Motivation: How do we integratively analyze large-scale multi-platform genomic data that are high dimensional and sparse? Furthermore, how can we incorporate prior knowledge, such as the association between genes, in the analysis systematically? Method: To solve this problem, we propose a Scalable Network Constrained Tucker decomposition method we call SNeCT. SNeCT adopts parallel stochastic gradient descent approach on the proposed parallelizable network constrained optimization function. SNeCT decomposition is applied to tensor constructed from large scale multi-platform multi-cohort cancer data, PanCan12, constrained on a network built from PathwayCommons database. Results: The decomposed factor matrices are applied to stratify cancers, to search for top-k similar patients, and to illustrate how the matrices can be used for personalized interpretation. In the stratification test, combined twelve-cohort data is clustered to form thirteen subclasses. The thirteen subclasses have a high correlation to tissue of origin in addition to other interesting observations, such as clear separation of OV cancers to two groups, and high clinical correlation within subclusters formed in cohorts BRCA and UCEC. In the top-k search, a new patient's genomic profile is generated and searched against existing patients based on the factor matrices. The similarity of the top-k patient to the query is high for 23 clinical features, including estrogen/progesterone receptor statuses of BRCA patients with average precision value ranges from 0.72 to 0.86 and from 0.68 to 0.86, respectively. We also provide an illustration of how the factor matrices can be used for interpretable personalized analysis of each patient.

In recent years, significant progress has been made in solving challenging problems across various domains using deep reinforcement learning (RL). Reproducing existing work and accurately judging the improvements offered by novel methods is vital to sustaining this progress. Unfortunately, reproducing results for state-of-the-art deep RL methods is seldom straightforward. In particular, non-determinism in standard benchmark environments, combined with variance intrinsic to the methods, can make reported results tough to interpret. Without significance metrics and tighter standardization of experimental reporting, it is difficult to determine whether improvements over the prior state-of-the-art are meaningful. In this paper, we investigate challenges posed by reproducibility, proper experimental techniques, and reporting procedures. We illustrate the variability in reported metrics and results when comparing against common baselines and suggest guidelines to make future results in deep RL more reproducible. We aim to spur discussion about how to ensure continued progress in the field by minimizing wasted effort stemming from results that are non-reproducible and easily misinterpreted.

Many optimization algorithms converge to stationary points. When the underlying problem is nonconvex, they may get trapped at local minimizers and occasionally stagnate near saddle points. We propose the Run-and-Inspect Method, which adds an "inspect" phase to existing algorithms that helps escape from non-global stationary points. The inspection samples a set of points in a radius $R$ around the current point. When a sample point yields a sufficient decrease in the objective, we move there and resume an existing algorithm. If no sufficient decrease is found, the current point is called an approximate $R$-local minimizer. We show that an $R$-local minimizer is globally optimal, up to a specific error depending on $R$, if the objective function can be implicitly decomposed into a smooth convex function plus a restricted function that is possibly nonconvex, nonsmooth. For high-dimensional problems, we introduce blockwise inspections to overcome the curse of dimensionality while still maintaining optimality bounds up to a factor equal to the number of blocks. Our method performs well on a set of artificial and realistic nonconvex problems by coupling with gradient descent, coordinate descent, EM, and prox-linear algorithms.

Natural gradient descent is an optimization method traditionally motivated from the perspective of information geometry, and works well for many applications as an alternative to stochastic gradient descent. In this paper we critically analyze this method and its properties, and show how it can be viewed as a type of approximate 2nd-order optimization method, where the Fisher information matrix can be viewed as an approximation of the Hessian. This perspective turns out to have significant implications for how to design a practical and robust version of the method. Additionally, we make the following contributions to the understanding of natural gradient and 2nd-order methods: a thorough analysis of the convergence speed of stochastic natural gradient descent (and more general stochastic 2nd-order methods) as applied to convex quadratics, a critical examination of the oft-used "empirical" approximation of the Fisher matrix, and an analysis of the (approximate) parameterization invariance property possessed by natural gradient methods, which we show still holds for certain choices of the curvature matrix other than the Fisher, but notably not the Hessian.

