We survey the current techniques to cope with the problem of string matching that allows errors. This is becoming a more and more relevant issue for many fast growing areas such as information retrieval and computational biology. We focus on online searching and mostly on edit distance, explaining the problem and its relevance, its statistical behavior, its history and current developments, and the central ideas of the algorithms and their complexities. We present a number of experiments to compare the performance of the different algorithms and show which are the best choices. We conclude with some directions for future work and open problems.

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A guided tour to approximate string matching

This book presents a practical approach to string matching problems, focusing on the algorithms and implementations that perform best in practice. It covers searching for simple, multiple, and extended strings, as well as regular expressions, exactly and approximately. It includes all of the most significant new developments in complex pattern searching. The clear explanations, step-by-step examples, algorithms pseudo-code, and implementation efficiency maps will enable researchers, professionals, and students in bioinformatics, computer science, and software engineering to choose the most appropriate algorithms for their applications.

Flexible Pattern Matching in Strings: Practical On-Line Search Algorithms for Texts and Biological Sequences

A distance measure for video sequences

A procedure for detecting a reordering requirement in a directed record stream during query execution in a relational database processing system. The query compiler component of a relational database processing system includes procedures for building query execution plans (QEPs) for evaluation preparatory to selecting an optimal plan for execution. These plans are constructed from the bottom up using an internal graphical representation for the user query that has a number of relation nodes interconnected by directed record streams (data flows). A relational operation within each node imposes an "order requirement" on the outflow stream represented by an order requirement vector OR. The records within each directed record stream have an "order property" represented by an order property vector OP. Order detection occurs when these two vectors are compared to determine whether the order property satisfies the order requirement. Order detection by normalization (ODN) according to this invention first normalizes the two order specification vectors to remove all attributes made redundant by the effects of predicates and functional dependencies. Query execution plans constructed using ODN are found to execute an order of magnitude faster than those constructed using order detection without normalization.

Semantic optimization of query order requirements using order detection by normalization in a query compiler system

The rapid growth of digital libraries, e-governance, and internet based applications has caused an exponential escalation in the volume of ‘Big-data’ particularly due to texts, images, audios and videos that are being both archived and transmitted on a daily basis. In order to make their storage and transfer efficient, different data compression techniques are used in the literature. The ultimate motive behind data compression is to transform a big size data into small size data, which eventually implies less space while archiving, and less time in transferring. However, in order to operate/analyze compressed data, it is usually necessary to decompress it, so as to bring back the data to its original form, which unfortunately warrants an additional computing cost. In this backdrop, if operating upon the compressed data itself can be made possible without going through the stage of decompression, then the advantage that could be accomplished due to compression would escalate. Further due to compression, from the data structure and storage perspectives, the original visibility structure of the data also being lost, it turns into a potential challenge to trace the original information in the compressed representation. This challenge is the motivation behind exploring the idea of direct processing on the compressed data itself in the literature. The proposed survey paper specifically focuses on compressed document images and brings out two original contributions. The first contribution is that it presents a critical study on different image analysis and image compression techniques, and highlights the motivational reasons for pursuing document image analysis in the compressed domain. The second contribution is that it summarizes the different compressed domain techniques in the literature so far based on the type of compression and operations performed by them. Overall, the paper aims to provide a perspective for pursuing further research in the area of document image analysis and pattern recognition directly based on the compressed data.

A review on document image analysis techniques directly in the compressed domain

Repetitive strings have been studied in such diverse fields as molecular biology data compression etc. Some important regularities that have been studied are perods, covers seeds and squares. A natural extension of the repetition problems is to allow errors. Among the four notions above aproximate squares and approximate periodes have been studied. In this paper, we introduce the notion of approximate covers which is an approximate version of covers. Given two strings P(｜P｜=m) and T(｜T｜=n) we propose and algorithm with finds the minimum distance t such that P is a t-approximate cover of T. The algorithm take O(m,n) time for the edit distance and time of finding a string which is an approximate cover of T is minimum distance is NP-complete.

Finding Approximate Covers of Strings

Efficient Algorithms for Approximate String Matching with Swaps

The authors present an algorithm for the HVH. . .VH multi-layer channel routing problem. First they determine the net groups to be positioned on the same track using a left-edge algorithm. The vertical constraint graph made from these net groups may contain many cycles. There is an attempt to remove the cycles through proper layer assignment and maze routing. >

Jee-Soo Lee

Papers

Finding Approximate Covers of Strings

Efficient Algorithms for Approximate String Matching with Swaps

HVH. . .VH multi-layer channel routing