Alexander Mathis

Alexander studied pure mathematics with a minor in logic and theory of science at the Ludwig Maximilians University in Munich. For his PhD also at LMU, he worked on optimal coding approaches to elucidate the properties of grid cells. As a postdoctoral fellow with Prof. Venkatesh N. Murthy at Harvard University and Prof. Matthias Bethge at Tuebingen AI, he decided to study olfactory behaviors such as odor-guided navigation, social behaviors and the cocktail party problem in mice. During this time, he increasingly got interested sensorimotor behaviors beyond olfaction and started working on proprioception, motor adaption, as well as computer vision tools for measuring animal behavior. In his group, he is interested in elucidating how the brain gives rise to adaptive behavior. One of the major goals is to synthesize large datasets into computationally useful information. For those purposes, he develops algorithms and systems to analyze animal behavior (e.g. DeepLabCut), neural data, as well as creates experimentally testable computational models.

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BIO-210: Applied software engineering for life sciences

We learn and apply software engineering principles to program projects in Python. Projects cover problems in life sciences, and will be developed over the course of the semester.

NX-414: Brain-like computation and intelligence

Recent advances in machine learning have contributed to the emergence of powerful models for how humans and other animals reason and behave. In this course we will compare and contrast how such brain models as well as brains create intelligent behaviour.

PHYS-754: Lecture series on scientific machine learning

This lecture presents ongoing work on how scientific questions can be tackled using machine learning. Machine learning enables extracting knowledge from data computationally and in an automatized way. We will learn on examples how this is influencing the very scientific method.

Deep learning

Deep learning is part of a broader family of machine learning methods, which is based on artificial neural networks with representation learning. The adjective "deep" in deep learning refers to the

Grid cell

A grid cell is a type of neuron within the entorhinal cortex that fires at regular intervals as an animal navigates an open area, allowing it to understand its position in space by storing and integ

Neural network

A neural network can refer to a neural circuit of biological neurons (sometimes also called a biological neural network), a network of artificial neurons or nodes in the case of an artificial neur

Multi-animal pose estimation, identification and tracking with DeepLabCut

Jessy Lauer, Mackenzie Mathis, Alexander Mathis, Tanmay Nath, Steffen Schneider, Shaokai Ye

Estimating the pose of multiple animals is a challenging computer vision problem: frequent interactions cause occlusions and complicate the association of detected keypoints to the correct individuals, as well as having highly similar looking animals that interact more closely than in typical multi-human scenarios. To take up this challenge, we build on DeepLabCut, an open-source pose estimation toolbox, and provide high-performance animal assembly and tracking-features required for multi-animal scenarios. Furthermore, we integrate the ability to predict an animal's identity to assist tracking (in case of occlusions). We illustrate the power of this framework with four datasets varying in complexity, which we release to serve as a benchmark for future algorithm development. DeepLabCut is extended to enable multi-animal pose estimation, animal identification and tracking, thereby enabling the analysis of social behaviors.

NATURE PORTFOLIO2022

Perspectives in machine learning for wildlife conservation

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

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 relevant information. We argue that animal ecologists can capitalize on large datasets generated by modern sensors by combining machine learning approaches with domain knowledge. Incorporating machine learning into ecological workflows could improve inputs for ecological models and lead to integrated hybrid modeling tools. This approach will require close interdisciplinary collaboration to ensure the quality of novel approaches and train a new generation of data scientists in ecology and conservation.

2022

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

Mackenzie Mathis, Alexander 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 characterize the behavior of mice freely interacting with a novel object. Novelty elicits a characteristic sequence of behavior, starting with investigatory approach and culminating in object engagement or avoidance. Dopamine in the tail of the striatum (TS) suppresses engagement, and dopamine responses were predictive of individual variability in behavior. Behavioral dy-namics and individual variability are explained by a reinforcement-learning (RL) model of threat prediction in which behavior arises from a novelty-induced initial threat prediction (akin to "shaping bonus") and a threat prediction that is learned through dopamine-mediated threat prediction errors. These results uncover an algorithmic similarity between reward-and threat-related dopamine sub-systems.

CELL PRESS2022