Publications by Alexander Mathis

Related publications (38)

Contrasting action and posture coding with hierarchical deep neural network models of proprioception

Alexander Mathis, Mackenzie Mathis, Matthias Bethge, Kai Jappe Sandbrink

Biological motor control is versatile, efficient, and depends on proprioceptive feedback. Muscles are flexible and undergo continuous changes, requiring distributed adaptive control mechanisms that continuously account for the body's state. The canonical r ...

eLIFE SCIENCES PUBL LTD2023

AmadeusGPT: a natural language interface for interactive animal behavioral analysis

Alexander Mathis, Mackenzie Mathis, Shaokai Ye, Jessy Lauer, Mu Zhou

The process of quantifying and analyzing animal behavior involves translating the naturally occurring descriptive language of their actions into machine-readable code. Yet, codifying behavior analysis is often challenging without deep understanding of anim ...

2023

Striatal dopamine explains novelty-induced behavioral dynamics and individual variability in threat prediction

Alexander Mathis, Mackenzie Mathis

Animals both explore and avoid novel objects in the environment, but the neural mechanisms that underlie these behaviors and their dynamics remain uncharacterized. Here, we used multi-point tracking (DeepLabCut) and behavioral segmentation (MoSeq) to chara ...

CELL PRESS2022

EPFL-Smart-Kitchen-30 Annotations and Poses

Silvestro Micera, Friedhelm Christoph Hummel, Solaiman Shokur, Alexander Mathis, Mahdi Hamidi Rad, Haozhe Qi, Franklin Leong, Andy Bonnetto, Matea Tashkovska

Understanding behavior requires datasets that capture humans while carrying out complex tasks. The kitchen is an excellent environment for assessing human motor and cognitive function, as many complex actions are naturally exhibited in kitchens from choppi ...

Zenodo2025

Task-driven neural network models predict neural dynamics of proprioception: Neural network model weights

Alexander Mathis, Alberto Silvio Chiappa, Alessandro Marin Vargas, Axel Bisi

Proprioception tells the brain the state of the body based on distributed sensors in the body. However, the principles that govern proprioceptive processing from those distributed sensors are poorly understood. Here, we employ a task-driven neural network ...

Zenodo2024

SuperAnimal pretrained pose estimation models for behavioral analysis

Alexander Mathis, Mackenzie Mathis, Shaokai Ye, Steffen Schneider, Jessy Lauer, Tian Qiu, Maxime Michel André Vidal, Anastasiia Filippova

Quantification of behavior is critical in diverse applications from neuroscience, veterinary medicine to animal conservation. A common key step for behavioral analysis is first extracting relevant keypoints on animals, known as pose estimation. However, re ...

Nature Research2024

Perspectives in machine learning for wildlife conservation

Devis Tuia, Alexander Mathis, Mackenzie Mathis, Benjamin Alexander Kellenberger

Inexpensive and accessible sensors are accelerating data acquisition in animal ecology. These technologies hold great potential for large-scale ecological understanding, but are limited by current processing approaches which inefficiently distill data into ...

Nature Research2022

HOISDF: Constraining 3D Hand-Object Pose Estimation with Global Signed Distance Fields: Processed data and trained models

Mathieu Salzmann, Alexander Mathis, Chen Zhao, Haozhe Qi

HOISDF: Constraining 3D Hand-Object Pose Estimation with Global Signed Distance Fields, CVPR 2024 Haozhe Qi, Chen Zhao, Mathieu Salzmann, Alexander Mathis. Affiliation: EPFL Date: June, 2024 Link to the CVPR article: https://openaccess.thecvf.com/conte ...

Zenodo2024

WildCLIP: Scene and animal attribute retrieval from camera trap data with domain-adapted vision-language models

Devis Tuia, Alexander Mathis, Marc Conrad Russwurm, Valentin Alexandre Guy Gabeff

WildCLIP: Scene and animal attribute retrieval from camera trap data with domain-adapted vision-language models ############# Authors: Valentin Gabeff, Marc Russwurm, Devis Tuia & Alexander Mathis Affiliation: EPFL Date: January, 2024 Link to the article: ...

