Merge branch 'theislab:main' into main

theislab · Jan 21, 2025 · 3bc51e4 · 3bc51e4
2 parents b0a7508 + c8387f4
commit 3bc51e4
Showing 1 changed file with 12 additions and 0 deletions.
diff --git a/_data/transformer-evaluation.yml b/_data/transformer-evaluation.yml
@@ -194,3 +194,15 @@
   evaluated_transformers: scGPT, Geneformer, scBERT
   tasks: Cell type annotation
   notes: Focused on imbalanced cell type classification. Geneformer appears to be outperformed by scGPT and scBERT, where the two latter perform similarly.
+- paper:
+    type: preprint
+    text: '[Csendes et al. 2024](https://www.biorxiv.org/content/10.1101/2024.09.30.615843v1)'
+    url: https://www.biorxiv.org/content/10.1101/2024.09.30.615843v1
+  code:
+    type: reproducible
+    text: "[ð\x9F\x9B\_ï¸\x8FGitHub](https://github.com/turbine-ai/PerturbSeqPredBenchmark)"
+    url: https://github.com/turbine-ai/PerturbSeqPredBenchmark
+  omic_modalities: scRNA-seq
+  evaluated_transformers: scGPT
+  tasks: Genetic perturbation effect prediction
+  notes: Simple baseline models can outperform scGPT on perturbational downstream tasks. The most widely used benchmarking datasets contain significant biases, making them suboptimal for evaluation.