Doob's Lagrangian: A Sample-Efficient Variational Approach to Transition Path Sampling
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Abstract (arXiv)
Rare event sampling in dynamical systems is a fundamental problem arising in the natural sciences, which poses significant computational challenges due to an exponentially large space of trajectories. For settings where the dynamical system of interest follows a Brownian motion with known drift, the question of conditioning the process to reach a given endpoint or desired rare event is definitively answered by Doob's h-transform. However, the naive estimation of this transform is infeasible, as it requires simulating sufficiently many forward trajectories to estimate rare event probabilities. In this work, we propose a variational formulation of Doob's h-transform as an optimization problem over trajectories between a given initial point and the desired ending point. To solve this optimization, we propose a simulation-free training objective with a model parameterization that imposes the desired boundary conditions by design. Our approach significantly reduces the search space over trajectories and avoids expensive trajectory simulation and inefficient importance sampling estimators which are required in existing methods. We demonstrate the ability of our method to find feasible transition paths on real-world molecular simulation and protein folding tasks.
Key facts. Cited by 25 papers in the map (data through 7 Oct 2026). Builds on 27 of its 84 references that are in the map. First posted on arXiv 10 Oct 2024.
Builds on
27 of 84 references.
References · 27
- 2022Flow Matching for Generative Modelingcited by 5,426
- 2016The Concrete Distribution: A Continuous Relaxation of Discrete Random Variablescited by 1,135
- 2021Diffusion Schr"odinger Bridge with Applications to Score-Based Generative Modelingcited by 594
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- 2021Likelihood Training of Schr"odinger Bridge using Forward-Backward SDEs Theorycited by 216
- 2023Diffusion Schr"odinger Bridge Matchingcited by 151
- 2022Diffusion-based Molecule Generation with Informative Prior Bridgescited by 104
- 2022Let us Build Bridges: Understanding and Extending Diffusion Generative Modelscited by 102
- 2014On the relation between optimal transport and Schr"odinger bridges: A stochastic control viewpointcited by 99
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- 2023Diffusion Bridge Mixture Transports, Schr"odinger Bridge Problems and Generative Modelingcited by 80
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- 2023From Molecules to Materials: Pre-training Large Generalizable Models for Atomic Property Predictioncited by 39
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- 2022Stochastic Optimal Control for Collective Variable Free Sampling of Molecular Transition Pathscited by 36
- 2020A reinforcement learning approach to rare trajectory samplingcited by 21
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- 2021Reinforcement learning of rare diffusive dynamicscited by 14
- 2020Molecular Latent Space Simulatorscited by 13
- 2023Transition Path Sampling with Boltzmann Generator-based MCMC Movescited by 8
- 2022Generative methods for sampling transition paths in molecular dynamicscited by 6
- 2022Conditioning Normalizing Flows for Rare Event Samplingcited by 5
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Citing papers per year: 2024: 1; 2025: 17; 2026: 7.
