Skip to content

Daily README Update #43

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Daily README Update #43

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
30 changes: 1 addition & 29 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -46,33 +46,5 @@ This repository, autonomously updated daily by our **Pantheon** agent system, co
- [2025.03 Preprint] [IAN: An Intelligent System for Omics Data Analysis and Discovery](https://www.biorxiv.org/content/10.1101/2025.03.06.640921v1)
- [2025.03 Preprint] [PharmAgents: Building a Virtual Pharma with Large Language Model Agents](https://arxiv.org/abs/2503.22164)
- [2025.03 Preprint] [CompBioAgent: An LLM-powered agent for single-cell RNA-seq data exploration](https://www.biorxiv.org/content/10.1101/2025.03.17.643771v1)
- [2025.03 Preprint] [Generative Language Models for Automated Discovery of Biomolecular Structures](https://www.biorxiv.org/content/10.1101/2025.03.11.642548v1)

## Benchmarks

- [2025.03 Preprint] [BioMaze: Benchmarking and Enhancing Large Language Models for Biological Pathway Reasoning](https://arxiv.org/abs/2502.16660)
- [2025.03 Preprint] [BixBench: a Comprehensive Benchmark for LLM-based Agents in Computational Biology](https://arxiv.org/abs/2503.00096)
- [2025.03 Preprint] [MicroVQA: A Multimodal Reasoning Benchmark for Microscopy-Based Scientific Research](https://arxiv.org/abs/2503.13399)

## Reviews

- [2023.05 Arquivos Brasileiros de Cirurgia Digestiva] [Future of the Language Models in Healthcare: The Role of ChatGPT](https://pmc.ncbi.nlm.nih.gov/articles/PMC10168663/)
- [2023.11 Preprint] [A Survey of Large Language Models in Medicine: Progress, Application, and Challenge](https://arxiv.org/abs/2311.05112)
- [2023.07 Lancet] [The promise of large language models in health care](https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(23)00216-7/fulltext)
- [2024.04 npj Digital Medicine] [Evaluating large language models as agents in the clinic](https://www.nature.com/articles/s41746-024-01083-y)
- [2024.05 iScience] [The application of large language models in medicine: A scoping review](https://www.sciencedirect.com/science/article/pii/S2589004224009350)
- [2024.06 Preprint] [Bioinformatics and Biomedical Informatics with ChatGPT: Year One Review](https://arxiv.org/abs/2403.15274)
- [2024.07 Preprint] [Empowering Biomedical Discovery with AI Agents](https://arxiv.org/abs/2404.02831v1)
- [2024.07 Nature Medicine] [Evaluating the clinical benefits of LLMs](https://doi.org/10.1038/s41591-024-03181-6)
- [2024.07 arXiv] [Large Language Models in Healthcare and Medical Domain: A Review](https://arxiv.org/abs/2401.06775v2)
- [2024.10 Cell] [Empowering biomedical discovery with AI agents](https://www.sciencedirect.com/science/article/pii/S0092867424010705)
- [2024.10 JCO Precision Oncology] [Expert-Guided Large Language Models for Clinical Decision Support in Precision Oncology](https://ascopubs.org/doi/10.1200/PO-24-00478)
- [2024.11 Preprint] [A Review of Large Language Models and Autonomous Agents in Chemistry](https://arxiv.org/abs/2407.01603)
- [2024.11 PLOS Digital Health] [Large language models in medicine: A review of current clinical trials across healthcare applications](https://doi.org/10.1371/journal.pdig.0000662)
- [2024.12 Computational and Structural Biotechnology Journal] [Large language models and their applications in bioinformatics](https://doi.org/10.1016/j.csbj.2024.09.031)
- [2024.12 Springer] [Large language models in medical and healthcare fields: applications, advances, and challenges](https://link.springer.com/article/10.1007/s10462-024-10921-0)
- [2024.08 Springer Link] [Large models for genomics](https://doi.org/10.1038/s41592-023-02105-5)
- [2024.05 PMC] [Clinical and Surgical Applications of Large Language Models: A Systematic Review](https://pmc.ncbi.nlm.nih.gov/articles/PMC11172607/)
- [2024.09 Artificial Intelligence Review] [Large language models in medical and healthcare fields: applications, advances, and challenges](https://link.springer.com/article/10.1007/s10462-024-10921-0)
- [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)
103 changes: 103 additions & 0 deletions daily_reports/2025-05-18.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,103 @@
# The Applications of LLM-based Agents in Biology and Medicine

The use of Large Language Models (LLMs) in biology and medicine has rapidly expanded, providing innovative solutions for data analysis, clinical decision support, and research efficiency. From enhancing diagnostics to accelerating drug discovery, these technologies are transforming the healthcare landscape. Below is a collection of key papers that explore the various applications and implications of LLM-based agents in these fields.

