An Investigation in Efficient Spatial Patterns Mining

The technical progress in computerized spatial data acquisition and storage results in the growth of vast spatial databases. Faced with large amounts of increasing spatial data, a terminal user has more difficulty in understanding them without the helpful knowledge from spatial databases. Thus, spatial data mining has been brought under the umbrella of data mining and is attracting more attention. Spatial data mining presents challenges. Differing from usual data, spatial data includes not only positional data and attribute data, but also spatial relationships among spatial events. Further, the instances of spatial events are embedded in a continuous space and share a variety of spatial relationships, so the mining of spatial patterns demands new techniques. In this thesis, several contributions were made. Some new techniques were proposed, i.e., fuzzy co-location mining, CPI-tree (Co-location Pattern Instance Tree), maximal co-location patterns mining, AOI-ags (Attribute-Oriented Induction based on Attributes’ Generalization Sequences), and fuzzy association prediction. Three algorithms were put forward on co-location patterns mining: the fuzzy co-location mining algorithm, the CPI-tree based co-location mining algorithm (CPI-tree algorithm) and the orderclique- based maximal prevalence co-location mining algorithm (order-clique-based algorithm). An attribute-oriented induction algorithm based on attributes’ generalization sequences (AOI-ags algorithm) is further given, which unified the attribute thresholds and the tuple thresholds. On the two real-world databases with time-series data, a fuzzy association prediction algorithm is designed. Also a cell-based spatial object fusion algorithm is proposed. Two fuzzy clustering methods using domain knowledge were proposed: Natural Method and Graph-Based Method, both of which were controlled by a threshold. The threshold was confirmed by polynomial regression. Finally, a prototype system on spatial co-location patterns’ mining was developed, and shows the relative efficiencies of the co-location techniques proposed The techniques presented in the thesis focus on improving the feasibility, usefulness, effectiveness, and scalability of related algorithm. In the design of fuzzy co-location Abstract mining algorithm, a new data structure, the binary partition tree, used to improve the process of fuzzy equivalence partitioning, was proposed. A prefix-based approach to partition the prevalent event set search space into subsets, where each sub-problem can be solved in main-memory, was also presented. The scalability of CPI-tree algorithm is guaranteed since it does not require expensive spatial joins or instance joins for identifying co-location table instances. In the order-clique-based algorithm, the co-location table instances do not need be stored after computing the Pi value of corresponding colocation, which dramatically reduces the executive time and space of mining maximal colocations. Some technologies, for example, partitions, equivalence partition trees, prune optimization strategies and interestingness, were used to improve the efficiency of the AOI-ags algorithm. To implement the fuzzy association prediction algorithm, the “growing window” and the proximity computation pruning were introduced to reduce both I/O and CPU costs in computing the fuzzy semantic proximity between time-series. For new techniques and algorithms, theoretical analysis and experimental results on synthetic data sets and real-world datasets were presented and discussed in the thesis

Fundamental structures of dynamic social networks

Social systems are in a constant state of flux with dynamics spanning from minute-by-minute changes to patterns present on the timescale of years. Accurate models of social dynamics are important for understanding spreading of influence or diseases, formation of friendships, and the productivity of teams. While there has been much progress on understanding complex networks over the past decade, little is known about the regularities governing the micro-dynamics of social networks. Here we explore the dynamic social network of a densely-connected population of approximately 1000 individuals and their interactions in the network of real-world person-to-person proximity measured via Bluetooth, as well as their telecommunication networks, online social media contacts, geo-location, and demographic data. These high-resolution data allow us to observe social groups directly, rendering community detection unnecessary. Starting from 5-minute time slices we uncover dynamic social structures expressed on multiple timescales. On the hourly timescale, we find that gatherings are fluid, with members coming and going, but organized via a stable core of individuals. Each core represents a social context. Cores exhibit a pattern of recurring meetings across weeks and months, each with varying degrees of regularity. Taken together, these findings provide a powerful simplification of the social network, where cores represent fundamental structures expressed with strong temporal and spatial regularity. Using this framework, we explore the complex interplay between social and geospatial behavior, documenting how the formation of cores are preceded by coordination behavior in the communication networks, and demonstrating that social behavior can be predicted with high precision.Comment: Main Manuscript: 16 pages, 4 figures. Supplementary Information: 39 pages, 34 figure