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- 2025No Trick, No Treat: Pursuits and Challenges Towards Simulation-free Training of Neural Samplerscited by 25
- 2025Consistent Sampling and Simulation: Molecular Dynamics with Energy-Based Diffusion Modelscited by 23
- 2025Trust Region Constrained Measure Transport in Path Space for Stochastic Optimal Control and Inferencecited by 22
- 2025SDE Matching: Scalable and Simulation-Free Training of Latent Stochastic Differential Equationscited by 19
- 2025Action-Minimization Meets Generative Modeling: Efficient Transition Path Sampling with the Onsager-Machlup Functionalcited by 18
- 2025Conditioning Diffusions Using Malliavin Calculuscited by 15
- 2026Conditional Diffusion Guidance under Hard Constraint: A Stochastic Analysis Approachcited by 10
- 2025ConfRover: Simultaneous Modeling of Protein Conformation and Dynamics via Autoregressioncited by 7
- 2025UniSim: A Unified Simulator for Time-Coarsened Dynamics of Biomoleculescited by 7
- 2025The Spacetime of Diffusion Models: An Information Geometry Perspectivecited by 6
- 2025Control Consistency Losses for Diffusion Bridgescited by 6
- 2024Generalized Flow Matching for Transition Dynamics Modelingcited by 4
13 more
- 2025Functional Adjoint Sampler: Scalable Sampling on Infinite Dimensional Spacescited by 4
- 2025Implicit Neural Representations for Chemical Reaction Pathscited by 3
- 2025Transferable Learning of Reaction Pathways from Geometric Priorscited by 2
- 2026FragmentFlow: Scalable Transition State Generation for Large Moleculescited by 2
- 2025Flows and Diffusions on the Neural Manifoldcited by 1
- 2025Entangled Schr"odinger Bridge Matchingcited by 1
- 2026Analytic Bridge Diffusions for Controlled Path Generationcited by 1
- 2026Intrinsic-Noise Consolidation: A Doob-Barrier-Conditioned Diffusion Turns Analog Device Noise into a Continual-Learning Resourcecited by 1
- 2026Twisted Schr"odinger Bridge Matchingcited by 1
- 2025Follow the MEP: Scalable Neural Representations for Minimum-Energy Path Discovery in Molecular Systemscited by 0
- 2025Machine-Learned Sampling of Conditioned Path Measurescited by 0
- 2026Stochastic Control Policies for Robust Molecular Transition Path Samplingcited by 0
- 2026Machine learning kinetics from molecular dynamics datacited by 0
- 2026Machine learning kinetics from molecular dynamics data15 Sep 2026
- 2026Stochastic Control Policies for Robust Molecular Transition Path Sampling13 Aug 2026
- 2026Twisted Schr"odinger Bridge Matching18 Jul 2026
- 2026Intrinsic-Noise Consolidation: A Doob-Barrier-Conditioned Diffusion Turns Analog Device Noise into a Continual-Learning Resource8 Jul 2026
- 2026Analytic Bridge Diffusions for Controlled Path Generation3 May 2026
- 2026Conditional Diffusion Guidance under Hard Constraint: A Stochastic Analysis Approach5 Feb 2026
- 2026FragmentFlow: Scalable Transition State Generation for Large Molecules2 Feb 2026
- 2025Control Consistency Losses for Diffusion Bridges4 Dec 2025
- 2025Entangled Schr"odinger Bridge Matching10 Nov 2025
- 2025Functional Adjoint Sampler: Scalable Sampling on Infinite Dimensional Spaces9 Nov 2025
- 2025Trust Region Constrained Measure Transport in Path Space for Stochastic Optimal Control and Inference17 Aug 2025
- 2025Flows and Diffusions on the Neural Manifold14 Jul 2025
13 more
- 2025Consistent Sampling and Simulation: Molecular Dynamics with Energy-Based Diffusion Models20 Jun 2025
- 2025Machine-Learned Sampling of Conditioned Path Measures2 Jun 2025
- 2025The Spacetime of Diffusion Models: An Information Geometry Perspective23 May 2025
- 2025ConfRover: Simultaneous Modeling of Protein Conformation and Dynamics via Autoregression23 May 2025
- 2025UniSim: A Unified Simulator for Time-Coarsened Dynamics of Biomolecules20 May 2025
