arXiv subjects

Alexander S. Ecker

Publications and source records attributed to Alexander S. Ecker.

At least 19 recordsLinked to original sources

arXiv2026

OmniMouse: Scaling properties of multi-modal, multi-task Brain Models on 150B Neural Tokens

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.

q-bio.NC↗

arXiv2026

SiLVi: Simple Interface for Labeling Video Interactions

Computer vision methods are increasingly used for the automated analysis of large volumes of video data collected through camera traps, drones, or direct observations of animals in the wild. While recent advances have focused primarily on detecting individual actions, much less work has addressed the detection and annotation of interactions -- a crucial aspect for understanding social and individualized animal behavior. Existing open-source annotation tools support either behavioral labeling without localization of individuals, or localization without the capacity to capture interactions. To bridge this gap, we present SiLVi, an open-source labeling software that integrates both functionalities. SiLVi enables researchers to annotate behaviors and interactions directly within video data, generating structured outputs suitable for training and validating computer vision models. By linking behavioral ecology with computer vision, SiLVi facilitates the development of automated approaches for fine-grained behavioral analyses. Although developed primarily in the context of animal behavior, SiLVi could be useful more broadly to annotate human interactions in other videos that require extracting dynamic scene graphs. The software, along with documentation and download instructions, is available at: https://silvi.eckerlab.org.

cs.CV↗

arXiv2026

PriVi: Towards A General-Purpose Video Model For Primate Behavior In The Wild

Non-human primates are our closest living relatives, and analyzing their behavior is central to research in cognition, evolution, and conservation. Computer vision could greatly aid this research, but existing methods often rely on human-centric pretrained models and focus on single datasets, which limits generalization. We address this limitation by shifting from a model-centric to a data-centric approach and introduce PriVi, a large-scale primate-centric video pretraining dataset. PriVi contains 424 hours of curated video, combining 174 hours from behavioral research across 11 settings with 250 hours of diverse web-sourced footage, assembled through a scalable data curation pipeline. We continue pretraining V-JEPA, a large-scale video model, on PriVi to learn primate-specific representations and evaluate it using a lightweight frozen classifier. Across four benchmark datasets, ChimpACT, PanAf500, BaboonLand, and ChimpBehave, our approach consistently outperforms prior work, including fully finetuned baselines, and scales favorably with fewer labels. These results demonstrate for the first time that domain-level pretraining, where pretraining is conducted on similar data but not the target dataset itself, works for video models. Our primate-centric pretraining substantially improves data efficiency and generalization, making it a promising approach for low-label applications. Dataset, code, and models are available: https://privi.eckerlab.org

cs.CV↗

arXiv2025

A Circular Argument : Does RoPE need to be Equivariant for Vision?

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.

cs.CV↗

arXiv2025

Clifford Algebraic Rotor Embeddings : Maybe embeddings should start to CARE

Rotary Positional Embeddings (RoPE) have demonstrated exceptional performance as a positional encoding method, consistently outperforming their baselines. While recent work has sought to extend RoPE to higher-dimensional inputs, many such extensions are non-commutative, thereby forfeiting RoPE's shift-equivariance property. Spherical RoPE is one such non-commutative variant, motivated by the idea of rotating embedding vectors on spheres rather than circles. However, spherical rotations are inherently non-commutative, making the choice of rotation sequence ambiguous. In this work, we explore a quaternion-based approach -- Quaternion Rotary Embeddings (QuatRo) -- in place of Euler angles, leveraging quaternions' ability to represent 3D rotations to parameterize the axes of rotation. We show Mixed RoPE and Spherical RoPE to be special cases of QuatRo. Further, we propose a generalization of QuatRo to Clifford Algebraic Rotary Embeddings (CARE) using geometric algebra. Viewing quaternions as the even subalgebra of Cl(3,0,0), we extend the notion of rotary embeddings from quaternions to Clifford rotors acting on multivectors. This formulation enables two key generalizations: (1) extending rotary embeddings to arbitrary dimensions, and (2) encoding positional information in multivectors of multiple grades, not just vectors. We present preliminary experiments comparing spherical, quaternion, and Clifford-based rotary embeddings.

cs.LG↗

arXiv2025

Do traveling waves make good positional encodings?

