Marissa A. Weis

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.

Marissa A. Weis, Maciej Wołczyk, Rajai Nasser et al.

Achieving cooperation among self-interested agents remains a fundamental challenge in multi-agent reinforcement learning. Recent work showed that mutual cooperation can be induced between "learning-aware" agents that account for and shape the learning dynamics of their co-players. However, existing approaches typically rely on hardcoded, often inconsistent, assumptions about co-player learning rules or enforce a strict separation between "naive learners" updating on fast timescales and "meta-learners" observing these updates. Here, we demonstrate that the in-context learning capabilities of sequence models allow for co-player learning awareness without requiring hardcoded assumptions or explicit timescale separation. We show that training sequence model agents against a diverse distribution of co-players naturally induces in-context best-response strategies, effectively functioning as learning algorithms on the fast intra-episode timescale. We find that the cooperative mechanism identified in prior work-where vulnerability to extortion drives mutual shaping-emerges naturally in this setting: in-context adaptation renders agents vulnerable to extortion, and the resulting mutual pressure to shape the opponent's in-context learning dynamics resolves into the learning of cooperative behavior. Our results suggest that standard decentralized reinforcement learning on sequence models combined with co-player diversity provides a scalable path to learning cooperative behaviors.

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.

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.

Alexander Meulemans, Rajai Nasser, Maciej Wołczyk et al.

The standard theory of model-free reinforcement learning assumes that the environment dynamics are stationary and that agents are decoupled from their environment, such that policies are treated as being separate from the world they inhabit. This leads to theoretical challenges in the multi-agent setting where the non-stationarity induced by the learning of other agents demands prospective learning based on prediction models. To accurately model other agents, an agent must account for the fact that those other agents are, in turn, forming beliefs about it to predict its future behavior, motivating agents to model themselves as part of the environment. Here, building upon foundational work on universal artificial intelligence (AIXI), we introduce a mathematical framework for prospective learning and embedded agency centered on self-prediction, where Bayesian RL agents predict both future perceptual inputs and their own actions, and must therefore resolve epistemic uncertainty about themselves as part of the universe they inhabit. We show that in multi-agent settings, self-prediction enables agents to reason about others running similar algorithms, leading to new game-theoretic solution concepts and novel forms of cooperation unattainable by classical decoupled agents. Moreover, we extend the theory of AIXI, and study universally intelligent embedded agents which start from a Solomonoff prior. We show that these idealized agents can form consistent mutual predictions and achieve infinite-order theory of mind, potentially setting a gold standard for embedded multi-agent learning.

Marissa A. Weis, Laura Hansel, Timo Lüddecke et al.

Unsupervised graph representation learning has recently gained interest in several application domains such as neuroscience, where modeling the diverse morphology of cell types in the brain is one of the key challenges. It is currently unknown how many excitatory cortical cell types exist and what their defining morphological features are. Here we present GraphDINO, a purely data-driven approach to learn low-dimensional representations of 3D neuronal morphologies from unlabeled large-scale datasets. GraphDINO is a novel transformer-based representation learning method for spatially-embedded graphs. To enable self-supervised learning on transformers, we (1) developed data augmentation strategies for spatially-embedded graphs, (2) adapted the positional encoding and (3) introduced a novel attention mechanism, AC-Attention, which combines attention-based global interaction between nodes and classic graph convolutional processing. We show, in two different species and across multiple brain areas, that this method yields morphological cell type clusterings that are on par with manual feature-based classification by experts, but without using prior knowledge about the structural features of neurons. Moreover, it outperforms previous approaches on quantitative benchmarks predicting expert labels. Our method could potentially enable data-driven discovery of novel morphological features and cell types in large-scale datasets. It is applicable beyond neuroscience in settings where samples in a dataset are graphs and graph-level embeddings are desired.

Marissa A. Weis, Kashyap Chitta, Yash Sharma et al.

Perceiving the world in terms of objects and tracking them through time is a crucial prerequisite for reasoning and scene understanding. Recently, several methods have been proposed for unsupervised learning of object-centric representations. However, since these models were evaluated on different downstream tasks, it remains unclear how they compare in terms of basic perceptual abilities such as detection, figure-ground segmentation and tracking of objects. To close this gap, we design a benchmark with four data sets of varying complexity and seven additional test sets featuring challenging tracking scenarios relevant for natural videos. Using this benchmark, we compare the perceptual abilities of four object-centric approaches: ViMON, a video-extension of MONet, based on recurrent spatial attention, OP3, which exploits clustering via spatial mixture models, as well as TBA and SCALOR, which use explicit factorization via spatial transformers. Our results suggest that the architectures with unconstrained latent representations learn more powerful representations in terms of object detection, segmentation and tracking than the spatial transformer based architectures. We also observe that none of the methods are able to gracefully handle the most challenging tracking scenarios despite their synthetic nature, suggesting that our benchmark may provide fruitful guidance towards learning more robust object-centric video representations.

Elliot Creager, David Madras, Jörn-Henrik Jacobsen et al.

We consider the problem of learning representations that achieve group and subgroup fairness with respect to multiple sensitive attributes. Taking inspiration from the disentangled representation learning literature, we propose an algorithm for learning compact representations of datasets that are useful for reconstruction and prediction, but are also \emph{flexibly fair}, meaning they can be easily modified at test time to achieve subgroup demographic parity with respect to multiple sensitive attributes and their conjunctions. We show empirically that the resulting encoder---which does not require the sensitive attributes for inference---enables the adaptation of a single representation to a variety of fair classification tasks with new target labels and subgroup definitions.

Santiago A. Cadena, Marissa A. Weis, Leon A. Gatys et al.

Visualizing features in deep neural networks (DNNs) can help understanding their computations. Many previous studies aimed to visualize the selectivity of individual units by finding meaningful images that maximize their activation. However, comparably little attention has been paid to visualizing to what image transformations units in DNNs are invariant. Here we propose a method to discover invariances in the responses of hidden layer units of deep neural networks. Our approach is based on simultaneously searching for a batch of images that strongly activate a unit while at the same time being as distinct from each other as possible. We find that even early convolutional layers in VGG-19 exhibit various forms of response invariance: near-perfect phase invariance in some units and invariance to local diffeomorphic transformations in others. At the same time, we uncover representational differences with ResNet-50 in its corresponding layers. We conclude that invariance transformations are a major computational component learned by DNNs and we provide a systematic method to study them.