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Matthieu Kirchmeyer

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6 papers

2 author rows

NeurIPS Conference 2025 Conference Paper

Unified all-atom molecule generation with neural fields

Matthieu Kirchmeyer
Pedro O. Pinheiro
Emma Willett
Karolis Martinkus
Joseph Kleinhenz
Emily Makowski
Andrew Watkins
Vladimir Gligorijevic

Generative models for structure-based drug design are often limited to a specific modality, restricting their broader applicability. To address this challenge, we introduce FuncBind, a framework based on computer vision to generate target-conditioned, all-atom molecules across atomic systems. FuncBind uses neural fields to represent molecules as continuous atomic densities and employs score-based generative models with modern architectures adapted from the computer vision literature. This modality-agnostic representation allows a single unified model to be trained on diverse atomic systems, from small to large molecules, and handle variable atom/residue counts, including non-canonical amino acids. FuncBind achieves competitive in silico performance in generating small molecules, macrocyclic peptides, and antibody complementarity-determining region loops, conditioned on target structures. FuncBind also generated in vitro novel antibody binders via de novo redesign of the complementarity-determining region H3 loop of two chosen co-crystal structures. As a final contribution, we introduce a new dataset and benchmark for structure-conditioned macrocyclic peptide generation.

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NeurIPS Conference 2024 Conference Paper

Score-based 3D molecule generation with neural fields

Matthieu Kirchmeyer
Pedro O. Pinheiro
Saeed Saremi

We introduce a new representation for 3D molecules based on their continuous atomic density fields. Using this representation, we propose a new model based on walk-jump sampling for unconditional 3D molecule generation in the continuous space using neural fields. Our model, FuncMol, encodes molecular fields into latent codes using a conditional neural field, samples noisy codes from a Gaussian-smoothed distribution with Langevin MCMC (walk), denoises these samples in a single step (jump), and finally decodes them into molecular fields. FuncMol performs all-atom generation of 3D molecules without assumptions on the molecular structure and scales well with the size of molecules, unlike most approaches. Our method achieves competitive results on drug-like molecules and easily scales to macro-cyclic peptides, with at least one order of magnitude faster sampling. The code is available at https: //github. com/prescient-design/funcmol.

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ICLR Conference 2023 Conference Paper

Continuous PDE Dynamics Forecasting with Implicit Neural Representations

Yuan Yin
Matthieu Kirchmeyer
Jean-Yves Franceschi
Alain Rakotomamonjy
Patrick Gallinari

Effective data-driven PDE forecasting methods often rely on fixed spatial and / or temporal discretizations. This raises limitations in real-world applications like weather prediction where flexible extrapolation at arbitrary spatiotemporal locations is required. We address this problem by introducing a new data-driven approach, DINo, that models a PDE's flow with continuous-time dynamics of spatially continuous functions. This is achieved by embedding spatial observations independently of their discretization via Implicit Neural Representations in a small latent space temporally driven by a learned ODE. This separate and flexible treatment of time and space makes DINo the first data-driven model to combine the following advantages. It extrapolates at arbitrary spatial and temporal locations; it can learn from sparse irregular grids or manifolds; at test time, it generalizes to new grids or resolutions. DINo outperforms alternative neural PDE forecasters in a variety of challenging generalization scenarios on representative PDE systems.

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NeurIPS Conference 2022 Conference Paper

Diverse Weight Averaging for Out-of-Distribution Generalization

Alexandre Rame
Matthieu Kirchmeyer
Thibaud Rahier
Alain Rakotomamonjy
Patrick Gallinari
Matthieu Cord

Standard neural networks struggle to generalize under distribution shifts in computer vision. Fortunately, combining multiple networks can consistently improve out-of-distribution generalization. In particular, weight averaging (WA) strategies were shown to perform best on the competitive DomainBed benchmark; they directly average the weights of multiple networks despite their nonlinearities. In this paper, we propose Diverse Weight Averaging (DiWA), a new WA strategy whose main motivation is to increase the functional diversity across averaged models. To this end, DiWA averages weights obtained from several independent training runs: indeed, models obtained from different runs are more diverse than those collected along a single run thanks to differences in hyperparameters and training procedures. We motivate the need for diversity by a new bias-variance-covariance-locality decomposition of the expected error, exploiting similarities between WA and standard functional ensembling. Moreover, this decomposition highlights that WA succeeds when the variance term dominates, which we show occurs when the marginal distribution changes at test time. Experimentally, DiWA consistently improves the state of the art on DomainBed without inference overhead.

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ICML Conference 2022 Conference Paper

Generalizing to New Physical Systems via Context-Informed Dynamics Model

Matthieu Kirchmeyer
Yuan Yin
Jérémie Donà
Nicolas Baskiotis
Alain Rakotomamonjy
Patrick Gallinari

Data-driven approaches to modeling physical systems fail to generalize to unseen systems that share the same general dynamics with the learning domain, but correspond to different physical contexts. We propose a new framework for this key problem, context-informed dynamics adaptation (CoDA), which takes into account the distributional shift across systems for fast and efficient adaptation to new dynamics. CoDA leverages multiple environments, each associated to a different dynamic, and learns to condition the dynamics model on contextual parameters, specific to each environment. The conditioning is performed via a hypernetwork, learned jointly with a context vector from observed data. The proposed formulation constrains the search hypothesis space for fast adaptation and better generalization across environments with few samples. We theoretically motivate our approach and show state-of-the-art generalization results on a set of nonlinear dynamics, representative of a variety of application domains. We also show, on these systems, that new system parameters can be inferred from context vectors with minimal supervision.

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ICLR Conference 2022 Conference Paper

Mapping conditional distributions for domain adaptation under generalized target shift

Matthieu Kirchmeyer
Alain Rakotomamonjy
Emmanuel de Bézenac
Patrick Gallinari

We consider the problem of unsupervised domain adaptation (UDA) between a source and a target domain under conditional and label shift a.k.a Generalized Target Shift (GeTarS). Unlike simpler UDA settings, few works have addressed this challenging problem. Recent approaches learn domain-invariant representations, yet they have practical limitations and rely on strong assumptions that may not hold in practice. In this paper, we explore a novel and general approach to align pretrained representations, which circumvents existing drawbacks. Instead of constraining representation invariance, it learns an optimal transport map, implemented as a NN, which maps source representations onto target ones. Our approach is flexible and scalable, it preserves the problem's structure and it has strong theoretical guarantees under mild assumptions. In particular, our solution is unique, matches conditional distributions across domains, recovers target proportions and explicitly controls the target generalization risk. Through an exhaustive comparison on several datasets, we challenge the state-of-the-art in GeTarS.

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