Lab Publications
Our publications fall into three groupings: Neuroscience, NeuroAI, & Computer Vision.
To see our work arranged according to these focus areas, please click here.
Below you will find lab publications in chronological order (bold names are lab members).
2024
Decoding the brain: From neural representations to mechanistic models. Cell, 2024
Mackenzie Weygandt Mathis, Adriana Perez Rotondo, Edward F. Chang, Andreas S. Tolias, Alexander Mathis.
Keypoint-MoSeq: parsing behavior by linking point tracking to pose dynamics. Nature Methods, 2024
Caleb Weinreb , Mohammed Abdal Monium Osman, Libby Zhang, Sherry Lin , Jonah Pearl , Sidharth Annapragada, Eli Conlin, Winthrop F. Gillis, Maya Jay, Shaokai Ye, Alexander Mathis, Mackenzie Weygandt Mathis, Talmo Pereira , Scott W. Linderman,* and Sandeep Robert Datta*
Ethological computational psychiatry: Challenges and opportunities. Current Opinion in Neurobiology, 2024
Ilya E. Monosov*, Jan Zimmermann*, Michael J. Frank*, Mackenzie W. Mathis*, Justin T. Baker* (*equal contributions)
SuperAnimal pretrained pose estimation models for behavioral analysis. Nature Communications, 2024
Shaokai Ye, Anastasiia Filippova, Jessy Lauer, Steffen Schneider, Maxime Vidal, Tian Qiu, Alexander Mathis & Mackenzie Weygandt Mathis
2023
Identifiable attribution maps using regularized contrastive learning. NeurIPS-W, 2023
Steffen Schneider, Rodrigo González Laiz, Markus Frey, Mackenzie W Mathis
AmadeusGPT: a natural language interface for interactive animal behavioral analysis. NeurIPS, 2023
Shaokai Ye, Jessy Lauer, Mu Zhou, Alexander Mathis, Mackenzie W. Mathis
Rethinking pose estimation in crowds: overcoming the detection information-bottleneck and ambiguity. ICCV, 2023
Mu Zhou*, Lucas Stoffl*, Mackenzie W. Mathis, Alexander Mathis
Contrasting action and posture coding with hierarchical deep neural network models of proprioception. eLife, 2023
Kai J. Sandbrink, Pranav Mamidanna, Claudio Michaelis, Matthias Bethge, Mackenzie Weygandt Mathis*, Alexander Mathis*
Project page: https://www.mathislab.org/deepdraw
Learnable latent embeddings for joint behavioural and neural analysis. Nature, 2023
Steffen Schneider, Jin Hwa Lee & Mackenzie Weygandt Mathis.
Brain dynamics uncovered using a machine-learning algorithm Nature Research Briefing, 2023
NeuroAI: If grid cells are the answer, is path integration the question? Current Biology, 2023
Dispatch Article for Sorscher et al 2023 Neuron
Markus Frey, Mackenzie W. Mathis, Alexander Mathis
Reaching an understanding of cortico-medullary control of forelimb behaviors. Cell, 2023
Preview article for Yang et al. 2023 Cell
Thomas T.J. Sainsbury, Mackenzie W. Mathis
The neocortical column as a universal template for perception and world-model learning. Nature Reviews Neuroscience, 2023
Mackenzie Weygandt Mathis
Next-generation brain observatories. Neuron, 2022
Christof Koch,* Karel Svoboda,* Amy Bernard, Michele A. Basso, Anne K. Churchland, Adrienne L. Fairhall, Peter A. Groblewski, Jerome A. Lecoq, Zachary F. Mainen, Mackenzie W. Mathis, Shawn R. Olsen, John w. Phillips, Alexandre Pouget, Shreya Saxena, Josh H. Siegle, and Anthony M. Zador (*corresponding; others are alphabetically listed)
2022
Striatal dopamine explains novelty-induced behavioral dynamics and individual variability in threat prediction. Neuron, 2022
Korleki Akiti, Iku Tsutsui-Kimura, Yudi Xie, Alexander Mathis, Jeffrey Markowitz, Rockwell Anyoha, Sandeep Robert Datta, Mackenzie Weygandt Mathis, Naoshige Uchida, Mitsuko Watabe-Uchida.
