amy x. lu 🌱

I’m a Senior Research Scientist at Isomorphic Labs in London. I’m interested in AI for drug discovery, and more broadly, in designing task-agnostic systems that can reason about the molecular-level world.

Until recently, I was a Computer Science PhD student in Pieter Abbeel’s group at UC Berkeley and Berkeley Artificial Intelligence Research, during which I was a part-time member of Genentech and Google Brain. You can find my full CV here.

amyxlu [at] berkeley [dot] edu

Amy X. Lu

News

2025-10-01 Invited talk at IDEALondon.
2025-07-07 I’ve joined Isomorphic Labs as a Research Scientist 🥳!
2025-04-28 PhD Dissertation Talk at the BAIR seminar series 👩‍🎓.
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Selected Publications

See Google Scholar for an up-to-date list of publications.
Genome modeling and design across all domains of life with Evo 2
Genome modeling and design across all domains of life with Evo 2
Garyk Brixi , Matthew G. Durrant , Jerome Ku , Michael Poli , Greg Brockman , Daniel Chang , Gabriel A. Gonzalez , Samuel H. King , David B. Li , Aditi T. Merchant , Mohsen Naghipourfar , Eric Nguyen , Chiara Ricci-Tam , David W. Romero , Gwanggyu Sun , Ali Taghibakshi , Anton Vorontsov , Brandon Yang , Myra Deng , Liv Gorton , Nam Nguyen , Nicholas K. Wang , Etowah Adams , Stephen A. Baccus , Steven Dillmann , Stefano Ermon , Daniel Guo , Rajesh Ilango , Ken Janik , Amy X. Lu , Reshma Mehta , Mohammad R.K. Mofrad , Madelena Y. Ng , Jaspreet Pannu , Christopher Ré , Jonathan C. Schmok , John St. John , Jeremy Sullivan , Kevin Zhu , Greg Zynda , Daniel Balsam , Patrick Collison , Anthony B. Costa , Tina Hernandez-Boussard , Eric Ho , Ming-Yu Liu , Thomas McGrath , Kimberly Powell , Dave P. Burke , Hani Goodarzi , Patrick D. Hsu , Brian L. Hie
bioRxiv, 2025
Paper / Code / Server
Evo 2 is a 40B parameter genomic foundation model capable of predicting functional impacts of genetic variations, autonomously learning biological features, and generating novel genomic sequences across all domains of life.
All-Atom Protein Generation with Latent Diffusion
All-Atom Protein Generation with Latent Diffusion
Amy X. Lu , Wilson Yan , Sarah A. Robinson , Simon Kelow , Kevin K. Yang , Vladimir Gligorijevic , Kyunghyun Cho , Richard Bonneau , Pieter Abbeel , Nathan Frey
bioRxiv, 2024
Paper / Code / Poster / Slides
PLAID is a multimodal protein generation model that generates all-atom protein structures from function and organism prompts, but requires only sequence training data.
Protein Language Model Fitness Is a Matter of Preference
Protein Language Model Fitness Is a Matter of Preference
Cade Gordon , Amy X. Lu , Pieter Abbeel
International Conference on Learning Representations (ICLR), 2025
Paper
Enabled by a one-pass pseudolikelihood algorithm, we find that pLMs capture artifacts of training data selection rather than true fitness landscape via influence functions.
Tokenized and Continuous Embedding Compressions of Protein Sequence and Structure
Tokenized and Continuous Embedding Compressions of Protein Sequence and Structure
Amy X. Lu , Wilson Yan , Kevin K. Yang , Vladimir Gligorijevic , Kyunghyun Cho , Pieter Abbeel , Richard Bonneau , Nathan Frey
Cell Patterns, 2024
Paper / Poster / Code
CHEAP is a joint embedding of protein sequence and structure that can be obtained from sequence alone, and unveil insights into the compressibilitiy, tokenizability, and mechanistic interpretability of protein folding models.
Self-Supervised Contrastive Learning of Protein Representations by Mutual Information Maximization
Self-Supervised Contrastive Learning of Protein Representations by Mutual Information Maximization
Amy X. Lu , Haoran Zhang , Marzyeh Ghassemi , Alan Moses
Machine Learning for Computational Biology (MLCB), 2020
Paper / Poster / Code
CPCProt uses contrastive learning to learn a parameter-efficient way of embedding proteins, and performs competitively with large language models.
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Talks

2025-10-01 In silico #002, IDEALondon [Slides]
2025-04-28 BAIR Seminar / UC Berkeley EECS PhD Dissertation Talk [Video] [Slides]
2025-03-03 Baker Lab Journal Club, UW Institute for Protein Design [Slides]
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Misc

I enjoy road biking. This year, I bikepacked 1,100 km down the coasts of California and Sweden, which gave me a bad sunburn. I have an ARCT Perfomer’s diploma from the Royal Conservatory of Music, and my favourite piano pieces are Chopin and Flo Rida covers. I love Berkeley Bowl peaches and 95% dark chocolate, and I’m a mother of two sons cats, Pascal and Gauss. If you need me for legal purposes, my name is Xiaoping Lu (逯晓萍).