Online Pattern Matching for String Edit Distance with Moves

Edit distance with moves (EDM) is a string-to-string distance measure that includes substring moves in addition to ordinal editing operations to turn one string to the other. Although optimizing EDM is intractable, it has many applications especially in error detections. Edit sensitive parsing (ESP) is an efficient parsing algorithm that guarantees an upper bound of parsing discrepancies between different appearances of the same substrings in a string. ESP can be used for computing an approximate EDM as the L1 distance between characteristic vectors built by node labels in parsing trees. However, ESP is not applicable to a streaming text data where a whole text is unknown in advance. We present an online ESP (OESP) that enables an online pattern matching for EDM. OESP builds a parse tree for a streaming text and computes the L1 distance between characteristic vectors in an online manner. For the space-efficient computation of EDM, OESP directly encodes the parse tree into a succinct representation by leveraging the idea behind recent results of a dynamic succinct tree. We experimentally test OESP on the ability to compute EDM in an online manner on benchmark datasets, and we show OESP's efficiency.Comment: This paper has been accepted to the 21st edition of the International Symposium on String Processing and Information Retrieval (SPIRE2014

An efficient algorithm for sequence comparison with block reversals

AbstractGiven two sequences X and Y that are strings over some alphabet set, we consider the distance d(X,Y) between them defined to be minimum number of character replacements and block (substring) reversals needed to transform X to Y (or vice versa). The operations are required to be disjoint. This is the “simplest” sequence comparison problem we know of that allows natural block edit operations. Block reversals arise naturally in genomic sequence comparison; they are also of interest in matching music data. We present an algorithm for exactly computing the distance d(X,Y); it takes time O(|X|log2|X|), and hence, is near-linear. Trivial approach takes quadratic time

Approximate Nearest Neighbors and Sequence Comparison With Block Operations

We study sequence nearest neighbors (SNN). Let D be a database of n sequences; we would like to preprocess D so that given any on-line query sequence Q we can quickly find a sequence S in D for which d(S; Q) d(S; T ) for any other sequence T in D. Here d(S; Q) denotes the distance between sequences S and Q, defined to be the minimum number of edit operations needed to transform one to another (all edit operations will be reversible so that d(S; T ) = d(T; S) for any two sequences T and S). These operations correspond to the notion of similarity between sequences that we wish to capture in a given application. Natural edit operations include character edits (inserts, replacements, deletes etc), block edits (moves, copies, deletes, reversals) and block numerical transformations (scaling by an additive or a multiplicative constant). The SNN problem arises in many applications. We present the first known efficient algorithm for "approximate" nearest neighbor search for sequences with p..

Approximate Nearest Neighbors and Sequence Comparison with Block Operations

We study sequence nearest neighbors (SNN). Let a database of sequences; we would like to preprocess so that given any on-line query sequence we can quickly find a sequence whic

Analyse de grappe des données de catégories et de séquences étude et application à la prédiction de la faillite personnelle

Cluster analysis is one of the most important and useful data mining techniques, and there are many applications of cluster analysis in pattern extraction, information retrieval, summarization, compression and other areas. The focus of this thesis is on clustering categorical and sequence data. Clustering categorical and sequence data is much more challenging than clustering numeric data because there is no inherently meaningful measure of similarity between the categorical objects and sequences. In this thesis, we design novel efficient and effective clustering algorithms for clustering categorical data and sequence respectively, and we perform extensive experiments to demonstrate the superior performance of our proposed algorithm. We also explore the extent to which the use of the proposed clustering algorithms can help to solve the personal bankruptcy prediction problem. Clustering categorical data poses two challenges: defining an inherently meaningful similarity measure, and effectively dealing with clusters which are often embedded in different subspaces. In this thesis, we view the task of clustering categorical data from an optimization perspective and propose a novel objective function. Based on the new formulation, we design a divisive hierarchical clustering algorithm for categorical data, named DHCC. In the bisection procedure of DHCC, the initialization of the splitting is based on multiple correspondence analysis (MCA). We devise a strategy for dealing with the key issue in the divisive approach, namely, when to terminate the splitting process. The proposed algorithm is parameter-free, independent of the order in which the data is processed, scalable to large data sets and capable of seamlessly discovering clusters embedded in subspaces. The prior knowledge about the data can be incorporated into the clustering process, which is known as semi-supervised clustering, to produce considerable improvement in learning accuracy. In this thesis, we view semi-supervised clustering of categorical data as an optimization problem with extra instance-level constraints, and propose a systematic and fully automated approach to guide the optimization process to a better solution in terms of satisfying the constraints, which would also be beneficial to the unconstrained objects. The proposed semi-supervised divisive hierarchical clustering algorithm for categorical data, named SDHCC, is parameter-free, fully automatic and effective in taking advantage of instance-level constraint background knowledge to improve the quality of the resultant dendrogram. Many existing sequence clustering algorithms rely on a pair-wise measure of similarity between sequences. Usually, such a measure is effective if there are significantly informative patterns in the sequences. However, it is difficult to define a meaningful pair-wise similarity measure if sequences are short and contain noise. In this thesis, we circumvent the obstacle of defining the pairwise similarity by defining the similarity between an individual sequence and a set of sequences. Based on the new similarity measure, which is based on the conditional probability distribution (CPD) model, we design a novel model-based K -means clustering algorithm for sequence clustering, which works in a similar way to the traditional K -means on vectorial data. Finally, we develop a personal bankruptcy prediction system whose predictors are mainly the bankruptcy features discovered by the clustering techniques proposed in this thesis. The mined bankruptcy features are represented in low-dimensional vector space. From the new feature space, which can be extended with some existing prediction-capable features (e.g., credit score), a support vector machine (SVM) classifier is built to combine these mined and already existing features. Our system is readily comprehensible and demonstrates promising prediction performance

Online Analysis of Dynamic Streaming Data

Die Arbeit zum Thema "Online Analysis of Dynamic Streaming Data" beschäftigt sich mit der Distanzmessung dynamischer, semistrukturierter Daten in kontinuierlichen Datenströmen um Analysen auf diesen Datenstrukturen bereits zur Laufzeit zu ermöglichen. Hierzu wird eine Formalisierung zur Distanzberechnung für statische und dynamische Bäume eingeführt und durch eine explizite Betrachtung der Dynamik von Attributen einzelner Knoten der Bäume ergänzt. Die Echtzeitanalyse basierend auf der Distanzmessung wird durch ein dichte-basiertes Clustering ergänzt, um eine Anwendung des Clustering, einer Klassifikation, aber auch einer Anomalieerkennung zu demonstrieren. Die Ergebnisse dieser Arbeit basieren auf einer theoretischen Analyse der eingeführten Formalisierung von Distanzmessungen für dynamische Bäume. Diese Analysen werden unterlegt mit empirischen Messungen auf Basis von Monitoring-Daten von Batchjobs aus dem Batchsystem des GridKa Daten- und Rechenzentrums. Die Evaluation der vorgeschlagenen Formalisierung sowie der darauf aufbauenden Echtzeitanalysemethoden zeigen die Effizienz und Skalierbarkeit des Verfahrens. Zudem wird gezeigt, dass die Betrachtung von Attributen und Attribut-Statistiken von besonderer Bedeutung für die Qualität der Ergebnisse von Analysen dynamischer, semistrukturierter Daten ist. Außerdem zeigt die Evaluation, dass die Qualität der Ergebnisse durch eine unabhängige Kombination mehrerer Distanzen weiter verbessert werden kann. Insbesondere wird durch die Ergebnisse dieser Arbeit die Analyse sich über die Zeit verändernder Daten ermöglicht