Clustering Algorithms for Microarray Data Mining

This thesis presents a systems engineering model of modern drug discovery processes and related systems integration requirements. Some challenging problems include the integration of public information content with proprietary corporate content, supporting different types of scientific analyses, and automated analysis tools motivated by diverse forms of biological data.To capture the requirements of the discovery system, we identify the processes, users, and scenarios to form a UML use case model. We then define the object-oriented system structure and attach behavioral elements. We also look at how object-relational database extensions can be applied for such analysis.The next portion of the thesis studies the performance of clustering algorithms based on LVQ, SVMs, and other machine learning algorithms, to two types of analyses - functional and phenotypic classification. We found that LVQ initialized with the LBG codebook yields comparable performance to the optimal separating surfaces generated by related SVM kernels. We also describe a novel similarity measure, called the unnormalized symmetric Kullback-Liebler measure, based on unnormalized expression values. Since the Mercer criterion cannot be applied to this measure, we compared the performance of this similarity measure with the log-Euclidean distance in the LVQ algorithm.The two distance measures perform similarly on cDNA arrays, while the unnormalized symmetric Kullback-Liebler measure outperforms the log-Euclidean distance on certain phenotypic classification problems. Pre-filtering algorithms to find discriminating instances based on PCA, the Find Similar function, and IB3 were also investigated. The Find Similar method gives the best performance in terms of multiple criteria

Automated anomaly recognition in real time data streams for oil and gas industry.

There is a growing demand for computer-assisted real-time anomaly detection - from the identification of suspicious activities in cyber security, to the monitoring of engineering data for various applications across the oil and gas, automotive and other engineering industries. To reduce the reliance on field experts' knowledge for identification of these anomalies, this thesis proposes a deep-learning anomaly-detection framework that can help to create an effective real-time condition-monitoring framework. The aim of this research is to develop a real-time and re-trainable generic anomaly-detection framework, which is capable of predicting and identifying anomalies with a high level of accuracy - even when a specific anomalous event has no precedent. Machine-based condition monitoring is preferable in many practical situations where fast data analysis is required, and where there are harsh climates or otherwise life-threatening environments. For example, automated conditional monitoring systems are ideal in deep sea exploration studies, offshore installations and space exploration. This thesis firstly reviews studies about anomaly detection using machine learning. It then adopts the best practices from those studies in order to propose a multi-tiered framework for anomaly detection with heterogeneous input sources, which can deal with unseen anomalies in a real-time dynamic problem environment. The thesis then applies the developed generic multi-tiered framework to two fields of engineering: data analysis and malicious cyber attack detection. Finally, the framework is further refined based on the outcomes of those case studies and is used to develop a secure cross-platform API, capable of re-training and data classification on a real-time data feed

Development of a WEB application

Ankara : The Department of Molecular Biology and Genetics and the Graduate School of Engineering and Science of Bilkent University, 2011.Thesis (Ph. D.) -- Bilkent University, 2011.Includes bibliographical references leaves 99-115.microRNAs, small non-coding RNA molecules with important roles in cellular machinery, target mRNAs for silencing by binding generally to their 3’ UTR sequences via partial base complementation. Thus, microRNAs with similar sequences also might exhibit expression and/or functional similarities. In this study, a modular tool, mESAdb (http://konulab.fen.bilkent.edu.tr/mirna/), was developed allowing for multivariate analysis of sequences and expression of microRNAs from multiple taxa. Its framework comprises PHP, JavaScript, packages in the R language, and a database storing mature microRNA sequences along with microRNA targets and selected expression data sets for human, mouse and zebrafish. mESAdb allows for: (i) mining of microRNA expression data sets for subsets of microRNAs selected manually or by a sequence motif; (ii) pair-wise multivariate analysis of expression data sets within and between taxa; and (iii) association of microRNA subsets with annotation databases, HuGE Navigator, KEGG and GO. mESAdb also permits user specified dataset upload for these analyses. Herein, utility of mESAdb was illustrated using different datasets and case studies. First, it was shown that microRNAs carrying the embryonic stem cell specific seed sequence, ‘AAGTGC’, were able to discriminate between normal and tumor tissues from hepatocellular carcinoma patients using dataset GSE10694. Second, mRNA targets of a set of liver specific microRNAs were annotated with human diseases based on HuGE Navigator. Third, the similarity between mouse and human tissue specificity of a given set of microRNAs was demonstrated. Forth, CHRNA5 targeting microRNAs were associated with estrogen receptor status in breast cancer using dataset GSE15885. Finally, a related tool under development for mRNA arrays planned for integration with mESAdb was presented.Kaya, Koray DoğanPh.D