- 2025Action-Minimization Meets Generative Modeling: Efficient Transition Path Sampling with the Onsager-Machlup Functional25 Apr 2025
- 2025Follow the MEP: Scalable Neural Representations for Minimum-Energy Path Discovery in Molecular Systems23 Apr 2025
- 2025Transferable Learning of Reaction Pathways from Geometric Priors21 Apr 2025
- 2025Conditioning Diffusions Using Malliavin Calculus4 Apr 2025
- 2025Implicit Neural Representations for Chemical Reaction Paths20 Feb 2025
- 2025No Trick, No Treat: Pursuits and Challenges Towards Simulation-free Training of Neural Samplers10 Feb 2025
- 2025SDE Matching: Scalable and Simulation-Free Training of Latent Stochastic Differential Equations4 Feb 2025
- 2024Generalized Flow Matching for Transition Dynamics Modeling19 Oct 2024
- 2025Consistent Sampling and Simulation: Molecular Dynamics with Energy-Based Diffusion Modelscited by 23
- 2025Action-Minimization Meets Generative Modeling: Efficient Transition Path Sampling with the Onsager-Machlup Functionalcited by 18
- 2026Conditional Diffusion Guidance under Hard Constraint: A Stochastic Analysis Approachcited by 10
- 2025The Spacetime of Diffusion Models: An Information Geometry Perspectivecited by 6
- 2024Generalized Flow Matching for Transition Dynamics Modelingcited by 4
- 2026Conditional Diffusion Guidance under Hard Constraint: A Stochastic Analysis Approach5 Feb 2026
- 2025Consistent Sampling and Simulation: Molecular Dynamics with Energy-Based Diffusion Models20 Jun 2025
- 2025The Spacetime of Diffusion Models: An Information Geometry Perspective23 May 2025
- 2025Action-Minimization Meets Generative Modeling: Efficient Transition Path Sampling with the Onsager-Machlup Functional25 Apr 2025
- 2024Generalized Flow Matching for Transition Dynamics Modeling19 Oct 2024
- 2025No Trick, No Treat: Pursuits and Challenges Towards Simulation-free Training of Neural Samplerscited by 25
- 2025Trust Region Constrained Measure Transport in Path Space for Stochastic Optimal Control and Inferencecited by 22
- 2025SDE Matching: Scalable and Simulation-Free Training of Latent Stochastic Differential Equationscited by 19
- 2025Conditioning Diffusions Using Malliavin Calculuscited by 15
- 2025ConfRover: Simultaneous Modeling of Protein Conformation and Dynamics via Autoregressioncited by 7
- 2025UniSim: A Unified Simulator for Time-Coarsened Dynamics of Biomoleculescited by 7
- 2025Control Consistency Losses for Diffusion Bridgescited by 6
- 2025Functional Adjoint Sampler: Scalable Sampling on Infinite Dimensional Spacescited by 4
- 2025Implicit Neural Representations for Chemical Reaction Pathscited by 3
- 2025Transferable Learning of Reaction Pathways from Geometric Priorscited by 2
- 2026FragmentFlow: Scalable Transition State Generation for Large Moleculescited by 2
- 2025Flows and Diffusions on the Neural Manifoldcited by 1
12 most cited of 20 All 20 (JSON)
- 2026Machine learning kinetics from molecular dynamics data15 Sep 2026
- 2026Stochastic Control Policies for Robust Molecular Transition Path Sampling13 Aug 2026
- 2026Twisted Schr"odinger Bridge Matching18 Jul 2026
- 2026Intrinsic-Noise Consolidation: A Doob-Barrier-Conditioned Diffusion Turns Analog Device Noise into a Continual-Learning Resource8 Jul 2026
- 2026Analytic Bridge Diffusions for Controlled Path Generation3 May 2026
- 2026FragmentFlow: Scalable Transition State Generation for Large Molecules2 Feb 2026
- 2025Control Consistency Losses for Diffusion Bridges4 Dec 2025
- 2025Entangled Schr"odinger Bridge Matching10 Nov 2025
- 2025Functional Adjoint Sampler: Scalable Sampling on Infinite Dimensional Spaces9 Nov 2025
- 2025Trust Region Constrained Measure Transport in Path Space for Stochastic Optimal Control and Inference17 Aug 2025
- 2025Flows and Diffusions on the Neural Manifold14 Jul 2025
- 2025Machine-Learned Sampling of Conditioned Path Measures2 Jun 2025
12 newest of 20 All 20 (JSON)