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

Probabilistic learning for selective dissemination of information

New methods and new systems are needed to filter or to selectively distribute the increasing volume of electronic information being produced nowadays. An effective information filtering system is one that provides the exact information that fulfills user's interests with the minimum effort by the user to describe it. Such a system will have to be adaptive to the user changing interest. In this paper we describe and evaluate a learning model for information filtering which is an adaptation of the generalized probabilistic model of information retrieval. The model is based on the concept of 'uncertainty sampling', a technique that allows for relevance feedback both on relevant and nonrelevant documents. The proposed learning model is the core of a prototype information filtering system called ProFile

Effective pattern discovery for text mining

Many data mining techniques have been proposed for mining useful patterns in text documents. However, how to effectively use and update discovered patterns is still an open research issue, especially in the domain of text mining. Since most existing text mining methods adopted term-based approaches, they all suffer from the problems of polysemy and synonymy. Over the years, people have often held the hypothesis that pattern (or phrase) based approaches should perform better than the term-based ones, but many experiments did not support this hypothesis. This paper presents an innovative technique, effective pattern discovery which includes the processes of pattern deploying and pattern evolving, to improve the effectiveness of using and updating discovered patterns for finding relevant and interesting information. Substantial experiments on RCV1 data collection and TREC topics demonstrate that the proposed solution achieves encouraging performance

An Intelligent System For Arabic Text Categorization

Text Categorization (classification) is the process of classifying documents into a predefined set of categories based on their content. In this paper, an intelligent Arabic text categorization system is presented. Machine learning algorithms are used in this system. Many algorithms for stemming and feature selection are tried. Moreover, the document is represented using several term weighting schemes and finally the k-nearest neighbor and Rocchio classifiers are used for classification process. Experiments are performed over self collected data corpus and the results show that the suggested hybrid method of statistical and light stemmers is the most suitable stemming algorithm for Arabic language. The results also show that a hybrid approach of document frequency and information gain is the preferable feature selection criterion and normalized-tfidf is the best weighting scheme. Finally, Rocchio classifier has the advantage over k-nearest neighbor classifier in the classification process. The experimental results illustrate that the proposed model is an efficient method and gives generalization accuracy of about 98%

Lexical Query Modeling in Session Search

Lexical query modeling has been the leading paradigm for session search. In this paper, we analyze TREC session query logs and compare the performance of different lexical matching approaches for session search. Naive methods based on term frequency weighing perform on par with specialized session models. In addition, we investigate the viability of lexical query models in the setting of session search. We give important insights into the potential and limitations of lexical query modeling for session search and propose future directions for the field of session search.Comment: ICTIR2016, Proceedings of the 2nd ACM International Conference on the Theory of Information Retrieval. 201