Added Yoav Kan-Tor et al. 2024 (#64)

* Smaller Font Size * scChat * Updated Filtersidebar * Added Yoav Kan-Tor et al. 2024 * add notes to gene embedding benchmark --------- Co-authored-by: Paul O.-P <[email protected]> Co-authored-by: Paul O.-P <[email protected]> Co-authored-by: Artur Szałata <[email protected]>
theislab · Dec 19, 2024 · cb47b68 · cb47b68
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diff --git a/_data/transformer-evaluation.yml b/_data/transformer-evaluation.yml
@@ -1,3 +1,15 @@
+- paper:
+    type: preprint
+    text: '[Yoav Kan-Tor et al. 2024](https://arxiv.org/abs/2412.04075)'
+    url: https://arxiv.org/abs/2412.04075
+  code:
+    type: reproducible
+    text: "[ð\x9F\x9B\_ï¸\x8FGitHub](https://github.com/BiomedSciAI/gene-benchmark)"
+    url: https://github.com/BiomedSciAI/gene-benchmark
+  omic_modalities: Natural Language, scRNAseq, protein sequence, DNA sequence
+  evaluated_transformers: Mistral, MPnet, CellPLM, GeneFormer, scGPT, DNABert2, ESM (plus bag-of-words, gene2vec)
+  tasks: genomic properties, gene regulatory functions, gene localization, gene biological processes, protein properties
+  notes: 'Evaluating model performance using gene embeddings allows comparing models utilizing different data modalities. The performance profile of a diverse set of models across ~300 gene related tasks was shown to be most influenced by the training modality.'
 - paper:
     type: preprint
     text: '[Ahlmann-Eltze et al. 2024](https://www.biorxiv.org/content/10.1101/2024.09.16.613342)'

diff --git a/_site/_data/transformer-evaluation.yml b/_site/_data/transformer-evaluation.yml
@@ -1,3 +1,15 @@
+- paper:
+    type: preprint
+    text: '[Yoav Kan-Tor et al. 2024](https://arxiv.org/abs/2412.04075)'
+    url: https://arxiv.org/abs/2412.04075
+  code:
+    type: reproducible
+    text: "[ð\x9F\x9B\_ï¸\x8FGitHub](https://github.com/BiomedSciAI/gene-benchmark)"
+    url: https://github.com/BiomedSciAI/gene-benchmark
+  omic_modalities: Natural Language, scRNAseq, protein sequence, DNA sequence
+  evaluated_transformers: Mistral, MPnet, CellPLM, GeneFormer, scGPT, DNABert2, ESM (plus bag-of-words, gene2vec)
+  tasks: genomic properties, gene regulatory functions, gene localization, gene biological processes, protein properties
+  notes: '-'
 - paper:
     type: preprint
     text: '[Ahlmann-Eltze et al. 2024](https://www.biorxiv.org/content/10.1101/2024.09.16.613342)'

diff --git a/_site/_pages/implementations.html b/_site/_pages/implementations.html
diff --git a/_site/assets/js/components/FilterButton.jsx b/_site/assets/js/components/FilterButton.jsx
@@ -6,7 +6,7 @@ const FILTER_OPTIONS = {
     { value: 'peer_reviewed', label: 'Peer Reviewed 📄' },
   ],
   code: [
-    { value: 'reproducible', label: 'Reproducible 🛠️' },
+    { value: 'reproducible', label: 'Training Code Available 🛠️' },
     { value: 'evaluation_only', label: 'Evaluation Only 🔍' },
     { value: 'none', label: 'None' },
   ],

diff --git a/_site/assets/js/components/FilterPanel.jsx b/_site/assets/js/components/FilterPanel.jsx
@@ -8,7 +8,7 @@ const FILTER_OPTIONS = {
     { value: 'peer_reviewed', label: 'Peer Reviewed 📄' },
   ],
   code: [
-    { value: 'reproducible', label: 'Reproducible 🛠️' },
+    { value: 'reproducible', label: 'Training Code Available 🛠️' },
     { value: 'evaluation_only', label: 'Evaluation Only 🔍' },
     { value: 'none', label: 'None' },
   ],

diff --git a/_site/assets/js/components/FilterSidebar.jsx b/_site/assets/js/components/FilterSidebar.jsx
@@ -8,7 +8,7 @@ const FILTER_OPTIONS = {
     { value: 'peer_reviewed', label: 'Peer Reviewed 📄' },
   ],
   code: [
-    { value: 'reproducible', label: 'Reproducible 🛠️' },
+    { value: 'reproducible', label: 'Training Code Available 🛠️' },
     { value: 'evaluation_only', label: 'Evaluation Only 🔍' },
     { value: 'none', label: 'None' },
   ],