Multi-animal pose estimation, identification and tracking with DeepLabCut. Nature Methods, 2022
Jessy Lauer, Mu Zhou, Shaokai Ye, William Menegas, Steffen Schneider, Tanmay Nath, Mohammed Mostafizur Rahman, Valentina Di Santo, Daniel Soberanes, Guoping Feng, Venkatesh N. Murthy, George Lauder, Catherine Dulac, Mackenzie Weygandt Mathis* & Alexander Mathis* (*co-senior)
Perspectives in machine learning for wildlife conservation. Nature Communications, 2022
Devis Tuia, Benjamin Kellenberger, Sara Beery, Blair R. Costelloe, Silvia Zuffi, Benjamin Risse, Alexander Mathis, Mackenzie W. Mathis, Frank van Langevelde, Tilo Burghardt, Roland Kays, Holger Klinck, Martin Wikelski, Iain D. Couzin, Grant van Horn, Margaret C. Crofoot, Charles V. Stewart & Tanya Berger-Wolf
2021
AcinoSet: A 3D Pose Estimation Dataset and Baseline Models for Cheetahs in the Wild. ICRA, 2021
Daniel Joska, Liam Clark, Naoya Muramatsu, Ricardo Jericevich, Fred Nicolls, Alexander Mathis, Mackenzie W. Mathis & Amir Patel.
Measuring and modeling the motor system with machine learning. Current Opinion in Neurobiology, 2021
Sebastien B. Hausmann, Alessandro Marin Vargas, Alexander Mathis, Mackenzie W. Mathis
Out-of-distribution generalization of internal models is correlated with reward. ICLR-W, 2021
Khushdeep S. Mann∗, Steffen Schneider∗, Alberto Chiappa, Jin H. Lee, Matthias Bethge, Alexander Mathis, Mackenzie W. Mathis
Motor control: Neural correlates of optimal feedback control theory. Current Biology, 2021
Mackenzie W. Mathis, Steffen Schneider.
Dispatch Review Paper on: Transient deactivation of dorsal premotor cortex or parietal area 5 impairs feedback control of the limb in macaques
Dynamic extrinsic pacing of the HOX clock in human axial progenitors controls motor neuron subtype specification. Development, 2021
Vincent Mouilleau, Célia Vaslin, Rémi Robert, Simona Gribaudo, Nour Nicolas, Margot Jarrige, Angélique Terray, Léa Lesueur, Mackenzie W. Mathis, Gist Croft, Mathieu Daynac, Virginie Rouiller-Fabre, Hynek Wichterle, Vanessa Ribes, Cécile Martinat, Stéphane Nedelec.
Pretraining boosts out-of-domain robustness for pose estimation. WACV, 2021
Alexander Mathis*, Thomas Biasi*, Steffen Schneider, Mert Yüksekgönül, Byron Rogers, Matthias Bethge, Mackenzie W. Mathis.
Also presented at the ICML 2020 Uncertainty & Robustness in Deep Learning Workshop.
- Watch Thomas Biasi give a talk at WACV!
- More details: horse10.deeplabcut.org
2020
Real-time, low-latency closed-loop feedback using markerless posture tracking.
eLife, 2020
Gary Kane, Gonçalo Lopes, Jonny L. Saunders, Alexander Mathis, Mackenzie W. Mathis.
Read more in the news!
Listen to an interview (french only)
Watch Gary Kane speak at NeuroMatch!
Generalized Invariant Risk Minimization: relating adaptation and invariant representation learning. NeurIPS-W, 2020
Steffen Schneider, Shubham Krishna, Luisa Eck, Wieland Brendel, Mackenzie W Mathis, Matthias Bethge.
