### Generative AI and Large Language Models in Biology and Medicine

This collection of papers explores the transformative role of generative AI and large language models (LLMs) in biological research and medical practice. These advanced technologies not only enhance scientific understanding but also address challenges in clinical settings, highlighting both their potential benefits and the ethical considerations that arise from their use.

#### Key Papers:
- **[Generative AI agents are transforming biology research: high resolution functional genome annotation for multiscale understanding of life](https://doi.org/10.1016/j.ebiom.2024.105446)**  
   eBioMedicine (Nov 8, 2024)  
   This Commentary describes key applications of generative AI in biology, detailing its potential to accelerate drug development and enhance synthetic biology.

- **[CRISPR-GPT: An LLM Agent for Automated Design of Gene-Editing Experiments](https://www.biorxiv.org/content/10.1101/2024.04.25.591003v3.full-text)**  
   bioRxiv (Apr 25, 2024)  
   Introduction of CRISPR-GPT, an LLM agent designed for the automated design of CRISPR gene-editing experiments, facilitating accessibility for non-expert researchers.

- **[BioDiscoveryAgent: An AI Agent for Designing Genetic Perturbation Experiments](https://openreview.net/forum?id=HAwZGLcye3)**  
   ICLR 2025 Conference Submission (Modified: Dec 2, 2024)  
   Dedicated to optimizing genetic perturbation experiments, showing significant improvements in gene prediction.

- **[Evaluating large language models as agents in the clinic](https://www.nature.com/articles/s41746-024-01083-y)**  
   npj Digital Medicine (Apr 3, 2024)  
   Proposes frameworks to evaluate LLM agents in clinical decision-making settings.

- **[The future landscape of large language models in medicine](https://www.nature.com/articles/s43856-023-00370-1)**  
   Communications Medicine (Oct 10, 2023)  
   Overview of LLMs' potential applications in medicine, discussing both democratization of medical knowledge and inherent risks.

- **[Large Language Models in Healthcare and Medical Domain: A Review](https://arxiv.org/abs/2401.06775v2)**  
   arXiv (Jul 8, 2024)  
   A comprehensive survey on the evolution and impact of LLMs within the healthcare sector, alongside challenges they face.

- **[On the limitations of large language models in clinical diagnosis](https://pmc.ncbi.nlm.nih.gov/articles/PMC10370243/)**  
   medRxiv (Feb 26, 2024)  
   Evaluates GPT-4 performance in clinical diagnostics, highlighting challenges in model accuracy.

- **[Large Language Models¡ªMisdiagnosing Diagnostic Excellence?](https://jamanetwork.com/journals/jamanetworkopen/fullarticle/2825399)**  
   JAMA Network Open (Oct 28, 2024)  
   Discusses the influence of LLMs on physician diagnostic performance in a clinical setting.

- **[Diagnostic reasoning prompts reveal the potential for large language model interpretability in medicine](https://www.nature.com/articles/s41746-024-01010-1)**  
   npj Digital Medicine (Jan 24, 2024)  
   Investigates if LLMs can replicate clinical reasoning while maintaining accuracy in diagnostics.

- **[A comparison of the diagnostic ability of large language models in challenging clinical cases](https://www.frontiersin.org/journals/artificial-intelligence/articles/10.3389/frai.2024.1379297/full)**  
   Frontiers in Artificial Intelligence (Aug 5, 2024)  
   Compares LLMs' diagnostic capabilities in complex clinical scenarios, finding performance variation.

- **[Challenges and barriers of using large language models (LLM) such as ChatGPT for diagnostic medicine with a focus on digital pathology ¨C a recent scoping review](https://diagnosticpathology.biomedcentral.com/articles/10.1186/s13000-024-01464-7)**  
   Diagnostic Pathology (Feb 27, 2024)  
   Reviews challenges faced in deploying LLMs in digital pathology and diagnostic medicine.

- **[Empowering biomedical discovery with AI agents](https://pubmed.ncbi.nlm.nih.gov/39486399/)**  
   Cell (Oct 31, 2024)  
   Discusses integration of AI models with biomedical tools to enhance research capabilities.

- **[ProCyon is a groundbreaking foundation model for modeling, generating, and predicting protein phenotypes](https://www.biorxiv.org/content/10.1101/2024.12.10.627665v1)**  
   bioRxiv (Dec 2024)  
   Explores a new foundation model for advancing protein phenotypes research.

- **[Impact and challenges of large language models in healthcare](https://arcadia.io/resources/large-language-models-in-healthcare)**  
   Arcadia (Jun 20, 2024)  
   Discusses LLMs' potential impact on healthcare delivery and patient engagement.

- **[Large language models and their applications in bioinformatics](https://www.sciencedirect.com/science/article/pii/S2001037024003209)**  
   Computational and Structural Biotechnology Journal (Dec 2024)  
   Reviews applications of LLMs in bioinformatics, focusing on current research advancements.

- **[Large language models in bioinformatics: applications and perspectives](https://pmc.ncbi.nlm.nih.gov/articles/PMC10802675/)**  
   ArXiv (Jan 8, 2024)  
   Surveys the emerging applications of LLMs across various bioinformatics fields.

- **[Enhancing Large Language Models for Clinical Decision Support by Incorporating Clinical Practice Guidelines](https://arxiv.org/html/2401.11120v1)**  
   arXiv (Jan 20, 2024)  
   Details methods for integrating clinical practice guidelines with LLMs to enhance clinical decision support.

- **[AI-based language models powering drug discovery and development](https://pmc.ncbi.nlm.nih.gov/articles/PMC8604259/)**  
   Drug Discov Today (Jun 30, 2021)  
   Summarizes advancements in AI LMs that are assisting drug discovery and development processes.

- **[Artificial intelligence in clinical pharmacology: A case study and scoping review of large language models and bioweapon potential](https://pubmed.ncbi.nlm.nih.gov/37658550/)**  
   Br J Clin Pharmacol (Mar 2024)  
   Reviews the implications of LLMs in clinical pharmacology alongside ethical considerations regarding bioweapon development.

- **[Large language models in medicine](https://www.nature.com/articles/s41591-023-02448-8)**  
   Nature Medicine (Jul 17, 2023)  
   Discusses the potential advantages and limitations of incorporating LLM technologies in clinical medicine.