Transformers rely on positional encoding to compensate for the inherent permutation invariance of self-attention. Traditional approaches use absolute sinusoidal embeddings or learned positional vectors, while more recent methods emphasize relative encodings to better capture translation equivariances. In this work, we propose RollPE, a novel positional encoding mechanism based on traveling waves, implemented by applying a circular roll operation to the query and key tensors in self-attention. This operation induces a relative shift in phase across positions, allowing the model to compute attention as a function of positional differences rather than absolute indices. We show this simple method significantly outperforms traditional absolute positional embeddings and is comparable to RoPE. We derive a continuous case of RollPE which implicitly imposes a topographic structure on the query and key space. We further derive a mathematical equivalence of RollPE to a particular configuration of RoPE. Viewing RollPE through the lens of traveling waves may allow us to simplify RoPE and relate it to processes of information flow in the brain.

cs.LG↗

arXiv2025

What should a neuron aim for? Designing local objective functions based on information theory

In modern deep neural networks, the learning dynamics of the individual neurons is often obscure, as the networks are trained via global optimization. Conversely, biological systems build on self-organized, local learning, achieving robustness and efficiency with limited global information. We here show how self-organization between individual artificial neurons can be achieved by designing abstract bio-inspired local learning goals. These goals are parameterized using a recent extension of information theory, Partial Information Decomposition (PID), which decomposes the information that a set of information sources holds about an outcome into unique, redundant and synergistic contributions. Our framework enables neurons to locally shape the integration of information from various input classes, i.e. feedforward, feedback, and lateral, by selecting which of the three inputs should contribute uniquely, redundantly or synergistically to the output. This selection is expressed as a weighted sum of PID terms, which, for a given problem, can be directly derived from intuitive reasoning or via numerical optimization, offering a window into understanding task-relevant local information processing. Achieving neuron-level interpretability while enabling strong performance using local learning, our work advances a principled information-theoretic foundation for local learning strategies.

cs.IT↗

arXiv2025

Domain-Adaptive Pretraining Improves Primate Behavior Recognition

Computer vision for animal behavior offers promising tools to aid research in ecology, cognition, and to support conservation efforts. Video camera traps allow for large-scale data collection, but high labeling costs remain a bottleneck to creating large-scale datasets. We thus need data-efficient learning approaches. In this work, we show that we can utilize self-supervised learning to considerably improve action recognition on primate behavior. On two datasets of great ape behavior (PanAf and ChimpACT), we outperform published state-of-the-art action recognition models by 6.1 %pt. accuracy and 6.3 %pt. mAP, respectively. We achieve this by utilizing a pretrained V-JEPA model and applying domain-adaptive pretraining (DAP), i.e. continuing the pretraining with in-domain data. We show that most of the performance gain stems from the DAP. Our method promises great potential for improving the recognition of animal behavior, as DAP does not require labeled samples. Code is available at https://github.com/ecker-lab/dap-behavior

cs.CV↗

arXiv2025

Learning to cluster neuronal function

Deep neural networks trained to predict neural activity from visual input and behaviour have shown great potential to serve as digital twins of the visual cortex. Per-neuron embeddings derived from these models could potentially be used to map the functional landscape or identify cell types. However, state-of-the-art predictive models of mouse V1 do not generate functional embeddings that exhibit clear clustering patterns which would correspond to cell types. This raises the question whether the lack of clustered structure is due to limitations of current models or a true feature of the functional organization of mouse V1. In this work, we introduce DECEMber -- Deep Embedding Clustering via Expectation Maximization-based refinement -- an explicit inductive bias into predictive models that enhances clustering by adding an auxiliary $t$-distribution-inspired loss function that enforces structured organization among per-neuron embeddings. We jointly optimize both neuronal feature embeddings and clustering parameters, updating cluster centers and scale matrices using the EM-algorithm. We demonstrate that these modifications improve cluster consistency while preserving high predictive performance and surpassing standard clustering methods in terms of stability. Moreover, DECEMber generalizes well across species (mice, primates) and visual areas (retina, V1, V4). The code is available at https://github.com/Nisone2000/sensorium/tree/neuroips_version.

