AIMC Topic: Computational Biology

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More Agility to Semantic Similarities Algorithm Implementations.

International journal of environmental research and public health
Algorithms for measuring semantic similarity between Gene Ontology (GO) terms has become a popular area of research in bioinformatics as it can help to detect functional associations between genes and potential impact to the health and well-being of ...

Using transfer learning from prior reference knowledge to improve the clustering of single-cell RNA-Seq data.

Scientific reports
In many research areas scientists are interested in clustering objects within small datasets while making use of prior knowledge from large reference datasets. We propose a method to apply the machine learning concept of transfer learning to unsuperv...

SpliceFinder: ab initio prediction of splice sites using convolutional neural network.

BMC bioinformatics
BACKGROUND: Identifying splice sites is a necessary step to analyze the location and structure of genes. Two dinucleotides, GT and AG, are highly frequent on splice sites, and many other patterns are also on splice sites with important biological fun...

Family history information extraction via deep joint learning.

BMC medical informatics and decision making
Family history (FH) information, including family members, side of family of family members (i.e., maternal or paternal), living status of family members, observations (diseases) of family members, etc., is very important in the decision-making proce...

A novel machine learning based approach for iPS progenitor cell identification.

PLoS computational biology
Identification of induced pluripotent stem (iPS) progenitor cells, the iPS forming cells in early stage of reprogramming, could provide valuable information for studying the origin and underlying mechanism of iPS cells. However, it is very difficult ...

Accurate classification of membrane protein types based on sequence and evolutionary information using deep learning.

BMC bioinformatics
BACKGROUND: Membrane proteins play an important role in the life activities of organisms. Knowing membrane protein types provides clues for understanding the structure and function of proteins. Though various computational methods for predicting memb...

Towards Improving Skin Cancer Diagnosis by Integrating Microarray and RNA-Seq Datasets.

IEEE journal of biomedical and health informatics
Many clinical studies have revealed the high biological similarities existing among different skin pathological states. These similarities create difficulties in the efficient diagnosis of skin cancer, and encourage to study and design new intelligen...

High-Throughput Prediction of MHC Class I and II Neoantigens with MHCnuggets.

Cancer immunology research
Computational prediction of binding between neoantigen peptides and major histocompatibility complex (MHC) proteins can be used to predict patient response to cancer immunotherapy. Current neoantigen predictors focus on estimation of MHC binding aff...

Interpretable deep neural network for cancer survival analysis by integrating genomic and clinical data.

BMC medical genomics
BACKGROUND: Understanding the complex biological mechanisms of cancer patient survival using genomic and clinical data is vital, not only to develop new treatments for patients, but also to improve survival prediction. However, highly nonlinear and h...