By lifting the ReLU function into a higher dimensional space, we develop a smooth multi-convex formulation for training feed-forward deep neural networks (DNNs). This allows us to develop a block coordinate descent (BCD) training algorithm consisting of a sequence of numerically well-behaved convex optimizations. Using ideas from proximal point methods in convex analysis, we prove that this BCD algorithm will converge globally to a stationary point with R-linear convergence rate of order one. In experiments with the MNIST database, DNNs trained with this BCD algorithm consistently yielded better test-set error rates than identical DNN architectures trained via all the stochastic gradient descent (SGD) variants in the Caffe toolbox.

We present a novel method for frequentist statistical inference in $M$-estimation problems, based on stochastic gradient descent (SGD) with a fixed step size: we demonstrate that the average of such SGD sequences can be used for statistical inference, after proper scaling. An intuitive analysis using the Ornstein-Uhlenbeck process suggests that such averages are asymptotically normal. From a practical perspective, our SGD-based inference procedure is a first order method, and is well-suited for large scale problems. To show its merits, we apply it to both synthetic and real datasets, and demonstrate that its accuracy is comparable to classical statistical methods, while requiring potentially far less computation.

In this paper, we consider the problem of machine teaching, the inverse problem of machine learning. Different from traditional machine teaching which views the learners as batch algorithms, we study a new paradigm where the learner uses an iterative algorithm and a teacher can feed examples sequentially and intelligently based on the current performance of the learner. We show that the teaching complexity in the iterative case is very different from that in the batch case. Instead of constructing a minimal training set for learners, our iterative machine teaching focuses on achieving fast convergence in the learner model. Depending on the level of information the teacher has from the learner model, we design teaching algorithms which can provably reduce the number of teaching examples and achieve faster convergence than learning without teachers.

Stochastic optimization algorithms with variance reduction have proven successful for minimizing large finite sums of functions. Unfortunately, these techniques are unable to deal with stochastic perturbations of input data, induced for example by data augmentation. In such cases, the objective is no longer a finite sum, and the main candidate for optimization is the stochastic gradient descent method (SGD). In this paper, we introduce a variance reduction approach for these settings when the objective is composite and strongly convex. The convergence rate outperforms SGD with a typically much smaller constant factor, which depends on the variance of gradient estimates only due to perturbations on a single example.

In this paper, we consider a class of finite-sum convex optimization problems defined over a distributed multiagent network with $m$ agents connected to a central server. In particular, the objective function consists of the average of $m$ ($\ge 1$) smooth components associated with each network agent together with a strongly convex term. Our major contribution is to develop a new randomized incremental gradient algorithm, namely random gradient extrapolation method (RGEM), which does not require any exact gradient evaluation even for the initial point, but can achieve the optimal ${\cal O}(\log(1/\epsilon))$ complexity bound in terms of the total number of gradient evaluations of component functions to solve the finite-sum problems. Furthermore, we demonstrate that for stochastic finite-sum optimization problems, RGEM maintains the optimal ${\cal O}(1/\epsilon)$ complexity (up to a certain logarithmic factor) in terms of the number of stochastic gradient computations, but attains an ${\cal O}(\log(1/\epsilon))$ complexity in terms of communication rounds (each round involves only one agent). It is worth noting that the former bound is independent of the number of agents $m$, while the latter one only linearly depends on $m$ or even $\sqrt m$ for ill-conditioned problems. To the best of our knowledge, this is the first time that these complexity bounds have been obtained for distributed and stochastic optimization problems. Moreover, our algorithms were developed based on a novel dual perspective of Nesterov's accelerated gradient method.

We present the Variational Adaptive Newton (VAN) method which is a black-box optimization method especially suitable for explorative-learning tasks such as active learning and reinforcement learning. Similar to Bayesian methods, VAN estimates a distribution that can be used for exploration, but requires computations that are similar to continuous optimization methods. Our theoretical contribution reveals that VAN is a second-order method that unifies existing methods in distinct fields of continuous optimization, variational inference, and evolution strategies. Our experimental results show that VAN performs well on a wide-variety of learning tasks. This work presents a general-purpose explorative-learning method that has the potential to improve learning in areas such as active learning and reinforcement learning.