Edit distance

About: Edit distance is a research topic. Over the lifetime, 2887 publications have been published within this topic receiving 71491 citations.

Efficient Similarity Search for Hierarchical Data in Large Databases

Abstract: Structured and semi-structured object representations are getting more and more important for modern database applications. Examples for such data are hierarchical structures including chemical compounds, XML data or image data. As a key feature, database systems have to support the search for similar objects where it is important to take into account both the structure and the content features of the objects. A successful approach is to use the edit distance for tree structured data. As the computation of this measure is NP-complete, constrained edit distances have been successfully applied to trees. While yielding good results, they are still computationally complex and, therefore, of limited benefit for searching in large databases. In this paper, we propose a filter and refinement architecture to overcome this problem. We present a set of new filter methods for structural and for content-based information in tree-structured data as well as ways to flexibly combine different filter criteria. The efficiency of our methods, resulting from the good selectivity of the filters is demonstrated in extensive experiments with real-world applications.

Support Vector Machines for Paraphrase Identification and Corpus Construction

Abstract: The lack of readily-available large corpora of aligned monolingual sentence pairs is a major obstacle to the development of Statistical Machine Translation-based paraphrase models. In this paper, we describe the use of annotated datasets and Support Vector Machines to induce larger monolingual paraphrase corpora from a comparable corpus of news clusters found on the World Wide Web. Features include: morphological variants; WordNet synonyms and hypernyms; loglikelihood-based word pairings dynamically obtained from baseline sentence alignments; and formal string features such as word-based edit distance. Use of this technique dramatically reduces the Alignment Error Rate of the extracted corpora over heuristic methods based on position of the sentences in the text.

Efficiently Indexing Large Sparse Graphs for Similarity Search

Abstract: The graph structure is a very important means to model schemaless data with complicated structures, such as protein-protein interaction networks, chemical compounds, knowledge query inferring systems, and road networks. This paper focuses on the index structure for similarity search on a set of large sparse graphs and proposes an efficient indexing mechanism by introducing the Q-Gram idea. By decomposing graphs to small grams (organized by κ-Adjacent Tree patterns) and pairing-up on those κ-Adjacent Tree patterns, the lower bound estimation of their edit distance can be calculated for candidate filtering. Furthermore, we have developed a series of techniques for inverted index construction and online query processing. By building the candidate set for the query graph before the exact edit distance calculation, the number of graphs need to proceed into exact matching can be greatly reduced. Extensive experiments on real and synthetic data sets have been conducted to show the effectiveness and efficiency of the proposed indexing mechanism.

An Error-Tolerant Approximate Matching Algorithm for Attributed Planar Graphs and Its Application to Fingerprint Classification

Abstract: Graph edit distance is a powerful error-tolerant similarity measure for graphs. For pattern recognition problems involving large graphs, however, the high computational complexity makes it sometimes impossible to apply edit distance algorithms. In the present paper we propose an efficient algorithm for edit distance computation of planar graphs. Given graphs embedded in the plane, we iteratively match small subgraphs by locally optimizing structural correspondences. Eventually we obtain a valid edit path and hence an upper bound of the edit distance. To demonstrate the efficiency of our approach, we apply the proposed algorithm to the problem of fingerprint classification.

Private genome analysis through homomorphic encryption

Abstract: The rapid development of genome sequencing technology allows researchers to access large genome datasets. However, outsourcing the data processing o the cloud poses high risks for personal privacy. The aim of this paper is to give a practical solution for this problem using homomorphic encryption. In our approach, all the computations can be performed in an untrusted cloud without requiring the decryption key or any interaction with the data owner, which preserves the privacy of genome data. We present evaluation algorithms for secure computation of the minor allele frequencies and χ2 statistic in a genome-wide association studies setting. We also describe how to privately compute the Hamming distance and approximate Edit distance between encrypted DNA sequences. Finally, we compare performance details of using two practical homomorphic encryption schemes - the BGV scheme by Gentry, Halevi and Smart and the YASHE scheme by Bos, Lauter, Loftus and Naehrig. The approach with the YASHE scheme analyzes data from 400 people within about 2 seconds and picks a variant associated with disease from 311 spots. For another task, using the BGV scheme, it took about 65 seconds to securely compute the approximate Edit distance for DNA sequences of size 5K and figure out the differences between them. The performance numbers for BGV are better than YASHE when homomorphically evaluating deep circuits (like the Hamming distance algorithm or approximate Edit distance algorithm). On the other hand, it is more efficient to use the YASHE scheme for a low-degree computation, such as minor allele frequencies or χ2 test statistic in a case-control study.