From 12a94dc794e03518448e25d209b5b6c25c71f2cd Mon Sep 17 00:00:00 2001
From: Xinyu Yuan <katarinayuan@pku.edu.cn>
Date: Tue, 4 Feb 2025 15:58:27 -0500
Subject: [PATCH] add scCello (#82)

* add scCello

* Update single-cell-transformers.yml

* Update single-cell-transformers.yml

---------

Co-authored-by: Paul <88028027+Paulos2411@users.noreply.github.com>
---
 _data/single-cell-transformers.yml | 32 +++++++++++++++---------------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/_data/single-cell-transformers.yml b/_data/single-cell-transformers.yml
index b5816e3..a707897 100644
--- a/_data/single-cell-transformers.yml
+++ b/_data/single-cell-transformers.yml
@@ -1,3 +1,19 @@
+- model: scCello
+  paper:
+    type: peer_reviewed
+    text: '[Yuan, Xinyu, et al. 2024](https://openreview.net/pdf?id=aeYNVtTo7o)'
+    url: https://openreview.net/pdf?id=aeYNVtTo7o
+  code:
+    type: reproducible
+    text: "[ð\x9F\x9B\_ï¸\x8FGithub](https://github.com/DeepGraphLearning/scCello)"
+    url: https://github.com/DeepGraphLearning/scCello
+  omic_modalities: scRNA-seq
+  pre_training_dataset: 23M / cross-tissue, human ([CELLxGENE](https://cellxgene.cziscience.com/))
+  input_embedding: 'Ordering: rank-based'
+  architecture: Encoder
+  ssl_tasks: 'Multi-level pre-training: MLM with CE loss for gene level modeling; an ontologybased cell-type coherence loss for intra-cellular level modeling; a relational alignment loss to inject cell-type lineage from cell ontology graph for inter-cellular level modeling'
+  supervised_tasks: 'fine-tuning tasks: cell type classification; zero-shot tasks: cell type annotation, marker gene prediction, novel cell type prediction, cancer drug prediction'
+
 - model: scGREAT
   paper:
     type: peer_reviewed
@@ -145,22 +161,6 @@
   supervised_tasks: '-'
 
 
-- model: scCello
-  paper:
-    type: preprint
-    text: '[Xinyu Yuan et al. 2024](https://github.com/theislab/single-cell-transformer-papers/issues/32)'
-    url: https://github.com/theislab/single-cell-transformer-papers/issues/32
-  code:
-    type: '-'
-    text: "[ð\x9F\x94\x8DGitHub](https://github.com/DeepGraphLearning/scCello)"
-    url: 'https://github.com/DeepGraphLearning/scCello'
-  omic_modalities: '-'
-  pre_training_dataset: '-'
-  input_embedding: '-'
-  architecture: '-'
-  ssl_tasks: '-'
-  supervised_tasks: '-'
-
 - model: scGenePT
   paper:
     type: preprint