Stochastic epidemic models provide an interpretable probabilistic description of the spread of a disease through a population. Yet, fitting these models when the epidemic process is only partially observed is a notoriously difficult task due to the intractability of the likelihood for many classical models. To remedy this issue, this article introduces a novel data-augmented MCMC algorithm for fast and exact Bayesian inference for the stochastic SIR model given discretely observed infection incidence counts. In a Metropolis-Hastings step, new event times of the latent data are jointly proposed from a surrogate process that closely resembles the SIR, and from which we can efficiently generate epidemics compatible with the observed data. The proposed DA-MCMC algorithm is fast and, since the latent data are generated from a faithful approximation of the target model, a large portion thereof can be updated per iteration without prohibitively lowering the acceptance rate. We find that the method explores the high-dimensional latent space efficiently and scales to outbreaks with hundreds of thousands of individuals, and we show that the Markov chain underlying the algorithm is uniformly ergodic. We validate its performance via thorough simulation experiments and a case study on the 2013-2015 Ebola outbreak in Western Africa.
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Although robust learning and local differential privacy are both widely studied fields of research, combining the two settings is just starting to be explored. We consider the problem of estimating a discrete distribution in total variation from $n$ contaminated data batches under a local differential privacy constraint. A fraction $1-\epsilon$ of the batches contain $k$ i.i.d. samples drawn from a discrete distribution $p$ over $d$ elements. To protect the users' privacy, each of the samples is privatized using an $\alpha$-locally differentially private mechanism. The remaining $\epsilon n $ batches are an adversarial contamination. The minimax rate of estimation under contamination alone, with no privacy, is known to be $\epsilon/\sqrt{k}+\sqrt{d/kn}$, up to a $\sqrt{\log(1/\epsilon)}$ factor. Under the privacy constraint alone, the minimax rate of estimation is $\sqrt{d^2/\alpha^2 kn}$. We show that combining the two constraints leads to a minimax estimation rate of $\epsilon\sqrt{d/\alpha^2 k}+\sqrt{d^2/\alpha^2 kn}$ up to a $\sqrt{\log(1/\epsilon)}$ factor, larger than the sum of the two separate rates. We provide a polynomial-time algorithm achieving this bound, as well as a matching information theoretic lower bound.
The variational autoencoder (VAE) is a popular deep latent variable model used to analyse high-dimensional datasets by learning a low-dimensional latent representation of the data. It simultaneously learns a generative model and an inference network to perform approximate posterior inference. Recently proposed extensions to VAEs that can handle temporal and longitudinal data have applications in healthcare, behavioural modelling, and predictive maintenance. However, these extensions do not account for heterogeneous data (i.e., data comprising of continuous and discrete attributes), which is common in many real-life applications. In this work, we propose the heterogeneous longitudinal VAE (HL-VAE) that extends the existing temporal and longitudinal VAEs to heterogeneous data. HL-VAE provides efficient inference for high-dimensional datasets and includes likelihood models for continuous, count, categorical, and ordinal data while accounting for missing observations. We demonstrate our model's efficacy through simulated as well as clinical datasets, and show that our proposed model achieves competitive performance in missing value imputation and predictive accuracy.
Stochastic partial differential equations (SPDEs) are the mathematical tool of choice for modelling spatiotemporal PDE-dynamics under the influence of randomness. Based on the notion of mild solution of an SPDE, we introduce a novel neural architecture to learn solution operators of PDEs with (possibly stochastic) forcing from partially observed data. The proposed Neural SPDE model provides an extension to two popular classes of physics-inspired architectures. On the one hand, it extends Neural CDEs and variants -- continuous-time analogues of RNNs -- in that it is capable of processing incoming sequential information arriving irregularly in time and observed at arbitrary spatial resolutions. On the other hand, it extends Neural Operators -- generalizations of neural networks to model mappings between spaces of functions -- in that it can parameterize solution operators of SPDEs depending simultaneously on the initial condition and a realization of the driving noise. By performing operations in the spectral domain, we show how a Neural SPDE can be evaluated in two ways, either by calling an ODE solver (emulating a spectral Galerkin scheme), or by solving a fixed point problem. Experiments on various semilinear SPDEs, including the stochastic Navier-Stokes equations, demonstrate how the Neural SPDE model is capable of learning complex spatiotemporal dynamics in a resolution-invariant way, with better accuracy and lighter training data requirements compared to alternative models, and up to 3 orders of magnitude faster than traditional solvers.