q-bio.NC↗

arXiv2025

Hierarchical clustering with maximum density paths and mixture models

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.

stat.ML↗

arXiv2024

MNIST-Nd: a set of naturalistic datasets to benchmark clustering across dimensions

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.

cs.LG↗

arXiv2024

Computer Vision for Primate Behavior Analysis in the Wild

Advances in computer vision as well as increasingly widespread video-based behavioral monitoring have great potential for transforming how we study animal cognition and behavior. However, there is still a fairly large gap between the exciting prospects and what can actually be achieved in practice today, especially in videos from the wild. With this perspective paper, we want to contribute towards closing this gap, by guiding behavioral scientists in what can be expected from current methods and steering computer vision researchers towards problems that are relevant to advance research in animal behavior. We start with a survey of the state-of-the-art methods for computer vision problems that are directly relevant to the video-based study of animal behavior, including object detection, multi-individual tracking, individual identification, and (inter)action recognition. We then review methods for effort-efficient learning, which is one of the biggest challenges from a practical perspective. Finally, we close with an outlook into the future of the emerging field of computer vision for animal behavior, where we argue that the field should develop approaches to unify detection, tracking, identification and (inter)action recognition in a single, video-based framework.

cs.CV↗

arXiv2024

The Dynamic Sensorium competition for predicting large-scale mouse visual cortex activity from videos

Understanding how biological visual systems process information is challenging due to the complex nonlinear relationship between neuronal responses and high-dimensional visual input. Artificial neural networks have already improved our understanding of this system by allowing computational neuroscientists to create predictive models and bridge biological and machine vision. During the Sensorium 2022, we introduced benchmarks for vision models with static input. However, animals operate and excel in dynamic environments, making it crucial to study and understand how the brain functions under these conditions. Moreover, many biological theories, such as predictive coding, suggest that previous input is crucial for current input processing. Currently, there is no standardized benchmark to identify state-of-the-art dynamic models of the mouse visual system. To address this gap, we propose the Sensorium 2023 Benchmark Competition with dynamic input. It includes the collection of a new large-scale dataset from the primary visual cortex of ten mice, containing responses from over 78,000 neurons to over 2 hours of dynamic stimuli per neuron. Participants in the main benchmark track will compete to identify the best predictive models of neuronal responses for dynamic input. We will also host a bonus track in which submission performance will be evaluated on out-of-domain input, using withheld neuronal responses to dynamic input stimuli whose statistics differ from the training set. Both tracks will offer behavioral data along with video stimuli. As before, we will provide code, tutorials, and strong pre-trained baseline models to encourage participation. We hope this competition will continue to strengthen the accompanying Sensorium benchmarks collection as a standard tool to measure progress in large-scale neural system identification models of the entire mouse visual hierarchy and beyond.

q-bio.NC↗

arXiv2024

Most discriminative stimuli for functional cell type clustering

Identifying cell types and understanding their functional properties is crucial for unraveling the mechanisms underlying perception and cognition. In the retina, functional types can be identified by carefully selected stimuli, but this requires expert domain knowledge and biases the procedure towards previously known cell types. In the visual cortex, it is still unknown what functional types exist and how to identify them. Thus, for unbiased identification of the functional cell types in retina and visual cortex, new approaches are needed. Here we propose an optimization-based clustering approach using deep predictive models to obtain functional clusters of neurons using Most Discriminative Stimuli (MDS). Our approach alternates between stimulus optimization with cluster reassignment akin to an expectation-maximization algorithm. The algorithm recovers functional clusters in mouse retina, marmoset retina and macaque visual area V4. This demonstrates that our approach can successfully find discriminative stimuli across species, stages of the visual system and recording techniques. The resulting most discriminative stimuli can be used to assign functional cell types fast and on the fly, without the need to train complex predictive models or show a large natural scene dataset, paving the way for experiments that were previously limited by experimental time. Crucially, MDS are interpretable: they visualize the distinctive stimulus patterns that most unambiguously identify a specific type of neuron.

