MorphoHELM: A Comprehensive Benchmark for Evaluating Representations for Microscopy-Based Morphology Assays
Emre Hayir, Lorin Crawford, Alex Lu
May 2026
Alex Lu
Senior Researcher
Publications
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Underrepresentation of children in public medical imaging datasets
S. Z. Hua, N. Heller, Ping He, Alexander J Towbin, Irene Chen, Alex Lu, L. Erdman
Nature Health | April 2026
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Transcription Factors: Disorderly Conduct
Eytan Weinstein, Alan M. Moses, Alex Lu
GEN Biotechnology | April 2026
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Enhancing AI and Dynamical Subseasonal Forecasts with Probabilistic Bias Correction
Hannah H Guan, S. Mouatadid, Paulo Orenstein, Judah Cohen, Haiyu Dong, Zekun Ni, Jeremy D. Berman, Genevieve Flaspohler, Alex Lu, Jakob Schloer, J. Talib, Jonathan A. Weyn, Lester Mackey
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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Multimodal Alignment Improves Generalizability of Genomic Biomarker Prediction in Computational Pathology
Ekaterina Redekop, Eric Zimmermann, Ava P. Amini, Alex Lu, Neil Tenenholtz, Jimmy Hall, Lorin Crawford, Kristen Severson
February 2026
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scGeneScope: A Treatment-Matched Single Cell Imaging and Transcriptomics Dataset and Benchmark for Treatment Response Modeling
Joel Dapello, Marcel Nassar, Ridvan Eksi, Ban Wang, Jules Gagnon-Marchand, Kenneth Gao, akram Baharlouei, Kyra Thrush, Nina Riehs, Amy Peterson, Aniket Tolpadi, Abhejit Rajagopal, Henry Miller, ashley conard, David Alvarez-Melis, Rory Stark, Simone Bianco, Morgan Levine, Ava P. Amini, Alex Lu, Nicolo Fusi, Ravi Pandya, Valentina Pedoia, Hana El-Samad
NeurIPS 2025 | October 2025
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Representation Learning Methods for Single-Cell Microscopy are Confounded by Background Cells
Arushi Gupta, Alan Moses, Alex Lu
June 2025
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Causal integration of chemical structures improves representations of microscopy images for morphological profiling
Yemin Yu, Neil Tenenholtz, Lester Mackey, Ying Wei, David Alvarez-Melis, Ava P. Amini, Alex Lu
April 2025
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Exploring Reduced Feature Sets for American Sign Language Dictionaries
Ben Kosa, Aashaka Desai, Alex Lu, Richard E. Ladner, Danielle Bragg
CHI 2025 | March 2025
Honorable Mention, CHI 2025
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ASL STEM Wiki: Dataset and Benchmark for Interpreting STEM Articles
Kayo Yin, Chinmay Singh, Fyodor O. Minakov, Vanessa Milan, Hal Daumé, Cyril Zhang, Alex Lu, Danielle Bragg
Proceedings of the 2024 Conference on Empirical Methods in Natural Language Processing | November 2024
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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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A Functional Map of the Human Intrinsically Disordered Proteome
I. Pritišanac, T. R. Alderson, Đesika Kolarić, Taraneh Zarin, Shuting Xie, Alex Lu, A. Alam, Abdullah Maqsood, Ji-Young Youn, J. Forman-Kay, A. Moses
March 2024
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Feature Reuse and Scaling: Understanding Transfer Learning with Protein Language Models
Francesca-Zhoufan Li, Ava P. Amini, Yisong Yue, Kevin Yang, Alex Lu
ICML 2024 | February 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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Assessing the limits of zero-shot foundation models in single-cell biology
