top of page

Select Publications

See Google Scholar for a more complete overview of our work. Also check out the Computational Behavior site for our previously released benchmark datasets and accompanying tutorials.

Neuron

How heterogeneity shapes dynamics and computation in the brain

David Dahmen, Axel Hutt, Giacomo Indiveri, Ann Kennedy, Jeremie Lefebvre, Luca Mazzucato, Adilson E Motter, Rishikesh Narayanan, Melika Payvand, Henrike Planert, Richard Gast

Neuron

2025

Much effort has been spent clustering neurons into transcriptomic or functional cell types and characterizing the differences between them. Beyond subdividing neurons into categories, we must recognize that no two neurons are identical and that graded physiological or transcriptomic properties exist within cells of a given type. This often overlooked “within-type” heterogeneity is a specific neuronal implementation of what statistical physics refers to as “disorder” and exhibits rich computational properties, the identification of which may shed crucial insights into theories of brain function. In this perspective article, we address this gap by highlighting theoretical frameworks for the study of neural tissue heterogeneity and discussing the benefits and implications of within-type heterogeneity for neural network dynamics, computation, and self-organization.

pdf_edited.jpg
link_edited.png
www_edited.jpg
Nature

A parabrachial hub for need-state control of enduring pain

Nitsan Goldstein, Amadeus Maes, Heather N Allen, Tyler S Nelson, Kayla A Kruger, Morgan Kindel, Albert TM Yeung, Nicholas K Smith, Jamie RE Carty, Lavinia Boccia, Niklas Blank, Emily Lo, Rachael E Villari, Ella Cho, Erin L Marble, Michelle Awh, Yasmina Dumiaty, Melissa J Chee, Rajesh Khanna, Christoph A Thaiss, Bradley K Taylor, Ann Kennedy, J Nicholas Betley

Nature

2025

Long-term sustained pain following acute physical injury is a prominent feature of chronic pain conditions. Populations of neurons that rapidly respond to noxious stimuli or tissue damage have been identified in the spinal cord and several nuclei in the brain. Understanding the central mechanisms that signal ongoing sustained pain, including after tissue healing, remains a challenge. Here we use spatial transcriptomics, neural manipulations, activity recordings and computational modelling to demonstrate that activity in an ensemble of anatomically and molecularly diverse parabrachial neurons that express the neuropeptide Y (NPY) receptor Y1 (Y1R neurons) is increased following injury and predicts functional coping behavior. Hunger, thirst or predator cues suppressed sustained pain, regardless of the injury type, by inhibiting parabrachial Y1R neurons via the release of NPY. Together, our results demonstrate an endogenous analgesic hub at pain-responsive parabrachial Y1R neurons.

pdf_edited.jpg
link_edited.png
www_edited.jpg
Current Opinion in Behavioral Sciences 59, 101437

Dynamics of neural activity in early nervous system evolution

Ann Kennedy, Brady Weissbourd

Current Opinion in Behavioral Sciences 59, 101437

2024

Endogenous activity, particularly periodic neural firing, appears across the animal kingdom and can arise through a diverse array of mechanisms. We speculate that periodic neural activity may have been a hallmark of the earliest nervous systems' function, and that modulation of this activity may have thus been an early site of behavioral control.

pdf_edited.jpg
link_edited.png
www_edited.jpg
Proceedings of the National Academy of Sciences 121 (3), e2311885121

Neural heterogeneity controls computations in spiking neural networks

Richard Gast, Sara Solla, and Ann Kennedy

Proceedings of the National Academy of Sciences 121 (3), e2311885121

2024

In contrast to information-encoding units in a computer, neurons are heterogeneous, i.e., they differ substantially in their electrophysiological properties. How does the brain make use of this heterogeneous substrate to carry out its function of processing information and generating adaptive behavior? We analyze a mathematical model of networks of heterogeneous spiking neurons and show that neural heterogeneity provides a previously unconsidered means of controlling computational properties of neural circuits.

pdf_edited.jpg
link_edited.png
www_edited.jpg
eLife 12, e84296

Using adversarial networks to extend brain computer interface decoding accuracy over time

Xuan Ma, Fabio Rizzoglio, Kevin L Bodkin, Eric Perreault, Lee E Miller, Ann Kennedy

eLife 12, e84296

2023

A critical barrier to intracortical brain-computer interface (iBCI) adoption is our inability to consistently record the same neurons over long spans of time; this signal drift requires iBCIs to be recalibrated every few days. Here, we show that domain adaptation methods can be used to "align" neural recordings between days, stabilizing iBCI performance for up to several months.

pdf_edited.jpg
link_edited.png
www_edited.jpg
ICML 32936-32990

MABe22: A multi-species multi-task benchmark for learned representations of behavior

