Added Models and Fixed Document Generation Error (#85)

* Update transformer-evaluation.yml

* Added Models and Fixed Document Generation

* BioLLM

.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

_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