arXiv subjects

Ann Kennedy

Publications and source records attributed to Ann Kennedy.

13 recordsLinked to original sources

arXiv2026

Local connectivity balance shapes population dynamics in random recurrent networks

Disordered dynamical systems comprising many interacting units, from ecological communities to neural circuits, are ubiquitous, and understanding how connectivity shapes their collective behavior is a central theoretical challenge. One long-recognized feature of neural circuits is local connectivity balance, in which the excitatory and inhibitory weights converging onto each unit approximately cancel. Although local connectivity balance has been proposed to serve functions such as gating incoming signals, its effect on collective network dynamics remains unclear. Here we analytically study randomly connected recurrent networks with varying degrees of local connectivity balance. We show that this balance leaves the connectivity spectrum unchanged yet drastically reshapes the dynamics in a manner that depends critically on the single-unit nonlinearity. Local balance suppresses unbounded growth of the network state and stabilizes network dynamics when the activation function scales linearly or faster, whereas it drives the network into chaos when the activation function is sub-linear or saturating. Importantly, these effects vanish for odd activation functions, which are commonly assumed in previous work. We further find that, for saturating nonlinearities, the effective dimension of the dynamics varies nonmonotonically with the degree of balance. We show that all these phenomena arise from a unifying mechanism: the suppression of a self-generated feedback input by local connectivity balance. Our results identify local connectivity balance as a previously overlooked control parameter for collective dynamics in realistic disordered networks.

q-bio.NC↗

arXiv2026

A multi-ensemble mean-field reduction method for networks of globally coupled phase oscillators with arbitrary parameter distributions

Understanding the dynamical properties of coupled phase oscillator systems with heterogeneous oscillator frequencies has been a long-standing challenge of complex systems theory. While the seminal work of Ott and Antonsen dramatically improved our theoretical understanding of coupled phase oscillators for a small family of oscillator frequency distributions, we here present a mean-field reduction method for arbitrary frequency distributions. Our method leverages the drastic dimensionality reduction obtained for Lorentzian frequency distributions, and combines it with a data-driven multi-ensemble approach. As such, the method renders the Ott-Antonsen equations directly applicable to empirical distributions of phase oscillator frequencies, often achieving a drastic dimensionality reduction and allowing to study real-world physical and biological systems by means of stability, sensitivity, and bifurcation analyses.

cond-mat.dis-nn↗

arXiv2025

BiomechGPT: Extending Motion-Language Models to Clinical Motion Understanding

Advances in markerless motion capture are making high-quality biomechanical data increasingly accessible, creating a growing need for scalable downstream analytics. Building a bespoke pipeline for each analysis task is time-consuming, motivating models that can flexibly handle diverse clinical questions within a single framework. Recent work has shown that fine-tuning language models to accept tokenized motion as an additional modality enables descriptive captioning of movement, raising the question of whether these models are also capable of clinically relevant motion understanding, where diverse tasks and annotations provide a natural testbed. We investigate whether such a multimodal motion--language model can answer detailed, clinically meaningful questions about movement. We collected 71 hours of biomechanical data from 750 participants, many with movement impairments, performing tasks commonly used in clinical assessment. To further expand the training dataset, we designed a cross-format tokenizer that directly encodes motion data from heterogeneous formats into a shared latent space without paired data, allowing a second dataset to be incorporated and enabling pooling annotations across datasets. From these tokenized representations, we constructed a multimodal dataset of motion-related question--answer pairs and used it to train BiomechGPT, a multimodal biomechanics--language model. BiomechGPT achieves competitive performance across a range of clinically relevant tasks, with performance scaling with both dataset and model size. It offers a new way for clinicians and researchers to interact with biomechanical data and represents a promising direction for rehabilitation-focused movement analysis. Project page: https://intelligentsensingandrehabilitation.github.io/BiomechGPT/

cs.CV↗

arXiv2023

MABe22: A Multi-Species Multi-Task Benchmark for Learned Representations of Behavior

We introduce MABe22, a large-scale, multi-agent video and trajectory benchmark to assess the quality of learned behavior representations. This dataset is collected from a variety of biology experiments, and includes triplets of interacting mice (4.7 million frames video+pose tracking data, 10 million frames pose only), symbiotic beetle-ant interactions (10 million frames video data), and groups of interacting flies (4.4 million frames of pose tracking data). Accompanying these data, we introduce a panel of real-life downstream analysis tasks to assess the quality of learned representations by evaluating how well they preserve information about the experimental conditions (e.g. strain, time of day, optogenetic stimulation) and animal behavior. We test multiple state-of-the-art self-supervised video and trajectory representation learning methods to demonstrate the use of our benchmark, revealing that methods developed using human action datasets do not fully translate to animal datasets. We hope that our benchmark and dataset encourage a broader exploration of behavior representation learning methods across species and settings.

