11,625 research outputs found
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
Assessing similarity of feature selection techniques in high-dimensional domains
Recent research efforts attempt to combine multiple feature selection techniques instead of using a single one. However, this combination is often made on an “ad hoc” basis, depending on the specific problem at hand, without considering the degree of diversity/similarity of the involved methods. Moreover, though it is recognized that different techniques may return quite dissimilar outputs, especially in high dimensional/small sample size domains, few direct comparisons exist that quantify these differences and their implications on classification performance. This paper aims to provide a contribution in this direction by proposing a general methodology for assessing the similarity between the outputs of different feature selection methods in high dimensional classification problems. Using as benchmark the genomics domain, an empirical study has been conducted to compare some of the most popular feature selection methods, and useful insight has been obtained about their pattern of agreement
Using bag-of-concepts to improve the performance of support vector machines in text categorization
This paper investigates the use of concept-based representations for text categorization. We introduce a new approach to create concept-based text representations, and apply it to a standard text categorization collection. The representations are used as input to a Support Vector Machine classifier, and the results show that there are certain categories for which concept-based representations constitute a viable supplement to word-based ones. We also demonstrate how the performance of the Support Vector Machine can be improved by combining representations
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