arXiv subjects

Frank Noé

Publications and source records attributed to Frank Noé.

At least 19 recordsLinked to original sources

arXiv2026

A strategic roadmap for an atomistic machine-learning ecosystem

Data-driven machine learning (ML) techniques have become an essential tool in many domains of science. Their application to atomistic simulations of matter is particularly widespread and impactful. This success is due largely to the existence of a well-developed and established physics-based modeling framework, ranging from first-principles electronic-structure calculations to molecular dynamics and statistical sampling, into which ML was integrated naturally to reshape long-standing trade-offs between accuracy, efficiency, and scale. Nevertheless, this integration raises both conceptual and practical challenges, from choosing between data-centric and physics-based modeling approaches to adapting established software stacks to modern hardware accelerators and ML libraries. As the field evolves rapidly, fueled in part by widespread enthusiasm but also by tangible impact, it seems appropriate to take a moment to consider the current state of the art and open challenges, and reflect on what can be done to better coordinate efforts across the community. With this goal in mind, several members of this community met in Lausanne in January 2026 at CECAM to discuss algorithms, models, software and hardware infrastructure, and the most promising scientific applications that have become possible thanks to the use of artificial intelligence in atomic-scale simulations. This strategic roadmap paper summarizes the outcomes of these discussions, suggesting some long-term goals, and some concrete actions, to establish a healthy, sustainable and impactful atomistic ML ecosystem.

physics.chem-ph↗

arXiv2026

An ab initio foundation model of wavefunctions that accurately describes chemical bond breaking

Reliable description of bond breaking remains a major challenge for quantum chemistry due to the multireference character of the electronic structure in dissociating species. Multireference methods in particular suffer from large computational cost, which under the normal paradigm has to be paid anew for each system at a full price, ignoring commonalities in electronic structure across molecules. Quantum Monte Carlo with deep neural networks uniquely offers to exploit such commonalities by pretraining transferable wavefunction models, but all such attempts were so far limited in scope. Here, we bring this paradigm to fruition with Orbformer, a transferable wavefunction model pretrained on 22,000 equilibrium and dissociating structures that can be fine-tuned on unseen molecules reaching an accuracy-cost ratio rivalling classical multireference methods. On established benchmarks as well as more challenging bond dissociations and Diels-Alder reactions, Orbformer is the only method that consistently converges to chemical accuracy (1 kcal/mol). This work turns the idea of amortizing the cost of solving the Schrödinger equation over many molecules into a practical approach in quantum chemistry.

physics.chem-ph↗

arXiv2026

Ab-initio simulation of excited-state potential energy surfaces with transferable deep quantum Monte Carlo

The accurate quantum chemical calculation of excited states is a challenging task, often requiring computationally demanding methods. When entire ground and excited potential energy surfaces (PESs) are desired, for instance to predict the interaction of light excitation and structural changes, one is often forced to use cheaper computational methods at the cost of reduced accuracy. Here we introduce a method for the geometrically transferable optimization of neural network wave functions that leverages weight sharing and dynamical ordering of electronic states. Our method enables the efficient prediction of ground and excited-state PESs and their intersections at the highest accuracy, demonstrating up to two orders of magnitude cost reduction compared to single-point calculations.We validate our approach on four challenging excited-state PESs, namely ethylene, the carbon dimer, the methylenimmonium cation, and a rubredoxin active site model containing 96 electrons, illustrating the potential of transferable deep-learning QMC as a practical framework for studying electronic excitations in molecules.

physics.chem-ph↗

arXiv2026

Learning Hamiltonian Flow Maps: Mean Flow Consistency for Large-Timestep Molecular Dynamics

Simulating the long-time evolution of Hamiltonian systems is limited by the small timesteps required for stable numerical integration. To overcome this constraint, we introduce a framework to learn Hamiltonian Flow Maps by predicting the mean phase-space evolution over a chosen time span, enabling stable large-timestep updates far beyond the stability limits of classical integrators. To this end, we impose a Mean Flow consistency condition for time-averaged Hamiltonian dynamics. Unlike prior approaches, this allows training on independent phase-space samples without access to future states, avoiding expensive trajectory generation. Validated across diverse Hamiltonian systems, our method in particular improves upon molecular dynamics simulations using machine-learned force fields (MLFF). Our models maintain comparable training and inference cost, but support significantly larger integration timesteps while trained directly on widely-available trajectory-free MLFF datasets.

