Approximating Clustering of Fingerprint Vectors with Missing Values

The problem of clustering fingerprint vectors is an interesting problem in Computational Biology that has been proposed in (Figureroa et al. 2004). In this paper we show some improvements in closing the gaps between the known lower bounds and upper bounds on the approximability of some variants of the biological problem. Namely we are able to prove that the problem is APX-hard even when each fingerprint contains only two unknown position. Moreover we have studied some variants of the orginal problem, and we give two 2-approximation algorithm for the IECMV and OECMV problems when the number of unknown entries for each vector is at most a constant.Comment: 13 pages, 4 figure

Structural textile pattern recognition and processing based on hypergraphs

The humanities, like many other areas of society, are currently undergoing major changes in the wake of digital transformation. However, in order to make collection of digitised material in this area easily accessible, we often still lack adequate search functionality. For instance, digital archives for textiles offer keyword search, which is fairly well understood, and arrange their content following a certain taxonomy, but search functionality at the level of thread structure is still missing. To facilitate the clustering and search, we introduce an approach for recognising similar weaving patterns based on their structures for textile archives. We first represent textile structures using hypergraphs and extract multisets of k-neighbourhoods describing weaving patterns from these graphs. Then, the resulting multisets are clustered using various distance measures and various clustering algorithms (K-Means for simplicity and hierarchical agglomerative algorithms for precision). We evaluate the different variants of our approach experimentally, showing that this can be implemented efficiently (meaning it has linear complexity), and demonstrate its quality to query and cluster datasets containing large textile samples. As, to the best of our knowledge, this is the first practical approach for explicitly modelling complex and irregular weaving patterns usable for retrieval, we aim at establishing a solid baseline

Detecting the community structure and activity patterns of temporal networks: a non-negative tensor factorization approach

The increasing availability of temporal network data is calling for more research on extracting and characterizing mesoscopic structures in temporal networks and on relating such structure to specific functions or properties of the system. An outstanding challenge is the extension of the results achieved for static networks to time-varying networks, where the topological structure of the system and the temporal activity patterns of its components are intertwined. Here we investigate the use of a latent factor decomposition technique, non-negative tensor factorization, to extract the community-activity structure of temporal networks. The method is intrinsically temporal and allows to simultaneously identify communities and to track their activity over time. We represent the time-varying adjacency matrix of a temporal network as a three-way tensor and approximate this tensor as a sum of terms that can be interpreted as communities of nodes with an associated activity time series. We summarize known computational techniques for tensor decomposition and discuss some quality metrics that can be used to tune the complexity of the factorized representation. We subsequently apply tensor factorization to a temporal network for which a ground truth is available for both the community structure and the temporal activity patterns. The data we use describe the social interactions of students in a school, the associations between students and school classes, and the spatio-temporal trajectories of students over time. We show that non-negative tensor factorization is capable of recovering the class structure with high accuracy. In particular, the extracted tensor components can be validated either as known school classes, or in terms of correlated activity patterns, i.e., of spatial and temporal coincidences that are determined by the known school activity schedule

Doctor of Philosophy

dissertationThe contributions of this dissertation are centered around designing new algorithms in the general area of sublinear algorithms such as streaming, core sets and sublinear verification, with a special interest in problems arising from data analysis including data summarization, clustering, matrix problems and massive graphs. In the first part, we focus on summaries and coresets, which are among the main techniques for designing sublinear algorithms for massive data sets. We initiate the study of coresets for uncertain data and study coresets for various types of range counting queries on uncertain data. We focus mainly on the indecisive model of locational uncertainty since it comes up frequently in real-world applications when multiple readings of the same object are made. In this model, each uncertain point has a probability density describing its location, defined as $k$ distinct locations. Our goal is to construct a subset of the uncertain points, including their locational uncertainty, so that range counting queries can be answered by examining only this subset. For each type of query we provide coreset constructions with approximation-size trade-offs. We show that random sampling can be used to construct each type of coreset, and we also provide significantly improved bounds using discrepancy-based techniques on axis-aligned range queries. In the second part, we focus on designing sublinear-space algorithms for approximate computations on massive graphs. In particular, we consider graph MAXCUT and correlation clustering problems and develop sampling based approaches to construct truly sublinear ($o(n)$) sized coresets for graphs that have polynomial (i.e., $n^{\delta}$ for any $\delta >0$) average degree. Our technique is based on analyzing properties of random induced subprograms of the linear program formulations of the problems. We demonstrate this technique with two examples. Firstly, we present a sublinear sized core set to approximate the value of the MAX CUT in a graph to a $(1+\epsilon)$ factor. To the best of our knowledge, all the known methods in this regime rely crucially on near-regularity assumptions. Secondly, we apply the same framework to construct a sublinear-sized coreset for correlation clustering. Our coreset construction also suggests 2-pass streaming algorithms for computing the MAX CUT and correlation clustering objective values which are left as future work at the time of writing this dissertation. Finally, we focus on streaming verification algorithms as another model for designing sublinear algorithms. We give the first polylog space and sublinear (in number of edges) communication protocols for any streaming verification problems in graphs. We present efficient streaming interactive proofs that can verify maximum matching exactly. Our results cover all flavors of matchings (bipartite/ nonbipartite and weighted). In addition, we also present streaming verifiers for approximate metric TSP and exact triangle counting, as well as for graph primitives such as the number of connected components, bipartiteness, minimum spanning tree and connectivity. In particular, these are the first results for weighted matchings and for metric TSP in any streaming verification model. Our streaming verifiers use only polylogarithmic space while exchanging only polylogarithmic communication with the prover in addition to the output size of the relevant solution. We also initiate a study of streaming interactive proofs (SIPs) for problems in data analysis and present efficient SIPs for some fundamental problems. We present protocols for clustering and shape fitting including minimum enclosing ball (MEB), width of a point set, $k$-centers and $k$-slab problem. We also present protocols for fundamental matrix analysis problems: We provide an improved protocol for rectangular matrix problems, which in turn can be used to verify $k$ (approximate) eigenvectors of an $n \times n$ integer matrix $A$. In general our solutions use polylogarithmic rounds of communication and polylogarithmic total communication and verifier space

An orientation field approach to modelling fibre-generated spatial point processes

This thesis introduces a new approach to analysing spatial point data clustered along or around a system of curves or fibres with additional background noise. Such data arise in catalogues of galaxy locations, recorded locations of earthquakes, aerial images of minefields, and pore patterns on fingerprints. Finding the underlying curvilinear structure of these point-pattern data sets may not only facilitate a better understanding of how they arise but also aid reconstruction of missing data. We base the space of fibres on the set of integral lines of an orientation field. Using an empirical Bayes approach, we estimate the field of orientations from anisotropic features of the data. The orientation field estimation draws on ideas from tensor field theory (an area recently motivated by the study of magnetic resonance imaging scans), using symmetric positive-definite matrices to estimate local anisotropies in the point pattern through the tensor method. We also propose a new measure of anisotropy, the modified square Fractional Anisotropy, whose statistical properties are estimated for tensors calculated via the tensor method. A continuous-time Markov chain Monte Carlo algorithm is used to draw samples from the posterior distribution of fibres, exploring models with different numbers of clusters, and fitting fibres to the clusters as it proceeds. The Bayesian approach permits inference on various properties of the clusters and associated fibres, and the resulting algorithm performs well on a number of very different curvilinear structures