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Differential co-expression analysis has been widely applied by scientists in understanding the biological mechanisms of diseases. However, the unknown differential patterns are often complicated; thus, models based on simplified parametric assumptions can be ineffective in identifying the differences. Meanwhile, the gene expression data involved in such analysis are in extremely high dimensions by nature, whose correlation matrices may not even be computable. Such a large scale seriously limits the application of most well-studied statistical methods. This paper introduces a simple yet powerful approach to the differential correlation analysis problem called compressed spectral screening. By leveraging spectral structures and random sampling techniques, our approach could achieve a highly accurate screening of features with complicated differential patterns while maintaining the scalability to analyze correlation matrices of $10^4$--$10^5$ variables within a few minutes on a standard personal computer. We have applied this screening approach in comparing a TCGA data set about Glioblastoma with normal subjects. Our analysis successfully identifies multiple functional modules of genes that exhibit different co-expression patterns. The findings reveal new insights about Glioblastoma's evolving mechanism. The validity of our approach is also justified by a theoretical analysis, showing that the compressed spectral analysis can achieve variable screening consistency.

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We study a new two-time-scale stochastic gradient method for solving optimization problems, where the gradients are computed with the aid of an auxiliary variable under samples generated by time-varying Markov random processes parameterized by the underlying optimization variable. These time-varying samples make gradient directions in our update biased and dependent, which can potentially lead to the divergence of the iterates. In our two-time-scale approach, one scale is to estimate the true gradient from these samples, which is then used to update the estimate of the optimal solution. While these two iterates are implemented simultaneously, the former is updated "faster" (using bigger step sizes) than the latter (using smaller step sizes). Our first contribution is to characterize the finite-time complexity of the proposed two-time-scale stochastic gradient method. In particular, we provide explicit formulas for the convergence rates of this method under different structural assumptions, namely, strong convexity, convexity, the Polyak-Lojasiewicz condition, and general non-convexity. We apply our framework to two problems in control and reinforcement learning. First, we look at the standard online actor-critic algorithm over finite state and action spaces and derive a convergence rate of O(k^(-2/5)), which recovers the best known rate derived specifically for this problem. Second, we study an online actor-critic algorithm for the linear-quadratic regulator and show that a convergence rate of O(k^(-2/3)) is achieved. This is the first time such a result is known in the literature. Finally, we support our theoretical analysis with numerical simulations where the convergence rates are visualized.

The superposition of data sets with internal parametric self-similarity is a longstanding and widespread technique for the analysis of many types of experimental data across the physical sciences. Typically, this superposition is performed manually, or recently by one of a few automated algorithms. However, these methods are often heuristic in nature, are prone to user bias via manual data shifting or parameterization, and lack a native framework for handling uncertainty in both the data and the resulting model of the superposed data. In this work, we develop a data-driven, non-parametric method for superposing experimental data with arbitrary coordinate transformations, which employs Gaussian process regression to learn statistical models that describe the data, and then uses maximum a posteriori estimation to optimally superpose the data sets. This statistical framework is robust to experimental noise, and automatically produces uncertainty estimates for the learned coordinate transformations. Moreover, it is distinguished from black-box machine learning in its interpretability -- specifically, it produces a model that may itself be interrogated to gain insight into the system under study. We demonstrate these salient features of our method through its application to four representative data sets characterizing the mechanics of soft materials. In every case, our method replicates results obtained using other approaches, but with reduced bias and the addition of uncertainty estimates. This method enables a standardized, statistical treatment of self-similar data across many fields, producing interpretable data-driven models that may inform applications such as materials classification, design, and discovery.

We provide a decision theoretic analysis of bandit experiments. The setting corresponds to a dynamic programming problem, but solving this directly is typically infeasible. Working within the framework of diffusion asymptotics, we define suitable notions of asymptotic Bayes and minimax risk for bandit experiments. For normally distributed rewards, the minimal Bayes risk can be characterized as the solution to a nonlinear second-order partial differential equation (PDE). Using a limit of experiments approach, we show that this PDE characterization also holds asymptotically under both parametric and non-parametric distribution of the rewards. The approach further describes the state variables it is asymptotically sufficient to restrict attention to, and therefore suggests a practical strategy for dimension reduction. The upshot is that we can approximate the dynamic programming problem defining the bandit experiment with a PDE which can be efficiently solved using sparse matrix routines. We derive the optimal Bayes and minimax policies from the numerical solutions to these equations. The proposed policies substantially dominate existing methods such as Thompson sampling. The framework also allows for substantial generalizations to the bandit problem such as time discounting and pure exploration motives.

We introduce a novel methodology for particle filtering in dynamical systems where the evolution of the signal of interest is described by a SDE and observations are collected instantaneously at prescribed time instants. The new approach includes the discretisation of the SDE and the design of efficient particle filters for the resulting discrete-time state-space model. The discretisation scheme converges with weak order 1 and it is devised to create a sequential dependence structure along the coordinates of the discrete-time state vector. We introduce a class of space-sequential particle filters that exploits this structure to improve performance when the system dimension is large. This is numerically illustrated by a set of computer simulations for a stochastic Lorenz 96 system with additive noise. The new space-sequential particle filters attain approximately constant estimation errors as the dimension of the Lorenz 96 system is increased, with a computational cost that increases polynomially, rather than exponentially, with the system dimension. Besides the new numerical scheme and particle filters, we provide in this paper a general framework for discrete-time filtering in continuous-time dynamical systems described by a SDE and instantaneous observations. Provided that the SDE is discretised using a weakly-convergent scheme, we prove that the marginal posterior laws of the resulting discrete-time state-space model converge to the posterior marginal posterior laws of the original continuous-time state-space model under a suitably defined metric. This result is general and not restricted to the numerical scheme or particle filters specifically studied in this manuscript.

