Word Sense Disambiguation for Exploiting Hierarchical Thesauri in Text Classification

The introduction of hierarchical thesauri (HT) that contain significant semantic information, has led researchers to investigate their potential for improving performance of the text classification task, extending the traditional “bag of words” representation, incorporating syntactic and semantic relationships among words. In this paper we address this problem by proposing a Word Sense Disambiguation (WSD) approach based on the intuition that word proximity in the document implies proximity also in the HT graph. We argue that the high precision exhibited by our WSD algorithm in various humanly-disambiguated benchmark datasets, is appropriate for the classification task. Moreover, we define a semantic kernel, based on the general concept of GVSM kernels, that captures the semantic relations contained in the hierarchical thesaurus. Finally, we conduct experiments using various corpora achieving a systematic improvement in classification accuracy using the SVM algorithm, especially when the training set is small

Designing Semantic Kernels as Implicit Superconcept Expansions

Recently, there has been an increased interest in the exploitation of background knowledge in the context of text mining tasks, especially text classification. At the same time, kernel-based learning algorithms like Support Vector Machines have become a dominant paradigm in the text mining community. Amongst other reasons, this is also due to their capability to achieve more accurate learning results by replacing standard linear kernel (bag-of-words) with customized kernel functions which incorporate additional apriori knowledge. In this paper we propose a new approach to the design of ‘semantic smoothing kernels’ by means of an implicit superconcept expansion using well-known measures of term similarity. The experimental evaluation on two different datasets indicates that our approach consistently improves performance in situations where (i) training data is scarce or (ii) the bag-ofwords representation is too sparse to build stable models when using the linear kernel

A Novel Kernel for Text Classification Based on Semantic and Statistical Information

In text categorization, a document is usually represented by a vector space model which can accomplish the classification task, but the model cannot deal with Chinese synonyms and polysemy phenomenon. This paper presents a novel approach which takes into account both the semantic and statistical information to improve the accuracy of text classification. The proposed approach computes semantic information based on HowNet and statistical information based on a kernel function with class-based weighting. According to our experimental results, the proposed approach could achieve state-of-the-art or competitive results as compared with traditional approaches such as the k-Nearest Neighbor (KNN), the Naive Bayes and deep learning models like convolutional networks

Automatic categorization of diverse experimental information in the bioscience literature

Background: Curation of information from bioscience literature into biological knowledge databases is a crucial way of capturing experimental information in a computable form. During the biocuration process, a critical first step is to identify from all published literature the papers that contain results for a specific data type the curator is interested in annotating. This step normally requires curators to manually examine many papers to ascertain which few contain information of interest and thus, is usually time consuming. We developed an automatic method for identifying papers containing these curation data types among a large pool of published scientific papers based on the machine learning method Support Vector Machine (SVM). This classification system is completely automatic and can be readily applied to diverse experimental data types. It has been in use in production for automatic categorization of 10 different experimental datatypes in the biocuration process at WormBase for the past two years and it is in the process of being adopted in the biocuration process at FlyBase and the Saccharomyces Genome Database (SGD). We anticipate that this method can be readily adopted by various databases in the biocuration community and thereby greatly reducing time spent on an otherwise laborious and demanding task. We also developed a simple, readily automated procedure to utilize training papers of similar data types from different bodies of literature such as C. elegans and D. melanogaster to identify papers with any of these data types for a single database. This approach has great significance because for some data types, especially those of low occurrence, a single corpus often does not have enough training papers to achieve satisfactory performance. Results: We successfully tested the method on ten data types from WormBase, fifteen data types from FlyBase and three data types from Mouse Genomics Informatics (MGI). It is being used in the curation work flow at WormBase for automatic association of newly published papers with ten data types including RNAi, antibody, phenotype, gene regulation, mutant allele sequence, gene expression, gene product interaction, overexpression phenotype, gene interaction, and gene structure correction. Conclusions: Our methods are applicable to a variety of data types with training set containing several hundreds to a few thousand documents. It is completely automatic and, thus can be readily incorporated to different workflow at different literature-based databases. We believe that the work presented here can contribute greatly to the tremendous task of automating the important yet labor-intensive biocuration effort

