A central challenge in neuroscience is understanding how neural system implements computation through its dynamics. We propose a nonlinear time series model aimed at characterizing interpretable dynamics from neural trajectories. Our model assumes low-dimensional continuous dynamics in a finite volume. It incorporates a prior assumption about globally contractional dynamics to avoid overly enthusiastic extrapolation outside of the support of observed trajectories. We show that our model can recover qualitative features of the phase portrait such as attractors, slow points, and bifurcations, while also producing reliable longterm future predictions in a variety of dynamical models and in real neural data.

We show that there are no spurious local minima in the non-convex factorized parametrization of low-rank matrix recovery from incoherent linear measurements. With noisy measurements we show all local minima are very close to a global optimum. Together with a curvature bound at saddle points, this yields a polynomial time global convergence guarantee for stochastic gradient descent from random initialization.

Estimating optimal phylogenetic trees or hierarchical clustering trees from metric data is an important problem in evolutionary biology and data analysis. Intuitively, the goodness-of-fit of a metric space to a tree depends on its inherent treeness, as well as other metric properties such as intrinsic dimension. Existing algorithms for embedding metric spaces into tree metrics provide distortion bounds depending on cardinality. Because cardinality is a simple property of any set, we argue that such bounds do not fully capture the rich structure endowed by the metric. We consider an embedding of a metric space into a tree proposed by Gromov. By proving a stability result, we obtain an improved additive distortion bound depending only on the hyperbolicity and doubling dimension of the metric. We observe that Gromov's method is dual to the well-known single linkage hierarchical clustering (SLHC) method. By means of this duality, we are able to transport our results to the setting of SLHC, where such additive distortion bounds were previously unknown.

Controlled interventions provide the most direct source of information for learning causal effects. In particular, a dose-response curve can be learned by varying the treatment level and observing the corresponding outcomes. However, interventions can be expensive and time-consuming. Observational data, where the treatment is not controlled by a known mechanism, is sometimes available. Under some strong assumptions, observational data allows for the estimation of dose-response curves. Estimating such curves nonparametrically is hard: sample sizes for controlled interventions may be small, while in the observational case a large number of measured confounders may need to be marginalized. In this paper, we introduce a hierarchical Gaussian process prior that constructs a distribution over the doseresponse curve by learning from observational data, and reshapes the distribution with a nonparametric affine transform learned from controlled interventions. This function composition from different sources is shown to speed-up learning, which we demonstrate with a thorough sensitivity analysis and an application to modeling the effect of therapy on cognitive skills of premature infants.

Recently proposed adversarial classification methods have shown promising results for cost sensitive and multivariate losses. In contrast with empirical risk minimization (ERM) methods, which use convex surrogate losses to approximate the desired non-convex target loss function, adversarial methods minimize non-convex losses by treating the properties of the training data as being uncertain and worst case within a minimax game. Despite this difference in formulation, we recast adversarial classification under zero-one loss as an ERM method with a novel prescribed loss function. We demonstrate a number of theoretical and practical advantages over the very closely related hinge loss ERM methods. This establishes adversarial classification under the zero-one loss as a method that fills the long standing gap in multiclass hinge loss classification, simultaneously guaranteeing Fisher consistency and universal consistency, while also providing dual parameter sparsity and high accuracy predictions in practice.

Sobolev quantities (norms, inner products, and distances) of probability density functions are important in the theory of nonparametric statistics, but have rarely been used in practice, due to a lack of practical estimators.

Stochastic gradient MCMC (SG-MCMC) has played an important role in largescale Bayesian learning, with well-developed theoretical convergence properties. In such applications of SG-MCMC, it is becoming increasingly popular to employ distributed systems, where stochastic gradients are computed based on some outdated parameters, yielding what are termed stale gradients. While stale gradients could be directly used in SG-MCMC, their impact on convergence properties has not been well studied. In this paper we develop theory to show that while the bias and MSE of an SG-MCMC algorithm depend on the staleness of stochastic gradients, its estimation variance (relative to the expected estimate, based on a prescribed number of samples) is independent of it. In a simple Bayesian distributed system with SG-MCMC, where stale gradients are computed asynchronously by a set of workers, our theory indicates a linear speedup on the decrease of estimation variance w.r.t. the number of workers.

A cluster tree provides a highly-interpretable summary of a density function by representing the hierarchy of its high-density clusters. It is estimated using the empirical tree, which is the cluster tree constructed from a density estimator. This paper addresses the basic question of quantifying our uncertainty by assessing the statistical significance of topological features of an empirical cluster tree. We first study a variety of metrics that can be used to compare different trees, analyze their properties and assess their suitability for inference. We then propose methods to construct and summarize confidence sets for the unknown true cluster tree. We introduce a partial ordering on cluster trees which we use to prune some of the statistically insignificant features of the empirical tree, yielding interpretable and parsimonious cluster trees. Finally, we illustrate the proposed methods on a variety of synthetic examples and furthermore demonstrate their utility in the analysis of a Graft-versus-Host Disease (GvHD) data set.

Bayesian optimization is a prominent method for optimizing expensive-to-evaluate black-box functions that is widely applied to tuning the hyperparameters of machine learning algorithms. Despite its successes, the prototypical Bayesian optimization approach - using Gaussian process models - does not scale well to either many hyperparameters or many function evaluations. Attacking this lack of scalability and flexibility is thus one of the key challenges of the field. We present a general approach for using flexible parametric models (neural networks) for Bayesian optimization, staying as close to a truly Bayesian treatment as possible. We obtain scalability through stochastic gradient Hamiltonian Monte Carlo, whose robustness we improve via a scale adaptation.

We consider the problem of community detection or clustering in the labeled Stochastic Block Model (LSBM) with a finite number K of clusters of sizes linearly growing with the global population of items n. Every pair of items is labeled independently at random, and label l appears with probability p(i, j, l) between two items in clusters indexed by i and j, respectively. The objective is to reconstruct the clusters from the observation of these random labels. Clustering under the SBM and their extensions has attracted much attention recently. Most existing work aimed at characterizing the set of parameters such that it is possible to infer clusters either positively correlated with the true clusters, or with a vanishing proportion of misclassified items, or exactly matching the true clusters. We find the set of parameters such that there exists a clustering algorithm with at most s misclassified items in average under the general LSBM and for any s = o(n), which solves one open problem raised in [2]. We further develop an algorithm, based on simple spectral methods, that achieves this fundamental performance limit within O(npolylog(n)) computations and without the a-priori knowledge of the model parameters.