Amy Wang

I’m a machine learning scientist working on generative models, LLM evaluation, and agentic systems for protein and antibody design. My work focuses on sequence-based modeling, affinity and developability prediction, and building discovery workflows that integrate biophysical constraints with experimental data.

As a Senior ML Scientist at Prescient Design (Genentech), I’ve developed ML methods in close partnership with experimental teams. My work has been adopted across the antibody portfolio, spanning discovery, developability optimization, and model evaluation.

I also have a decade of wet lab experience. I earned my PhD in Chemical Engineering from Stanford University in 2023, where I studied force-dependent cell adhesion proteins. As an undergraduate at MIT, I worked on protein–polymer systems for drug delivery.

CV | Google Scholar | Twitter
amywangsci [at] gmail.com

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Publications
Lab-in-the-loop therapeutic antibody design figure

Lab-in-the-loop therapeutic antibody design with deep learning
N.C. Frey, I. Hötzel, S.D. Stanton, R. Kelly, R.G. Alberstein, ..., A. Wang, ..., A. Regev, Y. Wu, K. Cho, R. Bonneau, V. Gligorijević

bioRxiv 2025

Concept bottleneck protein design figure

Concept Bottleneck Language Models For Protein Design
A.A. Ismail, T. Oikarinen, A. Wang, J. Adebayo, S.D. Stanton, H.C. Bravo, K. Cho, N.C. Frey

International Conference on Learning Representations (ICLR) 2025

Discrete diffusion protein design figure

Fine-tuning discrete diffusion models via reward optimization with applications to DNA and protein design
C. Wang, M. Uehara, Y. He, A. Wang, A. Lal, T. Jaakola, S. Levine, A. Regev, H. Wang, T. Biancalani

International Conference on Learning Representations (ICLR) 2025

Vinculin and alphaE-catenin figure

Multi-level force-dependent allosteric enhancement of αE-catenin binding to F-actin by vinculin
N.A. Bax*, A. Wang*, D.L. Huang, S. Pokutta, A.R. Dunn, W.I. Weis

Journal of Molecular Biology 2023 | PDF

Catch bond interaction figure

Mechanism of the cadherin-catenin F-actin catch bond interaction
A. Wang, A.R. Dunn, W.I. Weis

eLife 2022 | PDF

Therapeutic cell implant figure

A retrievable implant for the long-term encapsulation and survival of therapeutic xenogeneic cells
S. Bose, L.R. Volpatti*, D. Thiono*, V. Yesilyurt, C. McGladrigan, Y. Tang, A. Facklam, A. Wang, S. Jhunjhunwala, O. Veiseh, J. Hollister-Lock, C. Bhattacharya, G.C. Weir, D.L. Greiner, R. Langer, D.G. Anderson

Nature Biomedical Engineering 2020 | PDF

NKCC1 structure figure

Structure and mechanism of the cation-chloride cotransporter NKCC1
T.A. Chew*, B.J. Orlando*, J. Zhang*, N.R. Latorraca, A. Wang, S.A. Hollingsworth, D.H. Chen, R.O. Dror, M. Liao, L. Feng

Nature 2019 | PDF

Protein-polymer self-assembly figure

Predicting protein-polymer block copolymer self-assembly from protein properties
A. Huang, J.M. Paloni, A. Wang, A.C. Obermeyer, H.V. Sureka, H. Yao, B.D. Olsen

Biomacromolecules 2019 | PDF

Insulin-loaded nanoparticles figure

Design of insulin-loaded nanoparticles enabled by multistep control of nanoprecipitation and zinc chelation
S. Chopra, N. Bertrand, J. Lim, A. Wang, O. Farokhzad, R. Karnik

ACS Applied Materials & Interfaces 2017 | PDF
Patent Filed October 7, 2015.

Workshops
Therapeutic antibody design workshop figure

A guided design framework for the optimization of therapeutic-like antibodies
A. Wang, Z. Sang, S.D. Stanton, J.L. Hofmann, [...], N.C. Frey, A.M. Watkins, F. Seeger

Generative and Experimental Perspectives for Biomolecular Design, ICLR 2025 | PDF

SurfProp workshop figure

SurfProp: A surface-based property prediction framework for antibody developability and screening
P. Rao, H. Isaacson, J.L. Hofmann, D. Davidson, A. Wang, A.M. Watkins, R. Bonneau, S. Izadi, J.H. Lee, N.C. Frey, F. Seeger

GenBio Workshop, ICLR 2025 | PDF

Antibody inverse folding workshop figure

The Effects of Structural Conditioning on Antibody Inverse Folding
Z. Ma, D. Davidson, A. Wang, N. Frey, F. Seeger

Women in ML Workshop, NeurIPS 2023

Physics-based protein property prediction workshop figure

Learning from physics-based features improves protein property prediction
A. Wang, A.X. Lu, A.P. Amini, K.K. Yang

Machine Learning in Structural Biology Workshop, NeurIPS 2022
Internship project at Microsoft Research, BioML Group
PDF | Poster

Awards and Affiliations