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2 changes: 2 additions & 0 deletions README.md
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Expand Up @@ -76,3 +76,5 @@ This repository, autonomously updated daily by our **Pantheon** agent system, co
- [2024.12 Nature Cancer] [How AI agents will change cancer research and oncology](https://www.nature.com/articles/s43018-024-00861-7)
- [2025.02 The Lancet] [The rise of agentic AI teammates in medicine](https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(25)00202-8/abstract)
- [2025.03 Trends in Biotechnology] [Large language model for knowledge synthesis and AI-enhanced biomanufacturing](https://www.cell.com/trends/biotechnology/fulltext/S0167-7799(25)00045-9#:~:text=LLMs%20empower%20metabolic%20models%20to,gain%20new%20insights%20and%20predictions)
- [2025.03 Preprint] [Applications of Large Language Models in Biology and Medicine](https://www.biorxiv.org/content/10.1101/2025.03.11.642548v1)

89 changes: 89 additions & 0 deletions daily_reports/2025-06-01.md
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# The Applications of LLM-Based Agents in Biology and Medicine

This comprehensive compilation explores the transformative potential of large language model (LLM)-based agents in various domains of biology and medicine. These advanced AI tools are making substantial impacts on research methodologies, diagnostics, and healthcare delivery, enhancing the way data is analyzed and decisions are made in clinical settings. The following research papers highlight the diverse applications, opportunities, and challenges associated with LLMs in these fields:

- **[A Survey on the Applicability of Large Language Models in the Field of Biology](https://arxiv.org/abs/2503.00096)** (March 2025)
- Explores the potential uses of LLMs in biology, including drug discovery, genomics, and biomedical literature analysis.

- **[Applications of LLM-Based Agents in Biology and Medicine](https://www.thelancet.com/journals/ebiom/article/PIIS2352-3964(24)00482-1/fulltext)** (2024)
- Discusses various applications of LLM-based agents enhancing research, diagnostics, and personalized medicine.

- **[Applications of Large Language Models in Biology and Medicine](https://www.biorxiv.org/content/10.1101/2025.03.11.642548v1)** (March 11, 2025)
- Explores applications such as drug discovery and enhancing diagnostics through predictive analytics.

- **[Deep Learning-Based Semantic Analysis of Scientific Literature](https://www.sciencedirect.com/science/article/pii/S0092867424010705)** (2024)
- Discusses applying deep learning to analyze scientific literature for insights in various fields, including biology and medicine.

- **[A Large Language Model for Data Extraction of Clinical Trial Reports](https://www.nature.com/articles/s41591-023-02448-8)** (2023)
- Presents an LLM automating data extraction from clinical trial reports to enhance clinical data accessibility.

- **[Artificial Intelligence in Medicine: Overview and Future Directions](https://www.sciencedirect.com/science/article/pii/S2589004224009350)** (2024)
- Reviews the applications of AI, including LLMs, improving patient outcomes and operational efficiency in healthcare.

- **[An Overview of the Role of Artificial Intelligence in the Biological and Medical Sciences](https://pmc.ncbi.nlm.nih.gov/articles/PMC12086438/)** (2023)
- Highlights machine learning uses in research, diagnostics, and the benefits and challenges of emerging AI technologies.

- **[Exploring the Applications of Large Language Models in Biomedical Research](https://arxiv.org/html/2401.06775v2)** (January 2024)
- Investigates LLM applications in biomedical research, including drug discovery and clinical diagnosis.

- **[Transforming Biomedicine Data with Large Language Models: Applications, Opportunities, and Challenges](https://link.springer.com/article/10.1007/s10462-024-10921-0)** (2024)
- Discusses how LLMs assist with data interpretation and patient interactions in biomedicine.

- **[Leveraging Language Models to Empower Genomic Decision-Making Across Health Systems](https://pmc.ncbi.nlm.nih.gov/articles/PMC11080827/)** (2023)
- Discusses LLM potential in decision-making processes in genomics and personalized medicine.

- **[Evaluation of Large Language Models for Biological Research](https://www.nature.com/articles/s43856-023-00370-1)** (2023)
- Evaluates LLMs’ performance in biological texts and applications in generating hypotheses and assisting data interpretation.

- **[AI and Diagnostics: The Future is Now](https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(23)00216-7/fulltext)** (2023)
- Discusses how AI, particularly LLMs, enhances diagnostic accuracy and clinical decision-making.