cs.LG↗

arXiv2026

Enhanced Diffusion Sampling: Efficient Rare Event Sampling and Free Energy Calculation with Diffusion Models

The rare-event sampling problem has long been the central limiting factor in molecular dynamics (MD), especially in biomolecular simulation. Recently, diffusion models such as BioEmu have emerged as powerful equilibrium samplers that generate independent samples from complex molecular distributions, eliminating the cost of sampling rare transition events. However, a sampling problem remains when computing observables that rely on states which are rare in equilibrium, for example folding free energies. Here, we introduce enhanced diffusion sampling, enabling efficient exploration of rare-event regions while preserving unbiased thermodynamic estimators. The key idea is to perform quantitatively accurate steering protocols to generate biased ensembles and subsequently recover equilibrium statistics via exact reweighting. We instantiate our framework in three algorithms: UmbrellaDiff (umbrella sampling with diffusion models), MetaDiff (a batchwise analogue for metadynamics), and $Δ$G-Diff (free-energy differences via tilted ensembles). Across toy systems, protein folding landscapes and folding free energies, our methods achieve fast, accurate, and scalable estimation of equilibrium properties within GPU-minutes to hours per system-closing the rare-event sampling gap that remained after the advent of diffusion-model equilibrium samplers.

stat.ML↗

arXiv2026

MatterSim-MT: A multi-task foundation model for in silico materials characterization

Accurate property characterization is a major bottleneck in materials design. While first-principles methods and task-specific machine-learning models have driven important progress, they remain fundamentally limited in scalability and generalizability across the vast space of structures and properties relevant to real-world materials design. We present MatterSim-MT, a multi-task foundation model for in silico materials simulation and property characterization. The model is pretrained on over 35 million first-principles-labeled structures covering 89 elements, temperatures up to 5000 K and pressures up to 1000 GPa, and is fine-tuned on various properties including Bader charges, magnetic moments, Born effective charges, and dielectric matrices. Out of the box, MatterSim-MT not only serves as a foundation model for predicting material structure, dynamics and thermodynamics, its multi-task architecture also enables a wide range of complex simulations that cannot be captured by potential energy surfaces alone. For example, we demonstrate pressure-dependent LO-TO phonon splitting in SiC with close agreement with experiment, electric hysteresis in ferroelectric BaTiO3, and the cationic-to-anionic redox transition during delithiation of a Li-rich cathode material. Finally, we show that MatterSim-MT scales well with more data and parameters, can be efficiently fine-tuned to higher levels of theory, and can be efficiently extended to new systems via active learning. Overall, we believe this approach provides a scalable route to accurate in silico materials characterization.

cond-mat.mtrl-sci↗

arXiv2026

Excited Pfaffians: Generalized Neural Wave Functions Across Structure and State

Neural-network wave functions in Variational Monte Carlo (VMC) have achieved great success in accurately representing both ground and excited states. However, achieving sufficient numerical accuracy in state overlaps requires increasing the number of Monte Carlo samples, and consequently the computational cost, with the number of states. We present a nearly constant sample-size approach, Multi-State Importance Sampling (MSIS), that leverages samples from all states to estimate pairwise overlap. To efficiently evaluate all states for all samples, we introduce Excited Pfaffians. Inspired by Hartree-Fock, this architecture represents many states within a single neural network. Excited Pfaffians also serve as generalized wave functions, allowing a single model to represent multi-state potential energy surfaces. On the carbon dimer, we match the $O(N_s^4)$-scaling natural excited states while training $>200\times$ faster and modeling 50% more states. Our favorable scaling enables us to be the first to use neural networks to find all distinct energy levels of the beryllium atom. Finally, we demonstrate that a single wave function can represent excited states across various molecules.

