Vermeer: Autoregressive generative modeling of microscopy predicts protein localization
Subbarao Kambhampati, Eric Zimmermann, Emre Hayir, Kevin Kaichuang Yang, Fei Chen, Alex Lu
June 2026
Kevin Kaichuang Yang
Senior Researcher
Publications
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FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications
Kieran Didi, Sarah Alamdari, Alex Lu, Bruce Wittmann, Kadina E. Johnston, Ava P. Amini, Ali Madani, Maya Czeneszew, Christian Dallago, Kevin Kaichuang Yang
ICML 2026 | May 2026
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RosettaSearch: Multi-Objective Inference-Time Search for Protein Sequence Design
Meghana Kshirsagar, Ching-An Cheng, Allen Nie, Fanglei Xue, Rahul Dodhia, Juan M. Lavista Ferres, Kevin Kaichuang Yang, F. Dimaio
April 2026
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Evolutionary conditioning enables guided generation of functionally diverse enhancers
Andrew G. Duncan, Micaela Elisa Consens, Lorin Crawford, Jennifer A. Mitchell, Alan M. Moses, Kevin Kaichuang Yang, Alex Lu
April 2026
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Toward deep learning sequence–structure co-generation for protein design
Chentong Wang, Sarah Alamdari, Carles Domingo-Enrich, Ava P. Amini, Kevin Kaichuang Yang
Current Opinion in Structural Biology | March 2025
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Deep learning guided design of protease substrates
Carmen Martin-Alonso, Sarah Alamdari, Tahoura S. Samad, Kevin Kaichuang Yang, Sangeeta N. Bhatia, Ava P. Amini
bioRxiv | March 2025
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Benchmarking uncertainty quantification for protein engineering
Kevin P. Greenman, Ava P. Amini, Kevin Kaichuang Yang
PLOS Computational Biology | January 2025, Vol 21
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Protein generation with evolutionary diffusion: sequence is all you need
Sarah Alamdari, Nitya Thakkar, Rianne van den Berg, Neil Tenenholtz, Robert Strome, Alan M. Moses, Alex Lu, Nicolo Fusi, Ava P. Amini, Kevin Kaichuang Yang
bioRxiv | November 2024
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ProtNote: a multimodal method for protein-function annotation
Samir Char, Nathaniel Corley, Sarah Alamdari, Kevin Kaichuang Yang, Ava P. Amini
bioRxiv | October 2024
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Protein structure generation via folding diffusion
Kevin E. Wu, Kevin Kaichuang Yang, Rianne van den Berg, Sarah Alamdari, James Zou, Alex Lu, Ava P. Amini
Nature Communications | February 2024, Vol 15
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Deep self-supervised learning for biosynthetic gene cluster detection and product classification
Carolina Rios-Martinez, Nicholas Bhattacharya, Ava P. Amini, Lorin Crawford, Kevin Kaichuang Yang
PLOS Computational Biology | May 2023, Vol 19(5)
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From noise to protein with image models
Ava P. Amini, Kevin Kaichuang Yang
Nature Computational Science | May 2023, Vol 3: pp. 366-367
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Protein structure generation via folding diffusion
Kevin E. Wu, Kevin K. Yang, Rianne van den Berg, James Y. Zou, Alex X. Lu, Ava P. Amini
arXiv | September 2022
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A Topological Data Analytic Approach for Discovering Biophysical Signatures in Protein Dynamics
W. S. Tang, G. M. da Silva, H. Kirveslahti, E. Skeens, B. Feng, T. Sudijono, Kevin Kaichuang Yang, S. Mukherjee, B. Rubenstein, Lorin Crawford
bioRxiv | July 2021
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Machine learning-guided channelrhodopsin engineering enables minimally invasive optogenetics.
Claire N. Bedbrook, Kevin Kaichuang Yang, J. Elliott Robinson, Elisha D. Mackey, Viviana Gradinaru, Frances H. Arnold
Nature Methods | October 2019, Vol 16(11): pp. 1176-1184
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Machine-learning-guided directed evolution for protein engineering.
