Precision medicine aims for personalized prognosis and therapeutics by utilizing recent genome-scale high-throughput profiling techniques, including next-generation sequencing (NGS). However, translating NGS data faces several challenges. First, NGS count data are often overdispersed, requiring appropriate modeling. Second, compared to the number of involved molecules and system complexity, the number of available samples for studying complex disease, such as cancer, is often limited, especially considering disease heterogeneity. The key question is whether we may integrate available data from all different sources or domains to achieve reproducible disease prognosis based on NGS count data. In this paper, we develop a Bayesian Multi-Domain Learning (BMDL) model that derives domain-dependent latent representations of overdispersed count data based on hierarchical negative binomial factorization for accurate cancer subtyping even if the number of samples for a specific cancer type is small. Experimental results from both our simulated and NGS datasets from The Cancer Genome Atlas (TCGA) demonstrate the promising potential of BMDL for effective multi-domain learning without ``negative transfer'' effects often seen in existing multi-task learning and transfer learning methods.

This paper introduces a model-based reinforcement learning (MBRL) framework that incorporates the underlying decision problem in learning the transition model of the environment. This is in contrast with conventional approaches to MBRL that learn the model of the environment, for example by finding the maximum likelihood estimate, without taking into account the decision problem. Value-Aware Model Learning (VAML) framework argues that this might not be a good idea, especially if the true model of the environment does not belong to the model class from which we are estimating the model. The original VAML framework, however, may result in an optimization problem that is difficult to solve. This paper introduces a new MBRL class of algorithms, called Iterative VAML, that benefits from the structure of how the planning is performed (i.e., through approximate value iteration) to devise a simpler optimization problem. The paper theoretically analyzes Iterative VAML and provides finite sample error upper bound guarantee for it.

We present a new approach to the problems of evaluating and learning personalized decision policies from observational data of past contexts, decisions, and outcomes. Only the outcome of the enacted decision is available and the historical policy is unknown. These problems arise in personalized medicine using electronic health records and in internet advertising. Existing approaches use inverse propensity weighting (or, doubly robust versions) to make historical outcome (or, residual) data look like it were generated by a new policy being evaluated or learned. But this relies on a plug-in approach that rejects data points with a decision that disagrees with the new policy, leading to high variance estimates and ineffective learning. We propose a new, balance-based approach that too makes the data look like the new policy but does so directly by finding weights that optimize for balance between the weighted data and the target policy in the given, finite sample, which is equivalent to minimizing worst-case or posterior conditional mean square error. Our policy learner proceeds as a two-level optimization problem over policies and weights. We demonstrate that this approach markedly outperforms existing ones both in evaluation and learning, which is unsurprising given the wider support of balance-based weights. We establish extensive theoretical consistency guarantees and regret bounds that support this empirical success.

Stein variational gradient descent (SVGD) is a non-parametric inference algorithm that evolves a set of particles to fit a given distribution of interest. We analyze the non-asymptotic properties of SVGD, showing that there exists a set of functions, which we call the Stein matching set, whose expectations are exactly estimated by any set of particles that satisfies the fixed point equation of SVGD. This set is the image of Stein operator applied on the feature maps of the positive definite kernel used in SVGD. Our results provide a theoretical framework for analyzing the properties of SVGD with different kernels, shedding insight into optimal kernel choice. In particular, we show that SVGD with linear kernels yields exact estimation of means and variances on Gaussian distributions, while random Fourier features enable probabilistic bounds for distributional approximation. Our results offer a refreshing view of the classical inference problem as fitting Stein’s identity or solving the Stein equation, which may motivate more efficient algorithms.

We present a novel nonnegative tensor decomposition method, called Legendre decomposition, which factorizes an input tensor into a multiplicative combination of parameters. Thanks to the well-developed theory of information geometry, the reconstructed tensor is unique and always minimizes the KL divergence from an input tensor. We empirically show that Legendre decomposition can more accurately reconstruct tensors than other nonnegative tensor decomposition methods.

