# BASILISC

Cross-modal single-cell matching has returned a match but rarely a confidence. BASILISC places a Bayesian posterior over a siamese network of two modalities and defines uncertainty on the correspondence between a pair of cells, tested on multi-omics benchmarks where the true pairing is known. At the cell-type level, discarding the least certain fifth of pairs raises accuracy from 0.93 to 0.98; at the cell level, the posterior flags wrong matches that cross a cell-type boundary better than a deterministic read of the same scores, AUROC 0.68 against 0.64.

Cross-modal single-cell matching has returned a match but rarely a confidence. BASILISC places a Bayesian posterior over a siamese network of two modalities and defines uncertainty on the correspondence between a pair of cells, tested on multi-omics benchmarks where the true pairing is known. At the cell-type level, discarding the least certain fifth of pairs raises accuracy from 0.93 to 0.98; at the cell level, the posterior flags wrong matches that cross a cell-type boundary better than a deterministic read of the same scores, AUROC 0.68 against 0.64.