AIMC Topic: Transcriptome

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Transfer learning with convolutional neural networks for cancer survival prediction using gene-expression data.

PloS one
Precision medicine in oncology aims at obtaining data from heterogeneous sources to have a precise estimation of a given patient's state and prognosis. With the purpose of advancing to personalized medicine framework, accurate diagnoses allow prescri...

Network modeling of patients' biomolecular profiles for clinical phenotype/outcome prediction.

Scientific reports
Methods for phenotype and outcome prediction are largely based on inductive supervised models that use selected biomarkers to make predictions, without explicitly considering the functional relationships between individuals. We introduce a novel netw...

DeepTRIAGE: interpretable and individualised biomarker scores using attention mechanism for the classification of breast cancer sub-types.

BMC medical genomics
BACKGROUND: Breast cancer is a collection of multiple tissue pathologies, each with a distinct molecular signature that correlates with patient prognosis and response to therapy. Accurately differentiating between breast cancer sub-types is an import...

Hyper-Graph Regularized Constrained NMF for Selecting Differentially Expressed Genes and Tumor Classification.

IEEE journal of biomedical and health informatics
Non-negative Matrix Factorization (NMF) is a dimensionality reduction approach for learning a parts-based and linear representation of non-negative data. It has attracted more attention because of that. In practice, NMF not only neglects the manifold...

Predicting antimicrobial resistance in Pseudomonas aeruginosa with machine learning-enabled molecular diagnostics.

EMBO molecular medicine
Limited therapy options due to antibiotic resistance underscore the need for optimization of current diagnostics. In some bacterial species, antimicrobial resistance can be unambiguously predicted based on their genome sequence. In this study, we seq...

Application of Machine Learning in Developing a Novelty Five-Pseudogene Signature to Predict Prognosis of Head and Neck Squamous Cell Carcinoma: A New Aspect of "Junk Genes" in Biomedical Practice.

DNA and cell biology
Head and neck squamous cell carcinoma (HNSCC) is the sixth malignancy, which is characterized by poor prognosis or high mortality because of the lack of predicting markers. Aberrant cancer pseudogenes have been found predictive for prognosis. We aim ...

Investigating the gene expression profiles of cells in seven embryonic stages with machine learning algorithms.

Genomics
The development of embryonic cells involves several continuous stages, and some genes are related to embryogenesis. To date, few studies have systematically investigated changes in gene expression profiles during mammalian embryogenesis. In this stud...

scAI: an unsupervised approach for the integrative analysis of parallel single-cell transcriptomic and epigenomic profiles.

Genome biology
Simultaneous measurements of transcriptomic and epigenomic profiles in the same individual cells provide an unprecedented opportunity to understand cell fates. However, effective approaches for the integrative analysis of such data are lacking. Here,...