Summarizing a set of time series by averaging: From Steiner sequence to compact multiple alignment

AbstractSummarizing a set of sequences is an old topic that has been revived in the last decade, due to the increasing availability of sequential datasets. The definition of a consensus object is on the center of data analysis issues, since it crystallizes the underlying organization of the data.Dynamic Time Warping (DTW) is currently the most relevant similarity measure between sequences for a large panel of applications, since it makes it possible to capture temporal distortions. In this context, averaging a set of sequences is not a trivial task, since the average sequence has to be consistent with this similarity measure.The Steiner theory and several works in computational biology have pointed out the connection between multiple alignments and average sequences. Taking inspiration from these works, we introduce the notion of compact multiple alignment, which allows us to link these theories to the problem of summarizing under time warping. Having defined the link between the multiple alignment and the average sequence, the second part of this article focuses on the scan of the space of compact multiple alignments in order to provide an average sequence of a set of sequences. We propose to use a genetic algorithm based on a specific representation of the genotype inspired by genes. This representation of the genotype makes it possible to consistently paint the fitness landscape.Experiments carried out on standard datasets show that the proposed approach outperforms existing methods

Approximate String Matching With Dynamic Programming and Suffix Trees

The importance and the contribution of string matching algorithms to the modern society cannot be overstated. From basic search algorithms such as spell checking and data querying, to advanced algorithms such as DNA sequencing, trend analysis and signal processing, string matching algorithms form the foundation of many aspects in computing that have been pivotal in technological advancement. In general, string matching algorithms can be divided into the categories of exact string matching and approximate string matching. We study each area and examine some of the well known algorithms. We probe into one of the most intriguing data structure in string algorithms, the suffix tree. The lowest common ancestor extension of the suffix tree is the key to many advanced string matching algorithms. With these tools, we are able to solve string problems that were, until recently, thought intractable by many. Another interesting and relatively new data structure in string algorithms is the suffix array, which has significant breakthroughs in its linear time construction in recent years. Primarily, this thesis focuses on approximate string matching using dynamic programming and hybrid dynamic programming with suffix tree. We study both approaches in detail and see how the merger of exact string matching and approximate string matching algorithms can yield synergistic results in our experiments

Survey on representation techniques for malware detection system

Malicious programs are malignant software’s designed by hackers or cyber offenders with a harmful intent to disrupt computer operation. In various researches, we found that the balance between designing an accurate architecture that can detect the malware and track several advanced techniques that malware creators apply to get variants of malware are always a difficult line. Hence the study of malware detection techniques has become more important and challenging within the security field. This review paper provides a detailed discussion and full reviews for various types of malware, malware detection techniques, various researches on them, malware analysis methods and different dynamic programmingbased tools that could be used to represent the malware sampled. We have provided a comprehensive bibliography in malware detection, its techniques and analysis methods for malware researchers

Detecting and Modeling Polymorphic Shellcode

In this thesis, we address the problem of modeling and detecting polymorphic engines shellcode. By polymorphic engines, we mean programs having the ability to transform any piece of malware into many instances consisting of different code but having the same functionality as the original malware. Typically, polymorphic engines work by encrypting the target malware using various encryption techniques and providing a decryption module in order to execute the newly encrypted instance. Moreover, those engines have the ability to mutate their decryption routine making them unique from one instance to another and hard to detect. Our analysis focuses on polymorphic shellcode, which is shellcode that uses a polymorphic engine to mutate while keeping the original function of the code the same. We propose a new concept of signatures, shape signatures, which cope with the highly mutated nature of those engines. Those signatures try to identify the constant part as well as the mutated part of the deciphering routines. This combination is able to cope with the highly mutated nature of those engines in a much more efficient way compared to traditional signatures used in most intrusion detection systems. The second part of the thesis aims at modeling those polymorphic engines by showing that they exhibit commo

Eddy current defect response analysis using sum of Gaussian methods

This dissertation is a study of methods to automatedly detect and produce approximations of eddy current differential coil defect signatures in terms of a summed collection of Gaussian functions (SoG). Datasets consisting of varying material, defect size, inspection frequency, and coil diameter were investigated. Dimensionally reduced representations of the defect responses were obtained utilizing common existing reduction methods and novel enhancements to them utilizing SoG Representations. Efficacy of the SoG enhanced representations were studied utilizing common Machine Learning (ML) interpretable classifier designs with the SoG representations indicating significant improvement of common analysis metrics

Approximate Matching in Genomic Sequence Data

Ph.DDOCTOR OF PHILOSOPH

Mining a Small Medical Data Set by Integrating the Decision Tree and t-test

[[abstract]]Although several researchers have used statistical methods to prove that aspiration followed by the injection of 95% ethanol left in situ (retention) is an effective treatment for ovarian endometriomas, very few discuss the different conditions that could generate different recovery rates for the patients. Therefore, this study adopts the statistical method and decision tree techniques together to analyze the postoperative status of ovarian endometriosis patients under different conditions. Since our collected data set is small, containing only 212 records, we use all of these data as the training data. Therefore, instead of using a resultant tree to generate rules directly, we use the value of each node as a cut point to generate all possible rules from the tree first. Then, using t-test, we verify the rules to discover some useful description rules after all possible rules from the tree have been generated. Experimental results show that our approach can find some new interesting knowledge about recurrent ovarian endometriomas under different conditions.[[journaltype]]國外[[incitationindex]]EI[[booktype]]紙本[[countrycodes]]FI

Sequence queries on temporal graphs

Graphs that evolve over time are called temporal graphs. They can be used to describe and represent real-world networks, including transportation networks, social networks, and communication networks, with higher fidelity and accuracy. However, research is still limited on how to manage large scale temporal graphs and execute queries over these graphs efficiently and effectively. This thesis investigates the problems of temporal graph data management related to node and edge sequence queries. In temporal graphs, nodes and edges can evolve over time. Therefore, sequence queries on nodes and edges can be key components in managing temporal graphs. In this thesis, the node sequence query decomposes into two parts: graph node similarity and subsequence matching. For node similarity, this thesis proposes a modified tree edit distance that is metric and polynomially computable and has a natural, intuitive interpretation. Note that the proposed node similarity works even for inter-graph nodes and therefore can be used for graph de-anonymization, network transfer learning, and cross-network mining, among other tasks. The subsequence matching query proposed in this thesis is a framework that can be adopted to index generic sequence and time-series data, including trajectory data and even DNA sequences for subsequence retrieval. For edge sequence queries, this thesis proposes an efficient storage and optimized indexing technique that allows for efficient retrieval of temporal subgraphs that satisfy certain temporal predicates. For this problem, this thesis develops a lightweight data management engine prototype that can support time-sensitive temporal graph analytics efficiently even on a single PC