cs.LG↗

arXiv2026

Generative Pseudo-Force Fields for Molecular Generation

Generating stable molecular conformations typically forces a tradeoff between the physical realism of energy-based relaxation and the sampling efficiency of data-driven generative models. While machine learning force fields (MLFFs) can sample stable conformations by relaxing molecular geometries according to physical forces, they require costly ab-initio training data. Conversely, diffusion models (DMs) learn from equilibrium data alone but are dependent on noise schedules and time-step conditioning. In this work, we propose generative pseudo-force fields (GPFFs) to bridge these paradigms by training an MLFF on a quadratic pseudo-potential energy surface relative to reference equilibrium structures. Because no ab-initio calculations are required for the perturbed geometries, non-equilibrium training data can be generated on the fly by perturbing the equilibria with Gaussian noise. We show that GPFFs constitute a time-step-agnostic variant of variance exploding DMs: the score comes from the predicted pseudo-forces but because force magnitudes implicitly encode the noise level, no time-step conditioning is needed. Our GPFF can hence be used as a drop-in replacement in standard diffusion sampling (ancestral, Heun) but also facilitates more efficient, adaptive variants and an MLFF inspired direct denoising scheme. Our proposed sampling algorithms support arbitrary structural priors and geometric constraints. On QM9, GPFF has 100 % validity at 256 neural function evaluations (NFE) and over 50 % at just 6 NFE, outperforming diffusion baselines across all samplers. Combined with custom priors, we showcase the fast and accurate generation process of our method in a molecular editor for a drug design setting, where a molecule is generated in real time.

cs.LG↗

arXiv2026

Boltzmann Generators for Condensed Matter via Riemannian Flow Matching

Sampling equilibrium distributions is fundamental to statistical mechanics. While flow matching has emerged as scalable state-of-the-art paradigm for generative modeling, its potential for equilibrium sampling in condensed-phase systems remains largely unexplored. We address this by incorporating the periodicity inherent to these systems into continuous normalizing flows using Riemannian flow matching. The high computational cost of exact density estimation intrinsic to continuous normalizing flows is mitigated by using Hutchinson's trace estimator, utilizing a crucial bias-correction step based on cumulant expansion to render the stochastic estimates suitable for rigorous thermodynamic reweighting. Our approach is validated on monatomic ice, demonstrating the ability to train on systems of unprecedented size and obtain highly accurate free energy estimates without the need for traditional multistage estimators.

physics.comp-ph↗

arXiv2026

Enabling ab initio geometry optimization of strongly correlated systems with transferable deep quantum Monte Carlo

A faithful description of chemical processes requires exploring extended regions of the molecular potential energy surface (PES), which remains challenging for strongly correlated systems. Transferable deep-learning variational Monte Carlo (VMC) offers a promising route by efficiently solving the electronic Schrödinger equation jointly across molecular geometries at consistently high accuracy, yet its stochastic nature renders direct exploration of molecular configuration space nontrivial. Here, we present a framework for highly accurate ab initio exploration of PESs that combines transferable deep-learning VMC with a cost-effective estimation of energies, forces, and Hessians. By continuously sampling nuclear configurations during VMC optimization of electronic wave functions, we obtain transferable descriptions that achieve zero-shot chemical accuracy within chemically relevant distributions of molecular geometries. Throughout the subsequent characterization of molecular configuration space, the PES is evaluated only sparsely, with local approximations constructed by estimating VMC energies and forces at sampled geometries and aggregating the resulting noisy data using Gaussian process regression. Our method enables accurate and efficient exploration of complex PES landscapes, including structure relaxation, transition-state searches, and minimum-energy pathways, for both ground and excited states. This opens the door to studying bond breaking, formation, and large structural rearrangements in systems with pronounced multi-reference character.

physics.chem-ph↗

arXiv2026

Assessing generative modeling approaches for free energy estimates in condensed matter