Kasia Z. Kedzierska, Lorin Crawford, Ava P. Amini, Alex Lu
bioRxiv | November 2023
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ASL Citizen: A Community-Sourced Dataset for Advancing Isolated Sign Language Recognition
Aashaka Desai, Lauren Berger, Fyodor O. Minakov, Vanessa Milan, Chinmay Singh, Kriston Pumphrey, Richard E. Ladner, Hal Daumé III, Alex Lu, Naomi Caselli, Danielle Bragg
Advances in Neural Information Processing Systems (NeurIPS) 36 | June 2023
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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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Discovering molecular features of intrinsically disordered regions by using evolution for contrastive learning
Alex X. Lu, Amy X. Lu, Iva Pritišanac, Taraneh Zarin, Julie D. Forman-Kay, Alan M. Moses
PLOS Computational Biology | July 2022, Vol 18(6)
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MorphoHELM: A Comprehensive Benchmark for Evaluating Representations for Microscopy-Based Morphology Assays
Emre Hayir, Lorin Crawford, Alex Lu
May 2026
-
ASL Citizen: A Community-Sourced Dataset for Advancing Isolated Sign Language Recognition
Aashaka Desai, Lauren Berger, Fyodor O. Minakov, Vanessa Milan, Chinmay Singh, Kriston Pumphrey, Richard E. Ladner, Hal Daumé III, Alex Lu, Naomi Caselli, Danielle Bragg
Advances in Neural Information Processing Systems (NeurIPS) 36 | June 2023
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A Functional Map of the Human Intrinsically Disordered Proteome
I. Pritišanac, T. R. Alderson, Đesika Kolarić, Taraneh Zarin, Shuting Xie, Alex Lu, A. Alam, Abdullah Maqsood, Ji-Young Youn, J. Forman-Kay, A. Moses
March 2024
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A Functional Map of the Human Intrinsically Disordered Proteome
I. Pritišanac, T. R. Alderson, Đesika Kolarić, Taraneh Zarin, Shuting Xie, Alex Lu, A. Alam, Abdullah Maqsood, Ji-Young Youn, J. Forman-Kay, A. Moses
March 2024
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Underrepresentation of children in public medical imaging datasets
S. Z. Hua, N. Heller, Ping He, Alexander J Towbin, Irene Chen, Alex Lu, L. Erdman
Nature Health | April 2026
-
Transcription Factors: Disorderly Conduct
Eytan Weinstein, Alan M. Moses, Alex Lu
GEN Biotechnology | April 2026
-
Enhancing AI and Dynamical Subseasonal Forecasts with Probabilistic Bias Correction
Hannah H Guan, S. Mouatadid, Paulo Orenstein, Judah Cohen, Haiyu Dong, Zekun Ni, Jeremy D. Berman, Genevieve Flaspohler, Alex Lu, Jakob Schloer, J. Talib, Jonathan A. Weyn, Lester Mackey
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
-
Multimodal Alignment Improves Generalizability of Genomic Biomarker Prediction in Computational Pathology
Ekaterina Redekop, Eric Zimmermann, Ava P. Amini, Alex Lu, Neil Tenenholtz, Jimmy Hall, Lorin Crawford, Kristen Severson
February 2026
-
Causal integration of chemical structures improves representations of microscopy images for morphological profiling
Yemin Yu, Neil Tenenholtz, Lester Mackey, Ying Wei, David Alvarez-Melis, Ava P. Amini, Alex Lu
April 2025
-
Exploring Reduced Feature Sets for American Sign Language Dictionaries
Ben Kosa, Aashaka Desai, Alex Lu, Richard E. Ladner, Danielle Bragg
CHI 2025 | March 2025
Honorable Mention, CHI 2025
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ASL STEM Wiki: Dataset and Benchmark for Interpreting STEM Articles
Kayo Yin, Chinmay Singh, Fyodor O. Minakov, Vanessa Milan, Hal Daumé, Cyril Zhang, Alex Lu, Danielle Bragg
Proceedings of the 2024 Conference on Empirical Methods in Natural Language Processing | November 2024