The idea of approximating the Shapley value of an n-person game by Monte Carlo simulation was first suggested by Mann and Shapley (1960) and they also introduced four different heuristical methods to reduce the estimation error. Since 1960, several statistical methods have been developed to reduce the standard deviation of the estimate. In this paper, we develop an algorithm that uses a pair of negatively correlated samples to reduce the variance of the estimate. Although the observations generated are not independent, the sample is ergodic (obeys the strong law of large numbers), hence the name "ergodic sampling". Unlike Shapley and Mann, we do not use heuristics, the algorithm uses a small sample to learn the best ergodic transformation for a given game. We illustrate the algorithm on eight games with different characteristics to test the performance and understand how the proposed algorithm works. The experiments show that this method has at least as low variance as an independent sample, and in five test games, it significantly improves the quality of the estimation, up to 75 percent.
The problem of continuous inverse optimal control (over finite time horizon) is to learn the unknown cost function over the sequence of continuous control variables from expert demonstrations. In this article, we study this fundamental problem in the framework of energy-based model, where the observed expert trajectories are assumed to be random samples from a probability density function defined as the exponential of the negative cost function up to a normalizing constant. The parameters of the cost function are learned by maximum likelihood via an "analysis by synthesis" scheme, which iterates (1) synthesis step: sample the synthesized trajectories from the current probability density using the Langevin dynamics via back-propagation through time, and (2) analysis step: update the model parameters based on the statistical difference between the synthesized trajectories and the observed trajectories. Given the fact that an efficient optimization algorithm is usually available for an optimal control problem, we also consider a convenient approximation of the above learning method, where we replace the sampling in the synthesis step by optimization. Moreover, to make the sampling or optimization more efficient, we propose to train the energy-based model simultaneously with a top-down trajectory generator via cooperative learning, where the trajectory generator is used to fast initialize the synthesis step of the energy-based model. We demonstrate the proposed methods on autonomous driving tasks, and show that they can learn suitable cost functions for optimal control.
Many recent state-of-the-art (SOTA) optical flow models use finite-step recurrent update operations to emulate traditional algorithms by encouraging iterative refinements toward a stable flow estimation. However, these RNNs impose large computation and memory overheads, and are not directly trained to model such stable estimation. They can converge poorly and thereby suffer from performance degradation. To combat these drawbacks, we propose deep equilibrium (DEQ) flow estimators, an approach that directly solves for the flow as the infinite-level fixed point of an implicit layer (using any black-box solver), and differentiates through this fixed point analytically (thus requiring $O(1)$ training memory). This implicit-depth approach is not predicated on any specific model, and thus can be applied to a wide range of SOTA flow estimation model designs. The use of these DEQ flow estimators allows us to compute the flow faster using, e.g., fixed-point reuse and inexact gradients, consumes $4\sim6\times$ times less training memory than the recurrent counterpart, and achieves better results with the same computation budget. In addition, we propose a novel, sparse fixed-point correction scheme to stabilize our DEQ flow estimators, which addresses a longstanding challenge for DEQ models in general. We test our approach in various realistic settings and show that it improves SOTA methods on Sintel and KITTI datasets with substantially better computational and memory efficiency.