The accurate estimation of free energy differences between two states is a long-standing challenge in molecular simulations. Traditional approaches generally rely on sampling multiple intermediate states to ensure sufficient overlap in phase space and are, consequently, computationally expensive. Boltzmann Generators and related generative-model-based methods have recently addressed this challenge by learning a direct probability density transform between two states. However, it remains unclear which approach provides the best trade-off between efficiency, accuracy, and scalability. In this work, we review and benchmark selected generative approaches for condensed-matter systems, including discrete and continuous normalizing flows for targeted free energy perturbation and FEAT (Free Energy Estimators with Adaptive Transport) combined with the escorted Jarzynski equality, using coarse-grained monatomic ice and Lennard-Jones solids as benchmark systems. All models yield highly accurate free energy estimates and, depending on the system, may require fewer energy evaluations than traditional methods. Continuous flows and FEAT are most efficient in energy evaluations, whereas discrete flows have substantially lower inference cost. By releasing all data together with our results, we enable future benchmarking of free energy estimation methods in condensed-phase systems.

cond-mat.stat-mech↗

arXiv2026

Consistent Sampling and Simulation: Molecular Dynamics with Energy-Based Diffusion Models

In recent years, diffusion models trained on equilibrium molecular distributions have proven effective for sampling biomolecules. Beyond direct sampling, the score of such a model can also be used to derive the forces that act on molecular systems. However, while classical diffusion sampling usually recovers the training distribution, the corresponding energy-based interpretation of the learned score is often inconsistent with this distribution, even for low-dimensional toy systems. We trace this inconsistency to inaccuracies of the learned score at very small diffusion timesteps, where the model must capture the correct evolution of the data distribution. In this regime, diffusion models fail to satisfy the Fokker-Planck equation, which governs the evolution of the score. We interpret this deviation as one source of the observed inconsistencies and propose an energy-based diffusion model with a Fokker-Planck-derived regularization term to enforce consistency. We demonstrate our approach by sampling and simulating multiple biomolecular systems, including fast-folding proteins, and by introducing a state-of-the-art transferable Boltzmann emulator for dipeptides that supports simulation and achieves improved consistency and efficient sampling. Our code, model weights, and self-contained JAX and PyTorch notebooks are available at https://github.com/noegroup/ScoreMD.

cs.LG↗

arXiv2025

Scalable Boltzmann Generators for equilibrium sampling of large-scale materials

The use of generative models to sample equilibrium distributions of many-body systems, as first demonstrated by Boltzmann Generators, has attracted substantial interest due to their ability to produce unbiased and uncorrelated samples in `one shot'. Despite their promise and impressive results across the natural sciences, scaling these models to large systems remains a major challenge. In this work, we introduce a Boltzmann Generator architecture that addresses this scalability bottleneck with a focus on applications in materials science. We leverage augmented coupling flows in combination with graph neural networks to base the generation process on local environmental information, while allowing for energy-based training and fast inference. Compared to previous architectures, our model trains significantly faster, requires far less computational resources, and achieves superior sampling efficiencies. Crucially, the architecture is transferable to larger system sizes, which allows for the efficient sampling of materials with simulation cells of unprecedented size. We demonstrate the potential of our approach by applying it to several materials systems, including Lennard-Jones crystals, ice phases of mW water, and the phase diagram of silicon, for system sizes well above one thousand atoms. The trained Boltzmann Generators produce highly accurate equilibrium ensembles for various crystal structures, as well as Helmholtz and Gibbs free energies across a range of system sizes, able to reach scales where finite-size effects become negligible.

cond-mat.stat-mech↗

arXiv2025

Operator Forces For Coarse-Grained Molecular Dynamics

Coarse-grained (CG) molecular dynamics simulations extend the length and time scale of atomistic simulations by replacing groups of correlated atoms with CG beads. Machine-learned coarse-graining (MLCG) has recently emerged as a promising approach to construct highly accurate force fields for CG molecular dynamics. However, the calibration of MLCG force fields typically hinges on force matching, which demands extensive reference atomistic trajectories with corresponding force labels. In practice, atomistic forces are often not recorded, making traditional force matching infeasible on pre-existing datasets. Recently, noise-based kernels have been introduced to adapt force matching to the low-data regime, including situations in which reference atomistic forces are not present. While this approach produces force fields which recapitulate slow collective motion, it introduces significant local distortions due to the corrupting effects of the noise-based kernel. In this work, we introduce more general kernels based on normalizing flows that substantially reduce these local distortions while preserving global conformational accuracy. We demonstrate our method on small proteins, showing that flow-based kernels can generate high-quality CG forces solely from configurational samples.

