arXiv subjects

Frank Noé

Publications and source records attributed to Frank Noé.

At least 91 records · Page 5Linked to original sources

arXiv2020

Stochastic Normalizing Flows

The sampling of probability distributions specified up to a normalization constant is an important problem in both machine learning and statistical mechanics. While classical stochastic sampling methods such as Markov Chain Monte Carlo (MCMC) or Langevin Dynamics (LD) can suffer from slow mixing times there is a growing interest in using normalizing flows in order to learn the transformation of a simple prior distribution to the given target distribution. Here we propose a generalized and combined approach to sample target densities: Stochastic Normalizing Flows (SNF) -- an arbitrary sequence of deterministic invertible functions and stochastic sampling blocks. We show that stochasticity overcomes expressivity limitations of normalizing flows resulting from the invertibility constraint, whereas trainable transformations between sampling steps improve efficiency of pure MCMC/LD along the flow. By invoking ideas from non-equilibrium statistical mechanics we derive an efficient training procedure by which both the sampler's and the flow's parameters can be optimized end-to-end, and by which we can compute exact importance weights without having to marginalize out the randomness of the stochastic blocks. We illustrate the representational power, sampling efficiency and asymptotic correctness of SNFs on several benchmarks including applications to sampling molecular systems in equilibrium.

stat.ML↗

arXiv2020

Equivariant Flows: Exact Likelihood Generative Learning for Symmetric Densities

Normalizing flows are exact-likelihood generative neural networks which approximately transform samples from a simple prior distribution to samples of the probability distribution of interest. Recent work showed that such generative models can be utilized in statistical mechanics to sample equilibrium states of many-body systems in physics and chemistry. To scale and generalize these results, it is essential that the natural symmetries in the probability density -- in physics defined by the invariances of the target potential -- are built into the flow. We provide a theoretical sufficient criterion showing that the distribution generated by \textit{equivariant} normalizing flows is invariant with respect to these symmetries by design. Furthermore, we propose building blocks for flows which preserve symmetries which are usually found in physical/chemical many-body particle systems. Using benchmark systems motivated from molecular physics, we demonstrate that those symmetry preserving flows can provide better generalization capabilities and sampling efficiency.

stat.ML↗

arXiv2020

Deep neural network solution of the electronic Schrödinger equation

[New and updated results were published in Nature Chemistry, doi:10.1038/s41557-020-0544-y.] The electronic Schrödinger equation describes fundamental properties of molecules and materials, but can only be solved analytically for the hydrogen atom. The numerically exact full configuration-interaction method is exponentially expensive in the number of electrons. Quantum Monte Carlo is a possible way out: it scales well to large molecules, can be parallelized, and its accuracy has, as yet, only been limited by the flexibility of the used wave function ansatz. Here we propose PauliNet, a deep-learning wave function ansatz that achieves nearly exact solutions of the electronic Schrödinger equation. PauliNet has a multireference Hartree-Fock solution built in as a baseline, incorporates the physics of valid wave functions, and is trained using variational quantum Monte Carlo (VMC). PauliNet outperforms comparable state-of-the-art VMC ansatzes for atoms, diatomic molecules and a strongly-correlated hydrogen chain by a margin and is yet computationally efficient. We anticipate that thanks to the favourable scaling with system size, this method may become a new leading method for highly accurate electronic-strucutre calculations on medium-sized molecular systems.

physics.comp-ph↗

arXiv2020

Coupling particle-based reaction-diffusion simulations with reservoirs mediated by reaction-diffusion PDEs

Open biochemical systems of interacting molecules are ubiquitous in life-related processes. However, established computational methodologies, like molecular dynamics, are still mostly constrained to closed systems and timescales too small to be relevant for life processes. Alternatively, particle-based reaction-diffusion models are currently the most accurate and computationally feasible approach at these scales. Their efficiency lies in modeling entire molecules as particles that can diffuse and interact with each other. In this work, we develop modeling and numerical schemes for particle-based reaction-diffusion in an open setting, where the reservoirs are mediated by reaction-diffusion PDEs. We derive two important theoretical results. The first one is the mean-field for open systems of diffusing particles; the second one is the mean-field for a particle-based reaction-diffusion system with second-order reactions. We employ these two results to develop a numerical scheme that consistently couples particle-based reaction-diffusion processes with reaction-diffusion PDEs. This allows modeling open biochemical systems in contact with reservoirs that are time-dependent and spatially inhomogeneous, as in many relevant real-world applications.

