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Gene Expression

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Identifying longevity associated genes by integrating gene expression and curated annotations.

PLoS computational biology
Aging is a complex process with poorly understood genetic mechanisms. Recent studies have sought to classify genes as pro-longevity or anti-longevity using a variety of machine learning algorithms. However, it is not clear which types of features are...

A pitfall for machine learning methods aiming to predict across cell types.

Genome biology
Machine learning models that predict genomic activity are most useful when they make accurate predictions across cell types. Here, we show that when the training and test sets contain the same genomic loci, the resulting model may falsely appear to p...

A risk prediction model of gene signatures in ovarian cancer through bagging of GA-XGBoost models.

Journal of advanced research
INTRODUCTION: Ovarian cancer (OC) is one of the most frequent gynecologic cancers among women, and high-accuracy risk prediction techniques are essential to effectively select the best intervention strategies and clinical management for OC patients a...

MRI-based machine learning radiomics can predict HER2 expression level and pathologic response after neoadjuvant therapy in HER2 overexpressing breast cancer.

EBioMedicine
BACKGROUND: To use clinical and MRI radiomic features coupled with machine learning to assess HER2 expression level and predict pathologic response (pCR) in HER2 overexpressing breast cancer patients receiving neoadjuvant chemotherapy (NAC).

Unsupervised Clustering of Missense Variants in HNF1A Using Multidimensional Functional Data Aids Clinical Interpretation.

American journal of human genetics
Exome sequencing in diabetes presents a diagnostic challenge because depending on frequency, functional impact, and genomic and environmental contexts, HNF1A variants can cause maturity-onset diabetes of the young (MODY), increase type 2 diabetes ris...

Using autoencoders as a weight initialization method on deep neural networks for disease detection.

BMC medical informatics and decision making
BACKGROUND: As of today, cancer is still one of the most prevalent and high-mortality diseases, summing more than 9 million deaths in 2018. This has motivated researchers to study the application of machine learning-based solutions for cancer detecti...

Unsupervised generative and graph representation learning for modelling cell differentiation.

Scientific reports
Using machine learning techniques to build representations from biomedical data can help us understand the latent biological mechanism of action and lead to important discoveries. Recent developments in single-cell RNA-sequencing protocols have allow...

Data reduction and data visualization for automatic diagnosis using gene expression and clinical data.

Artificial intelligence in medicine
Accurate diagnoses of specific diseases require, in general, the review of the whole medical history of a patient. Currently, even though many advances have been made for disease monitoring, domain experts are still requested to perform direct analys...