Machine Learning Models Reveal the Importance of Clinical Biomarkers for the Diagnosis of Alzheimer's Disease.

Alzheimer's Disease (AD) is a neurodegenerative disease that causes complications with thinking capability, memory and behavior. AD is a major public health problem among the elderly in developed and developing countries. With the growth of AD around the world, there is a need to further expand our understanding of the roles different clinical measurements can have in the diagnosis of AD. In this work, we propose a machine learning-based technique to distinguish control subjects with no cognitive impairments, AD subjects, and subjects with mild cognitive impairment (MCI), often seen as precursors of AD. We utilized several machine learning (ML) techniques and found that Gradient Boosting Decision Trees achieved the highest performance above 84% classification accuracy. Also, we determined the importance of the features (clinical biomarkers) contributing to the proposed multi-class classification system. Further investigation on the biomarkers will pave the way to introduce better treatment plan for AD patients.

DeepCNPP: Deep Learning Architecture to Distinguish the Promoter of Human Long Non-Coding RNA Genes and Protein-Coding Genes.

Promoter region of protein-coding genes are gradually being well understood, yet no comparable studies exist for the promoter of long non-coding RNA (lncRNA) genes which has emerged as a global potential regulator in multiple cellular process and different diseases for human. To understand the difference in the transcriptional regulation pattern of these genes, previously, we proposed a machine learning based model to classify the promoter of protein-coding genes and lncRNA genes. In this study, we are presenting DeepCNPP (deep coding non-coding promoter predictor), an improved model based on deep learning (DL) framework to classify the promoter of lncRNA genes and protein-coding genes. We used convolution neural network (CNN) based deep network to classify the promoter of these two broad categories of human genes. Our computational model, built upon the sequence information only, was able to classify these two groups of promoters from human at a rate of 83.34% accuracy and outperformed the existing model. Further analysis and interpretation of the output from DeepCNPP architecture will enable us to understand the difference in transcription regulatory pattern for these two groups of genes.

DeepDSSR: Deep Learning Structure for Human Donor Splice Sites Recognition.

Human genes often, through alternative splicing of pre-messenger RNAs, produce multiple mRNAs and protein isoforms that may have similar or completely different functions. Identification of splice sites is, therefore, crucial to understand the gene structure and variants of mRNA and protein isoforms produced by the primary RNA transcripts. Although many computational methods have been developed to detect the splice sites in humans, this is still substantially a challenging problem and further improvement of the computational model is still foreseeable. Accordingly, we developed DeepDSSR (deep donor splice site recognizer), a novel deep learning based architecture, for predicting human donor splice sites. The proposed method, built upon publicly available and highly imbalanced benchmark dataset, is comparable with the leading deep learning based methods for detecting human donor splice sites. Performance evaluation metrics show that DeepDSSR outperformed the existing deep learning based methods. Future work will improve the predictive capabilities of our model, and we will build a model for the prediction of acceptor splice sites.