Alex Hernandez-Garcia

Torsional-GFN: a conditional conformation generator for small molecules

Alexandra Volokhova

Lena Nehale Ezzine

Piotr Gai'nski

Luca Scimeca

Emmanuel Bengio

Prudencio Tossou

Generating stable molecular conformations is crucial in several drug discovery applications, such as estimating the binding affinity of a mo… (see more)lecule to a target. Recently, generative machine learning methods have emerged as a promising, more efficient method than molecular dynamics for sampling of conformations from the Boltzmann distribution. In this paper, we introduce Torsional-GFN, a conditional GFlowNet specifically designed to sample conformations of molecules proportionally to their Boltzmann distribution, using only a reward function as training signal. Conditioned on a molecular graph and its local structure (bond lengths and angles), Torsional-GFN samples rotations of its torsion angles. Our results demonstrate that Torsional-GFN is able to sample conformations approximately proportional to the Boltzmann distribution for multiple molecules with a single model, and allows for zero-shot generalization to unseen bond lengths and angles coming from the MD simulations for such molecules. Our work presents a promising avenue for scaling the proposed approach to larger molecular systems, achieving zero-shot generalization to unseen molecules, and including the generation of the local structure into the GFlowNet model.

2025-07-15

ArXiv (preprint)

Multiscale Neural PDE Surrogates for Prediction and Downscaling: Application to Ocean Currents

Abdessamad El-Kabid

Loubna Benabbou

Redouane Lguensat

Accurate modeling of physical systems governed by partial differential equations is a central challenge in scientific computing. In oceanogr… (see more)aphy, high-resolution current data are critical for coastal management, environmental monitoring, and maritime safety. However, available satellite products, such as Copernicus data for sea water velocity at ~0.08 degrees spatial resolution and global ocean models, often lack the spatial granularity required for detailed local analyses. In this work, we (a) introduce a supervised deep learning framework based on neural operators for solving PDEs and providing arbitrary resolution solutions, and (b) propose downscaling models with an application to Copernicus ocean current data. Additionally, our method can model surrogate PDEs and predict solutions at arbitrary resolution, regardless of the input resolution. We evaluated our model on real-world Copernicus ocean current data and synthetic Navier-Stokes simulation datasets.

2025-07-01

arXiv (published)

RainShift: A Benchmark for Precipitation Downscaling Across Geographies

Paula Harder

Luca Schmidt

Francis Pelletier

Nicole Ludwig 0002

Matthew Chantry

Christian Lessig

David Rolnick

Earth System Models (ESM) are our main tool for projecting the impacts of climate change. However, running these models at sufficient resolu… (see more)tion for local-scale risk-assessments is not computationally feasible. Deep learning-based super-resolution models offer a promising solution to downscale ESM outputs to higher resolutions by learning from data. Yet, due to regional variations in climatic processes, these models typically require retraining for each geographical area-demanding high-resolution observational data, which is unevenly available across the globe. This highlights the need to assess how well these models generalize across geographic regions. To address this, we introduce RainShift, a dataset and benchmark for evaluating downscaling under geographic distribution shifts. We evaluate state-of-the-art downscaling approaches including GANs and diffusion models in generalizing across data gaps between the Global North and Global South. Our findings reveal substantial performance drops in out-of-distribution regions, depending on model and geographic area. While expanding the training domain generally improves generalization, it is insufficient to overcome shifts between geographically distinct regions. We show that addressing these shifts through, for example, data alignment can improve spatial generalization. Our work advances the global applicability of downscaling methods and represents a step toward reducing inequities in access to high-resolution climate information.

