AIMC Topic: Computational Biology

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Computational mechanisms underlying cortical responses to the affordance properties of visual scenes.

PLoS computational biology
Biologically inspired deep convolutional neural networks (CNNs), trained for computer vision tasks, have been found to predict cortical responses with remarkable accuracy. However, the internal operations of these models remain poorly understood, and...

A machine learning based framework to identify and classify long terminal repeat retrotransposons.

PLoS computational biology
Transposable elements (TEs) are repetitive nucleotide sequences that make up a large portion of eukaryotic genomes. They can move and duplicate within a genome, increasing genome size and contributing to genetic diversity within and across species. A...

Fuzzy set-based generalized multifactor dimensionality reduction analysis of gene-gene interactions.

BMC medical genomics
BACKGROUND: Gene-gene interactions (GGIs) are a known cause of missing heritability. Multifactor dimensionality reduction (MDR) is one of most commonly used methods for GGI detection. The generalized multifactor dimensionality reduction (GMDR) method...

Human Splice-Site Prediction with Deep Neural Networks.

Journal of computational biology : a journal of computational molecular cell biology
Accurate splice-site prediction is essential to delineate gene structures from sequence data. Several computational techniques have been applied to create a system to predict canonical splice sites. For classification tasks, deep neural networks (DNN...

Heterogeneity Analysis and Diagnosis of Complex Diseases Based on Deep Learning Method.

Scientific reports
Understanding genetic mechanism of complex diseases is a serious challenge. Existing methods often neglect the heterogeneity phenomenon of complex diseases, resulting in lack of power or low reproducibility. Addressing heterogeneity when detecting ep...

Annotating activation/inhibition relationships to protein-protein interactions using gene ontology relations.

BMC systems biology
BACKGROUND: Signaling pathways can be reconstructed by identifying 'effect types' (i.e. activation/inhibition) of protein-protein interactions (PPIs). Effect types are composed of 'directions' (i.e. upstream/downstream) and 'signs' (i.e. positive/neg...

Computational Approach to Investigating Key GO Terms and KEGG Pathways Associated with CNV.

BioMed research international
Choroidal neovascularization (CNV) is a severe eye disease that leads to blindness, especially in the elderly population. Various endogenous and exogenous regulatory factors promote its pathogenesis. However, the detailed molecular biological mechani...

Distinguishing butchery cut marks from crocodile bite marks through machine learning methods.

Scientific reports
All models of evolution of human behaviour depend on the correct identification and interpretation of bone surface modifications (BSM) on archaeofaunal assemblages. Crucial evolutionary features, such as the origin of stone tool use, meat-eating, foo...

Cox-nnet: An artificial neural network method for prognosis prediction of high-throughput omics data.

PLoS computational biology
Artificial neural networks (ANN) are computing architectures with many interconnections of simple neural-inspired computing elements, and have been applied to biomedical fields such as imaging analysis and diagnosis. We have developed a new ANN frame...

Ensemble of Rotation Trees for Imbalanced Medical Datasets.

Journal of healthcare engineering
Medical datasets are often predominately composed of "normal" examples with only a small percentage of "abnormal" ones and how to correctly recognize the abnormal examples is very meaningful. However, conventional classification learning methods try ...