Kevin Kaichuang Yang, Zachary Wu, Frances H Arnold
Nature Methods | July 2019, Vol 16(8): pp. 687-694
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Vermeer: Autoregressive generative modeling of microscopy predicts protein localization
Subbarao Kambhampati, Eric Zimmermann, Emre Hayir, Kevin Kaichuang Yang, Fei Chen, Alex Lu
June 2026
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RosettaSearch: Multi-Objective Inference-Time Search for Protein Sequence Design
Meghana Kshirsagar, Ching-An Cheng, Allen Nie, Fanglei Xue, Rahul Dodhia, Juan M. Lavista Ferres, Kevin Kaichuang Yang, F. Dimaio
April 2026
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Evolutionary conditioning enables guided generation of functionally diverse enhancers
Andrew G. Duncan, Micaela Elisa Consens, Lorin Crawford, Jennifer A. Mitchell, Alan M. Moses, Kevin Kaichuang Yang, Alex Lu
April 2026
-
Toward deep learning sequence–structure co-generation for protein design
Chentong Wang, Sarah Alamdari, Carles Domingo-Enrich, Ava P. Amini, Kevin Kaichuang Yang
Current Opinion in Structural Biology | March 2025
-
Deep learning guided design of protease substrates
Carmen Martin-Alonso, Sarah Alamdari, Tahoura S. Samad, Kevin Kaichuang Yang, Sangeeta N. Bhatia, Ava P. Amini
bioRxiv | March 2025
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Benchmarking uncertainty quantification for protein engineering
Kevin P. Greenman, Ava P. Amini, Kevin Kaichuang Yang
PLOS Computational Biology | January 2025, Vol 21
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Protein generation with evolutionary diffusion: sequence is all you need
Sarah Alamdari, Nitya Thakkar, Rianne van den Berg, Neil Tenenholtz, Robert Strome, Alan M. Moses, Alex Lu, Nicolo Fusi, Ava P. Amini, Kevin Kaichuang Yang
bioRxiv | November 2024
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ProtNote: a multimodal method for protein-function annotation
Samir Char, Nathaniel Corley, Sarah Alamdari, Kevin Kaichuang Yang, Ava P. Amini
bioRxiv | October 2024
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Protein structure generation via folding diffusion
Kevin E. Wu, Kevin Kaichuang Yang, Rianne van den Berg, Sarah Alamdari, James Zou, Alex Lu, Ava P. Amini
Nature Communications | February 2024, Vol 15
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Deep self-supervised learning for biosynthetic gene cluster detection and product classification
Carolina Rios-Martinez, Nicholas Bhattacharya, Ava P. Amini, Lorin Crawford, Kevin Kaichuang Yang
PLOS Computational Biology | May 2023, Vol 19(5)
-
From noise to protein with image models
Ava P. Amini, Kevin Kaichuang Yang
Nature Computational Science | May 2023, Vol 3: pp. 366-367
-
Protein structure generation via folding diffusion
Kevin E. Wu, Kevin K. Yang, Rianne van den Berg, James Y. Zou, Alex X. Lu, Ava P. Amini
arXiv | September 2022
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A Topological Data Analytic Approach for Discovering Biophysical Signatures in Protein Dynamics
W. S. Tang, G. M. da Silva, H. Kirveslahti, E. Skeens, B. Feng, T. Sudijono, Kevin Kaichuang Yang, S. Mukherjee, B. Rubenstein, Lorin Crawford
bioRxiv | July 2021
-
Machine learning-guided channelrhodopsin engineering enables minimally invasive optogenetics.
Claire N. Bedbrook, Kevin Kaichuang Yang, J. Elliott Robinson, Elisha D. Mackey, Viviana Gradinaru, Frances H. Arnold
Nature Methods | October 2019, Vol 16(11): pp. 1176-1184
-
Machine-learning-guided directed evolution for protein engineering.
Kevin Kaichuang Yang, Zachary Wu, Frances H Arnold
Nature Methods | July 2019, Vol 16(8): pp. 687-694
-
-
-
FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications
Kieran Didi, Sarah Alamdari, Alex Lu, Bruce Wittmann, Kadina E. Johnston, Ava P. Amini, Ali Madani, Maya Czeneszew, Christian Dallago, Kevin Kaichuang Yang
ICML 2026 | May 2026
-
RosettaSearch: Multi-Objective Inference-Time Search for Protein Sequence Design
Meghana Kshirsagar, Ching-An Cheng, Allen Nie, Fanglei Xue, Rahul Dodhia, Juan M. Lavista Ferres, Kevin Kaichuang Yang, F. Dimaio
April 2026
-
Evolutionary conditioning enables guided generation of functionally diverse enhancers
Andrew G. Duncan, Micaela Elisa Consens, Lorin Crawford, Jennifer A. Mitchell, Alan M. Moses, Kevin Kaichuang Yang, Alex Lu
April 2026
-
Toward deep learning sequence–structure co-generation for protein design
Chentong Wang, Sarah Alamdari, Carles Domingo-Enrich, Ava P. Amini, Kevin Kaichuang Yang
