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Stephen Lu
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Stephen Lu

@stephenzlu
馃嚚馃嚘 | ai for bio | cs phd @berkeley_ai | prev @bighatbio, @mcgillu
Berkeley, California
matrixmaster.me
Joined December 2019
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  • Pinned
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    Stephen Lu
    @stephenzlu
    Jun 8
    Antibody LMs learn what looks antibody-like, but not how selection turns naive germline antibodies into strong binders. @aakarshv1 and I are excited to share CoSiNE, a model that learns this germline-to-mature process for variant effect prediction and antibody design. (1/8)
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    Stephen Lu
    @stephenzlu
    Jul 5
    Heading to ICML! 鉁堬笍 @aakarshv1 and I will be presenting this work on Thursday during poster session 8. Come say hi at poster #808!
    user avatar
    Stephen Lu
    @stephenzlu
    Jun 8
    Antibody LMs learn what looks antibody-like, but not how selection turns naive germline antibodies into strong binders. @aakarshv1 and I are excited to share CoSiNE, a model that learns this germline-to-mature process for variant effect prediction and antibody design. (1/8)
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    Stephen Lu
    @stephenzlu
    Jul 17, 2025
    How close are we to an AI scientist that can make novel biological discoveries? Our recent work benchmarks key experimental abilities of frontier LLMs using insights from systems biology. We find that agents struggle at manipulating complex systems at scale 猬囷笍
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    Chris J. Maddison
    @cjmaddison
    Jul 16, 2025
    What makes a great scientist? Most AI scientist benchmarks miss the key skill: designing and analyzing experiments. 馃И We're introducing SciGym: the first simulated lab environment to benchmark #LLM on experimental design and analysis capabilities. #AI4SCIENCE #ICML25
    Picture of SCIGYM's title and authors
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    Stephen Lu
    @stephenzlu
    Jun 27, 2025
    馃殌 Just implemented Edit Flows => flow matching via edit operations (insert/delete/substitute)! No official code yet, so I built my own educational version on discretized sine functions. Watching the rates converge during training is very satisfying! (1/2)
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    Ricky T. Q. Chen
    @RickyTQChen
    Jun 11, 2025
    Padding in our non-AR sequence models? Yuck. 馃檯 馃憠 Instead of unmasking, our new work *Edit Flows* perform iterative refinements via position-relative inserts and deletes, operations naturally suited for variable-length sequence generation. Easily better than using mask tokens.
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