Biology subjects

Shin, B.

Publications and source records attributed to Shin, B..

2 recordsLinked to original sources

bioRxiv2017

Wx: a neural network-based feature selection algorithm for next-generation sequencing data

MotivationNext-generation sequencing (NGS), which allows the simultaneous sequencing of billions of DNA fragments simultaneously, has revolutionized how we study genomics and molecular biology by generating genome-wide molecular maps of molecules of interest. For example, an NGS-based transcriptomic assay called RNA-seq can be used to estimate the abundance of approximately 190,000 transcripts together. As the cost of next-generation sequencing sharply declines, researchers in many fields have been conducting research using NGS. The amount of information produced by NGS has made it difficult for researchers to choose the optimal set of target genes (or genomic loci).\n\nResultsWe have sought to resolve this issue by developing a neural network-based feature (gene) selection algorithm called Wx. The Wx algorithm ranks genes based on the discriminative index (DI) score that represents the classification power for distinguishing given groups. With a gene list ranked by DI score, researchers can institutively select the optimal set of genes from the highest-ranking ones. We applied the Wx algorithm to a TCGA pan-cancer gene-expression cohort to identify an optimal set of gene-expression biomarker (universal gene-expression biomarkers) candidates that can distinguish cancer samples from normal samples for 12 different types of cancer. The 14 gene-expression biomarker candidates identified by Wx were comparable to or outperformed previously reported universal gene expression biomarkers, highlighting the usefulness of the Wx algorithm for next-generation sequencing data. Thus, we anticipate that the Wx algorithm can complement current state-of-the-art analytical applications for the identification of biomarker candidates as an alternative method.\n\nAvailabilityhttps://github.com/deargen/DearWX\n\nContactkangk1204@dankook.ac.kr\n\nSupplementary informationSupplementary data are available at online.

bioinformatics↗

bioRxiv2017

Natural Language Processing for Classification of Acute, Communicable Findings on Unstructured Head CT Reports: Comparison of Neural Network and Non-Neural Machine Learning Techniques

Background and PurposeTo evaluate the accuracy of non-neural and neural network models to classify five categories (classes) of acute and communicable findings on unstructured head computed tomography (CT) reports.\n\nMaterials and MethodsThree radiologists annotated 1,400 head CT reports for language indicating the presence or absence of acute communicable findings (hemorrhage, stroke, hydrocephalus, and mass effect). This set was used to train, develop, and evaluate a non-neural classifier, support vector machine (SVM), in comparisons to two neural network models using convolutional neural networks (CNN) and neural attention model (NAM) Inter-rater agreement was computed using kappa statistics. Accuracy, receiver operated curves, and area under the curve were calculated and tabulated. P-values < 0.05 was significant and 95% confidence intervals were computed.\n\nResultsRadiologist agreement was 86-94% and Cohens kappa was 0.667-0.762 (substantial agreement). Accuracies of the CNN and NAM (range 0.90-0.94) were higher than SVM (range 0.88-0.92). NAM showed relatively equal accuracy with CNN for three classes, severity, mass effect, and hydrocephalus, higher accuracy for the acute bleed class, and lower accuracy for the acute stroke class. AUCs of all methods for all classes were above 0.92.\n\nConclusionsO_LINeural network models (CNN & NAM) generally had higher accuracies compared to the non-neural models (SVM) and have a range of accuracies that comparable to the inter-annotator agreement of three neuroradiologists.\nC_LIO_LIThe NAM method adds ability to hold the algorithm accountable for its classification via heat map generation, thereby adding an auditing feature to this neural network.\nC_LI\n\nAbbreviations

neuroscience↗