Harmony-Pytorch

Dec 30, 2025·
Dr. Bo Li
Dr. Bo Li
Yiming Yang
Yiming Yang
· 1 min read

Harmony-PyTorch is an efficient PyTorch implementation of Harmony algorithm, used for data integration and batch correction.

It has been adopted by rapids-singlecell (a GPU-accelerated single-cell analysis python package designed specific for NVIDIA devices; part of scverse) for its implementation on Harmony batch correction method. See release notes.

Python Data Integration Batch Correction PyTorch
Dr. Bo Li
Authors
Dr. Bo Li
Principal Scientist II
Dr. Bo Li is a Principal Scientist at Genentech, Inc. His research focuses on large-scale single-cell genomics data analysis. Before joining in Genentech, he was an Assistant Professor of Medicine at Harvard Medical School and the director of Bioinformatics and Computational Biology at Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital. He received his Ph.D. in computer science from UW-Madison and completed two postdoctoral trainings with Dr. Lior Pachter at UC Berkeley and Dr. Aviv Regev at Broad Institute. He is best known for developing RSEM, an impactful RNA-seq transcript quantification software. RSEM is cited 22,602 times (Google Scholar) and adopted by several big consortia such as TCGA, ENCODE, GTEx and TOPMed.
Yiming Yang
Authors
Yiming Yang
Bioinformatics Software Engineer
Yiming Yang is a bioinformatics software engineer in Li Lab.