q-bio.QM↗

arXiv2019

Deep learning Markov and Koopman models with physical constraints

The long-timescale behavior of complex dynamical systems can be described by linear Markov or Koopman models in a suitable latent space. Recent variational approaches allow the latent space representation and the linear dynamical model to be optimized via unsupervised machine learning methods. Incorporation of physical constraints such as time-reversibility or stochasticity into the dynamical model has been established for a linear, but not for arbitrarily nonlinear (deep learning) representations of the latent space. Here we develop theory and methods for deep learning Markov and Koopman models that can bear such physical constraints. We prove that the model is an universal approximator for reversible Markov processes and that it can be optimized with either maximum likelihood or the variational approach of Markov processes (VAMP). We demonstrate that the model performs equally well for equilibrium and systematically better for biased data compared to existing approaches, thus providing a tool to study the long-timescale processes of dynamical systems.

physics.comp-ph↗

arXiv2019

Neural Mode Jump Monte Carlo

Markov chain Monte Carlo methods are a powerful tool for sampling equilibrium configurations in complex systems. One problem these methods often face is slow convergence over large energy barriers. In this work, we propose a novel method which increases convergence in systems composed of many metastable states. This method aims to connect metastable regions directly using generative neural networks in order to propose new configurations in the Markov chain and optimizes the acceptance probability of large jumps between modes in configuration space. We provide a comprehensive theory and demonstrate the method on example systems.

physics.comp-ph↗

arXiv2019

Machine learning for protein folding and dynamics

Many aspects of the study of protein folding and dynamics have been affected by the recent advances in machine learning. Methods for the prediction of protein structures from their sequences are now heavily based on machine learning tools. The way simulations are performed to explore the energy landscape of protein systems is also changing as force-fields are started to be designed by means of machine learning methods. These methods are also used to extract the essential information from large simulation datasets and to enhance the sampling of rare events such as folding/unfolding transitions. While significant challenges still need to be tackled, we expect these methods to play an important role on the study of protein folding and dynamics in the near future. We discuss here the recent advances on all these fronts and the questions that need to be addressed for machine learning approaches to become mainstream in protein simulation.

physics.bio-ph↗

arXiv2019

Generating valid Euclidean distance matrices

Generating point clouds, e.g., molecular structures, in arbitrary rotations, translations, and enumerations remains a challenging task. Meanwhile, neural networks utilizing symmetry invariant layers have been shown to be able to optimize their training objective in a data-efficient way. In this spirit, we present an architecture which allows to produce valid Euclidean distance matrices, which by construction are already invariant under rotation and translation of the described object. Motivated by the goal to generate molecular structures in Cartesian space, we use this architecture to construct a Wasserstein GAN utilizing a permutation invariant critic network. This makes it possible to generate molecular structures in a one-shot fashion by producing Euclidean distance matrices which have a three-dimensional embedding.

cs.LG↗

arXiv2019

Machine learning for molecular simulation

Machine learning (ML) is transforming all areas of science. The complex and time-consuming calculations in molecular simulations are particularly suitable for a machine learning revolution and have already been profoundly impacted by the application of existing ML methods. Here we review recent ML methods for molecular simulation, with particular focus on (deep) neural networks for the prediction of quantum-mechanical energies and forces, coarse-grained molecular dynamics, the extraction of free energy surfaces and kinetics and generative network approaches to sample molecular equilibrium structures and compute thermodynamics. To explain these methods and illustrate open methodological problems, we review some important principles of molecular physics and describe how they can be incorporated into machine learning structures. Finally, we identify and describe a list of open challenges for the interface between ML and molecular simulation.

physics.chem-ph↗

arXiv2019

Special Topic: Markov Models of Molecular Kinetics

The Journal of Chemical Physics (JCP) article collection on Markov Models of Molecular Kinetics (MMMK) features recent advances developing and using Markov State Models (MSMs) in atomistic molecular simulations and related applications. This editorial provides a brief overview of the state of the art in the field and relates it to the articles in this JCP collection.

