From 33bdee152dea48d0b1ad29e8f81652d7076509f8 Mon Sep 17 00:00:00 2001
From: Jan Pennekamp <39992834+jpennekamp@users.noreply.github.com>
Date: Thu, 19 Dec 2024 23:43:23 +0100
Subject: [PATCH] add mcBERT (closes #39) (#65)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Artur Szałata <arturs6668@gmail.com>
---
 _data/single-cell-transformers.yml | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/_data/single-cell-transformers.yml b/_data/single-cell-transformers.yml
index 3c6b568..6e6c2c5 100644
--- a/_data/single-cell-transformers.yml
+++ b/_data/single-cell-transformers.yml
@@ -1,3 +1,18 @@
+- model: mcBERT
+  paper:
+    type: preprint
+    text: '[von Querfurth et al. 2024](https://doi.org/10.1101/2024.11.04.621897)'
+    url: https://doi.org/10.1101/2024.11.04.621897
+  code:
+    type: reproducible
+    text: "[ð\x9F\x9B\_ï¸\x8FGithub](https://github.com/COMSYS/mcBERT)"
+    url: https://github.com/COMSYS/mcBERT
+  omic_modalities: scRNA-seq
+  pre_training_dataset: 7M cells single tissue, human (see Table 1 in the paper; heart, kidney, PBMC, and lung)
+  input_embedding: Cells as tokens + value projection
+  architecture: Transformer Encoder / BERT
+  ssl_tasks: MLM on cell-level, based on unmasked cells of patient
+  supervised_tasks: Phenotype classification
 - model: CancerFoundation
   paper:
     type: preprint