Using Unsupervised Patterns to Extract Gene Regulation Relationships for Network Construction

BACKGROUND: The gene expression is usually described in the literature as a transcription factor X that regulates the target gene Y. Previously, some studies discovered gene regulations by using information from the biomedical literature and most of them require effort of human annotators to build the training dataset. Moreover, the large amount of textual knowledge recorded in the biomedical literature grows very rapidly, and the creation of manual patterns from literatures becomes more difficult. There is an increasing need to automate the process of establishing patterns. METHODOLOGY/PRINCIPAL FINDINGS: In this article, we describe an unsupervised pattern generation method called AutoPat. It is a gene expression mining system that can generate unsupervised patterns automatically from a given set of seed patterns. The high scalability and low maintenance cost of the unsupervised patterns could help our system to extract gene expression from PubMed abstracts more precisely and effectively. CONCLUSIONS/SIGNIFICANCE: Experiments on several regulators show reasonable precision and recall rates which validate AutoPat's practical applicability. The conducted regulation networks could also be built precisely and effectively. The system in this study is available at http://ikmbio.csie.ncku.edu.tw/AutoPat/

Optical tomography: Image improvement using mixed projection of parallel and fan beam modes

Mixed parallel and fan beam projection is a technique used to increase the quality images. This research focuses on enhancing the image quality in optical tomography. Image quality can be defined by measuring the Peak Signal to Noise Ratio (PSNR) and Normalized Mean Square Error (NMSE) parameters. The findings of this research prove that by combining parallel and fan beam projection, the image quality can be increased by more than 10%in terms of its PSNR value and more than 100% in terms of its NMSE value compared to a single parallel beam

Citation Handling: Processing Citation Texts in Scientific Documents

Citation sentences (sentences that cite other papers) play a key role in the summarization of scientific articles. However, a citation-based summarization system that depends on generic natural language processing components, such as parsers or sentence compressors, will perform poorly if those components cannot handle citations correctly. In this thesis, I examine the effect of citation handling on parsing, sentence compression, and multi-document summarization. There are two types of citations that occur in citation sentences: constituent citations and parenthetical citations. I propose an automatic citation classifier based on training data created through Mechanical Turk tasks. I demonstrate that the use of type-specific citation handling as pre-processing improves the performance of a state-of-the-art generic parser, both for quality of the parse trees and running time. Extrinsic evaluations demonstrate that improving the performance of a parser on citation sentences in turn improves the performance of a sentence compressor, Trimmer (Zajic et al., 2007), and a multi-document summarization system, MASCS, according to several summarization measures

The Structure and Dynamics of Co-Citation Clusters: A Multiple-Perspective Co-Citation Analysis

A multiple-perspective co-citation analysis method is introduced for characterizing and interpreting the structure and dynamics of co-citation clusters. The method facilitates analytic and sense making tasks by integrating network visualization, spectral clustering, automatic cluster labeling, and text summarization. Co-citation networks are decomposed into co-citation clusters. The interpretation of these clusters is augmented by automatic cluster labeling and summarization. The method focuses on the interrelations between a co-citation cluster's members and their citers. The generic method is applied to a three-part analysis of the field of Information Science as defined by 12 journals published between 1996 and 2008: 1) a comparative author co-citation analysis (ACA), 2) a progressive ACA of a time series of co-citation networks, and 3) a progressive document co-citation analysis (DCA). Results show that the multiple-perspective method increases the interpretability and accountability of both ACA and DCA networks.Comment: 33 pages, 11 figures, 10 tables. To appear in the Journal of the American Society for Information Science and Technolog