Book chapter
Exploring Pattern Structures of Syntactic Trees for Relation Extraction
In this paper we explore the possibility of defining an original pattern structure for managing syntactic trees. More precisely, we are interested in the extraction of relations such as drug-drug interactions (DDIs) in medical texts where sentences are represented as syntactic trees. In this specific pattern structure, called STPS, the similarity operator is based on rooted tree intersection. Moreover, we introduce “Lazy Pattern Structure Classification” (LPSC), which is a symbolic method able to extract and classify DDI sentences w.r.t. STPS. To decrease computation time, a projection and a set of tree-simplification operations are proposed. We evaluated the method by means of a 10-fold cross validation on the corpus of the DDI extraction challenge 2011, and we obtained very encouraging results that are reported at the end of the paper.
In book
A scalable method for mining graph patterns stable under subsampling is proposed. The existing subsample stability and robustness measures are not antimonotonic according to definitions known so far. We study a broader notion of antimonotonicity for graph patterns, so that measures of subsample stability become antimonotonic. Then we propose gSOFIA for mining the most subsample-stable graph patterns. The experiments on numerous graph datasets show that gSOFIA is very efficient for discovering subsample-stable graph patterns.
Formal Concept Analysis (FCA) is a mathematically well-founded theory aimed at data analysis and classi cation, introduced and detailed in the book of Bernhard Ganter and Rudolf Wille, \Formal Concept Analysis", Springer 1999. The area came into being in the early 1980s and has since then spawned over 10000 scienti c publications and a variety of practically deployed tools. FCA allows one to build from a data table with objects in rows and attributes in columns a taxonomic data structure called concept lattice, which can be used for many purposes, especially for Knowledge Discovery and Information Retrieval. The \Formal Concept Analysis Meets Information Retrieval" (FCAIR) workshop collocated with the 35th European Conference on Information Retrieval (ECIR 2013) was intended, on the one hand, to attract researchers from FCA community to a broad discussion of FCA-based research on information retrieval, and, on the other hand, to promote ideas, models, and methods of FCA in the community of Information Retrieval. This volume contains 11 contributions to FCAIR workshop (including 3 abstracts for invited talks and tutorial) held in Moscow, on March 24, 2013. All submissions were assessed by at least two reviewers from the program committee of the workshop to which we express our gratitude. We would also like to thank the co-organizers and sponsors of the FCAIR workshop: Russian Foundation for Basic Research, National Research University Higher School of Economics, and Yandex.
Many semantic text analysis problems employ string-to-text relevance measures. Research paper annotation problem is no exception. In general, research papers are annotated according to a system of topics, organized as a taxonomy, a hierarchy of topics (or concepts). For example the papers, published in journals of the international Association of Computing Machinery (ACM), the most influential organization in the Computer Science world, are annotated according to the Computing Classification System taxonomy (ACM CCS). String-to-text relevance measures should be used to automate the research paper annotation procedure since taxonomy topics are strings ant research papers or any of their constituents are texts. A relevance measure maps a string–text pair to a real number. The meaning of the mapping depends on the relevance model under consideration. Under any model, the higher the relevance value, the stronger the association between the string and the text. This paper explores the use of phrase-to-text relevance measures to annotate research papers in Computer Science by key phrases taken from the ACM Computing Classification System. Three phrase-to-text relevance measures are experimentally compared in this setting. The measures are: (a) cosine relevance score between conventional vector space representations of the texts coded with tf-idf weighting; (b) a popular characteristic of the probability of “elite” term generation BM25; and (c) a characteristic of the symbol conditional probability averaged over matching fragments in suffix trees representing texts and phrases, CPAMF, introduced by the authors. Our experiment is conducted over a set of texts published in journals of the ACM and manually annotated by their authors using topics from the ACM CCS. Applying any of the relevance measures to an article results in a list of taxonomy topics sorted in the descending order of their relevance values. The results are evaluated by comparing these sorted lists and lists of topics assigned to articles manually. The higher a manually assigned topic is placed in a relevance based sorted list of topics, the more accurate the sorted list is. The accuracy of the computational annotations is scored by using three different scoring functions: a) MAP, b) nDCG, c) Intersection at k, where (a) and (b) are taken from the literature, and (c) is introduced by the authors. It appears, CPAMF outperforms both the cosine measure and BM25 by a wide margin over all three scoring functions.
Symbolic classifiers allow for solving classification task and provide the reason for the classifier decision. Such classifiers were studied by a large number of researchers and known under a number of names including tests, JSM-hypotheses, version spaces, emerging patterns, proper predictors of a target class, representative sets etc. Here we consider such classifiers with restriction on counter-examples and discuss them in terms of pattern structures. We show how such classifiers are related. In particular, we discuss the equivalence between good maximally redundant tests and minimal JSM-hyposethes and between minimal representations of version spaces and good irredundant tests.
This paper addresses the important problem of efficiently mining numerical data with formal concept analysis (FCA). Classically, the only way to apply FCA is to binarize the data, thanks to a so-called scaling procedure. This may either involve loss of information, or produce large and dense binary data known as hard to process. In the context of gene expression data analysis, we propose and compare two FCA-based methods for mining numerical data and we show that they are equivalent. The first one relies on a particular scaling, encoding all possible intervals of attribute values, and uses standard FCA techniques. The second one relies on pattern structures without a priori transformation, and is shown to be more computationally efficient and to provide more readable results. Experiments with real-world gene expression data are discussed and give a practical basis for the comparison and evaluation of the methods.