-
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
-
Feature Reuse and Scaling: Understanding Transfer Learning with Protein Language Models
Francesca-Zhoufan Li, Ava P. Amini, Yisong Yue, Kevin Yang, Alex Lu
ICML 2024 | February 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
-
Assessing the limits of zero-shot foundation models in single-cell biology
Kasia Z. Kedzierska, Lorin Crawford, Ava P. Amini, Alex Lu
bioRxiv | November 2023
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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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Discovering molecular features of intrinsically disordered regions by using evolution for contrastive learning
Alex X. Lu, Amy X. Lu, Iva Pritišanac, Taraneh Zarin, Julie D. Forman-Kay, Alan M. Moses
PLOS Computational Biology | July 2022, Vol 18(6)
-
-
-
Underrepresentation of children in public medical imaging datasets
S. Z. Hua, N. Heller, Ping He, Alexander J Towbin, Irene Chen, Alex Lu, L. Erdman
Nature Health | April 2026
-
Transcription Factors: Disorderly Conduct
Eytan Weinstein, Alan M. Moses, Alex Lu
GEN Biotechnology | 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
-
Multimodal Alignment Improves Generalizability of Genomic Biomarker Prediction in Computational Pathology
Ekaterina Redekop, Eric Zimmermann, Ava P. Amini, Alex Lu, Neil Tenenholtz, Jimmy Hall, Lorin Crawford, Kristen Severson
February 2026
-
scGeneScope: A Treatment-Matched Single Cell Imaging and Transcriptomics Dataset and Benchmark for Treatment Response Modeling
Joel Dapello, Marcel Nassar, Ridvan Eksi, Ban Wang, Jules Gagnon-Marchand, Kenneth Gao, akram Baharlouei, Kyra Thrush, Nina Riehs, Amy Peterson, Aniket Tolpadi, Abhejit Rajagopal, Henry Miller, ashley conard, David Alvarez-Melis, Rory Stark, Simone Bianco, Morgan Levine, Ava P. Amini, Alex Lu, Nicolo Fusi, Ravi Pandya, Valentina Pedoia, Hana El-Samad
NeurIPS 2025 | October 2025
-
Representation Learning Methods for Single-Cell Microscopy are Confounded by Background Cells
Arushi Gupta, Alan Moses, Alex Lu
June 2025
-
Causal integration of chemical structures improves representations of microscopy images for morphological profiling
Yemin Yu, Neil Tenenholtz, Lester Mackey, Ying Wei, David Alvarez-Melis, Ava P. Amini, Alex Lu
April 2025
-
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
-
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
-
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
-
Discovering molecular features of intrinsically disordered regions by using evolution for contrastive learning
Alex X. Lu, Amy X. Lu, Iva Pritišanac, Taraneh Zarin, Julie D. Forman-Kay, Alan M. Moses
PLOS Computational Biology | July 2022, Vol 18(6)
-
-
-
Exploring Reduced Feature Sets for American Sign Language Dictionaries
Ben Kosa, Aashaka Desai, Alex Lu, Richard E. Ladner, Danielle Bragg
CHI 2025 | March 2025
Honorable Mention, CHI 2025
-
-
-
ASL STEM Wiki: Dataset and Benchmark for Interpreting STEM Articles
Kayo Yin, Chinmay Singh, Fyodor O. Minakov, Vanessa Milan, Hal Daumé, Cyril Zhang, Alex Lu, Danielle Bragg
Proceedings of the 2024 Conference on Empirical Methods in Natural Language Processing | November 2024
-
ASL Citizen: A Community-Sourced Dataset for Advancing Isolated Sign Language Recognition
Aashaka Desai, Lauren Berger, Fyodor O. Minakov, Vanessa Milan, Chinmay Singh, Kriston Pumphrey, Richard E. Ladner, Hal Daumé III, Alex Lu, Naomi Caselli, Danielle Bragg
Advances in Neural Information Processing Systems (NeurIPS) 36 | June 2023
-
-
-
MorphoHELM: A Comprehensive Benchmark for Evaluating Representations for Microscopy-Based Morphology Assays