SPONGY (SPam ONtoloGY): Email Classification Using Two-Level Dynamic Ontology

Email is one of common communication methods between people on the Internet. However, the increase of email misuse/abuse has resulted in an increasing volume of spam emails over recent years. An experimental system has been designed and implemented with the hypothesis that this method would outperform existing techniques, and the experimental results showed that indeed the proposed ontology-based approach improves spam filtering accuracy significantly. In this paper, two levels of ontology spam filters were implemented: a first level global ontology filter and a second level user-customized ontology filter. The use of the global ontology filter showed about 91% of spam filtered, which is comparable with other methods. The user-customized ontology filter was created based on the specific user’s background as well as the filtering mechanism used in the global ontology filter creation. The main contributions of the paper are (1) to introduce an ontology-based multilevel filtering technique that uses both a global ontology and an individual filter for each user to increase spam filtering accuracy and (2) to create a spam filter in the form of ontology, which is user-customized, scalable, and modularized, so that it can be embedded to many other systems for better performance

A COMPARATIVE STUDY ON ONTOLOGY GENERATION AND TEXT CLUSTERING USING VSM, LSI, AND DOCUMENT ONTOLOGY MODELS

Although using ontologies to assist information retrieval and text document processing has recently attracted more and more attention, existing ontology-based approaches have not shown advantages over the traditional keywords-based Latent Semantic Indexing (LSI) method. This paper proposes an algorithm to extract a concept forest (CF) from a document with the assistance of a natural language ontology, the WordNet lexical database. Using concept forests to represent the semantics of text documents, the semantic similarities of these documents are then measured as the commonalities of their concept forests. Performance studies of text document clustering based on different document similarity measurement methods show that the CF-based similarity measurement is an effective alternative to the existing keywords-based methods. Especially, this CF-based approach has obvious advantages over the existing keywords-based methods, including LSI, in dealing with text abstract databases, such as MEDLINE, or in P2P environments where it is impractical to collect the entire document corpus for analysis

Word Sense Disambiguation for Exploiting Hierarchical Thesauri in Text Classification

The introduction of hierarchical thesauri (HT) that contain significant semantic information, has led researchers to investigate their potential for improving performance of the text classification task, extending the traditional “bag of words” representation, incorporating syntactic and semantic relationships among words. In this paper we address this problem by proposing a Word Sense Disambiguation (WSD) approach based on the intuition that word proximity in the document implies proximity also in the HT graph. We argue that the high precision exhibited by our WSD algorithm in various humanly-disambiguated benchmark datasets, is appropriate for the classification task. Moreover, we define a semantic kernel, based on the general concept of GVSM kernels, that captures the semantic relations contained in the hierarchical thesaurus. Finally, we conduct experiments using various corpora achieving a systematic improvement in classification accuracy using the SVM algorithm, especially when the training set is small

CREATING A BIOMEDICAL ONTOLOGY INDEXED SEARCH ENGINE TO IMPROVE THE SEMANTIC RELEVANCE OF RETREIVED MEDICAL TEXT

Medical Subject Headings (MeSH) is a controlled vocabulary used by the National Library of Medicine to index medical articles, abstracts, and journals contained within the MEDLINE database. Although MeSH imposes uniformity and consistency in the indexing process, it has been proven that using MeSH indices only result in a small increase in precision over free-text indexing. Moreover, studies have shown that the use of controlled vocabularies in the indexing process is not an effective method to increase semantic relevance in information retrieval. To address the need for semantic relevance, we present an ontology-based information retrieval system for the MEDLINE collection that result in a 37.5% increase in precision when compared to free-text indexing systems. The presented system focuses on the ontology to: provide an alternative to text-representation for medical articles, finding relationships among co-occurring terms in abstracts, and to index terms that appear in text as well as discovered relationships. The presented system is then compared to existing MeSH and Free-Text information retrieval systems. This dissertation provides a proof-of-concept for an online retrieval system capable of providing increased semantic relevance when searching through medical abstracts in MEDLINE