I am a recent PhD graduate in Computer Science at Princeton University. I was very fortunate to be advised by Ben Raphael. Prior to working with Ben Raphael, I completed a Bachelor of Science in Math and Computer Science at Tufts University, where I worked with Lenore Cowen designing algorithms for protein-to-protein interaction networks.
My PhD research employed techniques from combinatorial and convex optimization to study problems in biology and machine learning. For example, I applied linear and convex optimization techniques to large-scale phylogenetic problems in cancer evolution (fastBE) and ancestral reconstruction (tree labeling polytope). In the last year of my PhD, I applied similar tools to design approximation algorithms for low-rank optimal transport.
Recent Updates
- (May 2026) Our paper on low-rank OT (transport clustering) was accepted for presentation at ICML 2026.
- (February 2026) Our papers LAML-Pro and POTTR were accepted for presentation at ISMB 2026 and RECOMB 2026, respectively.
- (July 2025) I presented our work fastppm at ISMB 2025.
- (January 2025) Our preprint Fast tumor phylogeny regression via tree-structured dual dynamic programming is now available on bioRxiv.
- (December 2024) The tree labeling polytope manuscript was accepted for presentation at RECOMB2025.
Selected Publications
Transport clustering: solving low-rank optimal transport via clustering
Henri Schmidt*, Peter Halmos*, and Benjamin J. Raphael
Presenting at ICML 2026. [openreview]
LAML-Pro: Joint maximum likelihood inference of cell genotypes and cell lineage trees
Gillian Chu*, Henri Schmidt*, and Benjamin J. Raphael
bioRxiv, March 27th, 2026. Presenting at ISMB 2026.
The tree labeling polytope: a unified approach to ancestral reconstruction problems
Henri Schmidt and Benjamin J. Raphael
bioRxiv, February 19th, 2025. Presented at RECOMB 2025. [slides]
Fast tumor phylogeny regression via tree-structured dual dynamic programming†
Henri Schmidt*, Yuanyuan Qi*, Benjamin J. Raphael, and Mohammed El-Kebir
Bioinformatics, Volume 41, July 2025. Presented at ISMB 2025. [slides]
Genome-wide CRISPR guide RNA design and specificity analysis with GuideScan2
Henri Schmidt*, Minsi Zhang*, Haralambos Mourelatos, Francisco J. Sánchez-Rivera, Scott W. Lowe, Andrea Ventura, Christina S. Leslie, Yuri Pritykin
Genome Biology, Volume 26, Article 41, February 26, 2025.