A survey on tree matching and XML retrieval

International audienceWith the increasing number of available XML documents, numerous approaches for retrieval have been proposed in the literature. They usually use the tree representation of documents and queries to process them, whether in an implicit or explicit way. Although retrieving XML documents can be considered as a tree matching problem between the query tree and the document trees, only a few approaches take advantage of the algorithms and methods proposed by the graph theory. In this paper, we aim at studying the theoretical approaches proposed in the literature for tree matching and at seeing how these approaches have been adapted to XML querying and retrieval, from both an exact and an approximate matching perspective. This study will allow us to highlight theoretical aspects of graph theory that have not been yet explored in XML retrieval

A clique-based method for the edit distance between unordered trees and its application to analysis of glycan structures

[Background]Measuring similarities between tree structured data is important for analysis of RNA secondary structures, phylogenetic trees, glycan structures, and vascular trees. The edit distance is one of the most widely used measures for comparison of tree structured data. However, it is known that computation of the edit distance for rooted unordered trees is NP-hard. Furthermore, there is almost no available software tool that can compute the exact edit distance for unordered trees. [Results]In this paper, we present a practical method for computing the edit distance between rooted unordered trees. In this method, the edit distance problem for unordered trees is transformed into the maximum clique problem and then efficient solvers for the maximum clique problem are applied. We applied the proposed method to similar structure search for glycan structures. The result suggests that our proposed method can efficiently compute the edit distance for moderate size unordered trees. It also suggests that the proposed method has the accuracy comparative to those by the edit distance for ordered trees and by an existing method for glycan search. [Conclusions]The proposed method is simple but useful for computation of the edit distance between unordered trees. The object code is available upon request

Discovering Shape Classes using Tree Edit-Distance and Pairwise Clustering

This paper describes work aimed at the unsupervised learning of shape-classes from shock trees. We commence by considering how to compute the edit distance between weighted trees. We show how to transform the tree edit distance problem into a series of maximum weight clique problems, and show how to use relaxation labeling to find an approximate solution. This allows us to compute a set of pairwise distances between graph-structures. We show how the edit distances can be used to compute a matrix of pairwise affinities using χ² statistics. We present a maximum likelihood method for clustering the graphs by iteratively updating the elements of the affinity matrix. This involves interleaved steps for updating the affinity matrix using an eigendecomposition method and updating the cluster membership indicators. We illustrate the new tree clustering framework on shock-graphs extracted from the silhouettes of 2D shapes

XML Matchers: approaches and challenges

Schema Matching, i.e. the process of discovering semantic correspondences between concepts adopted in different data source schemas, has been a key topic in Database and Artificial Intelligence research areas for many years. In the past, it was largely investigated especially for classical database models (e.g., E/R schemas, relational databases, etc.). However, in the latest years, the widespread adoption of XML in the most disparate application fields pushed a growing number of researchers to design XML-specific Schema Matching approaches, called XML Matchers, aiming at finding semantic matchings between concepts defined in DTDs and XSDs. XML Matchers do not just take well-known techniques originally designed for other data models and apply them on DTDs/XSDs, but they exploit specific XML features (e.g., the hierarchical structure of a DTD/XSD) to improve the performance of the Schema Matching process. The design of XML Matchers is currently a well-established research area. The main goal of this paper is to provide a detailed description and classification of XML Matchers. We first describe to what extent the specificities of DTDs/XSDs impact on the Schema Matching task. Then we introduce a template, called XML Matcher Template, that describes the main components of an XML Matcher, their role and behavior. We illustrate how each of these components has been implemented in some popular XML Matchers. We consider our XML Matcher Template as the baseline for objectively comparing approaches that, at first glance, might appear as unrelated. The introduction of this template can be useful in the design of future XML Matchers. Finally, we analyze commercial tools implementing XML Matchers and introduce two challenging issues strictly related to this topic, namely XML source clustering and uncertainty management in XML Matchers.Comment: 34 pages, 8 tables, 7 figure

