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Publication# Robust and Efficient Data Clustering with Signal Processing on Graphs

Résumé

Data is pervasive in today's world and has actually been for quite some time. With the increasing volume of data to process, there is a need for faster and at least as accurate techniques than what we already have. In particular, the last decade recorded the effervescence of social networks and ubiquitous sensing (through smartphones and the Internet of Things). These phenomena, including also the progresses in bioinformatics and traffic monitoring, pushed forward the research on graph analysis and called for more efficient techniques.

Clustering is an important field of machine learning because it belongs to the unsupervised techniques (i.e., one does not need to possess a ground truth about the data to start learning). With it, one can extract meaningful patterns from large data sources without requiring an expert to annotate a portion of the data, which can be very costly. However, the techniques of clustering designed so far all tend to be computationally demanding and have trouble scaling with the size of today's problems.

The emergence of Graph Signal Processing, attempting to apply traditional signal processing techniques on graphs instead of time, provided additional tools for efficient graph analysis. By considering the clustering assignment as a signal lying on the nodes of the graph, one may now apply the tools of GSP to the improvement of graph clustering and more generally data clustering at large.

In this thesis, we present several techniques using some of the latest developments of GSP in order to improve the scalability of clustering, while aiming for an accuracy resembling that of Spectral Clustering, a famous graph clustering technique that possess a solid mathematical intuition.

On the one hand, we explore the benefits of random signal filtering on a practical and theoretical aspect for the determination of the eigenvectors of the graph Laplacian. In practice, this attempt requires the design of polynomial approximations of the step function for which we provided an accelerated heuristic. We used this series of work in order to reduce the complexity of dynamic graphs clustering, the problem of defining a partition to a graph which is evolving in time at each snapshot. We also used them to propose a fast method for the determination of the subspace generated by the first eigenvectors of any symmetrical matrix. This element is useful for clustering as it serves in Spectral Clustering but it goes beyond that since it also serves in graph visualization (with Laplacian Eigenmaps) and data mining (with Principal Components Projection).

On the other hand, we were inspired by the latest works on graph filter localization in order to propose an extremely fast clustering technique. We tried to perform clustering by only using graph filtering and combining the results in order to obtain a partition of the nodes.

These different contributions are completed by experiments using both synthetic datasets and real-world problems. Since we think that research should be shared in order to progress, all the experiments made in this thesis are publicly available on my personal Github account.

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Genomic bioinformatics is a growing and developing field. Indeed, data analysis is becoming an integrative and essential part of any quantitative biological experiment as the technologies evolve and the wet lab methods used generate larger and larger quantities of data. Yet few standards have emerged and a plethora of analytical tools exist, none of which are established as a standard. The difficulties arise early on, even before processing any genomic data, as one first needs to visualize it. Several visualization methods exist, such as the UCSC genome browser, IGB or Argo, but none offer a satisfying interface or set of tools. Stemming from a pre-existing project at the bioinformatics and biostatistics core facility, this study presents a new solution to the multiple difficulties that at present beleaguer the field. A novel genome visualization tool is proposed where the user interface remains simple and incorporates a set of common statistical analysis functions. The software produced, entitled gFeatMiner, is capable of processing large scale genomic datasets for computing descriptive statistics and manipulate them in several ways. The program makes use of modern technologies and infrastructure paving the way for its development into an advanced data mining tool. In the second part of this study, a practical application is worked out. Examining the genes coding for ribosomal proteins in the model organism yeast (Saccharomyces cerevisiae) and using several available sets of data including multiple transcription factor binding profiles in vivo and in vitro, RNA polymerase activity and nucleosome enrichment, we attempt to better understand and reveal cellular mechanisms by clustering the numerous genes together using different criteria and machine learning strategies

2010Michael Bronstein, Xiaowen Dong, Pascal Frossard, Laura Toni

The effective representation, processing, analysis, and visualization of large-scale structured data, especially those related to complex domains, such as networks and graphs, are one of the key questions in modern machine learning. Graph signal processing (GSP), a vibrant branch of signal processing models and algorithms that aims at handling data supported on graphs, opens new paths of research to address this challenge. In this article, we review a few important contributions made by GSP concepts and tools, such as graph filters and transforms, to the development of novel machine learning algorithms. In particular, our discussion focuses on the following three aspects: exploiting data structure and relational priors, improving data and computational efficiency, and enhancing model interpretability. Furthermore, we provide new perspectives on the future development of GSP techniques that may serve as a bridge between applied mathematics and signal processing on one side and machine learning and network science on the other. Cross-fertilization across these different disciplines may help unlock the numerous challenges of complex data analysis in the modern age.

In many signal processing, machine learning and computer vision applications, one often has to deal with high dimensional and big datasets such as images, videos, web content, etc. The data can come in various forms, such as univariate or multivariate time series, matrices or high dimensional tensors. The goal of the data mining community is to reveal the hidden linear or non-linear structures in the datasets. Over the past couple of decades matrix factorization, owing to its intrinsic association with dimensionality reduction has been adopted as one of the key methods in this context. One can either use a single linear subspace to approximate the data (the standard Principal Component Analysis (PCA) approach) or a union of low dimensional subspaces where each data class belongs to a different subspace. In many cases, however, the low dimensional data follows some additional structure. Knowledge of such structure is beneficial, as we can use it to enhance the representativity of our models by adding structured priors. A nowadays standard way to represent pairwise affinity between objects is by using graphs. The introduction of graph-based priors to enhance matrix factorization models has recently brought them back to the highest attention of the data mining community. Representation of a signal on a graph is well motivated by the emerging field of signal processing on graphs, based on notions of spectral graph theory. The underlying assumption is that high-dimensional data samples lie on or close to a smooth low-dimensional manifold. Interestingly, the underlying manifold can be represented by its discrete proxy, i.e. a graph. A primary limitation of the state-of-the-art low-rank approximation methods is that they do not generalize for the case of non-linear low-rank structures. Furthermore, the standard low-rank extraction methods for many applications, such as low-rank and sparse decomposition, are computationally cumbersome. We argue, that for many machine learning and signal processing applications involving big data, an approximate low-rank recovery suffices. Thus, in this thesis, we present solutions to the above two limitations by presenting a new framework for scalable but approximate low-rank extraction which exploits the hidden structure in the data using the notion of graphs. First, we present a novel signal model, called

`Multilinear low-rank tensors on graphs (MLRTG)' which states that a tensor can be encoded as a multilinear combination of the low-frequency graph eigenvectors, where the graphs are constructed along the various modes of the tensor. Since the graph eigenvectors have the interpretation of \textit{non-linear} embedding of a dataset on the low-dimensional manifold, we propose a method called `

Graph Multilinear SVD (GMLSVD)' to recover PCA based linear subspaces from these eigenvectors. Finally, we propose a plethora of highly scalable matrix and tensor based problems for low-rank extraction which implicitly or explicitly make use of the GMLSVD framework. The core idea is to replace the expensive iterative SVD operations by updating the linear subspaces from the fixed non-linear ones via low-cost operations. We present applications in low-rank and sparse decomposition and clustering of the low-rank features to evaluate all the proposed methods. Our theoretical analysis shows that the approximation error of the proposed framework depends on the spectral properties of the graph Laplacians