A Comparative Performance Study of Feature Selection Methods for the Anti-spam Filtering Domain

In this paper we analyse the strengths and weaknesses of the mainly used feature selection methods in text categorization when they are applied to the spam problem domain. Several experiments with different feature selection methods and content-based filtering techniques are carried out and discussed. Information Gain, χ 2-text, Mutual Information and Document Frequency feature selection methods have been analysed in conjunction with Naïve Bayes, boosting trees, Support Vector Machines and ECUE models in different scenarios. From the experiments carried out the underlying ideas behind feature selection methods are identified and applied for improving the feature selection process of SpamHunting, a novel anti-spam filtering software able to accurate classify suspicious e-mails

New techniques for Arabic document classification

Text classification (TC) concerns automatically assigning a class (category) label to a text document, and has increasingly many applications, particularly in the domain of organizing, for browsing in large document collections. It is typically achieved via machine learning, where a model is built on the basis of a typically large collection of document features. Feature selection is critical in this process, since there are typically several thousand potential features (distinct words or terms). In text classification, feature selection aims to improve the computational e ciency and classification accuracy by removing irrelevant and redundant terms (features), while retaining features (words) that contain su cient information that help with the classification task. This thesis proposes binary particle swarm optimization (BPSO) hybridized with either K Nearest Neighbour (KNN) or Support Vector Machines (SVM) for feature selection in Arabic text classi cation tasks. Comparison between feature selection approaches is done on the basis of using the selected features in conjunction with SVM, Decision Trees (C4.5), and Naive Bayes (NB), to classify a hold out test set. Using publically available Arabic datasets, results show that BPSO/KNN and BPSO/SVM techniques are promising in this domain. The sets of selected features (words) are also analyzed to consider the di erences between the types of features that BPSO/KNN and BPSO/SVM tend to choose. This leads to speculation concerning the appropriate feature selection strategy, based on the relationship between the classes in the document categorization task at hand. The thesis also investigates the use of statistically extracted phrases of length two as terms in Arabic text classi cation. In comparison with Bag of Words text representation, results show that using phrases alone as terms in Arabic TC task decreases the classification accuracy of Arabic TC classifiers significantly while combining bag of words and phrase based representations may increase the classification accuracy of the SVM classifier slightly

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

Chi-square-based scoring function for categorization of MEDLINE citations

Objectives: Text categorization has been used in biomedical informatics for identifying documents containing relevant topics of interest. We developed a simple method that uses a chi-square-based scoring function to determine the likelihood of MEDLINE citations containing genetic relevant topic. Methods: Our procedure requires construction of a genetic and a nongenetic domain document corpus. We used MeSH descriptors assigned to MEDLINE citations for this categorization task. We compared frequencies of MeSH descriptors between two corpora applying chi-square test. A MeSH descriptor was considered to be a positive indicator if its relative observed frequency in the genetic domain corpus was greater than its relative observed frequency in the nongenetic domain corpus. The output of the proposed method is a list of scores for all the citations, with the highest score given to those citations containing MeSH descriptors typical for the genetic domain. Results: Validation was done on a set of 734 manually annotated MEDLINE citations. It achieved predictive accuracy of 0.87 with 0.69 recall and 0.64 precision. We evaluated the method by comparing it to three machine learning algorithms (support vector machines, decision trees, na\"ive Bayes). Although the differences were not statistically significantly different, results showed that our chi-square scoring performs as good as compared machine learning algorithms. Conclusions: We suggest that the chi-square scoring is an effective solution to help categorize MEDLINE citations. The algorithm is implemented in the BITOLA literature-based discovery support system as a preprocessor for gene symbol disambiguation process.Comment: 34 pages, 2 figure

KACST Arabic Text Classification Project: Overview and Preliminary Results

Electronically formatted Arabic free-texts can be found in abundance these days on the World Wide Web, often linked to commercial enterprises and/or government organizations. Vast tracts of knowledge and relations lie hidden within these texts, knowledge that can be exploited once the correct intelligent tools have been identified and applied. For example, text mining may help with text classification and categorization. Text classification aims to automatically assign text to a predefined category based on identifiable linguistic features. Such a process has different useful applications including, but not restricted to, E-Mail spam detection, web pages content filtering, and automatic message routing. In this paper an overview of King Abdulaziz City for Science and Technology (KACST) Arabic Text Classification Project will be illustrated along with some preliminary results. This project will contribute to the better understanding and elaboration of Arabic text classification techniques

Bounded Coordinate-Descent for Biological Sequence Classification in High Dimensional Predictor Space

We present a framework for discriminative sequence classification where the learner works directly in the high dimensional predictor space of all subsequences in the training set. This is possible by employing a new coordinate-descent algorithm coupled with bounding the magnitude of the gradient for selecting discriminative subsequences fast. We characterize the loss functions for which our generic learning algorithm can be applied and present concrete implementations for logistic regression (binomial log-likelihood loss) and support vector machines (squared hinge loss). Application of our algorithm to protein remote homology detection and remote fold recognition results in performance comparable to that of state-of-the-art methods (e.g., kernel support vector machines). Unlike state-of-the-art classifiers, the resulting classification models are simply lists of weighted discriminative subsequences and can thus be interpreted and related to the biological problem