Polina Turishcheva

Konstantin F. Willeke, Polina Turishcheva, Alex Gilbert et al. · stanford

Scaling data and artificial neural networks has transformed AI, driving breakthroughs in language and vision. 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. 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 vast recordings. The observation of systematic scaling raises the possibility of phase transitions in neural modeling, where larger and richer datasets might unlock qualitatively new capabilities, paralleling the emergent properties seen in large language models. Code available at https://github.com/enigma-brain/omnimouse.

Chase van de Geijn, Timo Lüddecke, Polina Turishcheva et al.

Rotary Positional Encodings (RoPE) have emerged as a highly effective technique for one-dimensional sequences in Natural Language Processing spurring recent progress towards generalizing RoPE to higher-dimensional data such as images and videos. The success of RoPE has been thought to be due to its positional equivariance, i.e. its status as a relative positional encoding. In this paper, we mathematically show RoPE to be one of the most general solutions for equivariant positional embedding in one-dimensional data. Moreover, we show Mixed RoPE to be the analogously general solution for M-dimensional data, if we require commutative generators -- a property necessary for RoPE's equivariance. However, we question whether strict equivariance plays a large role in RoPE's performance. We propose Spherical RoPE, a method analogous to Mixed RoPE, but assumes non-commutative generators. Empirically, we find Spherical RoPE to have the equivalent or better learning behavior compared to its equivariant analogues. This suggests that relative positional embeddings are not as important as is commonly believed, at least within computer vision. We expect this discovery to facilitate future work in positional encodings for vision that can be faster and generalize better by removing the preconception that they must be relative.

Martin Ritzert, Polina Turishcheva, Laura Hansel et al.

Hierarchical clustering is an effective, interpretable method for analyzing structure in data. It reveals insights at multiple scales without requiring a predefined number of clusters and captures nested patterns and subtle relationships, which are often missed by flat clustering approaches. However, existing hierarchical clustering methods struggle with high-dimensional data, especially when there are no clear density gaps between modes. In this work, we introduce t-NEB, a probabilistically grounded hierarchical clustering method, which yields state-of-the-art clustering performance on naturalistic high-dimensional data. t-NEB consists of three steps: (1) density estimation via overclustering; (2) finding maximum density paths between clusters; (3) creating a hierarchical structure via bottom-up cluster merging. t-NEB uses a probabilistic parametric density model for both overclustering and cluster merging, which yields both high clustering performance and a meaningful hierarchy, making it a valuable tool for exploratory data analysis. Code is available at https://github.com/ecker-lab/tneb clustering.

Finn Schmidt, Polina Turishcheva, Suhas Shrinivasan et al.

The neural activity in the visual processing is influenced by both external stimuli and internal brain states. Ideally, a neural predictive model should account for both of them. Currently, there are no dynamic encoding models that explicitly model a latent state and the entire neuronal response distribution. We address this gap by proposing a probabilistic model that predicts the joint distribution of the neuronal responses from video stimuli and stimulus-independent latent factors. After training and testing our model on mouse V1 neuronal responses, we find that it outperforms video-only models in terms of log-likelihood and achieves improvements in likelihood and correlation when conditioned on responses from other neurons. Furthermore, we find that the learned latent factors strongly correlate with mouse behavior and that they exhibit patterns related to the neurons' position on the visual cortex, although the model was trained without behavior and cortical coordinates. Our findings demonstrate that unsupervised learning of latent factors from population responses can reveal biologically meaningful structure that bridges sensory processing and behavior, without requiring explicit behavioral annotations during training.

Polina Turishcheva, Laura Hansel, Martin Ritzert et al.

Driven by advances in recording technology, large-scale high-dimensional datasets have emerged across many scientific disciplines. Especially in biology, clustering is often used to gain insights into the structure of such datasets, for instance to understand the organization of different cell types. However, clustering is known to scale poorly to high dimensions, even though the exact impact of dimensionality is unclear as current benchmark datasets are mostly two-dimensional. Here we propose MNIST-Nd, a set of synthetic datasets that share a key property of real-world datasets, namely that individual samples are noisy and clusters do not perfectly separate. MNIST-Nd is obtained by training mixture variational autoencoders with 2 to 64 latent dimensions on MNIST, resulting in six datasets with comparable structure but varying dimensionality. It thus offers the chance to disentangle the impact of dimensionality on clustering. Preliminary common clustering algorithm benchmarks on MNIST-Nd suggest that Leiden is the most robust for growing dimensions.

Polina Turishcheva, Jason Ramapuram, Sinead Williamson et al. · apple-ml, berkeley

Understanding model uncertainty is important for many applications. We propose Bootstrap Your Own Variance (BYOV), combining Bootstrap Your Own Latent (BYOL), a negative-free Self-Supervised Learning (SSL) algorithm, with Bayes by Backprop (BBB), a Bayesian method for estimating model posteriors. We find that the learned predictive std of BYOV vs. a supervised BBB model is well captured by a Gaussian distribution, providing preliminary evidence that the learned parameter posterior is useful for label free uncertainty estimation. BYOV improves upon the deterministic BYOL baseline (+2.83% test ECE, +1.03% test Brier) and presents better calibration and reliability when tested with various augmentations (eg: +2.4% test ECE, +1.2% test Brier for Salt & Pepper noise).