Statistical detection of a rare class of objects in a two-class classification problem can pose several challenges. Because the class of interest is rare in the training data, there is relatively little information in the known class response labels for model building. At the same time the available explanatory variables are often moderately high dimensional. In the four assays of our drug-discovery application, compounds are active or not against a specific biological target, such as lung cancer tumor cells, and active compounds are rare. Several sets of chemical descriptor variables from computational chemistry are available to classify the active versus inactive class; each can have up to thousands of variables characterizing molecular structure of the compounds. The statistical challenge is to make use of the richness of the explanatory variables in the presence of scant response information. Our algorithm divides the explanatory variables into subsets adaptively and passes each subset to a base classifier. The various base classifiers are then ensembled to produce one model to rank new objects by their estimated probabilities of belonging to the rare class of interest. The essence of the algorithm is to choose the subsets such that variables in the same group work well together; we call such groups phalanxes.

Exchangeable graphs arise via a sampling procedure from measurable functions known as graphons. A natural estimation problem is how well we can recover a graphon given a single graph sampled from it. One general framework for estimating a graphon uses step-functions obtained by partitioning the nodes of the graph according to some clustering algorithm. We propose an iterative step-function estimator (ISFE) that, given an initial partition, iteratively clusters nodes based on their edge densities with respect to the previous iteration's partition. We analyze ISFE and demonstrate its performance in comparison with other graphon estimation techniques.

In this paper the exact linear relation between the leading eigenvector of the unnormalized modularity matrix and the eigenvectors of the adjacency matrix is developed. Based on this analysis a method to approximate the leading eigenvector of the modularity matrix is given, and the relative error of the approximation is derived. A complete proof of the equivalence between normalized modularity clustering and normalized adjacency clustering is also given. A new metric is defined to describe the agreement of two clustering methods, and some applications and experiments are given to illustrate and corroborate the points that are made in the theoretical development.

We suggest a novel method of clustering and exploratory analysis of temporal event sequences data (also known as categorical time series) based on three-dimensional data grid models. A data set of temporal event sequences can be represented as a data set of three-dimensional points, each point is defined by three variables: a sequence identifier, a time value and an event value. Instantiating data grid models to the 3D-points turns the problem into 3D-coclustering. The sequences are partitioned into clusters, the time variable is discretized into intervals and the events are partitioned into clusters. The cross-product of the univariate partitions forms a multivariate partition of the representation space, i.e., a grid of cells and it also represents a nonparametric estimator of the joint distribution of the sequences, time and events dimensions. Thus, the sequences are grouped together because they have similar joint distribution of time and events, i.e., similar distribution of events along the time dimension. The best data grid is computed using a parameter-free Bayesian model selection approach. We also suggest several criteria for exploiting the resulting grid through agglomerative hierarchies, for interpreting the clusters of sequences and characterizing their components through insightful visualizations. Extensive experiments on both synthetic and real-world data sets demonstrate that data grid models are efficient, effective and discover meaningful underlying patterns of categorical time series data.

Data-aware methods for dimensionality reduction and matrix decomposition aim to find low-dimensional structure in a collection of data. Classical approaches discover such structure by learning a basis that can efficiently express the collection. Recently, "self expression", the idea of using a small subset of data vectors to represent the full collection, has been developed as an alternative to learning. Here, we introduce a scalable method for computing sparse SElf-Expressive Decompositions (SEED). SEED is a greedy method that constructs a basis by sequentially selecting incoherent vectors from the dataset. After forming a basis from a subset of vectors in the dataset, SEED then computes a sparse representation of the dataset with respect to this basis. We develop sufficient conditions under which SEED exactly represents low rank matrices and vectors sampled from a unions of independent subspaces. We show how SEED can be used in applications ranging from matrix approximation and denoising to clustering, and apply it to numerous real-world datasets. Our results demonstrate that SEED is an attractive low-complexity alternative to other sparse matrix factorization approaches such as sparse PCA and self-expressive methods for clustering.

Density mode clustering is a nonparametric clustering method. The clusters are the basins of attraction of the modes of a density estimator. We study the risk of mode-based clustering. We show that the clustering risk over the cluster cores --- the regions where the density is high --- is very small even in high dimensions. And under a low noise condition, the overall cluster risk is small even beyond the cores, in high dimensions.

