Amy X. Lu 🌱
I'm a Computer Science PhD student at UC Berkeley and BAIR advised by Pieter Abbeel, and a part-time researcher at Prescient Design (Genentech).
I'm broadly interested in artificial intelligence for drug discovery, especially via multimodal generation and biological foundation models. My long-term goal is to design generally intelligent systems to solve tasks that humans cannot, such as reasoning about the molecular-level world.
Previously, I was a Student Researcher at Google Brain and Machine Learning Engineer at insitro. I completed my Masters at the University of Toronto advised by Alan Moses and Marzyeh Ghassemi, and my undergrad at the University of Waterloo. My PhD is generously supported in part by the NSERC PGS-D award.
News
Publications
Generating All-Atom Protein Structure from Sequence-Only Training Data
Protein Language Model Fitness Is a Matter of Preference
Cade Gordon,
Tokenized and Continuous Embedding Compressions of Protein Sequence and Structure
TOPH: Adapting A Contrastive Question-Answering Framework for Protein Search
Ron Boger
Pretraining strategies for effective promoter-driven gene expression prediction
Aniketh Janardhan Reddy, Michael H. Herschl, Sathvik Kolli,
Data-Driven Optimization for Protein Design: Workflows, Algorithms and Metrics
Sathvik Kolli,
Discovering molecular features of intrinsically disordered regions by using evolution for contrastive learning
Alex X Lu,
Learned embeddings from deep learning to visualize and predict protein sets
Christian Dallago, Konstantin Schütze, Michael Heinzinger, Tobias Olenyi, Maria Littmann,
Evolution Is All You Need: Phylogenetic Augmentation for Contrastive Learning
Self-Supervised Contrastive Learning of Protein Representations by Mutual Information Maximization
Hurtful Words: Quantifying Biases in Clinical Contextual Word Embeddings
Haoran Zhang*,
The Cells Out of Sample (COOS) dataset and benchmarks for measuring out-of-sample generalization of image classifiers
Alex X Lu,
History and publication trends in the diffusion and early uptake of indirect comparison meta-analytic methods to study drugs: animated coauthorship networks over time
Joann K Ban, Mina Tadrous,
Invited Talks
Miscellaneous
Fun
I enjoy road biking through the East Bay redwoods, and playing the piano, especially Chopin and hip-hop covers. I'm usually coding to EDM or Beethoven's complete piano sonatas while eating 90% dark chocolate. My car and bikes are named after F. Scott Fitzgerald characters, and administrative entities call me Xiaoping Lu (逯晓萍).