About Me

Profile Picture of Markus Frey

I am a machine learning researcher with a Ph.D. in computational neuroscience, specializing in models that tackle complex problems at the intersection of AI and neuroscience. I did my PhD in computational neuroscience at the Kavli Institute for Systems Neuroscience with Christian Doeller & at University College London with Caswell Barry, followed by a PostDoc with Mackenzie Mathis at EPFL in Switzerland. I am currently a researcher at the Lamarr Institute & Fraunhofer IAIS, working on improving reasoning in large language models together with Mehdi Ali.

Selected Publications

Time-series attribution maps
Time-series attribution maps with regularized contrastive learning
S Schneider, RG Laiz, A Filippova, M Frey, MW Mathis

Here, Steffen developed a method for producing identifiable attribution maps in time-series data using regularized contrastive learning. I applied it to synthetic and real-world grid cell data.

NeurIPS Workshop (2024) & AISTATS (2025)
CellSeg3D
CellSeg3D: self-supervised 3D cell segmentation for fluorescence microscopy
C Achard, T Kousi, M Frey, M Vidal, Y Paychère, C Hofmann, A Iqbal, S B Hausmann, S Pagès, MW Mathis

In this study, Cyril built a self-supervised pipeline for segmenting cells in 3D fluorescence microscopy volumes, reducing the need for manual annotations.

eLife (2024)
NeuroAI grid cells
NeuroAI: If grid cells are the answer, is path integration the question?
M Frey, MW Mathis, A Mathis

Lots of ANNs have shown grid-cell like activity in their hidden units. We ask if this is an artifact of the objective function used. Includes cute animals.

Current Biology (2023)
Scene perception neural networks
Probing neural representations of scene perception in a hippocampally dependent task using artificial neural networks
M Frey, CF Doeller, C Barry

Here we were trying to build a neural network that simulates the egocentric to allocentric transformation circuit from visual areas to hippocampus. It works and we now also have a benchmark for ANNs that closely follows the four mountains test.

CVPR (2023)
DeepMReye
Magnetic resonance-based eye tracking using deep neural networks
M Frey, M Nau, CF Doeller

After lots of discussions in our lab meetings about the problems with eye-trackers we decided to build a deep learning framework that decodes eye position directly from MRI data.

Nature neuroscience (2021)
DeepInsight
Interpreting wide-band neural activity using convolutional neural networks
M Frey, S Tanni, C Perrodin, A O'Leary, M Nau, J Kelly, A Banino, D Bendor, J Lefort, CF Doeller, C Barry

DeepInsight – nicknamed the automatic John O' Keefe – decodes behavioral variables from wide-band neural recordings. This gives more objective measures of information content, compared to spike-based methods.

Elife (2021)
Directional tuning
Behavior-dependent directional tuning in the human visual-navigation network
M Nau, T Navarro Schröder, M Frey, CF Doeller

In this study, Matthis showed how directional tuning in the human visual-navigation network shifts depending on behavioral context during spatial navigation.

Nature communications (2020)
Tumor segmentation
Memory efficient brain tumor segmentation using an autoencoder-regularized u-net
M Frey, M Nau

We saw this challenge and thought it would be nice to compete. Top 5 in the end but with one of the most efficient implementations and a autoencoder regularization.

MICCAI (2020)
Head direction cells
Testing the efficacy of single-cell stimulation in biasing presubicular head direction activity
S Coletta, M Frey, K Nasr, P Preston-Ferrer, A Burgalossi

Here we tested a setup which I introduced during my master thesis, to see if stimulating individual neurons can shift the activity of head direction cells in the presubiculum. It can!

Journal of Neuroscience (2018)

Experiments

Project

Awesome NeuroAI

A curated list of papers and reviews from the intersection of deep learning and neuroscience, which I started collecting during my PhD and update from time to time.

GitHub Repository →
Project

The Human Move

Quantifying the psychological impact of chess moves using a simple heuristic based on engine evaluations. As seen on Hackernews.

GitHub Repository →
Blog

Exploring spatial representations in Visual Foundation Models

An exploration of neural representations in large vision models, with a focus on spatially selective cells that encode parts of the visual field.

Read More →

Timeline

Here are some posts from the last years, rescued from social media before the ecosystem collapsed.

2024
Jun 2024
Otto Hahn
2023
Jun 2023
DeepMReye
Apr 2023
DeepMReye open source
Mar 2023
PhD done