An investigation in efficient spatial patterns mining

The technical progress in computerized spatial data acquisition and storage results in the growth of vast spatial databases. Faced with large amounts of increasing spatial data, a terminal user has more difficulty in understanding them without the helpful knowledge from spatial databases. Thus, spatial data mining has been brought under the umbrella of data mining and is attracting more attention. Spatial data mining presents challenges. Differing from usual data, spatial data includes not only positional data and attribute data, but also spatial relationships among spatial events. Further, the instances of spatial events are embedded in a continuous space and share a variety of spatial relationships, so the mining of spatial patterns demands new techniques. In this thesis, several contributions were made. Some new techniques were proposed, i.e., fuzzy co-location mining, CPI-tree (Co-location Pattern Instance Tree), maximal co-location patterns mining, AOI-ags (Attribute-Oriented Induction based on Attributes’ Generalization Sequences), and fuzzy association prediction. Three algorithms were put forward on co-location patterns mining: the fuzzy co-location mining algorithm, the CPI-tree based co-location mining algorithm (CPI-tree algorithm) and the orderclique- based maximal prevalence co-location mining algorithm (order-clique-based algorithm). An attribute-oriented induction algorithm based on attributes’ generalization sequences (AOI-ags algorithm) is further given, which unified the attribute thresholds and the tuple thresholds. On the two real-world databases with time-series data, a fuzzy association prediction algorithm is designed. Also a cell-based spatial object fusion algorithm is proposed. Two fuzzy clustering methods using domain knowledge were proposed: Natural Method and Graph-Based Method, both of which were controlled by a threshold. The threshold was confirmed by polynomial regression. Finally, a prototype system on spatial co-location patterns’ mining was developed, and shows the relative efficiencies of the co-location techniques proposed The techniques presented in the thesis focus on improving the feasibility, usefulness, effectiveness, and scalability of related algorithm. In the design of fuzzy co-location Abstract mining algorithm, a new data structure, the binary partition tree, used to improve the process of fuzzy equivalence partitioning, was proposed. A prefix-based approach to partition the prevalent event set search space into subsets, where each sub-problem can be solved in main-memory, was also presented. The scalability of CPI-tree algorithm is guaranteed since it does not require expensive spatial joins or instance joins for identifying co-location table instances. In the order-clique-based algorithm, the co-location table instances do not need be stored after computing the Pi value of corresponding colocation, which dramatically reduces the executive time and space of mining maximal colocations. Some technologies, for example, partitions, equivalence partition trees, prune optimization strategies and interestingness, were used to improve the efficiency of the AOI-ags algorithm. To implement the fuzzy association prediction algorithm, the “growing window” and the proximity computation pruning were introduced to reduce both I/O and CPU costs in computing the fuzzy semantic proximity between time-series. For new techniques and algorithms, theoretical analysis and experimental results on synthetic data sets and real-world datasets were presented and discussed in the thesis.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