Emre Hayir, Lorin Crawford, Alex Lu
May 2026
-
Enhancing AI and Dynamical Subseasonal Forecasts with Probabilistic Bias Correction
Hannah H Guan, S. Mouatadid, Paulo Orenstein, Judah Cohen, Haiyu Dong, Zekun Ni, Jeremy D. Berman, Genevieve Flaspohler, Alex Lu, Jakob Schloer, J. Talib, Jonathan A. Weyn, Lester Mackey
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
-
Multimodal Alignment Improves Generalizability of Genomic Biomarker Prediction in Computational Pathology
Ekaterina Redekop, Eric Zimmermann, Ava P. Amini, Alex Lu, Neil Tenenholtz, Jimmy Hall, Lorin Crawford, Kristen Severson
February 2026
-
Representation Learning Methods for Single-Cell Microscopy are Confounded by Background Cells
Arushi Gupta, Alan Moses, Alex Lu
June 2025
-
Causal integration of chemical structures improves representations of microscopy images for morphological profiling
Yemin Yu, Neil Tenenholtz, Lester Mackey, Ying Wei, David Alvarez-Melis, Ava P. Amini, Alex Lu
April 2025
-
A Functional Map of the Human Intrinsically Disordered Proteome
I. Pritišanac, T. R. Alderson, Đesika Kolarić, Taraneh Zarin, Shuting Xie, Alex Lu, A. Alam, Abdullah Maqsood, Ji-Young Youn, J. Forman-Kay, A. Moses
March 2024
-
-
-
Underrepresentation of children in public medical imaging datasets
S. Z. Hua, N. Heller, Ping He, Alexander J Towbin, Irene Chen, Alex Lu, L. Erdman
Nature Health | April 2026
-
Transcription Factors: Disorderly Conduct
Eytan Weinstein, Alan M. Moses, Alex Lu
GEN Biotechnology | April 2026
-
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
-
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
-
Assessing the limits of zero-shot foundation models in single-cell biology
Kasia Z. Kedzierska, Lorin Crawford, Ava P. Amini, Alex Lu
bioRxiv | November 2023
-
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
-
Discovering molecular features of intrinsically disordered regions by using evolution for contrastive learning
Alex X. Lu, Amy X. Lu, Iva Pritišanac, Taraneh Zarin, Julie D. Forman-Kay, Alan M. Moses
PLOS Computational Biology | July 2022, Vol 18(6)
-
-
-
scGeneScope: A Treatment-Matched Single Cell Imaging and Transcriptomics Dataset and Benchmark for Treatment Response Modeling
Joel Dapello, Marcel Nassar, Ridvan Eksi, Ban Wang, Jules Gagnon-Marchand, Kenneth Gao, akram Baharlouei, Kyra Thrush, Nina Riehs, Amy Peterson, Aniket Tolpadi, Abhejit Rajagopal, Henry Miller, ashley conard, David Alvarez-Melis, Rory Stark, Simone Bianco, Morgan Levine, Ava P. Amini, Alex Lu, Nicolo Fusi, Ravi Pandya, Valentina Pedoia, Hana El-Samad
NeurIPS 2025 | October 2025
-
Exploring Reduced Feature Sets for American Sign Language Dictionaries
Ben Kosa, Aashaka Desai, Alex Lu, Richard E. Ladner, Danielle Bragg
CHI 2025 | March 2025
Honorable Mention, CHI 2025
-
ASL STEM Wiki: Dataset and Benchmark for Interpreting STEM Articles
Kayo Yin, Chinmay Singh, Fyodor O. Minakov, Vanessa Milan, Hal Daumé, Cyril Zhang, Alex Lu, Danielle Bragg
Proceedings of the 2024 Conference on Empirical Methods in Natural Language Processing | November 2024
-
Feature Reuse and Scaling: Understanding Transfer Learning with Protein Language Models
Francesca-Zhoufan Li, Ava P. Amini, Yisong Yue, Kevin Yang, Alex Lu
ICML 2024 | February 2024
-
ASL Citizen: A Community-Sourced Dataset for Advancing Isolated Sign Language Recognition
Aashaka Desai, Lauren Berger, Fyodor O. Minakov, Vanessa Milan, Chinmay Singh, Kriston Pumphrey, Richard E. Ladner, Hal Daumé III, Alex Lu, Naomi Caselli, Danielle Bragg
Advances in Neural Information Processing Systems (NeurIPS) 36 | June 2023
-