cs.LG↗

arXiv2023

BKinD-3D: Self-Supervised 3D Keypoint Discovery from Multi-View Videos

Quantifying motion in 3D is important for studying the behavior of humans and other animals, but manual pose annotations are expensive and time-consuming to obtain. Self-supervised keypoint discovery is a promising strategy for estimating 3D poses without annotations. However, current keypoint discovery approaches commonly process single 2D views and do not operate in the 3D space. We propose a new method to perform self-supervised keypoint discovery in 3D from multi-view videos of behaving agents, without any keypoint or bounding box supervision in 2D or 3D. Our method, BKinD-3D, uses an encoder-decoder architecture with a 3D volumetric heatmap, trained to reconstruct spatiotemporal differences across multiple views, in addition to joint length constraints on a learned 3D skeleton of the subject. In this way, we discover keypoints without requiring manual supervision in videos of humans and rats, demonstrating the potential of 3D keypoint discovery for studying behavior.

cs.CV↗

arXiv2023

PyRates -- A Code-Generation Tool for Dynamical Systems Modeling

Mathematical models allow us to gain a deeper understanding of real-world dynamical systems. One of the most powerful mathematical frameworks for modeling real-world phenomena are systems of differential equations. In the majority of fields that use differential equations, numerical methods are essential for conducting model-based research. Although many software solutions are available for the numerical study of differential equation systems, a common framework for implementing differential equation systems is lacking. This hinders progress in dynamical systems research and limits the shareability and reproducibility of results. PyRates is a Python-based software for modeling and analyzing dynamical systems. It provides a user-friendly interface for defining models, which is based on a graph-based, hierarchical structure that mirrors the modular organization of real-world dynamical systems. This design allows users to leverage the hierarchical structure of their systems and create their models with minimal effort. Importantly, the core of PyRates is a versatile code-generation system, which can translate user-defined models into "backend" implementations in various languages, including Python, Fortran, and Julia. This allows users to access a wide range of analysis methods for dynamical systems, eliminating the need for manual translation between code bases. We demonstrate PyRates's capabilities in three use cases, where it generates NumPy code for numerical simulations, Fortran code for bifurcation analysis, and PyTorch code for neural network optimization. Finally, PyRates can be used as a model definition interface for the creation of new dynamical systems tools. We developed two such software packages, PyCoBi and RectiPy, as extensions of PyRates for specific dynamical systems modeling applications.

cond-mat.dis-nn↗

arXiv2022

Unsupervised Learning of Neurosymbolic Encoders

We present a framework for the unsupervised learning of neurosymbolic encoders, which are encoders obtained by composing neural networks with symbolic programs from a domain-specific language. Our framework naturally incorporates symbolic expert knowledge into the learning process, which leads to more interpretable and factorized latent representations compared to fully neural encoders. We integrate modern program synthesis techniques with the variational autoencoding (VAE) framework, in order to learn a neurosymbolic encoder in conjunction with a standard decoder. The programmatic descriptions from our encoders can benefit many analysis workflows, such as in behavior modeling where interpreting agent actions and movements is important. We evaluate our method on learning latent representations for real-world trajectory data from animal biology and sports analytics. We show that our approach offers significantly better separation of meaningful categories than standard VAEs and leads to practical gains on downstream analysis tasks, such as for behavior classification.

cs.LG↗

arXiv2022

Macroscopic Dynamics of Neural Networks with Heterogeneous Spiking Thresholds

Mean-field theory links the physiological properties of individual neurons to the emergent dynamics of neural population activity. These models provide an essential tool for studying brain function at different scales; however, for their application to neural populations on large scale, they need to account for differences between distinct neuron types. The Izhikevich single neuron model can account for a broad range of different neuron types and spiking patterns, thus rendering it an optimal candidate for a mean-field theoretic treatment of brain dynamics in heterogeneous networks. Here, we derive the mean-field equations for networks of all-to-all coupled Izhikevich neurons with heterogeneous spiking thresholds. Using methods from bifurcation theory, we examine the conditions under which the mean-field theory accurately predicts the dynamics of the Izhikevich neuron network. To this end, we focus on three important features of the Izhikevich model that are subject here to simplifying assumptions: (i) spike-frequency adaptation, (ii) the spike reset conditions, and (iii) the distribution of single-cell spike thresholds across neurons. Our results indicate that, while the mean-field model is not an exact model of the Izhikevich network dynamics, it faithfully captures its different dynamic regimes and phase transitions. We thus present a mean-field model that can represent different neuron types and spiking dynamics. The model is comprised of biophysical state variables and parameters, incorporates realistic spike resetting conditions, and accounts for heterogeneity in neural spiking thresholds. These features allow for a broad applicability of the model as well as for a direct comparison to experimental data.