In this chapter we review the main literature related to kernel spectral clustering (KSC), an approach to clustering cast within a kernel-based optimization setting. KSC represents a least-squares support vector machine based formulation of spectral clustering described by a weighted kernel PCA objective. Just as in the classifier case, the binary clustering model is expressed by a hyperplane in a high dimensional space induced by a kernel. In addition, the multi-way clustering can be obtained by combining a set of binary decision functions via an Error Correcting Output Codes (ECOC) encoding scheme. Because of its model-based nature, the KSC method encompasses three main steps: training, validation, testing. In the validation stage model selection is performed to obtain tuning parameters, like the number of clusters present in the data. This is a major advantage compared to classical spectral clustering where the determination of the clustering parameters is unclear and relies on heuristics. Once a KSC model is trained on a small subset of the entire data, it is able to generalize well to unseen test points. Beyond the basic formulation, sparse KSC algorithms based on the Incomplete Cholesky Decomposition (ICD) and $L_0$, $L_1, L_0 + L_1$, Group Lasso regularization are reviewed. In that respect, we show how it is possible to handle large scale data. Also, two possible ways to perform hierarchical clustering and a soft clustering method are presented. Finally, real-world applications such as image segmentation, power load time-series clustering, document clustering and big data learning are considered.

Automatic classification of scientific articles based on common characteristics is an interesting problem with many applications in digital library and information retrieval systems. Properly organized articles can be useful for automatic generation of taxonomies in scientific writings, textual summarization, efficient information retrieval etc. Generating article bundles from a large number of input articles, based on the associated features of the articles is tedious and computationally expensive task. In this report we propose an automatic two-step approach for topic extraction and bundling of related articles from a set of scientific articles in real-time. For topic extraction, we make use of Latent Dirichlet Allocation (LDA) topic modeling techniques and for bundling, we make use of hierarchical agglomerative clustering techniques. We run experiments to validate our bundling semantics and compare it with existing models in use. We make use of an online crowdsourcing marketplace provided by Amazon called Amazon Mechanical Turk to carry out experiments. We explain our experimental setup and empirical results in detail and show that our method is advantageous over existing ones.

We consider the problem of clustering noisy finite-length observations of stationary ergodic random processes according to their nonparametric generative models without prior knowledge of the model statistics and the number of generative models. Two algorithms, both using the L1-distance between estimated power spectral densities (PSDs) as a measure of dissimilarity, are analyzed. The first algorithm, termed nearest neighbor process clustering (NNPC), to the best of our knowledge, is new and relies on partitioning the nearest neighbor graph of the observations via spectral clustering. The second algorithm, simply referred to as k-means (KM), consists of a single k-means iteration with farthest point initialization and was considered before in the literature, albeit with a different measure of dissimilarity and with asymptotic performance results only. We show that both NNPC and KM succeed with high probability under noise and even when the generative process PSDs overlap significantly, all provided that the observation length is sufficiently large. Our results quantify the tradeoff between the overlap of the generative process PSDs, the noise variance, and the observation length. Finally, we present numerical performance results for synthetic and real data.

We study exact recovery conditions for convex relaxations of point cloud clustering problems, focusing on two of the most common optimization problems for unsupervised clustering: $k$-means and $k$-median clustering. Motivations for focusing on convex relaxations are: (a) they come with a certificate of optimality, and (b) they are generic tools which are relatively parameter-free, not tailored to specific assumptions over the input. More precisely, we consider the distributional setting where there are $k$ clusters in $\mathbb{R}^m$ and data from each cluster consists of $n$ points sampled from a symmetric distribution within a ball of unit radius. We ask: what is the minimal separation distance between cluster centers needed for convex relaxations to exactly recover these $k$ clusters as the optimal integral solution? For the $k$-median linear programming relaxation we show a tight bound: exact recovery is obtained given arbitrarily small pairwise separation $\epsilon > 0$ between the balls. In other words, the pairwise center separation is $\Delta > 2+\epsilon$. Under the same distributional model, the $k$-means LP relaxation fails to recover such clusters at separation as large as $\Delta = 4$. Yet, if we enforce PSD constraints on the $k$-means LP, we get exact cluster recovery at center separation $\Delta > 2\sqrt2(1+\sqrt{1/m})$. In contrast, common heuristics such as Lloyd's algorithm (a.k.a. the $k$-means algorithm) can fail to recover clusters in this setting; even with arbitrarily large cluster separation, k-means++ with overseeding by any constant factor fails with high probability at exact cluster recovery. To complement the theoretical analysis, we provide an experimental study of the recovery guarantees for these various methods, and discuss several open problems which these experiments suggest.