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React-OT: Optimal Transport for Generating Transition State in Chemical Reactions
Apr 20, 2024
Transition states (TSs) are transient structures that are key in understanding reaction mechanisms and designing catalysts but challenging to be captured in experiments. Alternatively, many optimization algorithms have been developed to search for TSs computationally. Yet the cost of these algorithms driven by quantum chemistry methods (usually density functional theory) is still high, posing challenges for their applications in building large reaction networks for reaction exploration. Here we developed React-OT, an optimal transport approach for generating unique TS structures from reactants and products. React-OT generates highly accurate TS structures with a median structural root mean square deviation (RMSD) of 0.053{\AA} and median barrier height error of 1.06 kcal/mol requiring only 0.4 second per reaction. The RMSD and barrier height error is further improved by roughly 25% through pretraining React-OT on a large reaction dataset obtained with a lower level of theory, GFN2-xTB. We envision the great accuracy and fast inference of React-OT useful in targeting TSs when exploring chemical reactions with unknown mechanisms.
Augmented Bridge Matching
Nov 12, 2023Flow and bridge matching are a novel class of processes which encompass diffusion models. One of the main aspect of their increased flexibility is that these models can interpolate between arbitrary data distributions i.e. they generalize beyond generative modeling and can be applied to learning stochastic (and deterministic) processes of arbitrary transfer tasks between two given distributions. In this paper, we highlight that while flow and bridge matching processes preserve the information of the marginal distributions, they do \emph{not} necessarily preserve the coupling information unless additional, stronger optimality conditions are met. This can be problematic if one aims at preserving the original empirical pairing. We show that a simple modification of the matching process recovers this coupling by augmenting the velocity field (or drift) with the information of the initial sample point. Doing so, we lose the Markovian property of the process but preserve the coupling information between distributions. We illustrate the efficiency of our augmentation in learning mixture of image translation tasks.
Generalized Schrödinger Bridge Matching
Oct 03, 2023
Modern distribution matching algorithms for training diffusion or flow models directly prescribe the time evolution of the marginal distributions between two boundary distributions. In this work, we consider a generalized distribution matching setup, where these marginals are only implicitly described as a solution to some task-specific objective function. The problem setup, known as the Generalized Schr\"odinger Bridge (GSB), appears prevalently in many scientific areas both within and without machine learning. We propose Generalized Schr\"odinger Bridge Matching (GSBM), a new matching algorithm inspired by recent advances, generalizing them beyond kinetic energy minimization and to account for task-specific state costs. We show that such a generalization can be cast as solving conditional stochastic optimal control, for which efficient variational approximations can be used, and further debiased with the aid of path integral theory. Compared to prior methods for solving GSB problems, our GSBM algorithm always preserves a feasible transport map between the boundary distributions throughout training, thereby enabling stable convergence and significantly improved scalability. We empirically validate our claims on an extensive suite of experimental setups, including crowd navigation, opinion depolarization, LiDAR manifolds, and image domain transfer. Our work brings new algorithmic opportunities for training diffusion models enhanced with task-specific optimality structures.
Mirror Diffusion Models for Constrained and Watermarked Generation
Oct 02, 2023Modern successes of diffusion models in learning complex, high-dimensional data distributions are attributed, in part, to their capability to construct diffusion processes with analytic transition kernels and score functions. The tractability results in a simulation-free framework with stable regression losses, from which reversed, generative processes can be learned at scale. However, when data is confined to a constrained set as opposed to a standard Euclidean space, these desirable characteristics appear to be lost based on prior attempts. In this work, we propose Mirror Diffusion Models (MDM), a new class of diffusion models that generate data on convex constrained sets without losing any tractability. This is achieved by learning diffusion processes in a dual space constructed from a mirror map, which, crucially, is a standard Euclidean space. We derive efficient computation of mirror maps for popular constrained sets, such as simplices and $\ell_2$-balls, showing significantly improved performance of MDM over existing methods. For safety and privacy purposes, we also explore constrained sets as a new mechanism to embed invisible but quantitative information (i.e., watermarks) in generated data, for which MDM serves as a compelling approach. Our work brings new algorithmic opportunities for learning tractable diffusion on complex domains.
Improving Generative Model-based Unfolding with Schrödinger Bridges
Aug 23, 2023
Machine learning-based unfolding has enabled unbinned and high-dimensional differential cross section measurements. Two main approaches have emerged in this research area: one based on discriminative models and one based on generative models. The main advantage of discriminative models is that they learn a small correction to a starting simulation while generative models scale better to regions of phase space with little data. We propose to use Schroedinger Bridges and diffusion models to create SBUnfold, an unfolding approach that combines the strengths of both discriminative and generative models. The key feature of SBUnfold is that its generative model maps one set of events into another without having to go through a known probability density as is the case for normalizing flows and standard diffusion models. We show that SBUnfold achieves excellent performance compared to state of the art methods on a synthetic Z+jets dataset.
