We present a method to compute transport coefficients in molecular dynamics. Transport coefficients quantify the linear dependencies of fluxes in non-equilibrium systems subject to small external forcings. Whereas standard non-equilibrium approaches fix the forcing and measure the average flux induced in the system driven out of equilibrium, a dual philosophy consists in fixing the value of the flux, and measuring the average magnitude of the forcing needed to induce it. A deterministic version of this approach, named Norton dynamics, was studied in the 1980s by Evans and Morris. In this work, we introduce a stochastic version of this method, first developing a general formal theory for a broad class of diffusion processes, and then specializing it to underdamped Langevin dynamics, which are commonly used for molecular dynamics simulations. We provide numerical evidence that the stochastic Norton method provides an equivalent measure of the linear response, and in fact demonstrate that this equivalence extends well beyond the linear response regime. This work raises many intriguing questions, both from the theoretical and the numerical perspectives.
The Sparse Identification of Nonlinear Dynamics (SINDy) algorithm can be applied to stochastic differential equations to estimate the drift and the diffusion function using data from a realization of the SDE. The SINDy algorithm requires sample data from each of these functions, which is typically estimated numerically from the data of the state. We analyze the performance of the previously proposed estimates for the drift and diffusion function to give bounds on the error for finite data. However, since this algorithm only converges as both the sampling frequency and the length of trajectory go to infinity, obtaining approximations within a certain tolerance may be infeasible. To combat this, we develop estimates with higher orders of accuracy for use in the SINDy framework. For a given sampling frequency, these estimates give more accurate approximations of the drift and diffusion functions, making SINDy a far more feasible system identification method.
We investigate time-optimal Multi-Robot Coverage Path Planning (MCPP) for both unweighted and weighted terrains, which aims to minimize the coverage time, defined as the maximum travel time of all robots. Specifically, we focus on a reduction from MCPP to Rooted Min-Max Tree Cover (RMMTC). For the first time, we propose a Mixed Integer Programming (MIP) model to optimally solve RMMTC, resulting in an MCPP solution with a coverage time that is provably at most four times the optimal. Moreover, we propose two suboptimal yet effective heuristics that reduce the number of variables in the MIP model, thus improving its efficiency for large-scale MCPP instances. We show that both heuristics result in reduced-size MIP models that remain complete (i.e., guarantee to find a solution if one exists) for all RMMTC instances. Additionally, we explore the use of model optimization warm-startup to further improve the efficiency of both the original MIP model and the reduced-size MIP models. We validate the effectiveness of our MIP-based MCPP planner through experiments that compare it with two state-of-the-art MCPP planners on various instances, demonstrating a reduction in the coverage time by an average of 42.42% and 39.16% over them, respectively.
In this paper, practically computable low-order approximations of potentially high-dimensional differential equations driven by geometric rough paths are proposed and investigated. In particular, equations are studied that cover the linear setting, but we allow for a certain type of dissipative nonlinearity in the drift as well. In a first step, a linear subspace is found that contains the solution space of the underlying rough differential equation (RDE). This subspace is associated to covariances of linear Ito-stochastic differential equations which is shown exploiting a Gronwall lemma for matrix differential equations. Orthogonal projections onto the identified subspace lead to a first exact reduced order system. Secondly, a linear map of the RDE solution (quantity of interest) is analyzed in terms of redundant information meaning that state variables are found that do not contribute to the quantity of interest. Once more, a link to Ito-stochastic differential equations is used. Removing such unnecessary information from the RDE provides a further dimension reduction without causing an error. Finally, we discretize a linear parabolic rough partial differential equation in space. The resulting large-order RDE is subsequently tackled with the exact reduction techniques studied in this paper. We illustrate the enormous complexity reduction potential in the corresponding numerical experiments.
This article presents a general approximation-theoretic framework to analyze measure transport algorithms for probabilistic modeling. A primary motivating application for such algorithms is sampling -- a central task in statistical inference and generative modeling. We provide a priori error estimates in the continuum limit, i.e., when the measures (or their densities) are given, but when the transport map is discretized or approximated using a finite-dimensional function space. Our analysis relies on the regularity theory of transport maps and on classical approximation theory for high-dimensional functions. A third element of our analysis, which is of independent interest, is the development of new stability estimates that relate the distance between two maps to the distance~(or divergence) between the pushforward measures they define. We present a series of applications of our framework, where quantitative convergence rates are obtained for practical problems using Wasserstein metrics, maximum mean discrepancy, and Kullback--Leibler divergence. Specialized rates for approximations of the popular triangular Kn{\"o}the-Rosenblatt maps are obtained, followed by numerical experiments that demonstrate and extend our theory.
This paper revisits an adaptation of the random forest algorithm for Fr\'echet regression, addressing the challenge of regression in the context of random objects in metric spaces. Recognizing the limitations of previous approaches, we introduce a new splitting rule that circumvents the computationally expensive operation of Fr\'echet means by substituting with a medoid-based approach. We validate this approach by demonstrating its asymptotic equivalence to Fr\'echet mean-based procedures and establish the consistency of the associated regression estimator. The paper provides a sound theoretical framework and a more efficient computational approach to Fr\'echet regression, broadening its application to non-standard data types and complex use cases.