physics.chem-ph↗

arXiv2019

Kernel methods for detecting coherent structures in dynamical data

We illustrate relationships between classical kernel-based dimensionality reduction techniques and eigendecompositions of empirical estimates of reproducing kernel Hilbert space (RKHS) operators associated with dynamical systems. In particular, we show that kernel canonical correlation analysis (CCA) can be interpreted in terms of kernel transfer operators and that it can be obtained by optimizing the variational approach for Markov processes (VAMP) score. As a result, we show that coherent sets of particle trajectories can be computed by kernel CCA. We demonstrate the efficiency of this approach with several examples, namely the well-known Bickley jet, ocean drifter data, and a molecular dynamics problem with a time-dependent potential. Finally, we propose a straightforward generalization of dynamic mode decomposition (DMD) called coherent mode decomposition (CMD). Our results provide a generic machine learning approach to the computation of coherent sets with an objective score that can be used for cross-validation and the comparison of different methods.

math.DS↗

arXiv2019

Equivariant Flows: sampling configurations for multi-body systems with symmetric energies

Flows are exact-likelihood generative neural networks that transform samples from a simple prior distribution to the samples of the probability distribution of interest. Boltzmann Generators (BG) combine flows and statistical mechanics to sample equilibrium states of strongly interacting many-body systems such as proteins with 1000 atoms. In order to scale and generalize these results, it is essential that the natural symmetries of the probability density - in physics defined by the invariances of the energy function - are built into the flow. Here we develop theoretical tools for constructing such equivariant flows and demonstrate that a BG that is equivariant with respect to rotations and particle permutations can generalize to sampling nontrivially new configurations where a nonequivariant BG cannot.

stat.ML↗

arXiv2019

Diffusion-influenced reaction rates in the presence of pair interactions

The kinetics of bimolecular reactions in solution depends, among other factors, on intermolecular forces such as steric repulsion or electrostatic interaction. Microscopically, a pair of molecules first has to meet by diffusion before the reaction can take place. In this work, we establish an extension of Doi's volume reaction model to molecules interacting via pair potentials, which is a key ingredient for interacting-particle-based reaction-diffusion (iPRD) simulations. As a central result, we relate model parameters and macroscopic reaction rate constants in this situation. We solve the corresponding reaction-diffusion equation in the steady state and derive semi-analytical expressions for the reaction rate constant and the local concentration profiles. Our results apply to the full spectrum from well-mixed to diffusion--limited kinetics. For limiting cases, we give explicit formulas, and we provide a computationally inexpensive numerical scheme for the general case, including the intermediate, diffusion-influenced regime. The obtained rate constants decompose uniquely into encounter and formation rates, and we discuss the effect of the potential on both subprocesses, exemplified for a soft harmonic repulsion and a Lennard-Jones potential. The analysis is complemented by extensive stochastic iPRD simulations, and we find excellent agreement with the theoretical predictions.

cond-mat.soft↗

arXiv2019

Variational approach for learning Markov processes from time series data

Inference, prediction and control of complex dynamical systems from time series is important in many areas, including financial markets, power grid management, climate and weather modeling, or molecular dynamics. The analysis of such highly nonlinear dynamical systems is facilitated by the fact that we can often find a (generally nonlinear) transformation of the system coordinates to features in which the dynamics can be excellently approximated by a linear Markovian model. Moreover, the large number of system variables often change collectively on large time- and length-scales, facilitating a low-dimensional analysis in feature space. In this paper, we introduce a variational approach for Markov processes (VAMP) that allows us to find optimal feature mappings and optimal Markovian models of the dynamics from given time series data. The key insight is that the best linear model can be obtained from the top singular components of the Koopman operator. This leads to the definition of a family of score functions called VAMP-r which can be calculated from data, and can be employed to optimize a Markovian model. In addition, based on the relationship between the variational scores and approximation errors of Koopman operators, we propose a new VAMP-E score, which can be applied to cross-validation for hyper-parameter optimization and model selection in VAMP. VAMP is valid for both reversible and nonreversible processes and for stationary and non-stationary processes or realizations.

