AIMC Topic: Computational Biology

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OCLSTM: Optimized convolutional and long short-term memory neural network model for protein secondary structure prediction.

PloS one
Protein secondary structure prediction is extremely important for determining the spatial structure and function of proteins. In this paper, we apply an optimized convolutional neural network and long short-term memory neural network models to protei...

A Transfer Learning Based Super-Resolution Microscopy for Biopsy Slice Images: The Joint Methods Perspective.

IEEE/ACM transactions on computational biology and bioinformatics
Higher-resolution biopsy slice images reveal many details, which are widely used in medical practice. However, taking high-resolution slice images is more costly than taking low-resolution ones. In this paper, we propose a joint framework containing ...

Integrating Multi-Omic Data With Deep Subspace Fusion Clustering for Cancer Subtype Prediction.

IEEE/ACM transactions on computational biology and bioinformatics
One type of cancer usually consists of several subtypes with distinct clinical implications, thus the cancer subtype prediction is an important task in disease diagnosis and therapy. Utilizing one type of data from molecular layers in biological syst...

CNAPE: A Machine Learning Method for Copy Number Alteration Prediction from Gene Expression.

IEEE/ACM transactions on computational biology and bioinformatics
Detection of DNA copy number alteration in cancer cells is critical to understanding cancer initiation and progression. Widely used methods, such as DNA arrays and genomic DNA sequencing, are relatively expensive and require DNA samples at a microgra...

An Ontology-Independent Representation Learning for Similar Disease Detection Based on Multi-Layer Similarity Network.

IEEE/ACM transactions on computational biology and bioinformatics
To identify similar diseases has significant implications for revealing the etiology and pathogenesis of diseases and further research in the domain of biomedicine. Currently, most methods for the measurement of disease similarity utilize either asso...

Protein2Vec: Aligning Multiple PPI Networks with Representation Learning.

IEEE/ACM transactions on computational biology and bioinformatics
Research of Protein-Protein Interaction (PPI) Network Alignment is playing an important role in understanding the crucial underlying biological knowledge such as functionally homologous proteins and conserved evolutionary pathways across different sp...

FlyIT: Drosophila Embryogenesis Image Annotation based on Image Tiling and Convolutional Neural Networks.

IEEE/ACM transactions on computational biology and bioinformatics
With the rise of image-based transcriptomics, spatial gene expression data has become increasingly important for understanding gene regulations from the tissue level down to the cell level. Especially, the gene expression images of Drosophila embryos...

Cross-species Data Classification by Domain Adaptation via Discriminative Heterogeneous Maximum Mean Discrepancy.

IEEE/ACM transactions on computational biology and bioinformatics
Cross-species or Cross-platform data classification is a challenging problem in the field of bioinformatics, which aims to classify data samples in one species/platform by using labeled data samples in another species/platform. Traditional classifica...

CrystalM: A Multi-View Fusion Approach for Protein Crystallization Prediction.

IEEE/ACM transactions on computational biology and bioinformatics
Improving the accuracy of predicting protein crystallization is very important for protein crystallization projects, which is a critical step for the determination of protein structure by X-ray crystallography. At present, many machine learning metho...