Kevin Kaichuang Yang

Senior Researcher

出版物

表示方法:

- Vermeer: Autoregressive generative modeling of microscopy predicts protein localization
  
  Subbarao Kambhampati, Eric Zimmermann, Emre Hayir, Kevin Kaichuang Yang, Fei Chen, Alex Lu
  
  June 2026
  
  bioRxiv | June 2026
  
  DOI
- 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
  
  DOI
- 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
  
  arXiv | April 2026
  
  Publication
- 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
  
  bioRxiv | April 2026
  
  DOI
- Predicting evolutionary rate as a pretraining task improves genome language model representations
  
  Micaela Elisa Consens, Kevin Kaichuang Yang, Jimmy Hall, Ashley Conard, Bo Wang, Lorin Crawford, Alan M. Moses, Alex Lu
  
  ICML 2026 | February 2026
  
  DOI
- 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
  
  DOI Publication
- 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
  
  DOI
- Benchmarking uncertainty quantification for protein engineering
  
  Kevin P. Greenman, Ava P. Amini, Kevin Kaichuang Yang
  
  PLOS Computational Biology | January 2025, 巻21
  
  DOI Publication
- 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
  
  DOI Preprint アクセス
- ProtNote: a multimodal method for protein-function annotation
  
  Samir Char, Nathaniel Corley, Sarah Alamdari, Kevin Kaichuang Yang, Ava P. Amini
  
  bioRxiv | October 2024
  
  DOI Preprint
- 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, 巻15
  
  DOI PDF Publication
- 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, 巻19(5)
  
  DOI Publication
- From noise to protein with image models
  
  Ava P. Amini, Kevin Kaichuang Yang
  
  Nature Computational Science | May 2023, 巻3: pp. 366-367
  
  DOI Publication
- 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
  
  DOI
- 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
  
  DOI
- 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, 巻16(11): pp. 1176-1184
  
  DOI
- Machine-learning-guided directed evolution for protein engineering.
  
  Kevin Kaichuang Yang, Zachary Wu, Frances H Arnold
  
  Nature Methods | July 2019, 巻16(8): pp. 687-694
  
  DOI

- Vermeer: Autoregressive generative modeling of microscopy predicts protein localization
  
  Subbarao Kambhampati, Eric Zimmermann, Emre Hayir, Kevin Kaichuang Yang, Fei Chen, Alex Lu
  
  June 2026
  
  bioRxiv | June 2026
  
  DOI
- 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
  
  arXiv | April 2026
  
  Publication
- 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
  
  bioRxiv | April 2026
  
  DOI
- 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
  
  DOI Publication
- 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
  
  DOI
- Benchmarking uncertainty quantification for protein engineering
  
  Kevin P. Greenman, Ava P. Amini, Kevin Kaichuang Yang
  
  PLOS Computational Biology | January 2025, 巻21
  
  DOI Publication
- 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
  
  DOI Preprint アクセス
- ProtNote: a multimodal method for protein-function annotation
  
  Samir Char, Nathaniel Corley, Sarah Alamdari, Kevin Kaichuang Yang, Ava P. Amini
  
  bioRxiv | October 2024
  
  DOI Preprint
- 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, 巻15
  
  DOI PDF Publication
- 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, 巻19(5)
  
  DOI Publication
- From noise to protein with image models
  
  Ava P. Amini, Kevin Kaichuang Yang
  
  Nature Computational Science | May 2023, 巻3: pp. 366-367
  
  DOI Publication
- 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
  
  DOI
- 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
  
  DOI
- 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, 巻16(11): pp. 1176-1184
  
  DOI
- Machine-learning-guided directed evolution for protein engineering.
  
  Kevin Kaichuang Yang, Zachary Wu, Frances H Arnold
  
  Nature Methods | July 2019, 巻16(8): pp. 687-694
  
  DOI
- 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
  
  DOI
- 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
  
  arXiv | April 2026
  
  Publication
- 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
  
  bioRxiv | April 2026
  
  DOI
- Predicting evolutionary rate as a pretraining task improves genome language model representations
  
  Micaela Elisa Consens, Kevin Kaichuang Yang, Jimmy Hall, Ashley Conard, Bo Wang, Lorin Crawford, Alan M. Moses, Alex Lu
  
  ICML 2026 | February 2026
  
  DOI
- 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
  
  DOI Publication
- Benchmarking uncertainty quantification for protein engineering
  
  Kevin P. Greenman, Ava P. Amini, Kevin Kaichuang Yang
  
  PLOS Computational Biology | January 2025, 巻21
  
  DOI Publication
- 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
  
  DOI Preprint アクセス
- ProtNote: a multimodal method for protein-function annotation
  
  Samir Char, Nathaniel Corley, Sarah Alamdari, Kevin Kaichuang Yang, Ava P. Amini
  
  bioRxiv | October 2024
  
  DOI Preprint
- 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, 巻15
  
  DOI PDF Publication
- From noise to protein with image models
  
  Ava P. Amini, Kevin Kaichuang Yang
  
  Nature Computational Science | May 2023, 巻3: pp. 366-367
  
  DOI Publication
- 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
  
  DOI

- Vermeer: Autoregressive generative modeling of microscopy predicts protein localization
  
  Subbarao Kambhampati, Eric Zimmermann, Emre Hayir, Kevin Kaichuang Yang, Fei Chen, Alex Lu
  
