# GP-GPT: Large Language Model for Gene-Phenotype Mapping

arXiv: https://arxiv.org/abs/2409.09825 · HTML: https://mlsanity.com/paper/2409.09825/

## Key facts

- Cited by 11 papers in the map (data through 14 Oct 2026).
- Builds on 48 of its 122 references that are in the map.
- First posted on arXiv 15 Sep 2024.

## Builds on (most cited first, 30 of 48)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [Training language models to follow instructions with human feedback](https://mlsanity.com/paper/2203.02155/) (2022)
- [Exploring the Limits of Transfer Learning with a Unified Text-to-Text Transformer](https://mlsanity.com/paper/1910.10683/) (2019)
- [LoRA: Low-Rank Adaptation of Large Language Models](https://mlsanity.com/paper/2106.09685/) (2021)
- [Llama 2: Open Foundation and Fine-Tuned Chat Models](https://mlsanity.com/paper/2307.09288/) (2023)
- [Parameter-Efficient Transfer Learning for NLP](https://mlsanity.com/paper/1902.00751/) (2019)
- [QLoRA: Efficient Finetuning of Quantized LLMs](https://mlsanity.com/paper/2305.14314/) (2023)
- [BLOOM: A 176B-Parameter Open-Access Multilingual Language Model](https://mlsanity.com/paper/2211.05100/) (2022)
- [SciBERT: A Pretrained Language Model for Scientific Text](https://mlsanity.com/paper/1903.10676/) (2019)
- [Making Pre-trained Language Models Better Few-shot Learners](https://mlsanity.com/paper/2012.15723/) (2020)
- [Publicly Available Clinical BERT Embeddings](https://mlsanity.com/paper/1904.03323/) (2019)
- [Chameleon: Mixed-Modal Early-Fusion Foundation Models](https://mlsanity.com/paper/2405.09818/) (2024)
- [BioGPT: Generative Pre-trained Transformer for Biomedical Text Generation and Mining](https://mlsanity.com/paper/2210.10341/) (2022)
- [Sora: A Review on Background, Technology, Limitations, and Opportunities of Large Vision Models](https://mlsanity.com/paper/2402.17177/) (2024)
- [HyenaDNA: Long-Range Genomic Sequence Modeling at Single Nucleotide Resolution](https://mlsanity.com/paper/2306.15794/) (2023)
- [GeneGPT: Augmenting Large Language Models with Domain Tools for Improved Access to Biomedical Information](https://mlsanity.com/paper/2304.09667/) (2023)
- [GraphLLM: Boosting Graph Reasoning Ability of Large Language Model](https://mlsanity.com/paper/2310.05845/) (2023)
- [Interpretability at Scale: Identifying Causal Mechanisms in Alpaca](https://mlsanity.com/paper/2305.08809/) (2023)
- [BioT5: Enriching Cross-modal Integration in Biology with Chemical Knowledge and Natural Language Associations](https://mlsanity.com/paper/2310.07276/) (2023)
- [SciFive: a text-to-text transformer model for biomedical literature](https://mlsanity.com/paper/2106.03598/) (2021)
- [Advancing Multimodal Medical Capabilities of Gemini](https://mlsanity.com/paper/2405.03162/) (2024)
- [Large Language Models for Robotics: Opportunities, Challenges, and Perspectives](https://mlsanity.com/paper/2401.04334/) (2024)
- [BioRED: A Rich Biomedical Relation Extraction Dataset](https://mlsanity.com/paper/2204.04263/) (2022)
- [ProtST: Multi-Modality Learning of Protein Sequences and Biomedical Texts](https://mlsanity.com/paper/2301.12040/) (2023)
- [Understanding LLMs: A Comprehensive Overview from Training to Inference](https://mlsanity.com/paper/2401.02038/) (2024)
- [An Iterative Optimizing Framework for Radiology Report Summarization with ChatGPT](https://mlsanity.com/paper/2304.08448/) (2023)
- [When Brain-inspired AI Meets AGI](https://mlsanity.com/paper/2303.15935/) (2023)

## Built on by (most cited first, 11 of 11)

- [Opportunities and Challenges of Large Language Models for Low-Resource Languages in Humanities Research](https://mlsanity.com/paper/2412.04497/) (2024)
- [Transcending Language Boundaries: Harnessing LLMs for Low-Resource Language Translation](https://mlsanity.com/paper/2411.11295/) (2024)
- [Towards Next-Generation Medical Agent: How o1 is Reshaping Decision-Making in Medical Scenarios](https://mlsanity.com/paper/2411.14461/) (2024)
- [How Social is It? A Benchmark for LLMs' Capabilities in Multi-user Multi-turn Social Agent Tasks](https://mlsanity.com/paper/2505.04628/) (2025)
- [Large Language Models for Bioinformatics](https://mlsanity.com/paper/2501.06271/) (2025)
- [Breaking Bad Molecules: Are MLLMs Ready for Structure-Level Molecular Detoxification?](https://mlsanity.com/paper/2506.10912/) (2025)
- [Domain-Adaptive Diagnosis of Lewy Body Disease with Transferability Aware Transformer](https://mlsanity.com/paper/2507.08839/) (2025)
- [A Systematic Review on the Generative AI Applications in Human Medical Genomics](https://mlsanity.com/paper/2508.20275/) (2025)
- [A Deep Learning Pipeline for Epilepsy Genomic Analysis Using GPT-2 XL and NVIDIA H100](https://mlsanity.com/paper/2510.00392/) (2025)
- [Generative Artificial Intelligence in Bioinformatics: A Systematic Review of Models, Applications, and Methodological Advances](https://mlsanity.com/paper/2511.03354/) (2025)
- [Improving the Evaluation of Biomedical Question Answering with Few Human Preference Signals](https://mlsanity.com/paper/2610.16008/) (2026)

## Abstract (arXiv)

Pre-trained large language models(LLMs) have attracted increasing attention in biomedical domains due to their success in natural language processing. However, the complex traits and heterogeneity of multi-sources genomics data pose significant challenges when adapting these models to the bioinformatics and biomedical field. To address these challenges, we present GP-GPT, the first specialized large language model for genetic-phenotype knowledge representation and genomics relation analysis. Our model is fine-tuned in two stages on a comprehensive corpus composed of over 3,000,000 terms in genomics, proteomics, and medical genetics, derived from multiple large-scale validated datasets and scientific publications. GP-GPT demonstrates proficiency in accurately retrieving medical genetics information and performing common genomics analysis tasks, such as genomics information retrieval and relationship determination. Comparative experiments across domain-specific tasks reveal that GP-GPT outperforms state-of-the-art LLMs, including Llama2, Llama3 and GPT-4. These results highlight GP-GPT's potential to enhance genetic disease relation research and facilitate accurate and efficient analysis in the fields of genomics and medical genetics. Our investigation demonstrated the subtle changes of bio-factor entities' representations in the GP-GPT, which suggested the opportunities for the application of LLMs to advancing gene-phenotype research.