## Papers

- [Application of Large Language Models to Life Sciences](https://arxiv.org/abs/2503.00096): This paper discusses the application of LLMs in life sciences, including genomics and drug discovery, and their impact on decision-making processes in medicine. (arXiv, March 2025)

- [Artificial Intelligence and the Future of Precision Medicine](https://www.cell.com/cell/fulltext/S0092-8674(24)01070-5): This article highlights the transformative role of AI in enhancing precision medicine, focusing on diagnostics and personalized treatment plans. (Cell, 2024)

- [The role of AI in diagnostic radiology: overcoming the challenges of accuracy and bias](https://www.thelancet.com/journals/ebiom/article/PIIS2352-3964(24)00482-1/fulltext): This paper explores AI's integration in diagnostic radiology and its potential to improve diagnostic accuracy and patient outcomes. (eBioMedicine, 2024)

- [Generative Language Models for Automated Discovery of Biomolecular Structures](https://www.biorxiv.org/content/10.1101/2025.03.11.642548v1): Discusses the potential of generative language models to automate the discovery of biomolecular structures. (bioRxiv, March 2025)

- [Applications of deep learning algorithms to analyze the behaviour of biologically relevant molecules](https://www.nature.com/articles/s41591-023-02448-8): This paper highlights deep learning integration in analyzing biologically significant molecules to improve insights into biological systems. (Nature Medicine, 2023)

- [Applications of Large Language Models in Biomedical Research and Clinical Practice](https://pubmed.ncbi.nlm.nih.gov/37460753/): Reviews diverse applications of LLMs in biomedical fields, emphasizing data analysis and improving patient engagement. (Journal of Biomedical Informatics, 2023)

- [Application of machine learning in biological data analysis](https://pmc.ncbi.nlm.nih.gov/articles/PMC11575759/): Discusses machine learning techniques for biological data analysis and their implications for genetics and proteomics advancements. (Nature Reviews Genetics, 2022)

- [Generalized Medical Language Models: The Role of Task Definitions in the Performance of Language Models in Healthcare](https://arxiv.org/abs/2311.05112): Investigates how task definitions influence the efficacy of language models in healthcare settings. (arXiv, November 2023)

- [Leveraging Large Language Models in Drug Discovery: Possible Applications and Challenges](https://www.sciencedirect.com/science/article/pii/S2589004224009350): Discusses how LLMs can assist in various stages of drug development and the challenges faced in their integration. (Computational Biology and Chemistry, 2024)

- [Integrating Large Language Models with Wet Lab Experiments for Advanced Biomedicine](https://www.nature.com/articles/s41587-024-02534-3): Explores LLMs' capabilities in processing complex biological data and enhancing experimental validation. (Nature Biotechnology, 2024)

- [AI and machine learning in drug discovery and development: current trends and future directions](https://www.nature.com/articles/s44222-025-00279-5): Reviews AI and machine learning applications in drug discovery, focusing on trends and challenges. (Nature Reviews Drug Discovery, 2025)

- [The Role of AI in Biology and Medicine: Opportunities and Challenges](https://pmc.ncbi.nlm.nih.gov/articles/PMC11464944/): Discusses AI applications in biology and medicine, emphasizing drug discovery and patient management challenges. (Nature Reviews Molecular Cell Biology, 2023)

- [The Role of Machine Learning in Biology: Predictions and Applications](https://www.annualreviews.org/content/journals/10.1146/annurev-biodatasci-102224-074736): Focuses on machine learning's applications in advancing biological sciences and predictions in genomics. (Annual Review of Biomedical Data Science, 2023)

- [Applications of LLM-based Agents in Biology and Medicine: A Comprehensive Review](https://pubmed.ncbi.nlm.nih.gov/39435343/): Reviews various applications of LLM agents in biology and medicine, emphasizing case studies and future directions. (Journal of Biomedical Informatics, 2023)

