Foundation Models for Sensory and Behavioral Neuroscience
PI: Liam Paninski
Co-PI: Andreas Tolias, Stanford; Blake Richards, MILA
Abstract
Scaling data and artificial neural networks has transformed AI, driving breakthroughs in language, vision, and many other fields. Whether similar principles apply to modeling brain activity remains unclear. Here we leveraged a dataset of 3.1 million neurons from the visual cortex of 73 mice across 323 sessions, totaling more than 150 billion neural tokens recorded during natural movies, images and parametric stimuli, and behavior. We train multi-modal, multi-task models that support three regimes flexibly at test time: neural prediction, behavioral decoding, neural forecasting, or any combination of the three. Our model, OmniMouse, achieves state-of-the-art performance, outperforming specialized baselines across nearly all evaluation regimes. We find that performance scales reliably with more data, but gains from increasing model size saturate. This inverts the standard AI scaling story: in language and computer vision, massive datasets make parameter scaling the primary driver of progress, whereas in brain modeling -- even in the mouse visual cortex, a relatively simple system -- models remain data-limited despite recordings of growing scale.
Publications
- Bae, S., Azabou, M., Richards, B., & Cha, J. (2025). Decoding Dynamic Visual Experience from Calcium Imaging via Cell-Pattern-Aware Pretraining. arXiv. https://doi.org/10.48550/ARXIV.2510.18516
- Wang, Y., Yu, H., Blau, A., Zhang, Y., International Brain Laboratory, Paninski, L., Hurwitz, C., & Whiteway, M. R. (2026). Animal behavioral analysis and neural encoding with transformer-based self-supervised pretraining. In Proceedings of the International Conference on Learning Representations (ICLR 2026).
- Willeke, K. F., Turishcheva, P., Gilbert, A., Chakrabarty, G., Bedel, H. A., Fahey, P. G., Qiu, Y., Weis, M. A., Vystrčilová, M., Muhammad, T., Ntanavara, L., Froebe, R. E., Ponder, K., Tan, Z. H., Orhan, E., Cobos, E., Sanborn, S., Franke, K., Sinz, F. H., Tolias, A. S. (2025, October 8). OmniMouse: Scaling properties of multi-modal, multi-task Brain Models on 150B Neural Tokens. The Fourteenth International Conference on Learning Representations. https://openreview.net/forum?id=mEw4lhAn0F
- Xia, J., Zhang, Y., Wang, S., Allen, G. I., Paninski, L., Hurwitz, C. L., & Miller, K. D. (2025, October 29). Inpainting the Neural Picture: Inferring Unrecorded Brain Area Dynamics from Multi-Animal Datasets. The Thirty-ninth Annual Conference on Neural Information Processing Systems. https://openreview.net/forum?id=YufSVJxDgt
Resources
In progress
