AIMC Topic: Computational Biology

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A Technical Review of Convolutional Neural Network-Based Mammographic Breast Cancer Diagnosis.

Computational and mathematical methods in medicine
This study reviews the technique of convolutional neural network (CNN) applied in a specific field of mammographic breast cancer diagnosis (MBCD). It aims to provide several clues on how to use CNN for related tasks. MBCD is a long-standing problem, ...

LUADpp: an effective prediction model on prognosis of lung adenocarcinomas based on somatic mutational features.

BMC cancer
BACKGROUND: Lung adenocarcinoma is the most common type of lung cancers. Whole-genome sequencing studies disclosed the genomic landscape of lung adenocarcinomas. however, it remains unclear if the genetic alternations could guide prognosis prediction...

Enhancer prediction with histone modification marks using a hybrid neural network model.

Methods (San Diego, Calif.)
Enhancer is a DNA sequence of a genome that controls transcription of downstream target genes. Enhancers are known to be associated with certain epigenetic signatures. Machine learning tools, such as CSI-ANN, ChromHMM, and RFECS, were developed for p...

Group Lasso Regularized Deep Learning for Cancer Prognosis from Multi-Omics and Clinical Features.

Genes
Accurate prognosis of patients with cancer is important for the stratification of patients, the optimization of treatment strategies, and the design of clinical trials. Both clinical features and molecular data can be used for this purpose, for insta...

RNA sequencing and swarm intelligence-enhanced classification algorithm development for blood-based disease diagnostics using spliced blood platelet RNA.

Nature protocols
Blood-based diagnostics tests, using individual or panels of biomarkers, may revolutionize disease diagnostics and enable minimally invasive therapy monitoring. However, selection of the most relevant biomarkers from liquid biosources remains an imme...

PMAMCA: prediction of microRNA-disease association utilizing a matrix completion approach.

BMC systems biology
BACKGROUND: Numerous experimental results have indicated that microRNAs (miRNAs) play a vital role in biological processes, as well as outbreaks of diseases at the molecular level. Despite their important role in biological processes, knowledge regar...

Minimalistic Approach to Coreference Resolution in Lithuanian Medical Records.

Computational and mathematical methods in medicine
Coreference resolution is a challenging part of natural language processing (NLP) with applications in machine translation, semantic search and other information retrieval, and decision support systems. Coreference resolution requires linguistic prep...

The Development of Target-Specific Machine Learning Models as Scoring Functions for Docking-Based Target Prediction.

Journal of chemical information and modeling
The identification of possible targets for a known bioactive compound is of the utmost importance for drug design and development. Molecular docking is one possible approach for in-silico protein target prediction, whereas a molecule is docked into s...

Prediction of aptamer-protein interacting pairs based on sparse autoencoder feature extraction and an ensemble classifier.

Mathematical biosciences
Aptamer-protein interacting pairs play important roles in physiological functions and structural characterization. Identifying aptamer-protein interacting pairs is challenging and limited, despite of the tremendous applications of aptamers. Therefore...