Our latest paper on the interpretation on Neural Network Potentials is now published on Nature Communications: nature.com/articles/s41.... Congratulations to Klara Bonneau, Jonas Lederer and all authors. In collaboration with Klaus-Robert Müller's group.

Peering inside the black box by learning the relevance of many-body functions in neural network potentials - Nature Communications

Machine-learned force fields are becoming increasingly popular but suffer from their “black-box” nature. Here the authors adapt explainable AI techniques to coarse-grained graph neural network potenti...

nature.com

Our development of machine-learned transferable coarse-grained models in now on Nat Chem! doi.org/10.1038/s415... I am so proud of my group for this work! Particularly first authors Nick Charron, Klara Bonneau, Aldo Pasos-Trejo, Andrea Guljas.

Navigating protein landscapes with a machine-learned transferable coarse-grained model - Nature Chemistry

The development of a universal protein coarse-grained model has been a long-standing challenge. A coarse-grained model with chemical transferability has now been developed by combining deep-learning m...

doi.org

Extending the RANGE of Graph Neural Networks: Relaying Attention Nodes for Global Encoding Virtual nodes introduced that pass information via attention; reduces oversquashing; improves GNN on molecules; MD22!! P: arxiv.org/abs/2502.13797

Meet @cecclementi.bsky.social, Einstein Prof. of Physics at @freieuniversitaet.bsky.social 🇩🇪. An ELLIS Fellow, she pioneers #AI4Science & is a member of #ELLISProgram ML for Molecule Discovery. Her research spans Biophysics & Theoretical/Chemical Physics. #WomenInELLIS

Our new preprint is out: Extending the RANGE of Graph Neural Networks: Relaying Attention Nodes for Global Encoding. arxiv.org/abs/2502.13797 We present a new architecture to address the problem of "short-sightedness" of MLFF based on GNN, which outperform in speed and accuracy Ewald-based GNN.

Extending the RANGE of Graph Neural Networks: Relaying Attention Nodes for Global Encoding

Graph Neural Networks (GNNs) are routinely used in molecular physics, social sciences, and economics to model many-body interactions in graph-like systems. However, GNNs are inherently local and can s...

arxiv.org

Many thanks to our colloquium speaker Cecilia Clementi @cecclementi.bsky.social from FU Berlin, for providing a deeper understanding of how machine learning and molecular simulations are leveraged to model protein dynamics. Keep an eye out for the video release on the HITS YouTube channel!

Don't miss our next HITS-SIMPLAIX Joint Colloquium on 10 February at 2:00 PM CET! Cecilia Clementi @cecclementi.bsky.social will talk about Modeling Protein Dynamics with Machine Learning and Molecular Simulation. Sign up ow.ly/h0Wl50UQ2kX to join via Zoom or just come by. @simplaix.bsky.social

I made panettone tiramisu with mascarpone in the dough and inserts of pistachio coffee and chocolate. With my loyal sourdough starter.

Frank Noe@franknoe.bsky.social · 2y ago

@cecclementi.bsky.social made Panettone with pistachio and chocolate. Oh my god sooo good. My diet is so over. ❤️❤️❤️

Awesome paper! BioEmu from MSR: Scalable emulation of protein equilibrium ensembles with generative deep learning www.biorxiv.org/content/10.1... Looking forward to hearing more explanainers in tomorrow's reading group session on zoom at 9am PT / 12pm ET / 6pm CET: portal.valencelabs.com/logg

"[…] To me Physics was not defined by subject matter: the atom, the troposphere, a piece of glass, my bicycle, a magnet, these are all incidentally the subject matter." 🧵 John J. Hopfield (2024 Physics Nobel Prize)

In 2024 I made a family of ceramic whales by throwing the main body on the wheel and altering the form. 🐳 Now deciding what other pottery animal I can build in 2025. Open for suggestions 😀 #ceramic #pottery

I tried to make pandoro for the first time. It’s a recipe for pandoro al cappuccino e caramello from an Italian blog I follow. Not fully satisfied with the results but @franknoe.bsky.social is excited to eat it 😀. Next weekend I will try panettone.

Frank Noe@franknoe.bsky.social · 2y ago

@cecclementi.bsky.social made Pandoros ❤️😋😍. They contain about a million eggs, an impressive phase transition and a lot of work and love. Looking forward to breakfast.

Merry #fishmas! Blue ringed octopus in Lembeh Strait, Indonesia, during a 2018 diving trip with @franknoe.bsky.social

Merry #fishmas! Blenny from Bonaire, our favorite Caribbean Island, where @franknoe.bsky.social and I spent quite some time in 2021

Merry #fishmas! Sharks in Rangiroa, French Polynesia, in a 2016 diving trip with @franknoe.bsky.social

Merry #fishmas! Dolphin in Rangiroa, French Polynesia during a 2016 diving trip with @franknoe.bsky.social

Merry #fishmas! A couple of cuties from Raja Ampat, from a 2019 trip with @franknoe.bsky.social.

Merry #fishmas! Picture taken on a diving trip to Cocos Islands in summer 2014.

Merry #fishmas! This picture is from a diving trip in Raja Ampat 10 years ago but it is still one of my favorites.

Just a little Christmas feast with @cecclementi.bsky.social and team

Cecilia Clementi (@cecclementi.bsky.social) kicks off the afternoon session of the ELLIS ML4Molecules Workshop in Berlin!

Super excited to preprint our work on developing a Biomolecular Emulator (BioEmu): Scalable emulation of protein equilibrium ensembles with generative deep learning from @msftresearch.bsky.social ch AI for Science. www.biorxiv.org/content/10.1...

Please credit the exceptional team at @MSFTResearch AI for Science. I am privileged to be working with them: Sarah, Tim, @jjimenezluna.bsky.social, Michael, @yuxie.bsky.social Andrew F, Victor, Osama, Bas, Iryna, Yaoyi, Usman @cecclementi.bsky.social

CECAM crowd Lausanne @cecclementi.bsky.social Marilou Venkat Aaron Greg Michael Simon Rafa Pratyush Andy @chhdellago.bsky.social @grant.rotskoff.cc