Functional data analysis (FDA) methods have computational and theoretical appeals for some high dimensional data, but lack the scalability to modern large sample datasets. To tackle the challenge, we develop randomized algorithms for two important FDA methods: functional principal component analysis (FPCA) and functional linear regression (FLR) with scalar response. The two methods are connected as they both rely on the accurate estimation of functional principal subspace. The proposed algorithms draw subsamples from the large dataset at hand and apply FPCA or FLR over the subsamples to reduce the computational cost. To effectively preserve subspace information in the subsamples, we propose a functional principal subspace sampling probability, which removes the eigenvalue scale effect inside the functional principal subspace and properly weights the residual. Based on the operator perturbation analysis, we show the proposed probability has precise control over the first order error of the subspace projection operator and can be interpreted as an importance sampling for functional subspace estimation. Moreover, concentration bounds for the proposed algorithms are established to reflect the low intrinsic dimension nature of functional data in an infinite dimensional space. The effectiveness of the proposed algorithms is demonstrated upon synthetic and real datasets.
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We consider the "all-for-one" decentralized learning problem for generalized linear models. The features of each sample are partitioned among several collaborating agents in a connected network, but only one agent observes the response variables. To solve the regularized empirical risk minimization in this distributed setting, we apply the Chambolle--Pock primal--dual algorithm to an equivalent saddle-point formulation of the problem. The primal and dual iterations are either in closed-form or reduce to coordinate-wise minimization of scalar convex functions. We establish convergence rates for the empirical risk minimization under two different assumptions on the loss function (Lipschitz and square root Lipschitz), and show how they depend on the characteristics of the design matrix and the Laplacian of the network.
There are proposals that extend the classical generalized additive models (GAMs) to accommodate high-dimensional data ($p>>n$) using group sparse regularization. However, the sparse regularization may induce excess shrinkage when estimating smoothing functions, damaging predictive performance. Moreover, most of these GAMs consider an "all-in-all-out" approach for functional selection, rendering them difficult to answer if nonlinear effects are necessary. While some Bayesian models can address these shortcomings, using Markov chain Monte Carlo algorithms for model fitting creates a new challenge, scalability. Hence, we propose Bayesian hierarchical generalized additive models as a solution: we consider the smoothing penalty for proper shrinkage of curve interpolation and separation of smoothing function linear and nonlinear spaces. A novel spike-and-slab spline prior is proposed to select components of smoothing functions. Two scalable and deterministic algorithms, EM-Coordinate Descent and EM-Iterative Weighted Least Squares, are developed for different utilities. Simulation studies and metabolomics data analyses demonstrate improved predictive or computational performance against state-of-the-art models, mgcv, COSSO and sparse Bayesian GAM. The software implementation of the proposed models is freely available via an R package BHAM.
We study efficient distributed algorithms for the fundamental problem of principal component analysis and leading eigenvector computation on the sphere, when the data are randomly distributed among a set of computational nodes. We propose a new quantized variant of Riemannian gradient descent to solve this problem, and prove that the algorithm converges with high probability under a set of necessary spherical-convexity properties. We give bounds on the number of bits transmitted by the algorithm under common initialization schemes, and investigate the dependency on the problem dimension in each case.
Terpenes are a widespread class of natural products with significant chemical and biological diversity and many of these molecules have already made their way into medicines. Given the thousands of molecules already described, the full characterization of this chemical space can be a challenging task when relying in classical approaches. In this work we employ a data science-based approach to identify, compile and characterize the diversity of terpenes currently known in a systematic way. We worked with a natural product database, COCONUT, from which we extracted information for nearly 60000 terpenes. For these molecules, we conducted a subclass-by-subclass analysis in which we highlight several chemical and physical properties relevant to several fields, such as natural products chemistry, medicinal chemistry and drug discovery, among others. We were also interested in assessing the potential of this data for clustering and classification tasks. For clustering, we have applied and compared k-means with agglomerative clustering, both to the original data and following a step of dimensionality reduction. To this end, PCA, FastICA, Kernel PCA, t-SNE and UMAP were used and benchmarked. We also employed a number of methods for the purpose of classifying terpene subclasses using their physico-chemical descriptors. Light gradient boosting machine, k-nearest neighbors, random forests, Gaussian naiive Bayes and Multilayer perceptron, with the best-performing algorithms yielding accuracy, F1 score, precision and other metrics all over 0.9, thus showing the capabilities of these approaches for the classification of terpene subclasses.
We present a method to obtain the average and the typical value of the number of critical points of the empirical risk landscape for generalized linear estimation problems and variants. This represents a substantial extension of previous applications of the Kac-Rice method since it allows to analyze the critical points of high dimensional non-Gaussian random functions. We obtain a rigorous explicit variational formula for the annealed complexity, which is the logarithm of the average number of critical points at fixed value of the empirical risk. This result is simplified, and extended, using the non-rigorous Kac-Rice replicated method from theoretical physics. In this way we find an explicit variational formula for the quenched complexity, which is generally different from its annealed counterpart, and allows to obtain the number of critical points for typical instances up to exponential accuracy.