q-bio.NC↗

arXiv2024

Tailor-designed models for the turbulent velocity gradient through normalizing flow

Small-scale turbulence can be comprehensively described in terms of velocity gradients, which makes them an appealing starting point for low-dimensional modeling. Typical models consist of stochastic equations based on closures for non-local pressure and viscous contributions. The fidelity of the resulting models depends on the accuracy of the underlying modeling assumptions. Here, we discuss an alternative data-driven approach leveraging machine learning to derive a velocity gradient model which captures its statistics by construction. We use a normalizing flow to learn the velocity gradient probability density function (PDF) from direct numerical simulation (DNS) of incompressible turbulence. Then, by using the equation for the single-time PDF of the velocity gradient, we construct a deterministic, yet chaotic, dynamical system featuring the learned steady-state PDF by design. Finally, utilizing gauge terms for the velocity gradient single-time statistics, we optimize the time correlations as obtained from our model against the DNS data. As a result, the model time realizations statistically closely resemble the time series from DNS.

physics.flu-dyn↗

arXiv2023

Self-Supervised Graph Representation Learning for Neuronal Morphologies

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.

stat.ML↗

arXiv2022

A Broad Dataset is All You Need for One-Shot Object Detection

Is it possible to detect arbitrary objects from a single example? A central problem of all existing attempts at one-shot object detection is the generalization gap: Object categories used during training are detected much more reliably than novel ones. We here show that this generalization gap can be nearly closed by increasing the number of object categories used during training. Doing so allows us to improve generalization from seen to unseen classes from 45% to 89% and improve the state-of-the-art on COCO by 5.4 %AP50 (from 22.0 to 27.5). We verify that the effect is caused by the number of categories and not the number of training samples, and that it holds for different models, backbones and datasets. This result suggests that the key to strong few-shot detection models may not lie in sophisticated metric learning approaches, but instead simply in scaling the number of categories. We hope that our findings will help to better understand the challenges of few-shot learning and encourage future data annotation efforts to focus on wider datasets with a broader set of categories rather than gathering more samples per category.

cs.CV↗

arXiv2022

The Sensorium competition on predicting large-scale mouse primary visual cortex activity

The neural underpinning of the biological visual system is challenging to study experimentally, in particular as the neuronal activity becomes increasingly nonlinear with respect to visual input. Artificial neural networks (ANNs) can serve a variety of goals for improving our understanding of this complex system, not only serving as predictive digital twins of sensory cortex for novel hypothesis generation in silico, but also incorporating bio-inspired architectural motifs to progressively bridge the gap between biological and machine vision. The mouse has recently emerged as a popular model system to study visual information processing, but no standardized large-scale benchmark to identify state-of-the-art models of the mouse visual system has been established. To fill this gap, we propose the Sensorium benchmark competition. We collected a large-scale dataset from mouse primary visual cortex containing the responses of more than 28,000 neurons across seven mice stimulated with thousands of natural images, together with simultaneous behavioral measurements that include running speed, pupil dilation, and eye movements. The benchmark challenge will rank models based on predictive performance for neuronal responses on a held-out test set, and includes two tracks for model input limited to either stimulus only (Sensorium) or stimulus plus behavior (Sensorium+). We provide a starting kit to lower the barrier for entry, including tutorials, pre-trained baseline models, and APIs with one line commands for data loading and submission. We would like to see this as a starting point for regular challenges and data releases, and as a standard tool for measuring progress in large-scale neural system identification models of the mouse visual system and beyond.

q-bio.NC↗