Alex Lu

Senior Researcher

Publications

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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
  
  DOI Publication Publication Github
- 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
  
  Publication
- 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
  
  Publication Publication Project
- 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 Download
- 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
  
  DOI Publication
- 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
  
  DOI PDF Publication
- 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
  
  Preprint PDF Project
- 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
  
  Publication Publication Project
- 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
- 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)
  
  Publication Project

- 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
  
  DOI Publication Publication Github
- 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
  
  Publication
- 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
  
  Publication Publication Project
- 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 Download
- 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
  
  DOI Publication
- 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
  
  DOI PDF Publication
- 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
  
  Preprint PDF Project
- 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
- 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)
  
  Publication Project
- 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
  
  DOI Publication Publication Github
- 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 Download
- 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
  
  DOI PDF 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
- 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)
  
  Publication Project
- 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
  
  Publication
- 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
  
  Publication Publication Project
- 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
  
  Publication Publication Project
- 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
  
  Publication Publication Project

- 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
  
  DOI Publication Publication Github
- 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
  
  Publication
- 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
  
  Publication Publication Project
- 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
  
  DOI Publication
- 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
  
  Publication Publication Project
- 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 Download
- 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
  
  DOI PDF Publication
- 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
  
  Preprint PDF Project
- 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
- 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)
  
  Publication Project