An investigation in efficient spatial patterns mining

The technical progress in computerized spatial data acquisition and storage results in the growth of vast spatial databases. Faced with large amounts of increasing spatial data, a terminal user has more difficulty in understanding them without the helpful knowledge from spatial databases. Thus, spatial data mining has been brought under the umbrella of data mining and is attracting more attention. Spatial data mining presents challenges. Differing from usual data, spatial data includes not only positional data and attribute data, but also spatial relationships among spatial events. Further, the instances of spatial events are embedded in a continuous space and share a variety of spatial relationships, so the mining of spatial patterns demands new techniques. In this thesis, several contributions were made. Some new techniques were proposed, i.e., fuzzy co-location mining, CPI-tree (Co-location Pattern Instance Tree), maximal co-location patterns mining, AOI-ags (Attribute-Oriented Induction based on Attributes’ Generalization Sequences), and fuzzy association prediction. Three algorithms were put forward on co-location patterns mining: the fuzzy co-location mining algorithm, the CPI-tree based co-location mining algorithm (CPI-tree algorithm) and the orderclique- based maximal prevalence co-location mining algorithm (order-clique-based algorithm). An attribute-oriented induction algorithm based on attributes’ generalization sequences (AOI-ags algorithm) is further given, which unified the attribute thresholds and the tuple thresholds. On the two real-world databases with time-series data, a fuzzy association prediction algorithm is designed. Also a cell-based spatial object fusion algorithm is proposed. Two fuzzy clustering methods using domain knowledge were proposed: Natural Method and Graph-Based Method, both of which were controlled by a threshold. The threshold was confirmed by polynomial regression. Finally, a prototype system on spatial co-location patterns’ mining was developed, and shows the relative efficiencies of the co-location techniques proposed The techniques presented in the thesis focus on improving the feasibility, usefulness, effectiveness, and scalability of related algorithm. In the design of fuzzy co-location Abstract mining algorithm, a new data structure, the binary partition tree, used to improve the process of fuzzy equivalence partitioning, was proposed. A prefix-based approach to partition the prevalent event set search space into subsets, where each sub-problem can be solved in main-memory, was also presented. The scalability of CPI-tree algorithm is guaranteed since it does not require expensive spatial joins or instance joins for identifying co-location table instances. In the order-clique-based algorithm, the co-location table instances do not need be stored after computing the Pi value of corresponding colocation, which dramatically reduces the executive time and space of mining maximal colocations. Some technologies, for example, partitions, equivalence partition trees, prune optimization strategies and interestingness, were used to improve the efficiency of the AOI-ags algorithm. To implement the fuzzy association prediction algorithm, the “growing window” and the proximity computation pruning were introduced to reduce both I/O and CPU costs in computing the fuzzy semantic proximity between time-series. For new techniques and algorithms, theoretical analysis and experimental results on synthetic data sets and real-world datasets were presented and discussed in the thesis.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Advances in Big Data Analytics: Algorithmic Stability and Data Cleansing

Analysis of what has come to be called “big data” presents a number of challenges as data continues to grow in size, complexity and heterogeneity. To help addresses these challenges, we study a pair of foundational issues in algorithmic stability (robustness and tuning), with application to clustering in high-throughput computational biology, and an issue in data cleansing (outlier detection), with application to pre-processing in streaming meteorological measurement. These issues highlight major ongoing research aspects of modern big data analytics. First, a new metric, robustness, is proposed in the setting of biological data clustering to measure an algorithm’s tendency to maintain output coherence over a range of parameter settings. It is well known that different algorithms tend to produce different clusters, and that the choice of algorithm is often driven by factors such as data size and type, similarity measure(s) employed, and the sort of clusters desired. Even within the context of a single algorithm, clusters often vary drastically depending on parameter settings. Empirical comparisons performed over a variety of algorithms and settings show highly differential performance on transcriptomic data and demonstrate that many popular methods actually perform poorly. Second, tuning strategies are studied for maximizing biological fidelity when using the well-known paraclique algorithm. Three initialization strategies are compared, using ontological enrichment as a proxy for cluster quality. Although extant paraclique codes begin by simply employing the first maximum clique found, results indicate that by generating all maximum cliques and then choosing one of highest average edge weight, one can produce a small but statistically significant expected improvement in overall cluster quality. Third, a novel outlier detection method is described that helps cleanse data by combining Pearson correlation coefficients, K-means clustering, and Singular Spectrum Analysis in a coherent framework that detects instrument failures and extreme weather events in Atmospheric Radiation Measurement sensor data. The framework is tested and found to produce more accurate results than do traditional approaches that rely on a hand-annotated database