Improved sampling via learned diffusions
Jul 03, 2023Recently, a series of papers proposed deep learning-based approaches to sample from unnormalized target densities using controlled diffusion processes. In this work, we identify these approaches as special cases of the Schr\"odinger bridge problem, seeking the most likely stochastic evolution between a given prior distribution and the specified target. We further generalize this framework by introducing a variational formulation based on divergences between path space measures of time-reversed diffusion processes. This abstract perspective leads to practical losses that can be optimized by gradient-based algorithms and includes previous objectives as special cases. At the same time, it allows us to consider divergences other than the reverse Kullback-Leibler divergence that is known to suffer from mode collapse. In particular, we propose the so-called log-variance loss, which exhibits favorable numerical properties and leads to significantly improved performance across all considered approaches.
Deep Momentum Multi-Marginal Schrödinger Bridge
Mar 03, 2023
Reconstructing population dynamics using only samples from distributions at coarse time intervals is a crucial challenge. Recent data-driven approaches such as flow-based models or Schr\"odinger Bridge models have demonstrated appealing performance, yet the inferred sample trajectories either fail to account for the underlying stochasticity or are unnecessarily rigid. In this article, we propose $\underline{D}$eep $\underline{M}$omentum Multi-Marginal $\underline{S}$chr\"odinger $\underline{B}$ridge(DMSB), a novel computational framework that learns the smooth measure-valued spline for stochastic systems without violating the position marginal constraints across time. We first extend the scalable mean matching objective used in the state space SB algorithm into the phase space. We next carefully craft a multi-constraint optimization training method based on Bregman Iteration that enables effective phase space means matching training for the high-dimensional dataset. We demonstrate that the resulting training algorithm significantly outperforms baselines on both synthetic datasets and a real-world single-cell RNA sequence dataset.
I$^2$SB: Image-to-Image Schrödinger Bridge
Feb 12, 2023
We propose Image-to-Image Schr\"odinger Bridge (I$^2$SB), a new class of conditional diffusion models that directly learn the nonlinear diffusion processes between two given distributions. These diffusion bridges are particularly useful for image restoration, as the degraded images are structurally informative priors for reconstructing the clean images. I$^2$SB belongs to a tractable class of Schr\"odinger bridge, the nonlinear extension to score-based models, whose marginal distributions can be computed analytically given boundary pairs. This results in a simulation-free framework for nonlinear diffusions, where the I$^2$SB training becomes scalable by adopting practical techniques used in standard diffusion models. We validate I$^2$SB in solving various image restoration tasks, including inpainting, super-resolution, deblurring, and JPEG restoration on ImageNet 256x256 and show that I$^2$SB surpasses standard conditional diffusion models with more interpretable generative processes. Moreover, I$^2$SB matches the performance of inverse methods that additionally require the knowledge of the corruption operators. Our work opens up new algorithmic opportunities for developing efficient nonlinear diffusion models on a large scale. scale. Project page: https://i2sb.github.io/
Deep Generalized Schrödinger Bridge
Sep 20, 2022
Mean-Field Game (MFG) serves as a crucial mathematical framework in modeling the collective behavior of individual agents interacting stochastically with a large population. In this work, we aim at solving a challenging class of MFGs in which the differentiability of these interacting preferences may not be available to the solver, and the population is urged to converge exactly to some desired distribution. These setups are, despite being well-motivated for practical purposes, complicated enough to paralyze most (deep) numerical solvers. Nevertheless, we show that Schr\"odinger Bridge - as an entropy-regularized optimal transport model - can be generalized to accepting mean-field structures, hence solving these MFGs. This is achieved via the application of Forward-Backward Stochastic Differential Equations theory, which, intriguingly, leads to a computational framework with a similar structure to Temporal Difference learning. As such, it opens up novel algorithmic connections to Deep Reinforcement Learning that we leverage to facilitate practical training. We show that our proposed objective function provides necessary and sufficient conditions to the mean-field problem. Our method, named Deep Generalized Schr\"odinger Bridge (DeepGSB), not only outperforms prior methods in solving classical population navigation MFGs, but is also capable of solving 1000-dimensional opinion depolarization, setting a new state-of-the-art numerical solver for high-dimensional MFGs. Our code will be made available at https://github.com/ghliu/DeepGSB.
Likelihood Training of Schrödinger Bridge using Forward-Backward SDEs Theory
Oct 23, 2021
Schr\"odinger Bridge (SB) is an optimal transport problem that has received increasing attention in deep generative modeling for its mathematical flexibility compared to the Scored-based Generative Model (SGM). However, it remains unclear whether the optimization principle of SB relates to the modern training of deep generative models, which often rely on constructing parameterized log-likelihood objectives.This raises questions on the suitability of SB models as a principled alternative for generative applications. In this work, we present a novel computational framework for likelihood training of SB models grounded on Forward-Backward Stochastic Differential Equations Theory -- a mathematical methodology appeared in stochastic optimal control that transforms the optimality condition of SB into a set of SDEs. Crucially, these SDEs can be used to construct the likelihood objectives for SB that, surprisingly, generalizes the ones for SGM as special cases. This leads to a new optimization principle that inherits the same SB optimality yet without losing applications of modern generative training techniques, and we show that the resulting training algorithm achieves comparable results on generating realistic images on MNIST, CelebA, and CIFAR10.