We describe a seriation algorithm for ranking a set of items given pairwise comparisons between these items. Intuitively, the algorithm assigns similar rankings to items that compare similarly with all others. It does so by constructing a similarity matrix from pairwise comparisons, using seriation methods to reorder this matrix and construct a ranking. We first show that this spectral seriation algorithm recovers the true ranking when all pairwise comparisons are observed and consistent with a total order. We then show that ranking reconstruction is still exact when some pairwise comparisons are corrupted or missing, and that seriation based spectral ranking is more robust to noise than classical scoring methods. Finally, we bound the ranking error when only a random subset of the comparions are observed. An additional benefit of the seriation formulation is that it allows us to solve semi-supervised ranking problems. Experiments on both synthetic and real datasets demonstrate that seriation based spectral ranking achieves competitive and in some cases superior performance compared to classical ranking methods.

Modern malware is designed with mutation characteristics, namely polymorphism and metamorphism, which causes an enormous growth in the number of variants of malware samples. Categorization of malware samples on the basis of their behaviors is essential for the computer security community, because they receive huge number of malware everyday, and the signature extraction process is usually based on malicious parts characterizing malware families. Microsoft released a malware classification challenge in 2015 with a huge dataset of near 0.5 terabytes of data, containing more than 20K malware samples. The analysis of this dataset inspired the development of a novel paradigm that is effective in categorizing malware variants into their actual family groups. This paradigm is presented and discussed in the present paper, where emphasis has been given to the phases related to the extraction, and selection of a set of novel features for the effective representation of malware samples. Features can be grouped according to different characteristics of malware behavior, and their fusion is performed according to a per-class weighting paradigm. The proposed method achieved a very high accuracy ($\approx$ 0.998) on the Microsoft Malware Challenge dataset.

In machine learning, there is an ongoing revival of the use of variational Bayes (VB) to deal with complex probabilistic models with hidden variables. The revival is driven by the use of stochastic methods to approximate the VB lower bound and associated gradients. See for example [1, 2, 5]. The advantages include automated inference [3] and also that they are applicable to a much wider class of probabilistic models. While the basic recipes are limited in the flexibility of the approximate hidden-variable posteriors, there are ongoing efforts to make them more flexible.

Many modern datasets can be represented as graphs and hence spectral decompositions such as graph principal component analysis (PCA) can be useful. Distinct from previous graph decomposition approaches based on subspace projection of a single topological feature, e.g., the Fiedler vector of centered graph adjacency matrix (graph Laplacian), we propose spectral decomposition approaches to graph PCA and graph dictionary learning that integrate multiple features, including graph walk statistics, centrality measures and graph distances to reference nodes. In this paper we propose a new PCA method for single graph analysis, called multi-centrality graph PCA (MC-GPCA), and a new dictionary learning method for ensembles of graphs, called multi-centrality graph dictionary learning (MC-GDL), both based on spectral decomposition of multi-centrality matrices. As an application to cyber intrusion detection, MC-GPCA can be an effective indicator of anomalous connectivity pattern and MC-GDL can provide discriminative basis for attack classification.

A number of people are found in a room and involved in loud conversations in groups, just as it would happen in a cocktail party. There might also be some background noise, which could be music, car noise from outside, etc. Each person in this room is therefore forced to listen to a mixture of speech sounds coming from various directions, along with some noise. These sounds may come directly to one's ear or have first suffered a sequence of reverberations because of their reflections on the room's walls. The problem of focusing one's listening attention on a particular speaker among this cacophony of conversations and noise has been known as the cocktail party problem [6]. It consists of separating a mixture of speech signals of different characteristics with noise added to it. The signals are a-priori unknown (one listens only to a combination of them) as is also the way they have been mixed. The above scenario is a good analog for many other examples of situations that demand for a separation of mixed signals with no presupposed knowledge on the signals and the system mixing them.

