AIMC Topic: Machine Learning

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Machine learning integrates genomic signatures for subclassification beyond primary and secondary acute myeloid leukemia.

Blood
Although genomic alterations drive the pathogenesis of acute myeloid leukemia (AML), traditional classifications are largely based on morphology, and prototypic genetic founder lesions define only a small proportion of AML patients. The historical su...

Epitome: predicting epigenetic events in novel cell types with multi-cell deep ensemble learning.

Nucleic acids research
The accumulation of large epigenomics data consortiums provides us with the opportunity to extrapolate existing knowledge to new cell types and conditions. We propose Epitome, a deep neural network that learns similarities of chromatin accessibility ...

De Novo Identification and Visualization of Important Cell Populations for Classic Hodgkin Lymphoma Using Flow Cytometry and Machine Learning.

American journal of clinical pathology
OBJECTIVES: Automated classification of flow cytometry data has the potential to reduce errors and accelerate flow cytometry interpretation. We desired a machine learning approach that is accurate, is intuitively easy to understand, and highlights th...

CellProfiler Analyst 3.0: accessible data exploration and machine learning for image analysis.

Bioinformatics (Oxford, England)
SUMMARY: Image-based experiments can yield many thousands of individual measurements describing each object of interest, such as cells in microscopy screens. CellProfiler Analyst is a free, open-source software package designed for the exploration of...

PreTP-EL: prediction of therapeutic peptides based on ensemble learning.

Briefings in bioinformatics
Therapeutic peptides are important for understanding the correlation between peptides and their therapeutic diagnostic potential. The therapeutic peptides can be further divided into different types based on therapeutic function sharing different cha...

XOmiVAE: an interpretable deep learning model for cancer classification using high-dimensional omics data.

Briefings in bioinformatics
The lack of explainability is one of the most prominent disadvantages of deep learning applications in omics. This 'black box' problem can undermine the credibility and limit the practical implementation of biomedical deep learning models. Here we pr...

Drug sensitivity prediction from cell line-based pharmacogenomics data: guidelines for developing machine learning models.

Briefings in bioinformatics
The goal of precision oncology is to tailor treatment for patients individually using the genomic profile of their tumors. Pharmacogenomics datasets such as cancer cell lines are among the most valuable resources for drug sensitivity prediction, a cr...