In variable selection, a selection rule that prescribes the permissible sets of selected variables (called a "selection dictionary") is desirable due to the inherent structural constraints among the candidate variables. The methods that can incorporate such restrictions can improve model interpretability and prediction accuracy. Penalized regression can integrate selection rules by assigning the coefficients to different groups and then applying penalties to the groups. However, no general framework has been proposed to formalize selection rules and their applications. In this work, we establish a framework for structured variable selection that can incorporate universal structural constraints. We develop a mathematical language for constructing arbitrary selection rules, where the selection dictionary is formally defined. We show that all selection rules can be represented as a combination of operations on constructs, which can be used to identify the related selection dictionary. One may then apply some criteria to select the best model. We show that the theoretical framework can help to identify the grouping structure in existing penalized regression methods. In addition, we formulate structured variable selection into mixed-integer optimization problems which can be solved by existing software. Finally, we discuss the significance of the framework in the context of statistics.

This manuscript portrays optimization as a process. In many practical applications the environment is so complex that it is infeasible to lay out a comprehensive theoretical model and use classical algorithmic theory and mathematical optimization. It is necessary as well as beneficial to take a robust approach, by applying an optimization method that learns as one goes along, learning from experience as more aspects of the problem are observed. This view of optimization as a process has become prominent in varied fields and has led to some spectacular success in modeling and systems that are now part of our daily lives.

Spectral clustering (SC) is a popular clustering technique to find strongly connected communities on a graph. SC can be used in Graph Neural Networks (GNNs) to implement pooling operations that aggregate nodes belonging to the same cluster. However, the eigendecomposition of the Laplacian is expensive and, since clustering results are graph-specific, pooling methods based on SC must perform a new optimization for each new sample. In this paper, we propose a graph clustering approach that addresses these limitations of SC. We formulate a continuous relaxation of the normalized minCUT problem and train a GNN to compute cluster assignments that minimize this objective. Our GNN-based implementation is differentiable, does not require to compute the spectral decomposition, and learns a clustering function that can be quickly evaluated on out-of-sample graphs. From the proposed clustering method, we design a graph pooling operator that overcomes some important limitations of state-of-the-art graph pooling techniques and achieves the best performance in several supervised and unsupervised tasks.

Transfer learning aims at improving the performance of target learners on target domains by transferring the knowledge contained in different but related source domains. In this way, the dependence on a large number of target domain data can be reduced for constructing target learners. Due to the wide application prospects, transfer learning has become a popular and promising area in machine learning. Although there are already some valuable and impressive surveys on transfer learning, these surveys introduce approaches in a relatively isolated way and lack the recent advances in transfer learning. As the rapid expansion of the transfer learning area, it is both necessary and challenging to comprehensively review the relevant studies. This survey attempts to connect and systematize the existing transfer learning researches, as well as to summarize and interpret the mechanisms and the strategies in a comprehensive way, which may help readers have a better understanding of the current research status and ideas. Different from previous surveys, this survey paper reviews over forty representative transfer learning approaches from the perspectives of data and model. The applications of transfer learning are also briefly introduced. In order to show the performance of different transfer learning models, twenty representative transfer learning models are used for experiments. The models are performed on three different datasets, i.e., Amazon Reviews, Reuters-21578, and Office-31. And the experimental results demonstrate the importance of selecting appropriate transfer learning models for different applications in practice.

The area of Data Analytics on graphs promises a paradigm shift as we approach information processing of classes of data, which are typically acquired on irregular but structured domains (social networks, various ad-hoc sensor networks). Yet, despite its long history, current approaches mostly focus on the optimization of graphs themselves, rather than on directly inferring learning strategies, such as detection, estimation, statistical and probabilistic inference, clustering and separation from signals and data acquired on graphs. To fill this void, we first revisit graph topologies from a Data Analytics point of view, and establish a taxonomy of graph networks through a linear algebraic formalism of graph topology (vertices, connections, directivity). This serves as a basis for spectral analysis of graphs, whereby the eigenvalues and eigenvectors of graph Laplacian and adjacency matrices are shown to convey physical meaning related to both graph topology and higher-order graph properties, such as cuts, walks, paths, and neighborhoods. Next, to illustrate estimation strategies performed on graph signals, spectral analysis of graphs is introduced through eigenanalysis of mathematical descriptors of graphs and in a generic way. Finally, a framework for vertex clustering and graph segmentation is established based on graph spectral representation (eigenanalysis) which illustrates the power of graphs in various data association tasks. The supporting examples demonstrate the promise of Graph Data Analytics in modeling structural and functional/semantic inferences. At the same time, Part I serves as a basis for Part II and Part III which deal with theory, methods and applications of processing Data on Graphs and Graph Topology Learning from data.

Image segmentation is considered to be one of the critical tasks in hyperspectral remote sensing image processing. Recently, convolutional neural network (CNN) has established itself as a powerful model in segmentation and classification by demonstrating excellent performances. The use of a graphical model such as a conditional random field (CRF) contributes further in capturing contextual information and thus improving the segmentation performance. In this paper, we propose a method to segment hyperspectral images by considering both spectral and spatial information via a combined framework consisting of CNN and CRF. We use multiple spectral cubes to learn deep features using CNN, and then formulate deep CRF with CNN-based unary and pairwise potential functions to effectively extract the semantic correlations between patches consisting of three-dimensional data cubes. Effective piecewise training is applied in order to avoid the computationally expensive iterative CRF inference. Furthermore, we introduce a deep deconvolution network that improves the segmentation masks. We also introduce a new dataset and experimented our proposed method on it along with several widely adopted benchmark datasets to evaluate the effectiveness of our method. By comparing our results with those from several state-of-the-art models, we show the promising potential of our method.

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