SVD (singular value decomposition) is one of the basic tools of machine learning, allowing to optimize basis for a given matrix. However, sometimes we have a set of matrices $\{A_k\}_k$ instead, and would like to optimize a single common basis for them: find orthogonal matrices $U$, $V$, such that $\{U^T A_k V\}$ set of matrices is somehow simpler. For example DCT-II is orthonormal basis of functions commonly used in image/video compression - as discussed here, this kind of basis can be quickly automatically optimized for a given dataset. While also discussed gradient descent optimization might be computationally costly, there is proposed CSVD (common SVD): fast general approach based on SVD. Specifically, we choose $U$ as built of eigenvectors of $\sum_i (w_k)^q (A_k A_k^T)^p$ and $V$ of $\sum_k (w_k)^q (A_k^T A_k)^p$, where $w_k$ are their weights, $p,q>0$ are some chosen powers e.g. 1/2, optionally with normalization e.g. $A \to A - rc^T$ where $r_i=\sum_j A_{ij}, c_j =\sum_i A_{ij}$.
Computing a dense subgraph is a fundamental problem in graph mining, with a diverse set of applications ranging from electronic commerce to community detection in social networks. In many of these applications, the underlying context is better modelled as a weighted hypergraph that keeps evolving with time. This motivates the problem of maintaining the densest subhypergraph of a weighted hypergraph in a {\em dynamic setting}, where the input keeps changing via a sequence of updates (hyperedge insertions/deletions). Previously, the only known algorithm for this problem was due to Hu et al. [HWC17]. This algorithm worked only on unweighted hypergraphs, and had an approximation ratio of $(1+\epsilon)r^2$ and an update time of $O(\text{poly} (r, \log n))$, where $r$ denotes the maximum rank of the input across all the updates. We obtain a new algorithm for this problem, which works even when the input hypergraph is weighted. Our algorithm has a significantly improved (near-optimal) approximation ratio of $(1+\epsilon)$ that is independent of $r$, and a similar update time of $O(\text{poly} (r, \log n))$. It is the first $(1+\epsilon)$-approximation algorithm even for the special case of weighted simple graphs. To complement our theoretical analysis, we perform experiments with our dynamic algorithm on large-scale, real-world data-sets. Our algorithm significantly outperforms the state of the art [HWC17] both in terms of accuracy and efficiency.
Consider the problem of training robustly capable agents. One approach is to generate a diverse collection of agent polices. Training can then be viewed as a quality diversity (QD) optimization problem, where we search for a collection of performant policies that are diverse with respect to quantified behavior. Recent work shows that differentiable quality diversity (DQD) algorithms greatly accelerate QD optimization when exact gradients are available. However, agent policies typically assume that the environment is not differentiable. To apply DQD algorithms to training agent policies, we must approximate gradients for performance and behavior. We propose two variants of the current state-of-the-art DQD algorithm that compute gradients via approximation methods common in reinforcement learning (RL). We evaluate our approach on four simulated locomotion tasks. One variant achieves results comparable to the current state-of-the-art in combining QD and RL, while the other performs comparably in two locomotion tasks. These results provide insight into the limitations of current DQD algorithms in domains where gradients must be approximated. Source code is available at //github.com/icaros-usc/dqd-rl
Models for dependent data are distinguished by their targets of inference. Marginal models are useful when interest lies in quantifying associations averaged across a population of clusters. When the functional form of a covariate-outcome association is unknown, flexible regression methods are needed to allow for potentially non-linear relationships. We propose a novel marginal additive model (MAM) for modelling cluster-correlated data with non-linear population-averaged associations. The proposed MAM is a unified framework for estimation and uncertainty quantification of a marginal mean model, combined with inference for between-cluster variability and cluster-specific prediction. We propose a fitting algorithm that enables efficient computation of standard errors and corrects for estimation of penalty terms. We demonstrate the proposed methods in simulations and in application to (i) a longitudinal study of beaver foraging behaviour, and (ii) a spatial analysis of Loaloa infection in West Africa. R code for implementing the proposed methodology is available at //github.com/awstringer1/mam.
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