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add mcBERT (closes #39) (#65)
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Co-authored-by: Artur Szałata <[email protected]>
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jpennekamp and szalata authored Dec 19, 2024
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- 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: "\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
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