From ab394901608cf10a8f3194cf91e83ed7f0923286 Mon Sep 17 00:00:00 2001 From: Paul <88028027+Paulos2411@users.noreply.github.com> Date: Wed, 29 Jan 2025 17:04:37 +0100 Subject: [PATCH 1/3] Update transformer-evaluation.yml --- _data/transformer-evaluation.yml | 16 ---------------- 1 file changed, 16 deletions(-) diff --git a/_data/transformer-evaluation.yml b/_data/transformer-evaluation.yml index e60c041..3a09984 100644 --- a/_data/transformer-evaluation.yml +++ b/_data/transformer-evaluation.yml @@ -26,22 +26,6 @@ tasks: '-' notes: '-' - -- paper: - type: preprint - text: '[George Crowley et al. 2024](https://www.biorxiv.org/content/10.1101/2024.10.10.617605v1.full.pdf)' - url: https://www.biorxiv.org/content/10.1101/2024.10.10.617605v1.full.pdf - code: - type: 'reproducible' - text: '[ð\x9F\x9B\_ï¸\x8FGitHub](https://github.com/ggit12/anndictionary/)' - url: 'https://github.com/ggit12/anndictionary/' - omic_modalities: '-' - evaluated_transformers: '-' - tasks: '-' - notes: '-' - - - - paper: type: preprint text: '[George Crowley et al. 2024](https://www.biorxiv.org/content/10.1101/2024.10.10.617605v1.full.pdf)' From acdb42cce9bb4e71774f69e2d8d55f93264379fe Mon Sep 17 00:00:00 2001 From: Paulos2411 Date: Tue, 11 Feb 2025 13:33:16 +0100 Subject: [PATCH 2/3] Added Models and Fixed Document Generation --- .github/workflows/document-generation.yml | 6 ++-- _data/single-cell-transformers.yml | 35 +++++++++++++++++++++++ 2 files changed, 38 insertions(+), 3 deletions(-) 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..7cf9942 100644 --- a/_data/single-cell-transformers.yml +++ b/_data/single-cell-transformers.yml @@ -1,3 +1,38 @@ +- 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 From 4f0719e58a235df409e5267236e6bf1894aa2c22 Mon Sep 17 00:00:00 2001 From: Paulos2411 Date: Tue, 11 Feb 2025 13:40:41 +0100 Subject: [PATCH 3/3] BioLLM --- _data/single-cell-transformers.yml | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/_data/single-cell-transformers.yml b/_data/single-cell-transformers.yml index 7cf9942..6cfa862 100644 --- a/_data/single-cell-transformers.yml +++ b/_data/single-cell-transformers.yml @@ -1,3 +1,22 @@ +- 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