We analyze a class of stochastic gradient algorithms with momentum on a high-dimensional random least squares problem. Our framework, inspired by random matrix theory, provides an exact (deterministic) characterization for the sequence of loss values produced by these algorithms which is expressed only in terms of the eigenvalues of the Hessian. This leads to simple expressions for nearly-optimal hyperparameters, a description of the limiting neighborhood, and average-case complexity. As a consequence, we show that (small-batch) stochastic heavy-ball momentum with a fixed momentum parameter provides no actual performance improvement over SGD when step sizes are adjusted correctly. For contrast, in the non-strongly convex setting, it is possible to get a large improvement over SGD using momentum. By introducing hyperparameters that depend on the number of samples, we propose a new algorithm sDANA (stochastic dimension adjusted Nesterov acceleration) which obtains an asymptotically optimal average-case complexity while remaining linearly convergent in the strongly convex setting without adjusting parameters.
We propose a model-free reinforcement learning algorithm inspired by the popular randomized least squares value iteration (RLSVI) algorithm as well as the optimism principle. Unlike existing upper-confidence-bound (UCB) based approaches, which are often computationally intractable, our algorithm drives exploration by simply perturbing the training data with judiciously chosen i.i.d. scalar noises. To attain optimistic value function estimation without resorting to a UCB-style bonus, we introduce an optimistic reward sampling procedure. When the value functions can be represented by a function class $\mathcal{F}$, our algorithm achieves a worst-case regret bound of $\widetilde{O}(\mathrm{poly}(d_EH)\sqrt{T})$ where $T$ is the time elapsed, $H$ is the planning horizon and $d_E$ is the $\textit{eluder dimension}$ of $\mathcal{F}$. In the linear setting, our algorithm reduces to LSVI-PHE, a variant of RLSVI, that enjoys an $\widetilde{\mathcal{O}}(\sqrt{d^3H^3T})$ regret. We complement the theory with an empirical evaluation across known difficult exploration tasks.
Neural architecture search has attracted wide attentions in both academia and industry. To accelerate it, researchers proposed weight-sharing methods which first train a super-network to reuse computation among different operators, from which exponentially many sub-networks can be sampled and efficiently evaluated. These methods enjoy great advantages in terms of computational costs, but the sampled sub-networks are not guaranteed to be estimated precisely unless an individual training process is taken. This paper owes such inaccuracy to the inevitable mismatch between assembled network layers, so that there is a random error term added to each estimation. We alleviate this issue by training a graph convolutional network to fit the performance of sampled sub-networks so that the impact of random errors becomes minimal. With this strategy, we achieve a higher rank correlation coefficient in the selected set of candidates, which consequently leads to better performance of the final architecture. In addition, our approach also enjoys the flexibility of being used under different hardware constraints, since the graph convolutional network has provided an efficient lookup table of the performance of architectures in the entire search space.
Graph convolutional network (GCN) has been successfully applied to many graph-based applications; however, training a large-scale GCN remains challenging. Current SGD-based algorithms suffer from either a high computational cost that exponentially grows with number of GCN layers, or a large space requirement for keeping the entire graph and the embedding of each node in memory. In this paper, we propose Cluster-GCN, a novel GCN algorithm that is suitable for SGD-based training by exploiting the graph clustering structure. Cluster-GCN works as the following: at each step, it samples a block of nodes that associate with a dense subgraph identified by a graph clustering algorithm, and restricts the neighborhood search within this subgraph. This simple but effective strategy leads to significantly improved memory and computational efficiency while being able to achieve comparable test accuracy with previous algorithms. To test the scalability of our algorithm, we create a new Amazon2M data with 2 million nodes and 61 million edges which is more than 5 times larger than the previous largest publicly available dataset (Reddit). For training a 3-layer GCN on this data, Cluster-GCN is faster than the previous state-of-the-art VR-GCN (1523 seconds vs 1961 seconds) and using much less memory (2.2GB vs 11.2GB). Furthermore, for training 4 layer GCN on this data, our algorithm can finish in around 36 minutes while all the existing GCN training algorithms fail to train due to the out-of-memory issue. Furthermore, Cluster-GCN allows us to train much deeper GCN without much time and memory overhead, which leads to improved prediction accuracy---using a 5-layer Cluster-GCN, we achieve state-of-the-art test F1 score 99.36 on the PPI dataset, while the previous best result was 98.71 by [16]. Our codes are publicly available at //github.com/google-research/google-research/tree/master/cluster_gcn.
Network embedding aims to learn a latent, low-dimensional vector representations of network nodes, effective in supporting various network analytic tasks. While prior arts on network embedding focus primarily on preserving network topology structure to learn node representations, recently proposed attributed network embedding algorithms attempt to integrate rich node content information with network topological structure for enhancing the quality of network embedding. In reality, networks often have sparse content, incomplete node attributes, as well as the discrepancy between node attribute feature space and network structure space, which severely deteriorates the performance of existing methods. In this paper, we propose a unified framework for attributed network embedding-attri2vec-that learns node embeddings by discovering a latent node attribute subspace via a network structure guided transformation performed on the original attribute space. The resultant latent subspace can respect network structure in a more consistent way towards learning high-quality node representations. We formulate an optimization problem which is solved by an efficient stochastic gradient descent algorithm, with linear time complexity to the number of nodes. We investigate a series of linear and non-linear transformations performed on node attributes and empirically validate their effectiveness on various types of networks. Another advantage of attri2vec is its ability to solve out-of-sample problems, where embeddings of new coming nodes can be inferred from their node attributes through the learned mapping function. Experiments on various types of networks confirm that attri2vec is superior to state-of-the-art baselines for node classification, node clustering, as well as out-of-sample link prediction tasks. The source code of this paper is available at //github.com/daokunzhang/attri2vec.
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