  June 2026
  
  bioRxiv | June 2026
  
  DOI
- 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
  
  arXiv | April 2026
  
  Publication
- 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
  
  bioRxiv | April 2026
  
  DOI
- 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
  
  DOI
- Predicting evolutionary rate as a pretraining task improves genome language model representations
  
  Micaela Elisa Consens, Kevin Kaichuang Yang, Jimmy Hall, Ashley Conard, Bo Wang, Lorin Crawford, Alan M. Moses, Alex Lu
  
  ICML 2026 | February 2026
  
  DOI
- 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
  
  DOI Publication
- 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
  
  DOI
- Benchmarking uncertainty quantification for protein engineering
  
  Kevin P. Greenman, Ava P. Amini, Kevin Kaichuang Yang
  
  PLOS Computational Biology | January 2025, 巻21
  
  DOI Publication
- 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
  
  DOI Preprint アクセス
- ProtNote: a multimodal method for protein-function annotation
  
  Samir Char, Nathaniel Corley, Sarah Alamdari, Kevin Kaichuang Yang, Ava P. Amini
  
  bioRxiv | October 2024
  
  DOI Preprint
- 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, 巻15
  
  DOI PDF Publication
- 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, 巻19(5)
  
  DOI Publication
- From noise to protein with image models
  
  Ava P. Amini, Kevin Kaichuang Yang
  
  Nature Computational Science | May 2023, 巻3: pp. 366-367
  
  DOI Publication
- 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
  
  DOI
- 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
  
  DOI
- 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, 巻16(11): pp. 1176-1184
  
  DOI
- Machine-learning-guided directed evolution for protein engineering.
  
  Kevin Kaichuang Yang, Zachary Wu, Frances H Arnold
  
  Nature Methods | July 2019, 巻16(8): pp. 687-694
  
  DOI

Kevin Kaichuang Yang

出版物

Vermeer: Autoregressive generative modeling of microscopy predicts protein localization

FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications

RosettaSearch: Multi-Objective Inference-Time Search for Protein Sequence Design

Evolutionary conditioning enables guided generation of functionally diverse enhancers

Predicting evolutionary rate as a pretraining task improves genome language model representations

Toward deep learning sequence–structure co-generation for protein design

Deep learning guided design of protease substrates

Benchmarking uncertainty quantification for protein engineering

Protein generation with evolutionary diffusion: sequence is all you need

ProtNote: a multimodal method for protein-function annotation

Protein structure generation via folding diffusion

Deep self-supervised learning for biosynthetic gene cluster detection and product classification

From noise to protein with image models

Protein structure generation via folding diffusion

A Topological Data Analytic Approach for Discovering Biophysical Signatures in Protein Dynamics

Machine learning-guided channelrhodopsin engineering enables minimally invasive optogenetics.

Machine-learning-guided directed evolution for protein engineering.

Vermeer: Autoregressive generative modeling of microscopy predicts protein localization

RosettaSearch: Multi-Objective Inference-Time Search for Protein Sequence Design

Evolutionary conditioning enables guided generation of functionally diverse enhancers

Toward deep learning sequence–structure co-generation for protein design

Deep learning guided design of protease substrates

Benchmarking uncertainty quantification for protein engineering

Protein generation with evolutionary diffusion: sequence is all you need

ProtNote: a multimodal method for protein-function annotation

Protein structure generation via folding diffusion

Deep self-supervised learning for biosynthetic gene cluster detection and product classification

From noise to protein with image models

Protein structure generation via folding diffusion

A Topological Data Analytic Approach for Discovering Biophysical Signatures in Protein Dynamics

Machine learning-guided channelrhodopsin engineering enables minimally invasive optogenetics.

Machine-learning-guided directed evolution for protein engineering.

FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications

RosettaSearch: Multi-Objective Inference-Time Search for Protein Sequence Design

Evolutionary conditioning enables guided generation of functionally diverse enhancers

Predicting evolutionary rate as a pretraining task improves genome language model representations

Toward deep learning sequence–structure co-generation for protein design

Benchmarking uncertainty quantification for protein engineering

Protein generation with evolutionary diffusion: sequence is all you need

ProtNote: a multimodal method for protein-function annotation

Protein structure generation via folding diffusion

From noise to protein with image models

Protein structure generation via folding diffusion

Vermeer: Autoregressive generative modeling of microscopy predicts protein localization

RosettaSearch: Multi-Objective Inference-Time Search for Protein Sequence Design

Evolutionary conditioning enables guided generation of functionally diverse enhancers

FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications

Predicting evolutionary rate as a pretraining task improves genome language model representations

Toward deep learning sequence–structure co-generation for protein design

Deep learning guided design of protease substrates

Benchmarking uncertainty quantification for protein engineering

Protein generation with evolutionary diffusion: sequence is all you need

ProtNote: a multimodal method for protein-function annotation

Protein structure generation via folding diffusion

Deep self-supervised learning for biosynthetic gene cluster detection and product classification

From noise to protein with image models

Protein structure generation via folding diffusion

A Topological Data Analytic Approach for Discovering Biophysical Signatures in Protein Dynamics

Machine learning-guided channelrhodopsin engineering enables minimally invasive optogenetics.

Machine-learning-guided directed evolution for protein engineering.