physics.chem-ph↗

arXiv2025

Partitioning the electronic wave function using deep variational Monte Carlo

We propose a novel wave function partitioning method that integrates deep-learning variational Monte Carlo with ansätze based on generalized product functions. This approach effectively separates electronic wave functions (WFs) into multiple partial WFs representing, for example, the core and valence domains or different electronic shells. Although our ansätze do not explicitly include correlations between individual electron groups, we show that they accurately reproduce the underlying physics and chemical properties, such as dissociation curve, dipole moment, reaction energy, ionization energy, or atomic sizes. We identify the optimal number of core electrons and define physical core sizes for Li to Mg atoms. Our results demonstrate that core electrons can be effectively decoupled from valence electrons. We show that the core part of the WF remains nearly constant across different molecules and their geometries, enabling the transfer and reuse of the core part in WFs of more complex systems. This work provides a general framework for WF decomposition, offering potential advantages in computing and studying larger systems, and possibly paving the way for ab-initio development of effective core potentials. Though currently limited to small molecules due to scaling, we highlight several directions for extending our method it to larger systems.

physics.chem-ph↗

arXiv2025

Deep quantum Monte Carlo approach for polaritonic chemistry

Recent years have witnessed a surge of experimental and theoretical interest in controlling the properties of matter, such as its chemical reactivity, by confining it in optical cavities, where the enhancement of the light-matter coupling strength leads to the creation of hybrid light-matter states known as polaritons. However, ab initio calculations that account for the quantum nature of both the electromagnetic field and matter are challenging and have only started to be developed in recent years. We introduce a deep learning variational quantum Monte Carlo method to solve the electronic and photonic Schrödinger equation of molecules trapped in optical cavities. We extend typical electronic neural network wavefunction ansatzes to describe joint fermionic and bosonic systems, i.e. electron-photon systems, in a quantum Monte Carlo framework. We apply our method to hydrogen molecules in a cavity, computing both ground and excited states. We assess their energy, dipole moment, charge density shift due to the cavity, the state of the photonic field, and the entanglement developed between the electrons and photons. When possible, we compare our results with more conventional quantum chemistry methods proposed in the literature, finding good qualitative agreement, thus extending the range of scientific problems that can be tackled using machine learning techniques.

physics.chem-ph↗

arXiv2025

Dicke superradiant enhancement of the heat current in circuit QED

Collective effects, such as Dicke superradiant emission, can enhance the performance of a quantum device. Here, we study the heat current flowing between a cold and a hot bath through an ensemble of $N$ qubits, which are collectively coupled to the thermal baths. We find a regime where the collective coupling leads to a quadratic scaling of the heat current with $N$ in a finite-size scenario. Conversely, when approaching the thermodynamic limit, we prove that the collective scenario exhibits a parametric enhancement over the non-collective case. We then consider the presence of a third uncontrolled {\it parasitic} bath, interacting locally with each qubit, that models unavoidable couplings to the external environment. Despite having a non-perturbative effect on the steady-state currents, we show that the collective enhancement is robust to such an addition. Finally, we discuss the feasibility of realizing such a Dicke heat valve with superconducting circuits. Our findings indicate that in a minimal realistic experimental setting with two superconducting qubits, the collective advantage offers an enhancement of approximately $10\%$ compared to the non-collective scenario.

quant-ph↗

arXiv2025

Reinforcement learning optimization of the charging of a Dicke quantum battery

Quantum batteries are energy-storing devices, governed by quantum mechanics, that promise high charging performance thanks to collective effects. Due to its experimental feasibility, the Dicke battery - which comprises $N$ two-level systems coupled to a common photon mode - is one of the most promising designs for quantum batteries. However, the chaotic nature of the model severely hinders the extractable energy (ergotropy). Here, we use reinforcement learning to optimize the charging process of a Dicke battery either by modulating the coupling strength, or the system-cavity detuning. We find that the ergotropy and quantum mechanical energy fluctuations (charging precision) can be greatly improved with respect to standard charging strategies by countering the detrimental effect of quantum chaos. Notably, the collective speedup of the charging time can be preserved even when nearly fully charging the battery.

quant-ph↗