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A finite element solution of an ion channel dielectric continuum model such as Poisson-Boltzmann equation (PBE) and a system of Poisson-Nernst-Planck equations (PNP) requires tetrahedral meshes for an ion channel protein region, a membrane region, and an ionic solvent region as well as an interface fitted irregular tetrahedral mesh of a simulation box domain. However, generating these meshes is very difficult and highly technical due to the related three regions having very complex geometrical shapes. Currently, an ion channel mesh generation software package developed in Lu's research group is one available in the public domain. To significantly improve its mesh quality and computer performance, in this paper, new numerical schemes for generating membrane and solvent meshes are presented and implemented in Python, resulting in a new ion channel mesh generation software package. Numerical results are then reported to demonstrate the efficiency of the new numerical schemes and the quality of meshes generated by the new package for ion channel proteins with ion channel pores having different geometric complexities.

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Given its status as a classic problem and its importance to both theoreticians and practitioners, edit distance provides an excellent lens through which to understand how the theoretical analysis of algorithms impacts practical implementations. From an applied perspective, the goals of theoretical analysis are to predict the empirical performance of an algorithm and to serve as a yardstick to design novel algorithms that perform well in practice. In this paper, we systematically survey the types of theoretical analysis techniques that have been applied to edit distance and evaluate the extent to which each one has achieved these two goals. These techniques include traditional worst-case analysis, worst-case analysis parametrized by edit distance or entropy or compressibility, average-case analysis, semi-random models, and advice-based models. We find that the track record is mixed. On one hand, two algorithms widely used in practice have been born out of theoretical analysis and their empirical performance is captured well by theoretical predictions. On the other hand, all the algorithms developed using theoretical analysis as a yardstick since then have not had any practical relevance. We conclude by discussing the remaining open problems and how they can be tackled.

We study the stochastic $p$-Laplace system in a bounded domain. We propose two new space-time discretizations based on the approximation of time-averaged values. We establish linear convergence in space and $1/2$ convergence in time. Additionally, we provide a sampling algorithm to construct the necessary random input in an efficient way. The theoretical error analysis is complemented by numerical experiments.

We consider statistical models arising from the common set of solutions to a sparse polynomial system with general coefficients. The maximum likelihood degree counts the number of critical points of the likelihood function restricted to the model. We prove the maximum likelihood degree of a sparse polynomial system is determined by its Newton polytopes and equals the mixed volume of a related Lagrange system of equations.

We extend the Deep Galerkin Method (DGM) introduced in Sirignano and Spiliopoulos (2018)} to solve a number of partial differential equations (PDEs) that arise in the context of optimal stochastic control and mean field games. First, we consider PDEs where the function is constrained to be positive and integrate to unity, as is the case with Fokker-Planck equations. Our approach involves reparameterizing the solution as the exponential of a neural network appropriately normalized to ensure both requirements are satisfied. This then gives rise to nonlinear a partial integro-differential equation (PIDE) where the integral appearing in the equation is handled by a novel application of importance sampling. Secondly, we tackle a number of Hamilton-Jacobi-Bellman (HJB) equations that appear in stochastic optimal control problems. The key contribution is that these equations are approached in their unsimplified primal form which includes an optimization problem as part of the equation. We extend the DGM algorithm to solve for the value function and the optimal control \simultaneously by characterizing both as deep neural networks. Training the networks is performed by taking alternating stochastic gradient descent steps for the two functions, a technique inspired by the policy improvement algorithms (PIA).

Linear mixed models (LMMs) are instrumental for regression analysis with structured dependence, such as grouped, clustered, or multilevel data. However, selection among the covariates--while accounting for this structured dependence--remains a challenge. We introduce a Bayesian decision analysis for subset selection with LMMs. Using a Mahalanobis loss function that incorporates the structured dependence, we derive optimal linear coefficients for (i) any given subset of variables and (ii) all subsets of variables that satisfy a cardinality constraint. Crucially, these estimates inherit shrinkage or regularization and uncertainty quantification from the underlying Bayesian model, and apply for any well-specified Bayesian LMM. More broadly, our decision analysis strategy deemphasizes the role of a single "best" subset, which is often unstable and limited in its information content, and instead favors a collection of near-optimal subsets. This collection is summarized by key member subsets and variable-specific importance metrics. Customized subset search and out-of-sample approximation algorithms are provided for more scalable computing. These tools are applied to simulated data and a longitudinal physical activity dataset, and demonstrate excellent prediction, estimation, and selection ability.

