Extended Data Fig. 3: Full integration metrics per dataset.
From: Modeling fragment counts improves single-cell ATAC-seq analysis
Comparison of integration accuracy for Poisson VAE, Binary VAE, PeakVI9, Signac3 using LSI, cisTopic8 using LDA and SCALE10 on (a) the NeurIPS, (b) the Satpathy (c) the fly and (d) the sci-ATAC-seq3 datasets. For cisTopic and Signac, additional batch correction was performed using Harmony28. Metrics are categorized into batch correction and bioconservation categories. Reported is the mean over ten cross-validation runs. Overall scores were computed using a 40:60-weighted mean of batch correction and bioconservation scores.