q-bio.NC↗

arXiv2022

Effects of Neural Heterogeneity on Spiking Neural Network Dynamics

The brain is composed of complex networks of interacting neurons that express considerable heterogeneity in their physiology and spiking characteristics. How does neural heterogeneity affect macroscopic neural dynamics and how does it contribute to neurodynamic functions? In this letter, we address these questions by studying the macroscopic dynamics of networks of heterogeneous Izhikevich neurons. We derive mean-field equations for these networks and examine how heterogeneity in the spiking thresholds of Izhikevich neurons affects the emergent macroscopic dynamics. Our results suggest that the level of heterogeneity of inhibitory populations controls resonance and hysteresis properties of systems of coupled excitatory and inhibitory neurons. Neural heterogeneity may thus serve as a means to control the dynamic repertoire of mesoscopic brain circuits.

q-bio.NC↗

arXiv2022

Self-Supervised Keypoint Discovery in Behavioral Videos

We propose a method for learning the posture and structure of agents from unlabelled behavioral videos. Starting from the observation that behaving agents are generally the main sources of movement in behavioral videos, our method, Behavioral Keypoint Discovery (B-KinD), uses an encoder-decoder architecture with a geometric bottleneck to reconstruct the spatiotemporal difference between video frames. By focusing only on regions of movement, our approach works directly on input videos without requiring manual annotations. Experiments on a variety of agent types (mouse, fly, human, jellyfish, and trees) demonstrate the generality of our approach and reveal that our discovered keypoints represent semantically meaningful body parts, which achieve state-of-the-art performance on keypoint regression among self-supervised methods. Additionally, B-KinD achieve comparable performance to supervised keypoints on downstream tasks, such as behavior classification, suggesting that our method can dramatically reduce model training costs vis-a-vis supervised methods.

cs.CV↗

arXiv2021

The Multi-Agent Behavior Dataset: Mouse Dyadic Social Interactions

Multi-agent behavior modeling aims to understand the interactions that occur between agents. We present a multi-agent dataset from behavioral neuroscience, the Caltech Mouse Social Interactions (CalMS21) Dataset. Our dataset consists of trajectory data of social interactions, recorded from videos of freely behaving mice in a standard resident-intruder assay. To help accelerate behavioral studies, the CalMS21 dataset provides benchmarks to evaluate the performance of automated behavior classification methods in three settings: (1) for training on large behavioral datasets all annotated by a single annotator, (2) for style transfer to learn inter-annotator differences in behavior definitions, and (3) for learning of new behaviors of interest given limited training data. The dataset consists of 6 million frames of unlabeled tracked poses of interacting mice, as well as over 1 million frames with tracked poses and corresponding frame-level behavior annotations. The challenge of our dataset is to be able to classify behaviors accurately using both labeled and unlabeled tracking data, as well as being able to generalize to new settings.

cs.LG↗

arXiv2021

Interpreting Expert Annotation Differences in Animal Behavior

Hand-annotated data can vary due to factors such as subjective differences, intra-rater variability, and differing annotator expertise. We study annotations from different experts who labelled the same behavior classes on a set of animal behavior videos, and observe a variation in annotation styles. We propose a new method using program synthesis to help interpret annotation differences for behavior analysis. Our model selects relevant trajectory features and learns a temporal filter as part of a program, which corresponds to estimated importance an annotator places on that feature at each timestamp. Our experiments on a dataset from behavioral neuroscience demonstrate that compared to baseline approaches, our method is more accurate at capturing annotator labels and learns interpretable temporal filters. We believe that our method can lead to greater reproducibility of behavior annotations used in scientific studies. We plan to release our code.

cs.LG↗

arXiv2021

Task Programming: Learning Data Efficient Behavior Representations

Specialized domain knowledge is often necessary to accurately annotate training sets for in-depth analysis, but can be burdensome and time-consuming to acquire from domain experts. This issue arises prominently in automated behavior analysis, in which agent movements or actions of interest are detected from video tracking data. To reduce annotation effort, we present TREBA: a method to learn annotation-sample efficient trajectory embedding for behavior analysis, based on multi-task self-supervised learning. The tasks in our method can be efficiently engineered by domain experts through a process we call "task programming", which uses programs to explicitly encode structured knowledge from domain experts. Total domain expert effort can be reduced by exchanging data annotation time for the construction of a small number of programmed tasks. We evaluate this trade-off using data from behavioral neuroscience, in which specialized domain knowledge is used to identify behaviors. We present experimental results in three datasets across two domains: mice and fruit flies. Using embeddings from TREBA, we reduce annotation burden by up to a factor of 10 without compromising accuracy compared to state-of-the-art features. Our results thus suggest that task programming and self-supervision can be an effective way to reduce annotation effort for domain experts.

cs.CV↗