Brian Hie | Genome Modeling & Design Across All Domains of Life | Stanford HAI
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eventSeminar

Brian Hie | Genome Modeling & Design Across All Domains of Life

Status
Past
Date
Tuesday, September 30, 2025 12:00 PM - 1:15 PM PST/PDT
Location
Gates Computer Science Building 353 Jane Stanford Wy Room 119 Stanford, CA, 94305
Topics
Sciences (Social, Health, Biological, Physical)
Overview
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All of life encodes information with DNA. While tools for sequencing, synthesis, and editing of genomic code have transformed biological research, intelligently composing new biological systems would also require a deep understanding of the immense complexity encoded by genomes.

Overview
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Event Contact
Stanford HAI
stanford-hai@stanford.edu

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We introduce Evo 2, a biological foundation model trained on 9.3 trillion DNA base pairs from a highly curated genomic atlas spanning all domains of life. We train Evo 2 with 7B and 40B parameters to have an unprecedented 1 million token context window with single-nucleotide resolution. Evo 2 learns from DNA sequence alone to accurately predict the functional impacts of genetic variation—from noncoding pathogenic mutations to clinically significant BRCA1 variants—without task-specific finetuning. Applying mechanistic interpretability analyses, we reveal that Evo 2 autonomously learns a breadth of biological features, including exon–intron boundaries, transcription factor binding sites, protein structural elements, and prophage genomic regions. Beyond its predictive capabilities, Evo 2 generates mitochondrial, prokaryotic, and eukaryotic sequences at genome scale with greater naturalness and coherence than previous methods. Guiding Evo 2 via inference-time search enables controllable generation of epigenomic structure, for which we demonstrate the first inference-time scaling results in biology. We make Evo 2 fully open, including model parameters, training code, inference code, and the OpenGenome2 dataset, to accelerate the exploration and design of biological complexity.


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Speaker
Brian Hie
Assistant Professor of Chemical Engineering at Stanford University | HAI Faculty Affiliate, Stanford HAI

In collaboration with