MicroVQA: A Multimodal Reasoning Benchmark for Microscopy-Based Scientific Research

1 code implementation • 17 Mar 2025 • James Burgess, Jeffrey J Nirschl, Laura Bravo-Sánchez, Alejandro Lozano, Sanket Rajan Gupte, Jesus G. Galaz-Montoya, Yuhui Zhang, Yuchang Su, Disha Bhowmik, Zachary Coman, Sarina M. Hasan, Alexandra Johannesson, William D. Leineweber, Malvika G Nair, Ridhi Yarlagadda, Connor Zuraski, Wah Chiu, Sarah Cohen, Jan N. Hansen, Manuel D Leonetti, Chad Liu, Emma Lundberg, Serena Yeung-Levy

Scientific research demands sophisticated reasoning over multimodal data, a challenge especially prevalent in biology.

Benchmarking Multimodal Reasoning +4

CellFlow: Simulating Cellular Morphology Changes via Flow Matching

no code implementations • 13 Feb 2025 • Yuhui Zhang, Yuchang Su, Chenyu Wang, Tianhong Li, Zoe Wefers, Jeffrey Nirschl, James Burgess, Daisy Ding, Alejandro Lozano, Emma Lundberg, Serena Yeung-Levy

Building a virtual cell capable of accurately simulating cellular behaviors in silico has long been a dream in computational biology.

How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities

no code implementations • 18 Sep 2024 • Charlotte Bunne, Yusuf Roohani, Yanay Rosen, Ankit Gupta, Xikun Zhang, Marcel Roed, Theo Alexandrov, Mohammed AlQuraishi, Patricia Brennan, Daniel B. Burkhardt, Andrea Califano, Jonah Cool, Abby F. Dernburg, Kirsty Ewing, Emily B. Fox, Matthias Haury, Amy E. Herr, Eric Horvitz, Patrick D. Hsu, Viren Jain, Gregory R. Johnson, Thomas Kalil, David R. Kelley, Shana O. Kelley, Anna Kreshuk, Tim Mitchison, Stephani Otte, Jay Shendure, Nicholas J. Sofroniew, Fabian Theis, Christina V. Theodoris, Srigokul Upadhyayula, Marc Valer, Bo wang, Eric Xing, Serena Yeung-Levy, Marinka Zitnik, Theofanis Karaletsos, Aviv Regev, Emma Lundberg, Jure Leskovec, Stephen R. Quake

Accurate modeling of cells is important for this understanding as well as for determining the root causes of disease.

Enabling Global Image Data Sharing in the Life Sciences

no code implementations • 23 Jan 2024 • Peter Bajcsy, Sreenivas Bhattiprolu, Katy Boerner, Beth A Cimini, Lucy Collinson, Jan Ellenberg, Reto Fiolka, Maryellen Giger, Wojtek Goscinski, Matthew Hartley, Nathan Hotaling, Rick Horwitz, Florian Jug, Anna Kreshuk, Emma Lundberg, Aastha Mathur, Kedar Narayan, Shuichi Onami, Anne L. Plant, Fred Prior, Jason Swedlow, Adam Taylor, Antje Keppler

Coordinated collaboration is essential to realize the added value of and infrastructure requirements for global image data sharing in the life sciences.

Harmonizing the Generation and Pre-publication Stewardship of FAIR Image Data

no code implementations • 23 Jan 2024 • Nikki Bialy, Frank Alber, Brenda Andrews, Michael Angelo, Brian Beliveau, Lacramioara Bintu, Alistair Boettiger, Ulrike Boehm, Claire M. Brown, Mahmoud Bukar Maina, James J. Chambers, Beth A. Cimini, Kevin Eliceiri, Rachel Errington, Orestis Faklaris, Nathalie Gaudreault, Ronald N. Germain, Wojtek Goscinski, David Grunwald, Michael Halter, Dorit Hanein, John W. Hickey, Judith Lacoste, Alex Laude, Emma Lundberg, Jian Ma, Leonel Malacrida, Josh Moore, Glyn Nelson, Elizabeth Kathleen Neumann, Roland Nitschke, Shuichi Onami, Jaime A. Pimentel, Anne L. Plant, Andrea J. Radtke, Bikash Sabata, Denis Schapiro, Johannes Schöneberg, Jeffrey M. Spraggins, Damir Sudar, Wouter-Michiel Adrien Maria Vierdag, Niels Volkmann, Carolina Wählby, Siyuan, Wang, Ziv Yaniv, Caterina Strambio-De-Castillia

Together with the molecular knowledge of genes and proteins, biological images promise to significantly enhance the scientific understanding of complex cellular systems and to advance predictive and personalized therapeutic products for human health.

New views of old proteins: clarifying the enigmatic proteome

no code implementations • 17 Aug 2021 • Participants in a NIH Workshop on Functional, Integrative Proteomics, :, Kristin E. Burnum Johnson, Thomas P. Conrads, Richard R. Drake, Amy E. Herr, Ravi Iyengar, Ryan T. Kelly, Emma Lundberg, Michael J. MacCoss, Alexandra Naba, Garry P. Nolan, Pavel A. Pevzner, Karin D. Rodland, Salvatore Sechi, Nikolai Slavov, Jeffrey M. Spraggins, Jennifer E. Van Eyk, Marc Vidal, Christine Vogel, David R. Walt, Neil L. Kelleher

All human diseases involve proteins, yet our current tools to characterize and quantify them are limited.

Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging

no code implementations • 16 Jul 2021 • John W. Hickey, Elizabeth K. Neumann, Andrea J. Radtke, Jeannie M. Camarillo, Rebecca T. Beuschel, Alexandre Albanese, Elizabeth McDonough, Julia Hatler, Anne E. Wiblin, Jeremy Fisher, Josh Croteau, Eliza C. Small, Anup Sood, Richard M. Caprioli, R. Michael Angelo, Garry P. Nolan, Kwanghun Chung, Stephen M. Hewitt, Ronald N. Germain, Jeffrey M. Spraggins, Emma Lundberg, Michael P. Snyder, Neil L. Kelleher, Sinem K. Saka

Tissues and organs are composed of distinct cell types that must operate in concert to perform physiological functions.

ImJoy: an open-source computational platform for the deep learning era

4 code implementations • 30 May 2019 • Wei Ouyang, Florian Mueller, Martin Hjelmare, Emma Lundberg, Christophe Zimmer

Deep learning methods have shown extraordinary potential for analyzing very diverse biomedical data, but their dissemination beyond developers is hindered by important computational hurdles.

Deep Learning