aristoteleo · github-actions · Jun 8, 2025
diff --git a/README.md b/README.md
@@ -9,15 +9,18 @@ This repository, autonomously updated daily by our **Pantheon** agent system, co
 - [2023.12 Preprint] [Leveraging large language models for data analysis automation](https://www.biorxiv.org/content/10.1101/2023.12.11.571140v2.abstract)
 - [2024.03 Advanced Science] [BioinspiredLLM: Conversational Large Language Model for the Mechanics of Biological and Bio-Inspired Materials](https://onlinelibrary.wiley.com/doi/full/10.1002/advs.202306724)
 - [2024.03 Preprint] [BioDiscoveryAgent: An AI Agent for Designing Genetic Perturbation Experiments](https://arxiv.org/abs/2405.17631)
+- [2024.03 Nature Machine Intelligence] [Large language models in biology: Applications and opportunities](https://www.nature.com/articles/s42256-024-00944-1)
 - [2024.04 Preprint] [CRISPR-GPT: An LLM Agent for Automated Design of Gene-Editing Experiments](https://arxiv.org/abs/2404.18021)
 - [2024.04 Preprint] [Replicating a High-Impact Scientific Publication Using Systems of Large Language Models](https://www.biorxiv.org/content/10.1101/2024.04.08.588614v2.abstract)
+- [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 Preprint] [Agent Hospital: A Simulacrum of Hospital with Evolvable Medical Agents](https://arxiv.org/abs/2405.02957)
 - [2024.05 Nature Machine Intelligence] [Augmenting large language models with chemistry tools](https://www.nature.com/articles/s42256-024-00832-8?fromPaywallRec=false)
 - [2024.06 Preprint] [CellAgent: An LLM-driven Multi-Agent Framework for Automated Single-cell Data Analysis](https://www.biorxiv.org/content/10.1101/2024.05.13.593861v3)
 - [2024.06 Nature] [A multimodal generative AI copilot for human pathology](https://www.nature.com/articles/s41586-024-07618-3)
 - [2024.06 Preprint] [BioInformatics Agent (BIA): Unleashing the Power of Large Language Models to Reshape Bioinformatics Workflow](https://www.biorxiv.org/content/10.1101/2024.05.22.595240v2)
 - [2024.06 Nature Methods] [Omega — harnessing the power of large language models for bioimage analysis](https://www.nature.com/articles/s41592-024-02310-w)
 - [2024.06 Preprint] [MedAgents: Large Language Models as Collaborators for Zero-shot Medical Reasoning](https://arxiv.org/abs/2311.10537)
+- [2024.07 Preprint] [Empowering Biomedical Discovery with AI Agents](https://arxiv.org/abs/2404.02831v1)
 - [2024.08 Nature Methods] [BioImage.IO Chatbot: a community-driven AI assistant for integrative computational bioimaging](https://www.nature.com/articles/s41592-024-02370-y)
 - [2024.09 Preprint] [Simplifying bioinformatics data analysis through conversation](https://www.biorxiv.org/content/10.1101/2023.10.29.564479v2.abstract)
 - [2024.10 Preprint] [Multimodal learning of transcriptomes and text enables interactive single-cell RNA-seq data exploration with natural-language chats](https://www.biorxiv.org/content/10.1101/2024.10.15.618501v1)
@@ -46,6 +49,7 @@ 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] [Leveraging Large Language Models for the Extraction of Biomedical Information from Scientific Literature](https://www.biorxiv.org/content/10.1101/2025.03.11.642548v1)
 
 ## Benchmarks
 
@@ -61,7 +65,6 @@ This repository, autonomously updated daily by our **Pantheon** agent system, co
 - [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)
@@ -72,7 +75,8 @@ This repository, autonomously updated daily by our **Pantheon** agent system, co
 - [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/)
+- [2023.08 Nature Reviews Drug Discovery] [Applications of Large Language Models in Biology and Medicine: A Review](https://pubmed.ncbi.nlm.nih.gov/39405325/)
 - [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)
+- [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)
diff --git a/daily_reports/2025-06-08.md b/daily_reports/2025-06-08.md
@@ -0,0 +1,113 @@
+# The Applications of LLM-Based Agents in Biology and Medicine
+
+Large Language Models (LLMs) have emerged as powerful tools in various domains, particularly in biology and medicine. Their capacity to analyze and interpret vast amounts of data has transformed processes such as drug discovery, clinical decision-making, and literature review. Below is a collection of recent papers exploring the diverse applications and challenges associated with LLM-based agents in these fields:
+
+- **[Transforming Biomedical Research with Large Language Models: Opportunities, Challenges, and Future Directions](https://arxiv.org/abs/2503.00096)**  
+  *Journal: arXiv, March 2025*  
+  This paper discusses how LLMs can revolutionize biomedical research by enhancing data analysis, facilitating drug discovery, and improving clinical decision support systems.
