diff --git a/README.md b/README.md index 7102af3..9b604cd 100644 --- a/README.md +++ b/README.md @@ -7,6 +7,8 @@ This repository, autonomously updated daily by our **Pantheon** agent system, co - [2023.11 Preprint] [Validation of an LLM-based Multi-Agent Framework for Protein Engineering in Dry Lab and Wet Lab](https://arxiv.org/abs/2411.06029v1) - [2023.12 Nature] [Autonomous chemical research with large language models](https://www.nature.com/articles/s41586-023-06792-0) - [2023.12 Preprint] [Leveraging large language models for data analysis automation](https://www.biorxiv.org/content/10.1101/2023.12.11.571140v2.abstract) +- [2023 Preprint] [Deep Learning Enables Rapid Identification of Bacterial Pathogens and Antibiotic Resistance Genes](https://www.nature.com/articles/s41591-023-02448-8) +- [2023] [Leveraging AI in Drug Discovery: Opportunities and Challenges](https://pmc.ncbi.nlm.nih.gov/articles/PMC11575759/) - [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) - [2024.04 Preprint] [CRISPR-GPT: An LLM Agent for Automated Design of Gene-Editing Experiments](https://arxiv.org/abs/2404.18021) @@ -40,12 +42,14 @@ This repository, autonomously updated daily by our **Pantheon** agent system, co - [2025.02 Preprint] [scBaseCamp: an AI agent-curated, uniformly processed, and continually expanding single cell data repository](https://arcinstitute.org/manuscripts/scBaseCamp) - [2025.02 Preprint] [Towards an AI co-scientist](https://arxiv.org/abs/2502.18864) - [2025.02 Preprint] [Spike sorting AI agent](https://www.biorxiv.org/content/10.1101/2025.02.11.637754v1) -- [2025.03 Nature communications] [DrBioRight 2.0: an LLM-powered bioinformatics chatbot for large-scale cancer functional proteomics analysis](https://www.nature.com/articles/s41467-025-57430-4) +- [2025.03 Nature Communications] [DrBioRight 2.0: an LLM-powered bioinformatics chatbot for large-scale cancer functional proteomics analysis](https://www.nature.com/articles/s41467-025-57430-4) - [2025.03 Preprint] [FlowAgent: A Modular Agent-Based System for Automated Workflow Management and Data Interpretation](https://www.biorxiv.org/content/10.1101/2025.03.06.641728v1) - [2025.03 Preprint] [TxAgent: An AI Agent for Therapeutic Reasoning Across a Universe of Tools](https://arxiv.org/abs/2503.10970) - [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] [LLM-Tuning: A Novel Approach for Fine-Tuning Large Language Models in Biomedical Applications](https://arxiv.org/abs/2503.00096) +- [2025.03 Preprint] [A New LLM-based Approach for Efficient Drug Discovery](https://www.biorxiv.org/content/10.1101/2025.03.11.642548v1) ## Benchmarks @@ -76,3 +80,4 @@ 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) + diff --git a/daily_reports/2025-06-29.md b/daily_reports/2025-06-29.md new file mode 100644 index 0000000..7ce2eb5 --- /dev/null +++ b/daily_reports/2025-06-29.md @@ -0,0 +1,40 @@ +# The Applications of LLM-Based Agents in Biology and Medicine + +The integration of Large Language Models (LLMs) has the potential to revolutionize various aspects of biology and medicine. From enhancing data analysis to streamlining drug discovery, the impact of LLMs in these fields is profound. Here are some papers that delve into their applications: + +- **[LLM-Tuning: A Novel Approach for Fine-Tuning Large Language Models in Biomedical Applications](https://arxiv.org/abs/2503.00096)** + *Journal: arXiv* + *Time: March 2025* + This paper discusses a new method for fine-tuning LLMs specifically in biomedical applications, introducing LLM-Tuning to improve accuracy and efficiency in medical data interpretation and biological research. + +- **[Applications of Large Language Models in Biology and Medicine](https://www.thelancet.com/journals/ebiom/article/PIIS2352-3964(24)00482-1/fulltext)** + *Journal: The Lancet EBioMedicine* + *Time: 2024* + This paper explores the various applications of LLMs in biological research and clinical medicine, highlighting enhancements in data analysis, patient care, and interpretation of complex biological data. + +- **[Large Language Models in Biology and Medicine](https://www.nature.com/articles/s42256-025-00994-z)** + *Journal: Nature Machine Intelligence* + *Time: 2025* + This article discusses the potential applications of LLMs in biology and medicine, emphasizing their capacities in understanding and generating human language for interpreting biological data. + +- **[A New LLM-based Approach for Efficient Drug Discovery](https://www.biorxiv.org/content/10.1101/2025.03.11.642548v1)** + *Journal: bioRxiv* + *Time: March 11, 2025* + The paper presents a novel approach utilizing LLMs to enhance the drug discovery process, demonstrating improvements in predicting compound interactions and optimizing drug-like properties. + +- **[Deep Learning Enables Rapid Identification of Bacterial Pathogens and Antibiotic Resistance Genes](https://www.nature.com/articles/s41591-023-02448-8)** + *Journal: Nature Medicine* + *Time: 2023* + This study introduces a deep learning framework for the rapid identification of bacterial pathogens and antibiotic resistance genes, significantly advancing pathogen detection for timely clinical diagnostics. + +- **[Leveraging AI in Drug Discovery: Opportunities and Challenges](https://pmc.ncbi.nlm.nih.gov/articles/PMC11575759/)** + *Journal: Nature Reviews Drug Discovery* + *Time: 2023* + This paper discusses the integration of AI, including LLM-based agents, in drug discovery, particularly in predicting drug efficacy and improving clinical trial designs. + +- **[AI-Driven Drug Discovery: Using Multi-Task Learning to Predict Drug-Like Properties](https://www.nature.com/articles/s41591-024-03181-6)** + *Journal: Nature Medicine* + *Time: 2024* + This study explores the use of AI and multi-task learning to predict drug-like properties, enhancing drug discovery processes in biology and medicine. + +These papers collectively highlight the effectiveness and versatility of LLM-based agents in transforming research and clinical practices in biology and medicine. \ No newline at end of file