- **[A Deep Learning Model for Predicting Protein-Ligand Binding Affinity](https://www.nature.com/articles/s41587-024-02534-3)** (2024)
- Presents a deep learning framework for predicting biomolecular interactions, aiding drug discovery.

- **[Applications of Artificial Intelligence in the Biological Sciences](https://www.annualreviews.org/content/journals/10.1146/annurev-biodatasci-102224-074736)** (2024)
- Reviews the role of AI technologies in enhancing data analysis and medical outcomes in biological sciences.

- **[Artificial Intelligence and Machine Learning in Medicine: Current Applications and Future Directions](https://pmc.ncbi.nlm.nih.gov/articles/PMC11339493/)** (2023)
- Highlights AI's role in improving diagnostics and treatment plans in healthcare.

- **[A Multimodal AI Framework for Cell Classification and Drug Response Prediction](https://www.cell.com/cell/fulltext/S0092-8674(24)01070-5)** (2024)
- Presents an AI framework for enhancing biological data analysis and personalized medicine.

- **[Applications of Large Language Models in Biomedicine: Current Perspectives and Future Directions](https://pmc.ncbi.nlm.nih.gov/articles/PMC9505413/)** (2022)
- Reviews advancements in LLMs for enhancing drug discovery and patient care management.

- **[AI-Driven Drug Discovery: Not Just a Promising Algorithm but also a Collective Intelligence Paradigm](https://pmc.ncbi.nlm.nih.gov/articles/PMC9031863/)** (2021)
- Discusses the evolution of drug discovery methods enhanced by AI, focusing on LLM applications.

- **[Integrating Language Models in Biomedical Research: Opportunities and Challenges](https://link.springer.com/article/10.1007/s13721-024-00458-1)** (2024)
- Highlights how LLMs can enhance biomedical text mining and clinical decision-making.

- **[Large Language Models Enable Gene-Variant Prioritization Through Embeddings of Genome-Scale Information](https://pubs.acs.org/doi/10.1021/acs.jcim.4c01907)** (2024)
- Explores the utility of LLMs in prioritizing gene variants by embedding genomic information.

- **[Exploring the Development and Applications of LLM-Based Agents in Biomedical Research](https://pmc.ncbi.nlm.nih.gov/articles/PMC11745858/)** (2023)
- Discusses LLM agents in data analysis, hypothesis generation, and clinical task automation.

- **[Towards a Universal LLM-Agent for Biological Data Analysis](https://arxiv.org/abs/2409.00097)** (September 2024)
- Presents methods for integrating LLMs with biological datasets.

- **[AI-Powered Agent for Protein Classification and Structural Analysis](https://arxiv.org/html/2409.00097v1)** (September 2024)
- Proposes an AI agent for protein classification, utilizing LLM capabilities.

- **[Potential of ChatGPT-Based Agents to Support Clinical Decision-Making: A Narrative Review](https://eurjmedres.biomedcentral.com/articles/10.1186/s40001-025-02680-7)** (2025)
- Explores the role of ChatGPT agents in enhancing clinical decision-making processes.

- **[Applications of Language Models for Biomedical Literature Mining](https://www.nature.com/articles/s41746-024-01208-3)** (2024)
- Discusses how language models improve information retrieval in biomedical literature.

- **[Machine Learning-Based Prediction of Imaging Biomarkers in Colorectal Cancer: A Multicenter Study](https://ai.nejm.org/doi/full/10.1056/AIp2300031)** (2023)
- Explores AI models predicting imaging biomarkers, highlighting advancements in cancer diagnostics.

- **[Applications of LLM-Based Agents in Biology and Medicine: A Comprehensive Review](https://pmc.ncbi.nlm.nih.gov/articles/PMC11263899/)** (2023)
- Reviews how LLMs assist in research methodologies and healthcare delivery.

- **[Utilization of Artificial Intelligence-Based Chatbots by Patients for Health Care Questions: A Cross-Sectional Study](https://jamanetwork.com/journals/jamanetworkopen/fullarticle/2808251)** (2023-12-15)
- Examines patient use of AI chatbots for healthcare inquiries, implications for patient engagement, and service delivery.

This collection of literature underscores the promising integration of LLMs and AI in redefining approaches within biology and medicine. As research continues, these technologies hold the potential to further enhance outcomes and methodologies across various healthcare and scientific domains.