Computer aided drug design: Drug target directed in silico approaches

Ph.DDOCTOR OF PHILOSOPH

NEW METHODS FOR MINING SEQUENTIAL AND TIME SERIES DATA

Data mining is the process of extracting knowledge from large amounts of data. It covers a variety of techniques aimed at discovering diverse types of patterns on the basis of the requirements of the domain. These techniques include association rules mining, classification, cluster analysis and outlier detection. The availability of applications that produce massive amounts of spatial, spatio-temporal (ST) and time series data (TSD) is the rationale for developing specialized techniques to excavate such data. In spatial data mining, the spatial co-location rule problem is different from the association rule problem, since there is no natural notion of transactions in spatial datasets that are embedded in continuous geographic space. Therefore, we have proposed an efficient algorithm (GridClique) to mine interesting spatial co-location patterns (maximal cliques). These patterns are used as the raw transactions for an association rule mining technique to discover complex co-location rules. Our proposal includes certain types of complex relationships – especially negative relationships – in the patterns. The relationships can be obtained from only the maximal clique patterns, which have never been used until now. Our approach is applied on a well-known astronomy dataset obtained from the Sloan Digital Sky Survey (SDSS). ST data is continuously collected and made accessible in the public domain. We present an approach to mine and query large ST data with the aim of finding interesting patterns and understanding the underlying process of data generation. An important class of queries is based on the flock pattern. A flock is a large subset of objects moving along paths close to each other for a predefined time. One approach to processing a “flock query” is to map ST data into high-dimensional space and to reduce the query to a sequence of standard range queries that can be answered using a spatial indexing structure; however, the performance of spatial indexing structures rapidly deteriorates in high-dimensional space. This thesis sets out a preprocessing strategy that uses a random projection to reduce the dimensionality of the transformed space. We use probabilistic arguments to prove the accuracy of the projection and to present experimental results that show the possibility of managing the curse of dimensionality in a ST setting by combining random projections with traditional data structures. In time series data mining, we devised a new space-efficient algorithm (SparseDTW) to compute the dynamic time warping (DTW) distance between two time series, which always yields the optimal result. This is in contrast to other approaches which typically sacrifice optimality to attain space efficiency. The main idea behind our approach is to dynamically exploit the existence of similarity and/or correlation between the time series: the more the similarity between the time series, the less space required to compute the DTW between them. Other techniques for speeding up DTW, impose a priori constraints and do not exploit similarity characteristics that may be present in the data. Our experiments demonstrate that SparseDTW outperforms these approaches. We discover an interesting pattern by applying SparseDTW algorithm: “pairs trading” in a large stock-market dataset, of the index daily prices from the Australian stock exchange (ASX) from 1980 to 2002

Efficient processing of similarity queries with applications

Today, a myriad of data sources, from the Internet to business operations to scientific instruments, produce large and different types of data. Many application scenarios, e.g., marketing analysis, sensor networks, and medical and biological applications, call for identifying and processing similarities in big data. As a result, it is imperative to develop new similarity query processing approaches and systems that scale from low dimensional data to high dimensional data, from single machine to clusters of hundreds of machines, and from disk-based to memory-based processing. This dissertation introduces and studies several similarity-aware query operators, analyzes and optimizes their performance. The first contribution of this dissertation is an SQL-based Similarity Group-by operator (SGB, for short) that extends the semantics of the standard SQL Group-by operator to group data with similar but not necessarily equal values. We realize these SGB operators by extending the Standard SQL Group-by and introduce two new SGB operators for multi-dimensional data. We implement and test the new SGB operators and their algorithms inside an open-source centralized database server (PostgreSQL). In the second contribution of this dissertation, we study how to efficiently process Hamming-distance-based similarity queries (Hamming-distance select and Hamming-distance join) that are crucial to many applications. We introduce a new index, termed the HA-Index, that speeds up distance comparisons and eliminates redundancies when performing the two flavors of Hamming distance range queries (namely, the selects and joins). In the third and last contribution of this dissertation, we develop a system for similarity query processing and optimization in an in-memory and distributed setup for big spatial data. We propose a query scheduler and a distributed query optimizer that use a new cost model to optimize the cost of similarity query processing in this in-memory distributed setup. The scheduler and query optimizer generates query execution plans that minimize the effect of query skew. The query scheduler employs new spatial indexing techniques based on bloom filters to forward queries to the appropriate local sites. The proposed query processing and optimization techniques are prototyped inside Spark, a distributed main-memory computation system