AIMC Topic: Gene Expression Profiling

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Active learning using rough fuzzy classifier for cancer prediction from microarray gene expression data.

Journal of biomedical informatics
Cancer classification from microarray gene expression data is one of the important areas of research in the field of computational biology and bioinformatics. Traditional supervised techniques often fail to produce desired accuracy as the number of c...

Whale optimized mixed kernel function of support vector machine for colorectal cancer diagnosis.

Journal of biomedical informatics
Microarray technique is a prevalent method for the classification and prediction of colorectal cancer (CRC). Nevertheless, microarray data suffers from the curse of dimensionality when selecting feature genes of the disease based on imbalance samples...

Cell Identity Codes: Understanding Cell Identity from Gene Expression Profiles using Deep Neural Networks.

Scientific reports
Understanding cell identity is an important task in many biomedical areas. Expression patterns of specific marker genes have been used to characterize some limited cell types, but exclusive markers are not available for many cell types. A second appr...

Machine learning analysis of gene expression data reveals novel diagnostic and prognostic biomarkers and identifies therapeutic targets for soft tissue sarcomas.

PLoS computational biology
Based on morphology it is often challenging to distinguish between the many different soft tissue sarcoma subtypes. Moreover, outcome of disease is highly variable even between patients with the same disease. Machine learning on transcriptome sequenc...

Pancreatic cancer biomarker detection by two support vector strategies for recursive feature elimination.

Biomarkers in medicine
AIM: Pancreatic cancer is one of the worst malignant tumors in prognosis. Therefore, to reduce the mortality rate of pancreatic cancer, early diagnosis and prompt treatment are particularly important.

A robust fuzzy rule based integrative feature selection strategy for gene expression data in TCGA.

BMC medical genomics
BACKGROUND: Lots of researches have been conducted in the selection of gene signatures that could distinguish the cancer patients from the normal. However, it is still an open question on how to extract the robust gene features.

A Computational Framework for Genome-wide Characterization of the Human Disease Landscape.

Cell systems
A key challenge for the diagnosis and treatment of complex human diseases is identifying their molecular basis. Here, we developed a unified computational framework, URSA (Unveiling RNA Sample Annotation for Human Diseases), that leverages machine le...

A novel gene selection algorithm for cancer classification using microarray datasets.

BMC medical genomics
BACKGROUND: Microarray datasets are an important medical diagnostic tool as they represent the states of a cell at the molecular level. Available microarray datasets for classifying cancer types generally have a fairly small sample size compared to t...

Enhancing Confusion Entropy (CEN) for binary and multiclass classification.

PloS one
Different performance measures are used to assess the behaviour, and to carry out the comparison, of classifiers in Machine Learning. Many measures have been defined on the literature, and among them, a measure inspired by Shannon's entropy named the...

GOTrapper: a tool to navigate through branches of gene ontology hierarchy.

BMC bioinformatics
BACKGROUND: Gene Ontology (GO) is a useful resource of controlled vocabulary that provides information about annotated genes. Based on such resource, finding the biological function is useful for biologists to come up with different hypotheses and he...