Kleinberg [20] stated three axioms that any clustering procedure should satisfy and showed there is no clustering procedure that simultaneously satisfies all three. One of these, called the consistency axiom, requires that when the data is modified in a helpful way, i.e. if points in the same cluster are made more similar and those in different ones made less similar, the algorithm should output the same clustering. To circumvent this impossibility result, research has focused on considering clustering procedures that have a clustering quality measure (or a cost) and showing that a modification of Kleinberg's axioms that takes cost into account lead to feasible clustering procedures. In this work, we take a different approach, based on the observation that the consistency axiom fails to be satisfied when the "correct" number of clusters changes. We modify this axiom by making use of cost functions to determine the correct number of clusters, and require that consistency holds only if the number of clusters remains unchanged. We show that single linkage satisfies the modified axioms, and if the input is well-clusterable, some popular procedures such as k-means also satisfy the axioms, taking a step towards explaining the success of these objective functions for guiding the design of algorithms. 1 Introduction In a highly influential paper, Kleinberg [20] showed that clustering is impossible in the following sense: there exists no clustering function, i.e. a function that takes a point-set and a pairwise dis-similarity function

We suggest a general oracle-based framework that captures parallel stochastic optimization in different parallelization settings described by a dependency graph, and derive generic lower bounds in terms of this graph. We then use the framework and derive lower bounds to study several specific parallel optimization settings, including delayed updates and parallel processing with intermittent communication. We highlight gaps between lower and upper bounds on the oracle complexity, and cases where the ``natural'' algorithms are not known to be optimal.

The Probably Approximately Correct (PAC) Bayes framework (McAllester, 1999) can incorporate knowledge about the learning algorithm and (data) distribution through the use of distribution-dependent priors, yielding tighter generalization bounds on data-dependent posteriors. Using this flexibility, however, is difficult, especially when the data distribution is presumed to be unknown. We show how an e-differentially private data-dependent prior yields a valid PAC-Bayes bound, and then show how non-private mechanisms for choosing priors can also yield generalization bounds. As an application of this result, we show that a Gaussian prior mean chosen via stochastic gradient Langevin dynamics (SGLD; Welling and Teh, 2011) leads to a valid PAC-Bayes bound given control of the 2-Wasserstein distance to an e-differentially private stationary distribution. We study our datadependent bounds empirically, and show that they can be nonvacuous even when other distribution-dependent bounds are vacuous.

We present a number of novel contributions to the multiple-source adaptation problem. We derive new normalized solutions with strong theoretical guarantees for the cross-entropy loss and other similar losses. We also provide new guarantees that hold in the case where the conditional probabilities for the source domains are distinct. Moreover, we give new algorithms for determining the distribution-weighted combination solution for the cross-entropy loss and other losses. We report the results of a series of experiments with real-world datasets. We find that our algorithm outperforms competing approaches by producing a single robust model that performs well on any target mixture distribution. Altogether, our theory, algorithms, and empirical results provide a full solution for the multiple-source adaptation problem with very practical benefits.

Many probabilistic models of interest in scientific computing and machine learning have expensive, black-box likelihoods that prevent the application of standard techniques for Bayesian inference, such as MCMC, which would require access to the gradient or a large number of likelihood evaluations. We introduce here a novel sample-efficient inference framework, Variational Bayesian Monte Carlo (VBMC). VBMC combines variational inference with Gaussian-process based, active-sampling Bayesian quadrature, using the latter to efficiently approximate the intractable integral in the variational objective. Our method produces both a nonparametric approximation of the posterior distribution and an approximate lower bound of the model evidence, useful for model selection. We demonstrate VBMC both on several synthetic likelihoods and on a neuronal model with data from real neurons. Across all tested problems and dimensions (up to D = 10), VBMC performs consistently well in reconstructing the posterior and the model evidence with a limited budget of likelihood evaluations, unlike other methods that work only in very low dimensions. Our framework shows great promise as a novel tool for posterior and model inference with expensive, black-box likelihoods.