Navigating Diverse Datasets in the Face of Uncertainty

When exploring big volumes of data, one of the challenging aspects is their diversity of origin. Multiple files that have not yet been ingested into a database system may contain information of interest to a researcher, who must curate, understand and sieve their content before being able to extract knowledge. Performance is one of the greatest difficulties in exploring these datasets. On the one hand, examining non-indexed, unprocessed files can be inefficient. On the other hand, any processing before its understanding introduces latency and potentially un- necessary work if the chosen schema matches poorly the data. We have surveyed the state-of-the-art and, fortunately, there exist multiple proposal of solutions to handle data in-situ performantly. Another major difficulty is matching files from multiple origins since their schema and layout may not be compatible or properly documented. Most surveyed solutions overlook this problem, especially for numeric, uncertain data, as is typical in fields like astronomy. The main objective of our research is to assist data scientists during the exploration of unprocessed, numerical, raw data distributed across multiple files based solely on its intrinsic distribution. In this thesis, we first introduce the concept of Equally-Distributed Dependencies, which provides the foundations to match this kind of dataset. We propose PresQ, a novel algorithm that finds quasi-cliques on hypergraphs based on their expected statistical properties. The probabilistic approach of PresQ can be successfully exploited to mine EDD between diverse datasets when the underlying populations can be assumed to be the same. Finally, we propose a two-sample statistical test based on Self-Organizing Maps (SOM). This method can outperform, in terms of power, other classifier-based two- sample tests, being in some cases comparable to kernel-based methods, with the advantage of being interpretable. Both PresQ and the SOM-based statistical test can provide insights that drive serendipitous discoveries

New approaches for clustering high dimensional data

Clustering is one of the most effective methods for analyzing datasets that contain a large number of objects with numerous attributes. Clustering seeks to identify groups, or clusters, of similar objects. In low dimensional space, the similarity between objects is often evaluated by summing the difference across all of their attributes. High dimensional data, however, may contain irrelevant attributes which mask the existence of clusters. The discovery of groups of objects that are highly similar within some subsets of relevant attributes becomes an important but challenging task. My thesis focuses on various models and algorithms for this task. We first present a flexible clustering model, namely OP-Cluster (Order Preserving Cluster). Under this model, two objects are similar on a subset of attributes if the values of these two objects induce the same relative ordering of these attributes. OPClustering algorithm has demonstrated to be useful to identify co-regulated genes in gene expression data. We also propose a semi-supervised approach to discover biologically meaningful OP-Clusters by incorporating existing gene function classifications into the clustering process. This semi-supervised algorithm yields only OP-clusters that are significantly enriched by genes from specific functional categories. Real datasets are often noisy. We propose a noise-tolerant clustering algorithm for mining frequently occuring itemsets. This algorithm is called approximate frequent itemsets (AFI). Both the theoretical and experimental results demonstrate that our AFI mining algorithm has higher recoverability of real clusters than any other existing itemset mining approaches. Pair-wise dissimilarities are often derived from original data to reduce the complexities of high dimensional data. Traditional clustering algorithms taking pair-wise dissimilarities as input often generate disjoint clusters from pair-wise dissimilarities. It is well known that the classification model represented by disjoint clusters is inconsistent with many real classifications, such gene function classifications. We develop a Poclustering algorithm, which generates overlapping clusters from pair-wise dissimilarities. We prove that by allowing overlapping clusters, Poclustering fully preserves the information of any dissimilarity matrices while traditional partitioning algorithms may cause significant information loss

Addressing Challenges in a Graph-Based Analysis of High-Throughput Biological Data

Graph-based methods used in the analysis of DNA microarray technology can be powerful tools in the elucidation of biological relationships. As these methods are developed and applied to various types of data, challenges arise that test the limits of current algorithms. These challenges arise in all phases of data analysis: data normalization, modeling biological networks, and interpreting results. Spectral graph theory methods are investigated as means of threshold selection, a key step in constructing graphical models of biological data. Also important in constructing graphs is the selection of an appropriate gene-gene similarity metric, and an overview of similarity profiles for some biological data sets is present, along with a similarity thresholding method based upon structural properties of random graphs. The identification of altered relationships between two or more conditions is a goal of many microarray gene expression studies. Clique-based methods can identify sets of coexpressed genes within each group, but additional computational methods are required to uncover the differential relationships and sets of genes changing together between groups. Differential filters are reviewed to highlight those changing interactions and sets of changing genes. The effect of various normalization methods on these differential results is also studied. Finally, how methods commonly used in the analysis of gene expression data can be used to investigate relationships in noisy and incomplete historical ecosystem data is explored