diff --git a/_site/assets/js/dist/single-cell-transformers.bundle.js b/_site/assets/js/dist/single-cell-transformers.bundle.js
diff --git a/_site/assets/js/dist/single-cell-transformers.bundle.js.map b/_site/assets/js/dist/single-cell-transformers.bundle.js.map
diff --git a/_site/assets/js/dist/transformer-evaluation.bundle.js b/_site/assets/js/dist/transformer-evaluation.bundle.js
diff --git a/_site/assets/js/dist/transformer-evaluation.bundle.js.map b/_site/assets/js/dist/transformer-evaluation.bundle.js.map
diff --git a/_site/assets/js/dist/transformer-llms.bundle.js b/_site/assets/js/dist/transformer-llms.bundle.js
diff --git a/_site/assets/js/dist/transformer-llms.bundle.js.map b/_site/assets/js/dist/transformer-llms.bundle.js.map
diff --git a/_site/feed.xml b/_site/feed.xml
@@ -1 +1 @@
-<?xml version="1.0" encoding="utf-8"?><feed xmlns="http://www.w3.org/2005/Atom" ><generator uri="https://jekyllrb.com/" version="4.3.4">Jekyll</generator><link href="http://localhost:4000/single-cell-transformer-papers/feed.xml" rel="self" type="application/atom+xml" /><link href="http://localhost:4000/single-cell-transformer-papers/" rel="alternate" type="text/html" /><updated>2024-12-18T09:50:36+01:00</updated><id>http://localhost:4000/single-cell-transformer-papers/feed.xml</id><title type="html">Transformers in Single-Cell Omics</title><subtitle>A curated collection of papers on transformers in single-cell analysis</subtitle></feed>
+<?xml version="1.0" encoding="utf-8"?><feed xmlns="http://www.w3.org/2005/Atom" ><generator uri="https://jekyllrb.com/" version="4.3.4">Jekyll</generator><link href="http://localhost:4000/single-cell-transformer-papers/feed.xml" rel="self" type="application/atom+xml" /><link href="http://localhost:4000/single-cell-transformer-papers/" rel="alternate" type="text/html" /><updated>2024-12-18T20:50:24+01:00</updated><id>http://localhost:4000/single-cell-transformer-papers/feed.xml</id><title type="html">Transformers in Single-Cell Omics</title><subtitle>A curated collection of papers on transformers in single-cell analysis</subtitle></feed>
diff --git a/_site/implementations.html b/_site/implementations.html
diff --git a/_site/index.html b/_site/index.html
diff --git a/_site/single-cell-transformers.html b/_site/single-cell-transformers.html
diff --git a/_site/transformer-evaluation.html b/_site/transformer-evaluation.html
diff --git a/_site/transformer-llms.html b/_site/transformer-llms.html
diff --git a/assets/js/components/FilterButton.jsx b/assets/js/components/FilterButton.jsx
@@ -6,7 +6,7 @@ const FILTER_OPTIONS = {
     { value: 'peer_reviewed', label: 'Peer Reviewed 📄' },
   ],
   code: [
-    { value: 'reproducible', label: 'Reproducible 🛠️' },
+    { value: 'reproducible', label: 'Training Code Available 🛠️' },
     { value: 'evaluation_only', label: 'Evaluation Only 🔍' },
     { value: 'none', label: 'None' },
   ],

diff --git a/assets/js/components/FilterPanel.jsx b/assets/js/components/FilterPanel.jsx
@@ -8,7 +8,7 @@ const FILTER_OPTIONS = {
     { value: 'peer_reviewed', label: 'Peer Reviewed 📄' },
   ],
   code: [
-    { value: 'reproducible', label: 'Reproducible 🛠️' },
+    { value: 'reproducible', label: 'Training Code Available 🛠️' },
     { value: 'evaluation_only', label: 'Evaluation Only 🔍' },
     { value: 'none', label: 'None' },
   ],

diff --git a/assets/js/components/FilterSidebar.jsx b/assets/js/components/FilterSidebar.jsx
@@ -8,7 +8,7 @@ const FILTER_OPTIONS = {
     { value: 'peer_reviewed', label: 'Peer Reviewed 📄' },
   ],
   code: [
-    { value: 'reproducible', label: 'Reproducible 🛠️' },
+    { value: 'reproducible', label: 'Training Code Available 🛠️' },
     { value: 'evaluation_only', label: 'Evaluation Only 🔍' },
     { value: 'none', label: 'None' },
   ],

diff --git a/assets/js/dist/single-cell-transformers.bundle.js b/assets/js/dist/single-cell-transformers.bundle.js
diff --git a/assets/js/dist/single-cell-transformers.bundle.js.map b/assets/js/dist/single-cell-transformers.bundle.js.map
diff --git a/assets/js/dist/transformer-evaluation.bundle.js b/assets/js/dist/transformer-evaluation.bundle.js
diff --git a/assets/js/dist/transformer-evaluation.bundle.js.map b/assets/js/dist/transformer-evaluation.bundle.js.map
diff --git a/assets/js/dist/transformer-llms.bundle.js b/assets/js/dist/transformer-llms.bundle.js
diff --git a/assets/js/dist/transformer-llms.bundle.js.map b/assets/js/dist/transformer-llms.bundle.js.map
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		@@ -1 +1 @@
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