The geometry of syntax and semantics for directed file transformations

We introduce a conceptual framework that associates syntax and semantics with vertical and horizontal directions in principal bundles and related constructions. This notion of geometry corresponds to a mechanism for performing goal-directed file transformations such as "eliminate unsafe syntax" and suggests various engineering practices

Matching hierarchical structures for shape recognition

In this thesis we aim to develop a framework for clustering trees and rep- resenting and learning a generative model of graph structures from a set of training samples. The approach is applied to the problem of the recognition and classification of shape abstracted in terms of its morphological skeleton. We make five contributions. The first is an algorithm to approximate tree edit-distance using relaxation labeling. The second is the introduction of the tree union, a representation capable of representing the modes of structural variation present in a set of trees. The third is an information theoretic approach to learning a generative model of tree structures from a training set. While the skeletal abstraction of shape was chosen mainly as a exper- imental vehicle, we, nonetheless, make some contributions to the fields of skeleton extraction and its graph representation. In particular, our fourth contribution is the development of a skeletonization method that corrects curvature effects in the Hamilton-Jacobi framework, improving its localiza- tion and noise sensitivity. Finally, we propose a shape-measure capable of characterizing shapes abstracted in terms of their skeleton. This measure has a number of interesting properties. In particular, it varies smoothly as the shape is deformed and can be easily computed using the presented skeleton extraction algorithm. Each chapter presents an experimental analysis of the proposed approaches applied to shape recognition problems

Social Network Data Management

With the increasing usage of online social networks and the semantic web's graph structured RDF framework, and the rising adoption of networks in various fields from biology to social science, there is a rapidly growing need for indexing, querying, and analyzing massive graph structured data. Facebook has amassed over 500 million users creating huge volumes of highly connected data. Governments have made RDF datasets containing billions of triples available to the public. In the life sciences, researches have started to connect disparate data sets of research results into one giant network of valuable information. Clearly, networks are becoming increasingly popular and growing rapidly in size, requiring scalable solutions for network data management. This thesis focuses on the following aspects of network data management. We present a hierarchical index structure for external memory storage of network data that aims to maximize data locality. We propose efficient algorithms to answer subgraph matching queries against network databases and discuss effective pruning strategies to improve performance. We show how adaptive cost models can speed up subgraph matching query answering by assigning budgets to index retrieval operations and adjusting the query plan while executing. We develop a cloud oriented social network database, COSI, which handles massive network datasets too large for a single computer by partitioning the data across multiple machines and achieving high performance query answering through asynchronous parallelization and cluster-aware heuristics. Tracking multiple standing queries against a social network database is much faster with our novel multi-view maintenance algorithm, which exploits common substructures between queries. To capture uncertainty inherent in social network querying, we define probabilistic subgraph matching queries over deterministic graph data and propose algorithms to answer them efficiently. Finally, we introduce a general relational machine learning framework and rule-based language, Probabilistic Soft Logic, to learn from and probabilistically reason about social network data and describe applications to information integration and information fusion

A Survey on Metric Learning for Feature Vectors and Structured Data

The need for appropriate ways to measure the distance or similarity between data is ubiquitous in machine learning, pattern recognition and data mining, but handcrafting such good metrics for specific problems is generally difficult. This has led to the emergence of metric learning, which aims at automatically learning a metric from data and has attracted a lot of interest in machine learning and related fields for the past ten years. This survey paper proposes a systematic review of the metric learning literature, highlighting the pros and cons of each approach. We pay particular attention to Mahalanobis distance metric learning, a well-studied and successful framework, but additionally present a wide range of methods that have recently emerged as powerful alternatives, including nonlinear metric learning, similarity learning and local metric learning. Recent trends and extensions, such as semi-supervised metric learning, metric learning for histogram data and the derivation of generalization guarantees, are also covered. Finally, this survey addresses metric learning for structured data, in particular edit distance learning, and attempts to give an overview of the remaining challenges in metric learning for the years to come.Comment: Technical report, 59 pages. Changes in v2: fixed typos and improved presentation. Changes in v3: fixed typos. Changes in v4: fixed typos and new method