Publication Imaging Transformer for MRI Denoising: a Scalable Model Architecture that enables SNR<<1 Imaging Hui Xue, Sarah M. Hooper, Rhodri H. Davies, T. Treibel, Iain Pierce, John Stairs, Joseph Naegele, Charlotte Manisty, James C. Moon, A. Campbell-Washburn, Peter Kellman, Michael Hansen April 2025 Project
Publication 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 Github
Publication 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
Publication Consequences of training data composition for deep learning models in single-cell biology Ajay Nadig, Akshaya Thoutam, Madeline Hughes, Anay Gupta, Andrew W. Navia, Nicolo Fusi, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin Crawford bioRxiv | February 2025 Project
Publication Addressing biomedical data challenges and opportunities to inform a large-scale data lifecycle for enhanced data sharing, interoperability, analysis, and collaboration across stakeholders Vivek Sriram, Ashley Conard, Ilyana Rosenberg, Dokyoon Kim, Scott Saponas, Amanda K. Hall Scientific Reports | February 2025, Vol 15
Publication Exploring Scalable Medical Image Encoders Beyond Text Supervision Fernando Pérez-García, Harshita Sharma, Sam Bond-Taylor, Kenza Bouzid, Valentina Salvatelli, Maximilian Ilse, Shruthi Bannur, Daniel Coelho de Castro, Anton Schwaighofer, Matthew P Lungren, Noel Codella, Stephanie Hyland, Javier Alvarez-Valle, Ozan Oktay Nature Machine Intelligence | January 2025, Vol 7: pp. 119-130 Access Project
Publication BioAgents: Democratizing Bioinformatics Analysis with Multi-Agent Systems Nikita Mehandru, Amanda K. Hall, Olesya Melnichenko, Yulia Dubinina, Daniel Tsirulnikov, David Bamman, Ahmed Alaa, Scott Saponas, V. Malladi January 2025
Publication Benchmarking uncertainty quantification for protein engineering Kevin P. Greenman, Ava P. Amini, Kevin Kaichuang Yang PLOS Computational Biology | January 2025, Vol 21
Publication Evaluating the role of pre-training dataset size and diversity on single-cell foundation model performance Alan DenAdel, Madeline Hughes, Akshaya Thoutam, Anay Gupta, Nicolo Fusi, Andrew W. Navia, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin Crawford bioRxiv | December 2024 Project
Publication MAIRA-Seg: Enhancing Radiology Report Generation with Segmentation-Aware Multimodal Large Language Models Harshita Sharma, Valentina Salvatelli, Shaury Srivastav, Kenza Bouzid, Shruthi Bannur, Daniel Coelho de Castro, Maximilian Ilse, Sam Bond-Taylor, Mercy Ranjit, Fabian Falck, Fernando Pérez-García, Anton Schwaighofer, Hannah Richardson (nee Murfet), Maria Teodora Wetscherek, Stephanie Hyland, Javier Alvarez-Valle Machine Learning for Health Symposium 2024 | December 2024 Project
