Stefan Gugler ⚗️
Stefan Gugler

Postdoctoral Researcher (SNSF Postdoc.Mobility Fellow)

About Me

I am a postdoc at TU Berlin in the machine learning group of Prof. Dr. Klaus-Robert Müller. My research concerns novel machine learning methods like probabilistic diffusion models and their applications to theoretical chemistry.

Interests
  • Diffusion models for molecules
  • Chemical reaction network exploration
  • ML force fields and MD
  • Explainable AI for chemistry
  • Multi-reference quantum chemistry
Education
  • PhD in Theoretical Chemistry

    ETH Zurich, with Markus Reiher

  • MSc Interdisciplinary Sciences

    MIT, with Heather J. Kulik
    ETH Zurich

  • BSc Interdisciplinary Sciences

    ETH Zurich

Research

I did my PhD at the Laboratory for Physical Chemistry (now: Institute of Molecular Physical Science) at ETH Zurich. I worked in the research group of Prof. Markus Reiher. I developed procedures to apply methods from the field of machine learning and artificial intelligence to theoretical chemistry. My first paper applies Gaussian process regression and Bayesian sampling to dispersion interaction between organic compounds to yield more accurate results as well as streamline the pipeline of starting new reference calculations for compounds too dissimilar to the training set.

Before, I worked at MIT under Prof. Heather J. Kulik for my Master thesis, on transition metal complexes for multifidelity machine learning. The work was published and won an MSDE award. Another collaboration was published and a follow up to my thesis.

From 2013 to 2018 I studied Interdisciplinary Science at ETH Zurich with a major in Computational and Physical Chemistry.

Selected Publications
(2026). How simple can you go? An off-the-shelf transformer approach to molecular dynamics. The Journal of Chemical Physics.
(2026). ReactionAtlas: Ab origine exploration of chemical reaction networks with machine learning. arXiv preprint arXiv:2606.30778.
(2024). Molecular relaxation by reverse diffusion with time step prediction. Machine Learning: Science and Technology, 5, 035038.
(2022). Quantum chemical roots of machine-learning molecular similarity descriptors. Journal of Chemical Theory and Computation.
(2020). Enumeration of de novo inorganic complexes for chemical discovery and machine learning. Molecular Systems Design & Engineering.
Recent Talks
  • 06/2026 Generative exploration of chemical reaction networks. CNRS / Université de Lorraine, Nancy (invited)
  • 12/2025 How simple can you go? Machine learning molecular dynamics with minimal physical constraints. Pacifichem 2025, Honolulu
  • 10/2025 Machine learning and AI for the sciences: toward understanding. Latvian Institute of Organic Synthesis, Riga (invited)
  • 09/2025 Chemical reaction network exploration with diffusion probabilistic models. Young WATOC, Oslo; DTU Energy, Copenhagen (invited)
  • 08/2025 Generative computational chemistry: From reverse diffusion to XAI. University of Basel (invited)
  • 12/2024 Accelerating computational chemistry with machine learning. University of Freiburg (invited)