Add BABEL method (ATAC->GEX prediction) - #19
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Ports BABEL (Wu et al. 2021, PNAS) as a train/predict method pair for predicting RNA expression from scATAC-seq accessibility. Uses a dense RNA encoder/decoder and a chromosome-split ATAC encoder/decoder, trained jointly with a negative binomial loss for RNA and BCE for binarized ATAC accessibility. Verified end-to-end via viash run against real bmmc_multiome/swap data (Docker build, training, prediction): 0.34 mean per-cell correlation with ground truth, in line with the existing knnr_py baseline on the same data.As BABEl is not installable in its original implmentation, code was rewritten here.
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Ports BABEL (Wu et al. 2021, PNAS) as a train/predict method pair for predicting RNA expression from scATAC-seq accessibility. Uses a dense RNA encoder/decoder and a chromosome-split ATAC encoder/decoder, trained jointly with a negative binomial loss for RNA and BCE for binarized ATAC accessibility.
Verified end-to-end via viash run against real bmmc_multiome/swap data (Docker build, training, prediction): 0.34 mean per-cell correlation with ground truth, in line with the existing knnr_py baseline on the same data.As BABEl is not installable in its original implmentation, code was rewritten here.
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Proposed changes are described in the CHANGELOG.md
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