We provide a decision theoretic analysis of bandit experiments. The setting corresponds to a dynamic programming problem, but solving this directly is typically infeasible. Working within the framework of diffusion asymptotics, we define suitable notions of asymptotic Bayes and minimax risk for bandit experiments. For normally distributed rewards, the minimal Bayes risk can be characterized as the solution to a nonlinear second-order partial differential equation (PDE). Using a limit of experiments approach, we show that this PDE characterization also holds asymptotically under both parametric and non-parametric distribution of the rewards. The approach further describes the state variables it is asymptotically sufficient to restrict attention to, and therefore suggests a practical strategy for dimension reduction. The upshot is that we can approximate the dynamic programming problem defining the bandit experiment with a PDE which can be efficiently solved using sparse matrix routines. We derive the optimal Bayes and minimax policies from the numerical solutions to these equations. The proposed policies substantially dominate existing methods such as Thompson sampling. The framework also allows for substantial generalizations to the bandit problem such as time discounting and pure exploration motives.

We consider M-estimation problems, where the target value is determined using a minimizer of an expected functional of a Levy process. With discrete observations from the Levy process, we can produce a "quasi-path" by shuffling increments of the Levy process, we call it a quasi-process. Under a suitable sampling scheme, a quasi-process can converge weakly to the true process according to the properties of the stationary and independent increments. Using this resampling technique, we can estimate objective functionals similar to those estimated using the Monte Carlo simulations, and it is available as a contrast function. The M-estimator based on these quasi-processes can be consistent and asymptotically normal.

Recently, numerous studies have demonstrated the presence of bias in machine learning powered decision-making systems. Although most definitions of algorithmic bias have solid mathematical foundations, the corresponding bias detection techniques often lack statistical rigor, especially for non-iid data. We fill this gap in the literature by presenting a rigorous non-parametric testing procedure for bias according to Predictive Rate Parity, a commonly considered notion of algorithmic bias. We adapt traditional asymptotic results for non-parametric estimators to test for bias in the presence of dependence commonly seen in user-level data generated by technology industry applications and illustrate how these approaches can be leveraged for mitigation. We further propose modifications of this methodology to address bias measured through marginal outcome disparities in classification settings and extend notions of predictive rate parity to multi-objective models. Experimental results on real data show the efficacy of the proposed detection and mitigation methods.

Imitation learning is a promising approach to help robots acquire dexterous manipulation capabilities without the need for a carefully-designed reward or a significant computational effort. However, existing imitation learning approaches require sophisticated data collection infrastructure and struggle to generalize beyond the training distribution. One way to address this limitation is to gather additional data that better represents the full operating conditions. In this work, we investigate characteristics of such additional demonstrations and their impact on performance. Specifically, we study the effects of corrective and randomly-sampled additional demonstrations on learning a policy that guides a five-fingered robot hand through a pick-and-place task. Our results suggest that corrective demonstrations considerably outperform randomly-sampled demonstrations, when the proportion of additional demonstrations sampled from the full task distribution is larger than the number of original demonstrations sampled from a restrictive training distribution. Conversely, when the number of original demonstrations are higher than that of additional demonstrations, we find no significant differences between corrective and randomly-sampled additional demonstrations. These results provide insights into the inherent trade-off between the effort required to collect corrective demonstrations and their relative benefits over randomly-sampled demonstrations. Additionally, we show that inexpensive vision-based sensors, such as LeapMotion, can be used to dramatically reduce the cost of providing demonstrations for dexterous manipulation tasks. Our code is available at //github.com/GT-STAR-Lab/corrective-demos-dexterous-manipulation.

One of the most important problems in system identification and statistics is how to estimate the unknown parameters of a given model. Optimization methods and specialized procedures, such as Empirical Minimization (EM) can be used in case the likelihood function can be computed. For situations where one can only simulate from a parametric model, but the likelihood is difficult or impossible to evaluate, a technique known as the Two-Stage (TS) Approach can be applied to obtain reliable parametric estimates. Unfortunately, there is currently a lack of theoretical justification for TS. In this paper, we propose a statistical decision-theoretical derivation of TS, which leads to Bayesian and Minimax estimators. We also show how to apply the TS approach on models for independent and identically distributed samples, by computing quantiles of the data as a first step, and using a linear function as the second stage. The proposed method is illustrated via numerical simulations.

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