qizhipei/awesome-biomolecule-language-cross-modeling

Awesome-Biomolecule-Language-Cross-Modeling: a curated list of resources for paper "Leveraging Biomolecule and Natural Language through Multi-Modal Learning: A Survey"

Qizhi Pei

• 🔭 I’m Qizhi Pei, a second-year PhD student from Gaoling School of Artificial Intelligence, RUC.
• 🌱 I’m currently doing research about AI4Science, especially for 3D biomolecular modeling and multi-modal learning on biomolecule.
• 📫 How to reach me:
  • Website: https://qizhipei.github.io
  • Email: [email protected]

awesome-biomolecule-language-cross-modeling's Issues

scGPT

Would scGPT worth to be added ?
https://www.nature.com/articles/s41592-024-02201-0
https://github.com/bowang-lab/scGPT

Add dataset of GIMLET

The work GIMLET: A Unified Graph-Text Model for Instruction-Based Molecule Zero-Shot Learning also releases instruction datasets for both pretraining and testing available at their github code https://github.com/zhao-ht/GIMLET and on huggingface: https://huggingface.co/datasets/haitengzhao/molecule_property_instruction. Hope this can be added to the dataset list ^^

Add several datasets from https://github.com/kjappelbaum/awesome-chemistry-datasets

You can refer to kjappelbaum's awesome-chemistry-datasets to add more datasets

Like:
text datasets

• BC5CDR:1500 PubMed articles with 4409 annotated chemicals, 5818 diseases and 3116 chemical-disease interactions (named entity recognition)
• BioCreative V: BC5CDR corpus consists of 1500 PubMed articles with 4409 annotated chemicals, 5818 diseases and 3116 chemical-disease interactions.
• Elsevier Corpus: This is a corpus of 40k (40,001) open access (OA) CC-BY articles from across Elsevier’s journals represent the first cross-discipline research of data at this scale to support NLP and ML research.
• Europe PMC - Bulk download of full text and SI of > 5 million articles.
  ...

Would it better to sort along time?

Thx for your great job. Would it be easier to follow if articles in various fields were arranged in chronological order? If need help, glad to join this project.