Chen (Benjamin) Hsieh

I'm a bioinformatics PhD candidate at the University of Georgia, defending in Fall/Winter 2026. My dissertation is on gene duplication in Populus . Lately much of my attention has turned to genomic foundation models , and this fall I'm also consulting part-time with the Computational Biology Consulting Group at IOB.

One question I keep returning to: these models post strong benchmark numbers, yet biologically meaningless edits can still flip their predictions. I test them under constraints a biologist would accept, then look inside to understand what changed.

Five peer-reviewed papers, mostly in plant genomics. I am looking for computational biology and ML research roles beginning Fall 2026, particularly the evaluation and interpretation of models over biological sequence data. My resume is here , and I am always glad to hear from you by email .

Featured right now

Current research · under review
Adversarial Robustness of Genomic Foundation Models
Biologically-valid adversarial edits still flip predictions from six DNA/RNA foundation models. LoRA-based defenses cut attack success roughly in half. Read more →
Open source · on PyPI
Open-Source Research Tooling
SLURM cost reporting, GPU/HPC job templates, and portable agentic research workflows — the infrastructure from my own research, packaged for reuse. Read more →

Projects

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A few things people ask

When do you graduate?

December 2026, and I can start work from Fall 2026.

What kind of role are you looking for?

Two, and I would rather be plain about both. Primarily computational biology and ML research — the evaluation and interpretation of models over biological sequence data. I am also preparing for management consulting, which the case training and the PhD Consulting Club role were for. The consulting page covers both.

Is the foundation-model work published?

Not yet. It was submitted to a workshop in August 2026 and is under review. Until that clears, the numbers on that page are our internal results, not peer-reviewed findings.

What is CBCG?

The Computational Biology Consulting Group at the UGA Institute of Bioinformatics, led by Dr. Casey Bergman. It helps labs with computational problems they'd otherwise improvise. More on the consulting page .

Can I use your code?

Yes. The research tooling is on GitHub , and some of it is on PyPI. If something is broken or undocumented, let me know and I'll see to it.

Elsewhere