Current Opinion in Structural Biology | March 2025
-
Benchmarking uncertainty quantification for protein engineering
Kevin P. Greenman, Ava P. Amini, Kevin Kaichuang Yang
PLOS Computational Biology | January 2025, Vol 21
-
Protein generation with evolutionary diffusion: sequence is all you need
Sarah Alamdari, Nitya Thakkar, Rianne van den Berg, Neil Tenenholtz, Robert Strome, Alan M. Moses, Alex Lu, Nicolo Fusi, Ava P. Amini, Kevin Kaichuang Yang
bioRxiv | November 2024
-
ProtNote: a multimodal method for protein-function annotation
Samir Char, Nathaniel Corley, Sarah Alamdari, Kevin Kaichuang Yang, Ava P. Amini
bioRxiv | October 2024
-
Protein structure generation via folding diffusion
Kevin E. Wu, Kevin Kaichuang Yang, Rianne van den Berg, Sarah Alamdari, James Zou, Alex Lu, Ava P. Amini
Nature Communications | February 2024, Vol 15
-
From noise to protein with image models
Ava P. Amini, Kevin Kaichuang Yang
Nature Computational Science | May 2023, Vol 3: pp. 366-367
-
Protein structure generation via folding diffusion
Kevin E. Wu, Kevin K. Yang, Rianne van den Berg, James Y. Zou, Alex X. Lu, Ava P. Amini
arXiv | September 2022
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Vermeer: Autoregressive generative modeling of microscopy predicts protein localization
Subbarao Kambhampati, Eric Zimmermann, Emre Hayir, Kevin Kaichuang Yang, Fei Chen, Alex Lu
June 2026
-
RosettaSearch: Multi-Objective Inference-Time Search for Protein Sequence Design
Meghana Kshirsagar, Ching-An Cheng, Allen Nie, Fanglei Xue, Rahul Dodhia, Juan M. Lavista Ferres, Kevin Kaichuang Yang, F. Dimaio
April 2026
-
Evolutionary conditioning enables guided generation of functionally diverse enhancers
Andrew G. Duncan, Micaela Elisa Consens, Lorin Crawford, Jennifer A. Mitchell, Alan M. Moses, Kevin Kaichuang Yang, Alex Lu
April 2026
-
-
-
FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications
Kieran Didi, Sarah Alamdari, Alex Lu, Bruce Wittmann, Kadina E. Johnston, Ava P. Amini, Ali Madani, Maya Czeneszew, Christian Dallago, Kevin Kaichuang Yang
ICML 2026 | May 2026
-
-
-
Toward deep learning sequence–structure co-generation for protein design
Chentong Wang, Sarah Alamdari, Carles Domingo-Enrich, Ava P. Amini, Kevin Kaichuang Yang
Current Opinion in Structural Biology | March 2025
-
Deep learning guided design of protease substrates
Carmen Martin-Alonso, Sarah Alamdari, Tahoura S. Samad, Kevin Kaichuang Yang, Sangeeta N. Bhatia, Ava P. Amini
bioRxiv | March 2025
-
Benchmarking uncertainty quantification for protein engineering
Kevin P. Greenman, Ava P. Amini, Kevin Kaichuang Yang
PLOS Computational Biology | January 2025, Vol 21
-
Protein generation with evolutionary diffusion: sequence is all you need
Sarah Alamdari, Nitya Thakkar, Rianne van den Berg, Neil Tenenholtz, Robert Strome, Alan M. Moses, Alex Lu, Nicolo Fusi, Ava P. Amini, Kevin Kaichuang Yang
bioRxiv | November 2024
-
ProtNote: a multimodal method for protein-function annotation
Samir Char, Nathaniel Corley, Sarah Alamdari, Kevin Kaichuang Yang, Ava P. Amini
bioRxiv | October 2024
-
Protein structure generation via folding diffusion
Kevin E. Wu, Kevin Kaichuang Yang, Rianne van den Berg, Sarah Alamdari, James Zou, Alex Lu, Ava P. Amini
Nature Communications | February 2024, Vol 15
-
Deep self-supervised learning for biosynthetic gene cluster detection and product classification
Carolina Rios-Martinez, Nicholas Bhattacharya, Ava P. Amini, Lorin Crawford, Kevin Kaichuang Yang
PLOS Computational Biology | May 2023, Vol 19(5)
-
From noise to protein with image models
Ava P. Amini, Kevin Kaichuang Yang
Nature Computational Science | May 2023, Vol 3: pp. 366-367
-
Protein structure generation via folding diffusion
Kevin E. Wu, Kevin K. Yang, Rianne van den Berg, James Y. Zou, Alex X. Lu, Ava P. Amini
arXiv | September 2022
-
A Topological Data Analytic Approach for Discovering Biophysical Signatures in Protein Dynamics
W. S. Tang, G. M. da Silva, H. Kirveslahti, E. Skeens, B. Feng, T. Sudijono, Kevin Kaichuang Yang, S. Mukherjee, B. Rubenstein, Lorin Crawford
bioRxiv | July 2021
-
Machine learning-guided channelrhodopsin engineering enables minimally invasive optogenetics.
Claire N. Bedbrook, Kevin Kaichuang Yang, J. Elliott Robinson, Elisha D. Mackey, Viviana Gradinaru, Frances H. Arnold
Nature Methods | October 2019, Vol 16(11): pp. 1176-1184
-
Machine-learning-guided directed evolution for protein engineering.
Kevin Kaichuang Yang, Zachary Wu, Frances H Arnold
Nature Methods | July 2019, Vol 16(8): pp. 687-694
-