Models with intractable normalizing functions have numerous applications. Because the normalizing constants are functions of the parameters of interest, standard Markov chain Monte Carlo cannot be used for Bayesian inference for these models. A number of algorithms have been developed for such models. Some have the posterior distribution as their asymptotic distribution. Other ``asymptotically inexact'' algorithms do not possess this property. There is limited guidance for evaluating approximations based on these algorithms. Hence it is very hard to tune them. We propose two new diagnostics that address these problems for intractable normalizing function models. Our first diagnostic, inspired by the second Bartlett identity, is in principle broadly applicable to Monte Carlo approximations beyond the normalizing function problem. We develop an approximate version of this diagnostic that is applicable to intractable normalizing function problems. Our second diagnostic is a Monte Carlo approximation to a kernel Stein discrepancy-based diagnostic introduced by Gorham and Mackey (2017). We provide theoretical justification for our methods and apply them to several algorithms in challenging simulated and real data examples including an Ising model, an exponential random graph model, and a Conway--Maxwell--Poisson regression model, obtaining interesting insights about the algorithms in these contexts.
In this paper, we explore the new design space of extra-linguistic cues inspired by graphical tropes used in graphic novels and animation to enhance the expressiveness of social robots. To achieve this, we identified a set of cues that can be used to generate expressions, including smoke/steam/fog, water droplets, and bubbles. We prototyped devices that can generate these fluid expressions for a robot and conducted design sessions where eight designers explored the use and utility of the cues in conveying the robot's internal states in various design scenarios. Our analysis of the 22 designs, the associated design justifications, and the interviews with designers revealed patterns in how each cue was used, how they were combined with nonverbal cues, and where the participants drew their inspiration from. These findings informed the design of an integrated module called EmoPack, which can be used to augment the expressive capabilities of any robot platform.
Partial orders are a natural model for the social hierarchies that may constrain "queue-like" rank-order data. However, the computational cost of counting the linear extensions of a general partial order on a ground set with more than a few tens of elements is prohibitive. Vertex-series-parallel partial orders (VSPs) are a subclass of partial orders which admit rapid counting and represent the sorts of relations we expect to see in a social hierarchy. However, no Bayesian analysis of VSPs has been given to date. We construct a marginally consistent family of priors over VSPs with a parameter controlling the prior distribution over VSP depth. The prior for VSPs is given in closed form. We extend an existing observation model for queue-like rank-order data to represent noise in our data and carry out Bayesian inference on "Royal Acta" data and Formula 1 race data. Model comparison shows our model is a better fit to the data than Plackett-Luce mixtures, Mallows mixtures, and "bucket order" models and competitive with more complex models fitting general partial orders.
PyVBMC is a Python implementation of the Variational Bayesian Monte Carlo (VBMC) algorithm for posterior and model inference for black-box computational models (Acerbi, 2018, 2020). VBMC is an approximate inference method designed for efficient parameter estimation and model assessment when model evaluations are mildly-to-very expensive (e.g., a second or more) and/or noisy. Specifically, VBMC computes: - a flexible (non-Gaussian) approximate posterior distribution of the model parameters, from which statistics and posterior samples can be easily extracted; - an approximation of the model evidence or marginal likelihood, a metric used for Bayesian model selection. PyVBMC can be applied to any computational or statistical model with up to roughly 10-15 continuous parameters, with the only requirement that the user can provide a Python function that computes the target log likelihood of the model, or an approximation thereof (e.g., an estimate of the likelihood obtained via simulation or Monte Carlo methods). PyVBMC is particularly effective when the model takes more than about a second per evaluation, with dramatic speed-ups of 1-2 orders of magnitude when compared to traditional approximate inference methods. Extensive benchmarks on both artificial test problems and a large number of real models from the computational sciences, particularly computational and cognitive neuroscience, show that VBMC generally - and often vastly - outperforms alternative methods for sample-efficient Bayesian inference, and is applicable to both exact and simulator-based models (Acerbi, 2018, 2019, 2020). PyVBMC brings this state-of-the-art inference algorithm to Python, along with an easy-to-use Pythonic interface for running the algorithm and manipulating and visualizing its results.
Since hardware resources are limited, the objective of training deep learning models is typically to maximize accuracy subject to the time and memory constraints of training and inference. We study the impact of model size in this setting, focusing on Transformer models for NLP tasks that are limited by compute: self-supervised pretraining and high-resource machine translation. We first show that even though smaller Transformer models execute faster per iteration, wider and deeper models converge in significantly fewer steps. Moreover, this acceleration in convergence typically outpaces the additional computational overhead of using larger models. Therefore, the most compute-efficient training strategy is to counterintuitively train extremely large models but stop after a small number of iterations. This leads to an apparent trade-off between the training efficiency of large Transformer models and the inference efficiency of small Transformer models. However, we show that large models are more robust to compression techniques such as quantization and pruning than small models. Consequently, one can get the best of both worlds: heavily compressed, large models achieve higher accuracy than lightly compressed, small models.