Zenodo2024

Decoding the brain: From neural representations to mechanistic models

Alexander Mathis, Mackenzie Mathis, Adriana Perez Rotondo

A central principle in neuroscience is that neurons within the brain act in concert to produce perception, cognition, and adaptive behavior. Neurons are organized into specialized brain areas, dedicated to different functions to varying extents, and their ...

CELL PRESS2024

NeuroAI: If grid cells are the answer, is path integration the question?

Alexander Mathis, Mackenzie Mathis, Markus Frey

Spatially modulated neurons known as grid cells are thought to play an important role in spatial cognition. A new study has found that units with grid-cell-like properties can emerge within artificial neural networks trained to path integrate, and develope ...

CELL PRESS2023

Real-time, low-latency closed-loop feedback using markerless posture tracking

Alexander Mathis, Mackenzie Mathis

The ability to control a behavioral task or stimulate neural activity based on animal behavior in real-time is an important tool for experimental neuroscientists. Ideally, such tools are noninvasive, low-latency, and provide interfaces to trigger external ...

2020

Deep-learning models of the ascending proprioceptive pathway are subject to illusions

Olaf Blanke, Alexander Mathis, Merkourios Simos, Adriana Perez Rotondo, Florian Axel Raphaël David

Proprioception is essential for perception and action. Like any other sense, proprioception is also subject to illusions. In this study, we model classic proprioceptive illusions in which tendon vibrations lead to biases in estimating the state of the body ...

Wiley2025

WildCLIP: Scene and Animal Attribute Retrieval from Camera Trap Data with Domain-Adapted Vision-Language Models

Devis Tuia, Alexander Mathis, Marc Conrad Russwurm, Valentin Alexandre Guy Gabeff

Wildlife observation with camera traps has great potential for ethology and ecology, as it gathers data non-invasively in an automated way. However, camera traps produce large amounts of uncurated data, which is time-consuming to annotate. Existing methods ...

2024

Task-driven neural network models predict neural dynamics of proprioception

Alexander Mathis, Alberto Silvio Chiappa, Alessandro Marin Vargas, Axel Bisi

Proprioception tells the brain the state of the body based on distributed sensory neurons. Yet, the principles that govern proprioceptive processing are poorly understood. Here, we employ a task -driven modeling approach to investigate the neural code of p ...

Cell Press2024

Acquiring musculoskeletal skills with curriculum-based reinforcement learning - model weights

Abigaïl Rebecca Lise Ingster, Alexander Mathis, Alberto Silvio Chiappa

Here we provide the weights of the neural network policies used for the analysis presented in our article. The archives whose names start with a number (01 - 32) correspond to the 32 curriculum steps to train the Baoding Balls policy which ranked first at ...

Zenodo2024

Pretraining boosts out-of-domain robustness for pose estimation

Alexander Mathis, Mackenzie Mathis, Matthias Bethge, Steffen Schneider

Neural networks are highly effective tools for pose estimation. However, as in other computer vision tasks, robustness to out-of-domain data remains a challenge, especially for small training sets that are common for real-world applications. Here, we probe ...

IEEE COMPUTER SOC2021

AcinoSet: A 3D Pose Estimation Dataset and Baseline Models for Cheetahs in the Wild

Alexander Mathis, Mackenzie Mathis

Animals are capable of extreme agility, yet understanding their complex dynamics, which have ecological, biomechanical and evolutionary implications, remains challenging. Being able to study this incredible agility will be critical for the development of n ...

IEEE2021

Keypoint-MoSeq: parsing behavior by linking point tracking to pose dynamics

Alexander Mathis, Mackenzie Mathis, Shaokai Ye

Keypoint tracking algorithms can flexibly quantify animal movement from videos obtained in a wide variety of settings. However, it remains unclear how to parse continuous keypoint data into discrete actions. This challenge is particularly acute because key ...

Nature Publishing Group2024

Perspectives on Individual Animal Identification from Biology and Computer Vision

Alexander Mathis, Maxime Michel André Vidal

Identifying individual animals is crucial for many biological investigations. In response to some of the limitations of current identification methods, new automated computer vision approaches have emerged with strong performance. Here, we review current a ...

OXFORD UNIV PRESS INC2021