I am a current Quantitative Researcher at Squarepoint Capital and a recent PhD graduate from Princeton University. During my PhD, I was very fortunate to be advised by Ben Raphael, with whom I tackled problems in phylogenetics and machine learning.

In detail, I applied linear and convex optimization techniques to large-scale phylogenetic problems in cancer evolution (fastBE) and ancestral reconstruction (tree labeling polytope). In my final year, I applied similar tools to design constant-factor approximation algorithms for low-rank optimal transport. I also worked on a handful of practical problems during my PhD. Most notably, I designed a tool for CRISPR guideRNA design that played a very small role in correcting a disease-causing genetic variant in a seven month-old patient, see the New York Times coverage of the story.

Selected Publications

Transport clustering: solving low-rank optimal transport via clustering
Henri Schmidt*, Peter Halmos*, and Benjamin J. Raphael
International Conference on Machine Learning, July 2026. [poster]

LAML-Pro: Joint maximum likelihood inference of cell genotypes and cell lineage trees
Gillian Chu*, Henri Schmidt*, and Benjamin J. Raphael
Bioinformatics, July 7th, 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.

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