2025-07-01

arXiv (published)

Torsional-GFN: a conditional conformation generator for small molecules

Alexandra Volokhova

Lena Nehale Ezzine

Piotr Gaiński

Luca Scimeca

Emmanuel Bengio

Prudencio Tossou

2025-06-11

ICML.cc/2025/Workshop/GenBio (poster)

openreview.net

Learning Decision Trees as Amortized Structure Inference

Mohammed Mahfoud

Ghait Boukachab

Michał Koziarski

Stefan Bauer

Nikolay Malkin

2025-03-10

ArXiv (preprint)

Learning Decision Trees as Amortized Structure Inference

Mohammed Mahfoud

Ghait Boukachab

Michał Koziarski

Stefan Bauer

Nikolay Malkin

2025-03-05

ICLR.cc/2025/Workshop/FPI (poster)

openreview.net

OBELiX: A Curated Dataset of Crystal Structures and Experimentally Measured Ionic Conductivities for Lithium Solid-State Electrolytes

Félix Therrien

Jamal Abou Haibeh

Divya Sharma

Rhiannon Hendley

Sun Sun

Alain Tchagang

Jiang Su

Samuel Huberman

Hongyu Guo

Homin Shin

Solid-state electrolyte batteries are expected to replace liquid electrolyte lithium-ion batteries in the near future thanks to their higher… (see more) theoretical energy density and improved safety. However, their adoption is currently hindered by their lower effective ionic conductivity, a quantity that governs charge and discharge rates. Identifying highly ion-conductive materials using conventional theoretical calculations and experimental validation is both time-consuming and resource-intensive. While machine learning holds the promise to expedite this process, relevant ionic conductivity and structural data is scarce. Here, we present OBELiX, a domain-expert-curated database of

2025-02-20

ArXiv (preprint)

OBELiX: A Curated Dataset of Crystal Structures and Experimentally Measured Ionic Conductivities for Lithium Solid-State Electrolytes

F'elix Therrien

Jamal Abou Haibeh

Divya Sharma

Rhiannon Hendley

Alex Hern'andez-Garc'ia

Sun Sun

Alain Tchagang

Jiang Su

Samuel Huberman

Hongyu Guo

Homin Shin

Solid-state electrolyte batteries are expected to replace liquid electrolyte lithium-ion batteries in the near future thanks to their higher… (see more) theoretical energy density and improved safety. However, their adoption is currently hindered by their lower effective ionic conductivity, a quantity that governs charge and discharge rates. Identifying highly ion-conductive materials using conventional theoretical calculations and experimental validation is both time-consuming and resource-intensive. While machine learning holds the promise to expedite this process, relevant ionic conductivity and structural data is scarce. Here, we present OBELiX, a domain-expert-curated database of

2025-02-20

ArXiv (preprint)

Improved Off-policy Reinforcement Learning in Biological Sequence Design

Minsu Kim

Jinkyoo Park

Designing biological sequences with desired properties is a significant challenge due to the combinatorially vast search space and the high … (see more)cost of evaluating each candidate sequence. To address these challenges, reinforcement learning (RL) methods, such as GFlowNets, utilize proxy models for rapid reward evaluation and annotated data for policy training. Although these approaches have shown promise in generating diverse and novel sequences, the limited training data relative to the vast search space often leads to the misspecification of proxy for out-of-distribution inputs. We introduce

2024-10-06

ArXiv (preprint)

Improved Off-policy Reinforcement Learning in Biological Sequence Design

Minsu Kim

Alex Hern'andez-Garc'ia

Jinkyoo Park

Designing biological sequences with desired properties is a significant challenge due to the combinatorially vast search space and the high … (see more)cost of evaluating each candidate sequence. To address these challenges, reinforcement learning (RL) methods, such as GFlowNets, utilize proxy models for rapid reward evaluation and annotated data for policy training. Although these approaches have shown promise in generating diverse and novel sequences, the limited training data relative to the vast search space often leads to the misspecification of proxy for out-of-distribution inputs. We introduce

2024-10-06

ArXiv (preprint)

PhAST: Physics-Aware, Scalable, and Task-specific GNNs for Accelerated Catalyst Design

Alexandre AGM Duval

Victor Schmidt

Santiago Miret