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Bayesian phylogenetic inference is often conducted via local or sequential search over topologies and branch lengths using algorithms such as random-walk Markov chain Monte Carlo (MCMC) or Combinatorial Sequential Monte Carlo (CSMC). However, when MCMC is used for evolutionary parameter learning, convergence requires long runs with inefficient exploration of the state space. We introduce Variational Combinatorial Sequential Monte Carlo (VCSMC), a powerful framework that establishes variational sequential search to learn distributions over intricate combinatorial structures. We then develop nested CSMC, an efficient proposal distribution for CSMC and prove that nested CSMC is an exact approximation to the (intractable) locally optimal proposal. We use nested CSMC to define a second objective, VNCSMC which yields tighter lower bounds than VCSMC. We show that VCSMC and VNCSMC are computationally efficient and explore higher probability spaces than existing methods on a range of tasks.

Inferring parameter distributions of complex industrial systems from noisy time series data requires methods to deal with the uncertainty of the underlying data and the used simulation model. Bayesian inference is well suited for these uncertain inverse problems. Standard methods used to identify uncertain parameters are Markov Chain Monte Carlo (MCMC) methods with explicit evaluation of a likelihood function. However, if the likelihood is very complex, such that its evaluation is computationally expensive, or even unknown in its explicit form, Approximate Bayesian Computation (ABC) methods provide a promising alternative. In this work both methods are first applied to artificially generated data and second on a real world problem, by using data of an electric motor test bench. We show that both methods are able to infer the distribution of varying parameters with a Bayesian hierarchical approach. But the proposed ABC method is computationally much more efficient in order to achieve results with similar accuracy. We suggest to use summary statistics in order to reduce the dimension of the data which significantly increases the efficiency of the algorithm. Further the simulation model is replaced by a Polynomial Chaos Expansion (PCE) surrogate to speed up model evaluations. We proof consistency for the proposed surrogate-based ABC method with summary statistics under mild conditions on the (approximated) forward model.

We develop a mathematical and numerical framework to solve state estimation problems for applications that present variations in the shape of the spatial domain. This situation arises typically in a biomedical context where inverse problems are posed on certain organs or portions of the body which inevitably involve morphological variations. If one wants to provide fast reconstruction methods, the algorithms must take into account the geometric variability. We develop and analyze a method which allows to take this variability into account without needing any a priori knowledge on a parametrization of the geometrical variations. For this, we rely on morphometric techniques involving Multidimensional Scaling, and couple them with reconstruction algorithms that make use of reduced model spaces pre-computed on a database of geometries. We prove the potential of the method on a synthetic test problem inspired from the reconstruction of blood flows and quantities of medical interest with Doppler ultrasound imaging.

Markov chain Monte Carlo (MCMC) algorithms have long been the main workhorses of Bayesian inference. Among them, Hamiltonian Monte Carlo (HMC) has recently become very popular due to its efficiency resulting from effective use of the gradients of the target distribution. In privacy-preserving machine learning, differential privacy (DP) has become the gold standard in ensuring that the privacy of data subjects is not violated. Existing DP MCMC algorithms either use random-walk proposals, or do not use the Metropolis--Hastings (MH) acceptance test to ensure convergence without decreasing their step size to zero. We present a DP variant of HMC using the MH acceptance test that builds on a recently proposed DP MCMC algorithm called the penalty algorithm, and adds noise to the gradient evaluations of HMC. We prove that the resulting algorithm converges to the correct distribution, and is ergodic. We compare DP-HMC with the existing penalty, DP-SGLD and DP-SGNHT algorithms, and find that DP-HMC has better or equal performance than the penalty algorithm, and performs more consistently than DP-SGLD or DP-SGNHT.

Projection-free conditional gradient (CG) methods are the algorithms of choice for constrained optimization setups in which projections are often computationally prohibitive but linear optimization over the constraint set remains computationally feasible. Unlike in projection-based methods, globally accelerated convergence rates are in general unattainable for CG. However, a very recent work on Locally accelerated CG (LaCG) has demonstrated that local acceleration for CG is possible for many settings of interest. The main downside of LaCG is that it requires knowledge of the smoothness and strong convexity parameters of the objective function. We remove this limitation by introducing a novel, Parameter-Free Locally accelerated CG (PF-LaCG) algorithm, for which we provide rigorous convergence guarantees. Our theoretical results are complemented by numerical experiments, which demonstrate local acceleration and showcase the practical improvements of PF-LaCG over non-accelerated algorithms, both in terms of iteration count and wall-clock time.