Selected Oral: Watch Steffen Schneider give a talk at NeurIPS workshop!
A Primer on Motion Capture with Deep Learning: Principles, Pitfalls, and Perspectives. Neuron, 2020
Alexander Mathis, Steffen Schneider, Jessy Lauer, Mackenzie W Mathis
Deep learning tools for the measurement of animal behavior in neuroscience. Current Opinion in Neurobiology, 2020
Mackenzie W. Mathis & Alexander Mathis.
2019
A new spin on fidgets. Nature Neuroscience, 2019
New & Views on: Single-trial neural dynamics are dominated by richly varied movements
Mackenzie W. Mathis
Using DeepLabCut for 3D markerless pose estimation across species and behaviors. Nature Protocols, 2019
Tanmay Nath*, Alexander Mathis*, An Chi Chen, Amir Patel, Matthias Bethge, and Mackenzie W. Mathis.
2018
DeepLabCut: markerless pose estimation of user-defined body parts with deep learning. Nature Neuroscience, 2018
Alexander Mathis, Pranav Mamidanna, Kevin M. Cury, Taiga Abe, Venkatesh N. Murthy, Mackenzie W Mathis* & Matthias Bethge* ; *co-senior authors
Read more in the Harvard Gazette, NVIDIA Developer News or The Atlantic
Commentary: Behavior Tracking Cuts Deep [Lab Animal], Behavior Tracking Gets Real [Nature Neuroscience].
Project Page: www.deeplabcut.org
Work Completed Before Lab Opening in 2017:
By MW Mathis (note, also went by MW Amoroso):
Mathis MW, Mathis A, Uchida N. Somatosensory Cortex Plays an Essential Role in Forelimb Motor Adaptation in Mice, Neuron. 2017. 10.1016/j.neuron.2017.02.049.
News piece at the Dept. website
Ho R, Sances S, Gowing G, Amoroso, MW, et al. ALS disrupts spinal motor neuron maturation and aging pathways within gene co-expression networks. Nature Neuroscience, 2016.
Li H, Kuwajima T, Oakley D, et al. Protein Prenylation Constitutes an Endogenous Brake on Axonal Growth.
Cell Reports. 2016.16 (2) :545 - 558.
Cohen JY, Amoroso MW, Uchida N. Serotonergic neurons signal reward and punishment on multiple timescales.
eLife. 2015. 10.7554/eLife.06346
Read the eLife Insight here (By Peter Dayan and Quentin Huys)
Recommended by F1000
Re D B, Le Verche V, Yu C, Amoroso, MW, et al. Necroptosis Drives Motor Neuron Death in Models of Both Sporadic and Familial ALS. Neuron. 2014. 81 :1001 - 1008.
Read the Neuron review here (By Sheila K. Pirooznia, Valina L. Dawson, Ted M. Dawson)
Amoroso MW, Croft GF, Williams DJ, et al. Accelerated High-Yield Generation of Limb-Innervating Motor Neurons from Human Stem Cells. Journal of Neuroscience. 2013. 33 (2) :574 - 586.
Read the Journal of Neuroscience Journal Club article here
Nédelec S, Peljto M, Shi P, et al. Concentration-Dependent Requirement for Local Protein Synthesis in Motor Neuron Subtype-Specific Response to Axon Guidance Cues. Journal of Neuroscience, 2012. 32 (4) :1496 - 1506.
Takazawa T, Croft GF, Amoroso MW, et al. Maturation of Spinal Motor Neurons Derived from Human Embryonic Stem Cells. PLOS ONE, 2012. 7 (7) :e40154.
Boulting GL*, Kiskinis E*, Croft GF*, Amoroso, MW*, Oakley, D* et al. A functionally characterized test set of human induced pluripotent stem cells. Nature Biotechnology, 2011. 29 (3) :279 - 286.
*co-first authors
Bock C, Kiskinis E, Verstappen G, et al. Reference Maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines. Cell, 2011. 144 (3) :439 - 452.