Uncertainty principles such as Heisenberg's provide limits on the time-frequency concentration of a signal, and constitute an important theoretical tool for designing and evaluating linear signal transforms. Generalizations of such principles to the graph setting can inform dictionary design for graph signals, lead to algorithms for reconstructing missing information from graph signals via sparse representations, and yield new graph analysis tools. While previous work has focused on generalizing notions of spreads of a graph signal in the vertex and graph spectral domains, our approach is to generalize the methods of Lieb in order to develop uncertainty principles that provide limits on the concentration of the analysis coefficients of any graph signal under a dictionary transform whose atoms are jointly localized in the vertex and graph spectral domains. One challenge we highlight is that due to the inhomogeneity of the underlying graph data domain, the local structure in a single small region of the graph can drastically affect the uncertainty bounds for signals concentrated in different regions of the graph, limiting the information provided by global uncertainty principles. Accordingly, we suggest a new way to incorporate a notion of locality, and develop local uncertainty principles that bound the concentration of the analysis coefficients of each atom of a localized graph spectral filter frame in terms of quantities that depend on the local structure of the graph around the center vertex of the given atom. Finally, we demonstrate how our proposed local uncertainty measures can improve the random sampling of graph signals.

KECA roughly reduces to a sorting of the importance of kernel eigenvectors by entropy instead of by variance as in Kernel Principal Components Analysis. In this work, we propose an extension of the KECA method, named Optimized KECA (OKECA), that directly extracts the optimal features retaining most of the data entropy by means of compacting the information in very few features (often in just one or two). The proposed method produces features which have higher expressive power . In particular, it is based on the Independent Component Analysis (ICA) framework, and introduces an extra rotation to the eigen-decomposition, which is optimized via gradient ascent search. This maximum entropy preservation suggests that OKECA features are more efficient than KECA features for density estimation. In addition, a critical issue in both methods is the selection of the kernel parameter since it critically affects the resulting performance. Here we analyze the most common kernel length-scale selection criteria. Results of both methods are illustrated in different synthetic and real problems. Results show that 1) OKECA returns projections with more expressive power than KECA, 2) the most successful rule for estimating the kernel parameter is based on maximum likelihood, and 3) OKECA is more robust to the selection of the length-scale parameter in kernel density estimation.

In Bipartite Correlation Clustering (BCC) we are given a complete bipartite graph $G$ with `+' and `-' edges, and we seek a vertex clustering that maximizes the number of agreements: the number of all `+' edges within clusters plus all `-' edges cut across clusters. BCC is known to be NP-hard. We present a novel approximation algorithm for $k$-BCC, a variant of BCC with an upper bound $k$ on the number of clusters. Our algorithm outputs a $k$-clustering that provably achieves a number of agreements within a multiplicative ${(1-\delta)}$-factor from the optimal, for any desired accuracy $\delta$. It relies on solving a combinatorially constrained bilinear maximization on the bi-adjacency matrix of $G$. It runs in time exponential in $k$ and $\delta^{-1}$, but linear in the size of the input. Further, we show that, in the (unconstrained) BCC setting, an ${(1-\delta)}$-approximation can be achieved by $O(\delta^{-1})$ clusters regardless of the size of the graph. In turn, our $k$-BCC algorithm implies an Efficient PTAS for the BCC objective of maximizing agreements.

We consider a composite convex minimization problem associated with regularized empirical risk minimization, which often arises in machine learning. We propose two new stochastic gradient methods that are based on stochastic dual averaging method with variance reduction. Our methods generate a sparser solution than the existing methods because we do not need to take the average of the history of the solutions. This is favorable in terms of both interpretability and generalization. Moreover, our methods have theoretical support for both a strongly and a non-strongly convex regularizer and achieve the best known convergence rates among existing nonaccelerated stochastic gradient methods.

Manifold Learning (ML) is a class of algorithms seeking a low-dimensional nonlinear representation of high-dimensional data. Thus ML algorithms are, at least in theory, most applicable to high-dimensional data and sample sizes to enable accurate estimation of the manifold. Despite this, most existing manifold learning implementations are not particularly scalable. Here we present a Python package that implements a variety of manifold learning algorithms in a modular and scalable fashion, using fast approximate neighbors searches and fast sparse eigendecompositions. The package incorporates theoretical advances in manifold learning, such as the unbiased Laplacian estimator introduced by Coifman and Lafon (2006) and the estimation of the embedding distortion by the Riemannian metric method introduced by Perraul-Joncas and Meila (2013). In benchmarks, even on a single-core desktop computer, our code embeds millions of data points in minutes, and takes just 200 minutes to embed the main sample of galaxy spectra from the Sloan Digital Sky Survey -- consisting of 0.6 million samples in 3750-dimensions -- a task which has not previously been possible.