [ScispaCy: Fast and Robust Models for Biomedical Natural Language Processing](https://mlsanity.com/paper/1902.07669/) (2019)
- [Self-Alignment Pretraining for Biomedical Entity Representations](https://mlsanity.com/paper/2010.11784/) (2020)
- [Large Language Models are Few-Shot Clinical Information Extractors](https://mlsanity.com/paper/2205.12689/) (2022)
- [Constituency Parsing with a Self-Attentive Encoder](https://mlsanity.com/paper/1805.01052/) (2018)
- [Biomedical Entity Representations with Synonym Marginalization](https://mlsanity.com/paper/2005.00239/) (2020)
- [Knowledge-Rich Self-Supervision for Biomedical Entity Linking](https://mlsanity.com/paper/2112.07887/) (2021)
- [Learning Domain-Specialised Representations for Cross-Lingual Biomedical Entity Linking](https://mlsanity.com/paper/2105.14398/) (2021)
- [Enhancing Phenotype Recognition in Clinical Notes Using Large Language Models: PhenoBCBERT and PhenoGPT](https://mlsanity.com/paper/2308.06294/) (2023)
- [PhenoTagger: A Hybrid Method for Phenotype Concept Recognition using Human Phenotype Ontology](https://mlsanity.com/paper/2009.08478/) (2020)
- [An evaluation of GPT models for phenotype concept recognition](https://mlsanity.com/paper/2309.17169/) (2023)
- [Disease Entity Recognition and Normalization is Improved with Large Language Model Derived Synthetic Normalized Mentions](https://mlsanity.com/paper/2410.07951/) (2024)

## Built on by (most cited first, 10 of 10)

- [CentaurEval: Benchmarking Human-in-the-Loop Value in Agentic Coding](https://mlsanity.com/paper/2512.04111/) (2025)
- [Render-in-the-Loop: Vector Graphics Generation via Visual Self-Feedback](https://mlsanity.com/paper/2604.20730/) (2026)
- [MedSynapse-V: Bridging Visual Perception and Clinical Intuition via Latent Memory Evolution](https://mlsanity.com/paper/2604.26283/) (2026)
- [GRASP: Plan-Guided Graph Retrieval with Adaptive Fusion and Reranking on Semi-Structured Knowledge Bases](https://mlsanity.com/paper/2605.30237/) (2026)
- [SAKE: Self-aware Knowledge Exploitation-Exploration for Grounded Multimodal Named Entity Recognition](https://mlsanity.com/paper/2604.20146/) (2026)
- [SynGR: Unleashing the Potential of Cross-Modal Synergy for Generative Recommendation](https://mlsanity.com/paper/2605.18920/) (2026)
- [Toward Workflow-Aware Benchmarking for Healthcare NLP Agents](https://mlsanity.com/paper/2609.00296/) (2026)
- [MOSAIC: Orchestrating Collaborative Knowledge Tracing with Hierarchical Semantic Alignment](https://mlsanity.com/paper/2606.29049/) (2026)
- [Neighborhood-Aware Dual Biomedical Entity Linking](https://mlsanity.com/paper/2608.04144/) (2026)
- [DR-LabStack: Design and Implementation of a Clinician-Facing Web System for Diabetic Retinopathy Prediction](https://mlsanity.com/paper/2609.10796/) (2026)

## Abstract (arXiv)

Motivation: Phenotype concept recognition (CR) is a fundamental task in biomedical text mining. However, existing methods either require ontology-specific training, making them struggle to generalize across diverse text styles and evolving biomedical terminology, or depend on general-purpose large language models (LLMs) that lack necessary domain knowledge. Results: To address these limitations, we propose AutoPCR, a prompt-based phenotype CR method designed to automatically generalize to new ontologies and unseen data without ontology-specific training. To further boost performance, we also introduce an optional self-supervised training strategy. Experiments show that AutoPCR achieves the best average and most robust performance across datasets. Further ablation and transfer studies demonstrate its inductive capability and generalizability to new ontologies. Availability and Implementation: Our code is available at https://github.com/yctao7/AutoPCR. Contact: drjieliu@umich.edu