diff --git a/.github/workflows/document-generation.yml b/.github/workflows/document-generation.yml index 61a82a9..bacf47f 100644 --- a/.github/workflows/document-generation.yml +++ b/.github/workflows/document-generation.yml @@ -14,7 +14,7 @@ jobs: # Setup Python for notebook conversion - name: Set up Python - uses: actions/setup-python@v2 + uses: actions/setup-python@v4 with: python-version: '3.x' @@ -54,13 +54,13 @@ jobs: # Upload artifacts - name: Upload PDF artifacts - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: pdfs path: _pages/*.pdf - name: Upload Notebook artifacts - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: notebooks path: _pages/*.ipynb \ No newline at end of file diff --git a/_data/single-cell-transformers.yml b/_data/single-cell-transformers.yml index a707897..6cfa862 100644 --- a/_data/single-cell-transformers.yml +++ b/_data/single-cell-transformers.yml @@ -1,3 +1,57 @@ +- model: BioLLM + paper: + type: preprint + text: '[Ping Qiu, et al. 2024](https://www.biorxiv.org/content/10.1101/2024.11.22.624786v1.full.pdf)' + url: https://www.biorxiv.org/content/10.1101/2024.11.22.624786v1.full.pdf + code: + type: reproducible + text: "[ð\x9F\x9B\_ï¸\x8FGithub](https://github.com/BGIResearch/BioLLM)" + url: https://github.com/BGIResearch/BioLLM + omic_modalities: '-' + pre_training_dataset: '-' + input_embedding: '-' + architecture: '-' + ssl_tasks: '-' + supervised_tasks: '-' + + + + +- model: scGPT-spatial + paper: + type: preprint + text: '[Chloe Wang, et al. 2024](https://www.biorxiv.org/content/10.1101/2025.02.05.636714v1.full.pdf)' + url: https://www.biorxiv.org/content/10.1101/2025.02.05.636714v1.full.pdf + code: + type: reproducible + text: "[ð\x9F\x9B\_ï¸\x8FGithub](https://github.com/bowang-lab/scGPT-spatial)" + url: https://github.com/bowang-lab/scGPT-spatial + omic_modalities: '-' + pre_training_dataset: '-' + input_embedding: '-' + architecture: '-' + ssl_tasks: '-' + supervised_tasks: '-' + + +- model: MAMMAL - Molecular Aligned Multi-Modal Architecture and Language + paper: + type: preprint + text: '[Yoel Shoshan, et al. 2024](https://arxiv.org/pdf/2410.22367)' + url: https://arxiv.org/pdf/2410.22367 + code: + type: reproducible + text: "[ð\x9F\x9B\_ï¸\x8FGithub](https://github.com/BiomedSciAI/biomed-multi-alignment)" + url: https://github.com/BiomedSciAI/biomed-multi-alignment + omic_modalities: '-' + pre_training_dataset: '-' + input_embedding: '-' + architecture: '-' + ssl_tasks: '-' + supervised_tasks: '-' + + + - model: scCello paper: type: peer_reviewed