This curated reading list focuses on the intersection of AI and biology, offering a selection of key papers and resources. Currently includes the following areas:
- Protein 🔥
- Foundation models 🔥
- Large deep learning models for biology (e.g., biomolecule, biomedical, ...)
- Others
- unclassified yet (e.g., RNA, BioText, ...)
🚀 This list is currently collected manually in tabular form:
| Tag | Title | Pub.&Year | Notes |
|---|---|---|---|
| [Survey] / [Benchmark] / Abbreviation | Paper title | e.g., bioRxiv '2024 | code, blog, or some important notes |
🚀 A glimpse into AI4Science: Scientific discovery in the age of artificial intelligence (Nature '2023)
- A recent comprehensive survey: Advances of Deep Learning in Protein Science: A Comprehensive Survey (Science China Information Sciences' 2024)
- A recent comprehensive "Protein desigen & Structure prediction" benchmark: ProteinBench: A Holistic Evaluation of Protein Foundation Models (Arxiv' 2024)
| Topic | What's it about? |
|---|---|
| Immunity-related | HLA, T-cell receptor (TCR), Antibody, Antigen, ... |
| Protein representation | Protein Language model, structure representation, ... |
| Protein meets LLM | After the emergence of ChatGPT |
| Protein design | Design protein sequence |
| Structure prediction | Sequence to structure, AlphaFold and its applications |
| Protein interaction | Protein-protein/ligand interaction, Docking |
| [To be updated] |
- Must-read article: The Next Frontier For Large Language Models Is Biology (2023)
- For protein foundation models, see Protein section: Protein representation, Protein meets LLM, ...
| Title | Pub.&Year | Notes | |
|---|---|---|---|
| [Survey] | Leveraging Biomolecule and Natural Language through Multi-Modal Learning: A Survey | Arxiv '2024 | |
| [Survey] | Foundation Model for Advancing Healthcare: Challenges, Opportunities, and Future Directions | Arxiv '2024 | pape list |
| BioBridge | BioBridge: Bridging Biomedical Foundation Models via Knowledge Graphs | ICLR '2024 | code |
| Title | Pub.&Year | Notes | |
|---|---|---|---|
| Geneformer | Transfer learning enables predictions in network biology | Nature '2023 | |
| CancerGPT | CancerGPT: Few-shot Drug Pair Synergy Prediction using Large Pre-trained Language Models | npj Digital Medicine '2024 | |