stat.ML↗

arXiv2019

Boltzmann Generators -- Sampling Equilibrium States of Many-Body Systems with Deep Learning

Computing equilibrium states in condensed-matter many-body systems, such as solvated proteins, is a long-standing challenge. Lacking methods for generating statistically independent equilibrium samples in "one shot", vast computational effort is invested for simulating these system in small steps, e.g., using Molecular Dynamics. Combining deep learning and statistical mechanics, we here develop Boltzmann Generators, that are shown to generate unbiased one-shot equilibrium samples of representative condensed matter systems and proteins. Boltzmann Generators use neural networks to learn a coordinate transformation of the complex configurational equilibrium distribution to a distribution that can be easily sampled. Accurate computation of free energy differences and discovery of new configurations are demonstrated, providing a statistical mechanics tool that can avoid rare events during sampling without prior knowledge of reaction coordinates.

stat.ML↗

arXiv2019

Deflation reveals dynamical structure in nondominant reaction coordinates

The output of molecular dynamics simulations is high-dimensional, and the degrees of freedom among the atoms are related in intricate ways. Therefore, a variety of analysis frameworks have been introduced in order to distill complex motions into lower-dimensional representations that model the system dynamics. These dynamical models have been developed to optimally approximate the system's global kinetics. However, the separate aims of optimizing global kinetics and modeling a process of interest diverge when the process of interest is not the slowest process in the system. Here, we introduce deflation into state-of-the-art methods in molecular kinetics in order to preserve the use of variational optimization tools when the slowest dynamical mode is not the same as the one we seek to model and understand. First, we showcase deflation for a simple toy system and introduce the deflated variational approach to Markov processes (dVAMP). Using dVAMP, we show that nondominant reaction coordinates produced using deflation are more informative than their counterparts generated without deflation. Then, we examine a protein folding system in which the slowest dynamical mode is not folding. Following a dVAMP analysis, we show that deflation can be used to obscure this undesired slow process from a kinetic model, in this case a VAMPnet. The incorporation of deflation into current methods opens the door for enhanced sampling strategies and more flexible, targeted model building.

q-bio.BM↗

arXiv2019

Variational Selection of Features for Molecular Kinetics

The modeling of atomistic biomolecular simulations using kinetic models such as Markov state models (MSMs) has had many notable algorithmic advances in recent years. The variational principle has opened the door for a nearly fully automated toolkit for selecting models that predict the long-time kinetics from molecular dynamics simulations. However, one yet-unoptimized step of the pipeline involves choosing the features, or collective variables, from which the model should be constructed. In order to build intuitive models, these collective variables are often sought to be interpretable and familiar features, such as torsional angles or contact distances in a protein structure. However, previous approaches for evaluating the chosen features rely on constructing a full MSM, which in turn requires additional hyperparameters to be chosen, and hence leads to a computationally expensive framework. Here, we present a method to optimize the feature choice directly, without requiring the construction of the final kinetic model. We demonstrate our rigorous preprocessing algorithm on a canonical set of twelve fast-folding protein simulations, and show that our procedure leads to more efficient model selection.

physics.bio-ph↗

arXiv2019

Identification of kinetic order parameters for non-equilibrium dynamics

A popular approach to analyze the dynamics of high-dimensional many-body systems, such as macromolecules, is to project the trajectories onto a space of slowly-varying collective variables, where subsequent analyses are made, such as clustering or estimation of free energy profiles or Markov state models (MSMs). However, existing "dynamical" dimension reduction methods, such as the time-lagged independent component analysis (TICA) are only valid if the dynamics obeys detailed balance (microscopic reversibility) and typically require long, equilibrated simulation trajectories. Here we develop a dimension reduction method for non-equilibrium dynamics based on the recently developed Variational Approach for Markov Processes (VAMP) by Wu and Noé. VAMP is illustrated by obtaining a low-dimensional description of a single file ion diffusion model and by identifying long-lived states from molecular dynamics simulations of the KcsA channel protein in an external electrochemical potential. This analysis provides detailed insights into the coupling of conformational dynamics, the configuration of the selectivity filter, and the conductance of the channel. We recommend VAMP as a replacement for the less general TICA method.

physics.chem-ph↗