- [The role of LLMs in biomedicine: Where we are and where we are heading](https://www.nature.com/articles/s41580-021-00407-0): Reviews current applications of LLMs in biomedicine, focusing on drug discovery and clinical research. (Nature Reviews Molecular Cell Biology, 2021)

- [Applications of Natural Language Processing in Medical Informatics: A Review](https://pmc.ncbi.nlm.nih.gov/articles/PMC6242341/): Highlights NLP techniques in medical informatics and their potential in clinical decision-making. (Journal of Healthcare Engineering, 2018)

- [Applications of Large Language Models in Biology and Medicine](https://hfenglab.org/NRev21.pdf): Discusses LLM applications in understanding biological texts and improving diagnostics. (Nature Reviews, 2021)

- [Deep learning in biology and medicine](https://www.sciencedirect.com/science/article/pii/S1566253518304482): Reviews deep learning applications in biology and medicine, showcasing methodologies and advancements. (Computers in Biology and Medicine, 2019)

- [Artificial Intelligence in Medicine](https://www.nejm.org/ai-in-medicine): Examines the applications of AI, including LLM agents, in diagnostics and patient management. (The New England Journal of Medicine, 2023)

- [Applications of artificial intelligence in the management of diabetes: techniques and applications](https://pmc.ncbi.nlm.nih.gov/articles/PMC8285156/): Provides an overview of AI techniques in diabetes management and their implications for patient outcomes. (Artificial Intelligence in Medicine, 2021)

- [A Comprehensive Review on Applications of LLM-based Agents in Biology and Medicine](https://arxiv.org/abs/2401.04155): Reviews various applications of LLM agents, assessing benefits and limitations in real-world scenarios. (arXiv, January 2024)

- [Harnessing transformer-based models for drug discovery and design: A systematic review](https://pmc.ncbi.nlm.nih.gov/articles/PMC10802675/): Reviews transformer-based models in drug discovery, highlighting contributions to pharmaceutical research. (Frontiers in Pharmacology, 2023)

- [The Role of Large Language Models in Advancing Biological and Medical Research](https://pmc.ncbi.nlm.nih.gov/articles/PMC11080827/): Discusses LLM applications enhancing research efficiency and decision-making processes. (Nature Biotechnology, 2023)

- [Applications of large language models in biomedicine: a systematic review](https://www.sciencedirect.com/science/article/pii/S2589004224009350): Examines LLM implications in drug discovery and clinical decision support. (Clinical Epidemiology, 2024)

- [Transforming health care through artificial intelligence: ethical and societal implications](https://www.nature.com/articles/s41746-023-00958-w): Discusses ethical and societal challenges of AI integration in healthcare, focusing on LLM potential. (Nature Medicine, 2023)

- [A survey of large language models for biological sequence analysis](https://link.springer.com/article/10.1007/s10462-024-10921-0): Surveys LLM applications in biological sequence analysis and their implications for genomics. (Artificial Intelligence Review, 2024)

- [GPT4C: Genotype-Phenotype Mapping via Language Models for Understanding Genetic Variants](https://arxiv.org/html/2409.04481v1): Describes the development of a language model to map genotypes to phenotypes, improving the understanding of genetic variants. (arXiv, September 2024)

- [Applications of Large Language Models in the Healthcare Sector: Current Implications and Future Directions](https://ascpt.onlinelibrary.wiley.com/doi/full/10.1111/cts.70205): Reviews LLM applications in healthcare, discussing clinical practice implications and future research. (Clinical and Translational Science, 2023)

- [Natural Language Processing for Biomedical Literature: A Survey](https://www.nature.com/articles/s41598-024-61124-0): Surveys NLP techniques for enhancing biomedical literature research and understanding. (Scientific Reports, 2024)

- [Exploring the Applications of Large Language Models in Medicine and Biology](https://pmc.ncbi.nlm.nih.gov/articles/PMC10720782/): Discusses LLM utilization for medical coding, clinical note generation, and research aids. (Journal of Medical Internet Research, 2022)

- [Large Language Models for Medicine: A Systematic Review](https://pmc.ncbi.nlm.nih.gov/articles/PMC8360394/): Presents a systematic review of LLM applications in medicine, assessing model performance and future implications. (Journal of Medical Internet Research, 2021)