In studies of maternal exposure to air pollution a children's health outcome is regressed on exposures observed during pregnancy. The distributed lag nonlinear model (DLNM) is a statistical method commonly implemented to estimate an exposure-time-response function when it is postulated the exposure effect is nonlinear. Previous implementations of the DLNM estimate an exposure-time-response surface parameterized with a bivariate basis expansion. However, basis functions such as splines assume smoothness across the entire exposure-time-response surface, which may be unrealistic in settings where the exposure is associated with the outcome only in a specific time window. We propose a framework for estimating the DLNM based on Bayesian additive regression trees. Our method operates using a set of regression trees that each assume piecewise constant relationships across the exposure-time space. In a simulation, we show that our model outperforms spline-based models when the exposure-time surface is not smooth, while both methods perform similarly in settings where the true surface is smooth. Importantly, the proposed approach is lower variance and more precisely identifies critical windows during which exposure is associated with a future health outcome. We apply our method to estimate the association between maternal exposure to PM$_{2.5}$ and birth weight in a Colorado USA birth cohort.

We propose a fast algorithm for the probabilistic solution of boundary value problems (BVPs), which are ordinary differential equations subject to boundary conditions. In contrast to previous work, we introduce a Gauss--Markov prior and tailor it specifically to BVPs, which allows computing a posterior distribution over the solution in linear time, at a quality and cost comparable to that of well-established, non-probabilistic methods. Our model further delivers uncertainty quantification, mesh refinement, and hyperparameter adaptation. We demonstrate how these practical considerations positively impact the efficiency of the scheme. Altogether, this results in a practically usable probabilistic BVP solver that is (in contrast to non-probabilistic algorithms) natively compatible with other parts of the statistical modelling tool-chain.

Despite remarkable success in a variety of applications, it is well-known that deep learning can fail catastrophically when presented with out-of-distribution data. Toward addressing this challenge, we consider the domain generalization problem, wherein predictors are trained using data drawn from a family of related training domains and then evaluated on a distinct and unseen test domain. We show that under a natural model of data generation and a concomitant invariance condition, the domain generalization problem is equivalent to an infinite-dimensional constrained statistical learning problem; this problem forms the basis of our approach, which we call Model-Based Domain Generalization. Due to the inherent challenges in solving constrained optimization problems in deep learning, we exploit nonconvex duality theory to develop unconstrained relaxations of this statistical problem with tight bounds on the duality gap. Based on this theoretical motivation, we propose a novel domain generalization algorithm with convergence guarantees. In our experiments, we report improvements of up to 30 percentage points over state-of-the-art domain generalization baselines on several benchmarks including ColoredMNIST, Camelyon17-WILDS, FMoW-WILDS, and PACS.

This paper proposes a Reinforcement Learning (RL) algorithm to synthesize policies for a Markov Decision Process (MDP), such that a linear time property is satisfied. We convert the property into a Limit Deterministic Buchi Automaton (LDBA), then construct a product MDP between the automaton and the original MDP. A reward function is then assigned to the states of the product automaton, according to accepting conditions of the LDBA. With this reward function, our algorithm synthesizes a policy that satisfies the linear time property: as such, the policy synthesis procedure is "constrained" by the given specification. Additionally, we show that the RL procedure sets up an online value iteration method to calculate the maximum probability of satisfying the given property, at any given state of the MDP - a convergence proof for the procedure is provided. Finally, the performance of the algorithm is evaluated via a set of numerical examples. We observe an improvement of one order of magnitude in the number of iterations required for the synthesis compared to existing approaches.

We develop an approach to risk minimization and stochastic optimization that provides a convex surrogate for variance, allowing near-optimal and computationally efficient trading between approximation and estimation error. Our approach builds off of techniques for distributionally robust optimization and Owen's empirical likelihood, and we provide a number of finite-sample and asymptotic results characterizing the theoretical performance of the estimator. In particular, we show that our procedure comes with certificates of optimality, achieving (in some scenarios) faster rates of convergence than empirical risk minimization by virtue of automatically balancing bias and variance. We give corroborating empirical evidence showing that in practice, the estimator indeed trades between variance and absolute performance on a training sample, improving out-of-sample (test) performance over standard empirical risk minimization for a number of classification problems.