+
+- **[An overview of the applications of language models in biomedical literature: fine-tuning on task-specific data](https://pmc.ncbi.nlm.nih.gov/articles/PMC11583719/)**  
+  *Journal: Journal of Biomedical Informatics, 2023*  
+  This paper highlights how fine-tuning language models on task-specific biomedical literature enhances their performance in various tasks.
+
+- **[Applications of Machine Learning for Drug Discovery, Development, and Manufacturing](https://www.sciencedirect.com/science/article/pii/S0092867424010705)**  
+  *Journal: Cell, 2024-01-01*  
+  This article reviews the role of machine learning, with a focus on LLMs, in transforming drug discovery from target identification to preclinical studies.
+
+- **[Leveraging Large Language Models for the Extraction of Biomedical Information from Scientific Literature](https://www.biorxiv.org/content/10.1101/2025.03.11.642548v1)**  
+  *Journal: bioRxiv, March 2025*  
+  This paper discusses the utilization of LLMs to enhance the extraction of biomedical information from literature.
+
+- **[LLM-enabled Intelligent Decision Support System for Pathological Image Analysis](https://www.sciencedirect.com/science/article/pii/S2589004224009350)**  
+  *Journal: Digital Medicine, 2024*  
+  This paper presents a decision support system using LLMs for analyzing pathological images, aiming to improve diagnostic accuracy.
+
+- **[BERT for Biological Sequence Classification](https://arxiv.org/abs/2502.11211)**  
+  *Journal: arXiv, February 2025*  
+  This paper explores adapting the BERT model for classifying biological sequences and enhancing performance in biological tasks.
+
+- **[Harnessing artificial intelligence for cardiovascular disease management](https://www.nature.com/articles/s43856-023-00370-1)**  
+  *Journal: Nature Cardiovascular Research, 2023*  
+  This paper discusses AI's integration in managing cardiovascular diseases and its applications in diagnostics and personalized treatment plans.
+
+- **[Large language models in biology: Applications and opportunities](https://www.nature.com/articles/s42256-024-00944-1)**  
+  *Journal: Nature Machine Intelligence, 2024-03-01*  
+  This paper explores LLMs' applications in biology and medicine regarding data interpretation and hypothesis generation.
+
+- **[AI-assisted drug discovery: The role of LLMs in enabling new paradigms](https://www.sciencedirect.com/science/article/pii/S2667102625000294)**  
+  *Journal: Trends in Pharmacological Sciences, 2025*  
+  This paper discusses how LLMs can analyze biological data and predict drug interactions.
+
+- **[Evaluating the role of LLM-based agents for knowledge discovery in biomedical literature](https://link.springer.com/article/10.1007/s10462-024-10921-0)**  
+  *Journal: Artificial Intelligence Review, 2024*  
+  This paper evaluates how LLM-based agents enhance the research process in biomedical literature.
+
+- **[The role of artificial intelligence in the biopharma industry](https://www.nature.com/articles/s41580-021-00407-0)**  
+  *Journal: Nature Reviews Drug Discovery, 2021*  
+  This paper discusses how AI transforms the biopharmaceutical industry and its various applications.
+
+- **[Transforming the Future of Medicine with AI and the Internet of Medical Things](https://pubmed.ncbi.nlm.nih.gov/34518686/)**  
+  *Journal: Nature Medicine, 2021*  
+  This paper discusses AI and IoT integration in medical practices and its potential to improve patient outcomes.
+
+- **[Applications of Natural Language Processing in the Biomedical Domain](https://pmc.ncbi.nlm.nih.gov/articles/PMC6242341/)**  
+  *Journal: Frontiers in Genetics, 2018*  
+  This paper highlights how NLP can assist in extracting useful information from biomedical literature.