Jennifer J Sun, Markus Marks, Andrew Wesley Ulmer, Dipam Chakraborty, Brian Geuther, Edward Hayes, Heng Jia, Vivek Kumar, Sebastian Oleszko, Zachary Partridge, Milan Peelman, Alice Robie, Catherine E Schretter, Keith Sheppard, Chao Sun, Param Uttarwar, Julian Morgan Wagner, Erik Werner, Joseph Parker, Pietro Perona, Yisong Yue, Kristin Branson, Ann Kennedy

ICML 32936-32990

2023

The past decade has seen a proliferation of methods for discovering a vocabulary of animals' actions in a data-driven manner; such methods typically work by recording the spontaneous actions of animals and looking for recurring structure. However, assessing the quality of a learned representation is not easy. In the Multi-Agent Behavior (MABe22) benchmark, we present three large datasets of interacting agents for use in representation learning; each dataset is accompanied by ground-truth labels of animals' states and actions. We propose that a "good" representation of animal behavior is one from which this relevant state and action information can be decoded without having been provided during representation learning.

pdf_edited.jpg
link_edited.png
www_edited.jpg
Physical Review E

Macroscopic dynamics of neural networks with heterogeneous spiking thresholds

Richard Gast, Sara A Solla, Ann Kennedy

Physical Review E

2023

Next-generation mean-field models are a powerful mathematical tool for modeling the emergent dynamics of spiking neural networks. However, the typical mean-field model treats neurons as identical and interchangeable units, neglecting the biological reality of both distinct neuronal cell types and of variation within a cell type. To address both points, we derive mean-field models for biologically interpretable Izhikevich model neurons and introduce neuronal heterogeneity in the form of distributed spike thresholds, contrasting dynamics of spiking and mean-field models to show where the mean-field assumptions break down.

pdf_edited.jpg
link_edited.png
www_edited.jpg
Cell 186(1) 178-193

An approximate line attractor in the hypothalamus encodes an aggressive state

Aditya Nair, Tomomi Karigo, Bin Yang, Surya Ganguli, Mark J Schnitzer, Scott W Linderman, David J Anderson, Ann Kennedy

Cell 186(1) 178-193

2023

The ventrolateral portion of ventromedial hypothalamus (VMHvl) plays a central role in regulating within-species aggression. While many VMHvl neurons show complex dynamics that are difficult to interpret, population-level analysis using a switching linear dynamical system reveals a single dimension of VMHvl activity that acts like a leaky integrator: neuronal activity along this dimension grows in magnitude as animals escalate social encounters from investigation to outright attack. Across animals, the time constant of dynamics along this dimension is highly correlated with aggression, suggesting that this time constant might be tuned to adjust an animal's willingness to fight.

pdf_edited.jpg
link_edited.png
www_edited.jpg
Current Opinion in Neurobiology 74 102549

The what, how, and why of naturalistic behavior

Ann Kennedy

Current Opinion in Neurobiology 74 102549

2022

Theories and models of behavior vary in their objective, language, and level of mechanistic detail. In this review, we present a delineation of behavior models into broad categories: descriptive models that identify what an agent did, generative models that tell us how an agent can be expected to behave given a set of conditions, and normative models that identify why a behavior occurred by defining the underlying principles that inform its structure.

pdf_edited.jpg
link_edited.png
www_edited.jpg
Neural Information Processing Systems, Datasets and Benchmarks Track

The Multi-Agent Behavior Dataset: Mouse Dyadic Social Interactions

Jennifer J Sun, Tomomi Karigo, Dipam Chakraborty, Sharada Mohanty, Benjamin Wild, Quan Sun, Chen Chen, David Anderson, Pietro Perona, Yisong Yue, Ann Kennedy

Neural Information Processing Systems, Datasets and Benchmarks Track

2021

The development of new algorithms for automated behavior analysis is throttled by a lack of large, high quality datasets that can be used to benchmark algorithm performance: without these datasets, any lab aiming to develop and test a new method must first collect their own training data. Here, we document and release three benchmark datasets for supervised behavior classification, alongside the results of an accompanying online behavior classification competition, the 2021 Multi-Agent Behavior Challenge.

pdf_edited.jpg
link_edited.png
www_edited.jpg
eLife 10 e63720

The Mouse Action Recognition System (MARS) software pipeline for automated analysis of social behaviors in mice

Cristina Segalin, Jalani Williams, Tomomi Karigo, May Hui, Moriel Zelikowsky, Jennifer J Sun, Pietro Perona, David J Anderson, Ann Kennedy

eLife 10 e63720

2021

We present the Mouse Action Recognition System (MARS), a computer vision and machine learning platform for markerless pose estimation and supervised behavior classification in socially interacting mice. MARS automatically detects three types of social interaction with human-level accuracy, permitting high-throughput social behavior screening. Accompanying platform BENTO supports analysis and visualization of joint neural and behavioral datasets.

pdf_edited.jpg
link_edited.png
www_edited.jpg
bottom of page