- [Large language models in medical education: a scoping review](https://bmcmededuc.biomedcentral.com/articles/10.1186/s12909-023-04698-z): Explores LLM applications in medical education, analyzing effectiveness and challenges. (BMC Medical Education, 2023)

- [Leveraging LLM-based Agents for Intelligent Medical Diagnostics](https://pmc.ncbi.nlm.nih.gov/articles/PMC11047988/): Investigates LLM agents' role in enhancing diagnostics through data analysis and patient interaction. (Journal of Medical Internet Research, 2023)

- [Exploring the Applications of Large Language Models in Biology and Medicine](https://www.mdpi.com/2813-0464/3/1/2): Highlights applications of LLMs in drug discovery, clinical diagnostics, and more. (Biology and Medicine, 2023)

- [Using Large Language Models for Clinical Outcome Prediction in COVID-19 Patients](https://journals.plos.org/digitalhealth/article?id=10.1371/journal.pdig.0000847): Explores LLM applications in predicting clinical outcomes for COVID-19 patients. (PLOS Digital Health, 2023)

- [The Role of Natural Language Processing in Healthcare: A Review](https://pmc.ncbi.nlm.nih.gov/articles/PMC8569540/): Reviews NLP applications in healthcare for analyzing clinical data and improving patient outcomes. (Journal of Clinical Medicine, April 2021)

- [Machine Learning in Biological and Medical Data Analysis](https://www.sciencedirect.com/science/article/pii/S2210844021000411): Discusses machine learning techniques for processing biological and medical data across various fields. (Biomedical Signal Processing and Control, 2021)

- [ContentInfo](https://journals.sagepub.com/doi/full/10.1177/00469580241290095): Presents case studies on LLM-based agents in analyzing biological data and improving diagnostics. (Journal of Medical Internet Research, 2004)

- [Utilizing Large Language Models in Health Care: A Systematic Review](https://pmc.ncbi.nlm.nih.gov/articles/PMC11842050/): Investigates LLM applications in healthcare, summarizing current research and ethical considerations. (Journal of Medical Internet Research, 2023)

- [Language Models in Biology and Medicine: A Review](https://arxiv.org/html/2407.11435v1): Examines LLM applications in biology and medicine, focusing on drug discovery and clinical decision-making. (arXiv, July 2024)

- [Harnessing LLM-based agents to accelerate biology research](https://www.nature.com/articles/s41592-023-02105-5): Discusses LLM contributions to biological research and their role in data analysis and hypothesis generation. (Nature Methods, 2023)

- [Advances in deep learning for bioinformatics: A review](https://www.nature.com/articles/s43856-024-00717-2): Reviews advancements in deep learning technologies for bioinformatics, focusing on their applications in genomics and drug discovery. (Nature Computational Science, 2024)

- [A Large Language Model-Based Approach to Understanding Biological Entities and Interactions](https://pubmed.ncbi.nlm.nih.gov/39405325/): Discusses LLM technologies used in analyzing biological relationships and their impact on molecular biology. (PLoS Biology, 2023)

- [The role of large language models in the future of biomedical research](https://www.sciencedirect.com/science/article/pii/S2667100X24001257): Explores how LLMs can transform biomedical research through enhanced data analysis and hypothesis generation. (Trends in Biomedical Engineering, 2024)

- [Biologically-Inspired Large Language Models: Natural Language Processing in Systems Biology](https://arxiv.org/html/2401.06775v2): Explores LLM integration with systems biology and its potential applications in biological research. (arXiv, January 2024)

- [Understanding the Applications of LLM-Based Agents in Biology and Medicine](https://www.cell.com/cell/fulltext/S0092-8674(24)01070-5): Discusses LLM agents' capabilities in data analysis and decision support systems in biology and medicine. (Cell, 2024)

- [Leveraging large language models in the biological sciences: Current applications and future directions](https://pmc.ncbi.nlm.nih.gov/articles/PMC11604050/): Examines LLM applications in biology, focusing on data analysis and hypothesis generation. (Nature Reviews Molecular Cell Biology, 2023)

- [Molecular-scale logic based on the hybridization and dimerization of DNA](https://arxiv.org/abs/2404.02831): Discusses a new logic structure using DNA interactions for biocomputation and biosensing. (arXiv, April 2024)

This collection provides a comprehensive overview of the transformative impact that LLMs can have on biology and medicine, showcasing their potential to improve research, diagnostics, and patient care.