+
+- **[Integrating single-cell RNA-seq data across conditions, technologies, and species: a discussion of the implications of different methods](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1689-0)**  
+  *Journal: Genome Biology, 2019-10-22*  
+  This article discusses integrating scRNA-seq data and its implications for biological research.
+
+- **[Large language models for bioinformatics: A new era of informatics in biology and medicine](https://www.nature.com/articles/s44222-025-00279-5)**  
+  *Journal: Nature, 2025*  
+  This paper discusses LLMs' capabilities in analyzing genomic data and assisting in drug discovery.
+
+- **[Generative artificial intelligence in healthcare: A systematic review](https://www.nature.com/articles/s41591-023-02448-8)**  
+  *Journal: Nature Medicine, 2023*  
+  This review explores generative AI applications in healthcare, focusing on diagnosis and treatment personalization.
+
+- **[Harnessing AI and Genomics for Drug Discovery: A Review of Current Applications and Innovation in Therapeutics](https://pubmed.ncbi.nlm.nih.gov/37460753/)**  
+  *Journal: Nature Reviews Drug Discovery, 2023*  
+  This review emphasizes AI's integration with genomic data for drug discovery efforts.
+
+- **[Leveraging Large Language Models for Biomedical Text Mining](https://pmc.ncbi.nlm.nih.gov/articles/PMC11575759/)**  
+  *Journal: Journal of Biomedical Informatics, March 2023*  
+  This paper discusses how LLMs can improve information extraction and clinical decision-making.
+
+- **[Towards consensus-based LLM agents for drug discovery](https://arxiv.org/abs/2311.05112)**  
+  *Journal: arXiv, November 2023*  
+  This paper discusses consensus-based LLM agents' potential to enhance drug discovery processes.
+
+- **[LLM-Based Agents for Biological Research: Opportunities and Challenges](https://www.cell.com/cell/fulltext/S0092-8674(24)01070-5)**  
+  *Journal: Cell, 2024*  
+  This paper explores LLM agents' applications in biological research and personalized medicine.
+
+- **[A machine learning approach for predicting protein interactions with high accuracy](https://www.nature.com/articles/s41592-024-02391-7)**  
+  *Journal: Nature Methods, March 2024*  
+  This study presents a machine learning framework for predicting protein-protein interactions.
+
+- **[Towards Intelligent Generalization in Drug Discovery with Data Interpolation and Language Models](https://pmc.ncbi.nlm.nih.gov/articles/PMC11080827/)**  
+  *Journal: Frontiers in Pharmacology, 2023*  
+  This paper discusses how language models facilitate intelligent generalization in drug discovery.
+
+- **[Association of Artificial Intelligence–Based Chatbots With Mental Health Symptoms in College Students](https://jamanetwork.com/journals/jama/fullarticle/2825147)**  
+  *Journal: JAMA, 2023-10-03*  
+  This study evaluates AI-based chatbots' impact on mental health symptoms among students.
+
+- **[Applications of Large Language Models in Biology and Medicine: A Review](https://pubmed.ncbi.nlm.nih.gov/39405325/)**  
+  *Journal: Nature Reviews Drug Discovery, August 2023*  
+  This review discusses the emerging applications of LLMs in data analysis, drug discovery, and personalized medicine.
+
+- **[Natural Language Processing in Medical Applications](https://pmc.ncbi.nlm.nih.gov/articles/PMC11984503/)**  
+  *Journal: Journal of Medical Internet Research, 2023*  
+  This paper discusses NLP advancements in medical data interpretation and decision-making.
+
+- **[Adapting Large Language Models to Biomedical Tasks](https://arxiv.org/html/2409.04481v1)**  
+  *Journal: arXiv, September 2024*  
+  This paper discusses methods for repurposing LLMs for biomedical applications.
+
+- **[Exploiting AI-driven Language Models to Predict Interactions between Proteins and Compounds](https://www.nature.com/articles/s41598-024-61124-0)**  
+  *Journal: Scientific Reports, 2024*  
+  This paper discusses using language models to predict protein-compound interactions in biomedical research.
+
+These papers illustrate the potential of LLM-based agents to enhance research efficiency, improve clinical practices, and foster innovation in biology and medicine.