Prediction in cancer genomics using topological signatures and machine learning

DOI10.1007/978-3-030-43408-3_10MaRDI QIDQ5118370zbMATH OpenOpenAlexFDO

Authors Georgina Gonzalez, Arina Ushakova, R. Sazdanović, J. Arsuaga

Publication date 8 September 2020

Published in Topological Data Analysis (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/978-3-030-43408-3_10

zbMATH Keywords

predictionmachine learningcancer genomicstopological signatures

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Learning and adaptive systems in artificial intelligence (68T05) Inference from stochastic processes and prediction (62M20) Protein sequences, DNA sequences (92D20) Persistent homology and applications, topological data analysis (55N31) Topological data analysis (62R40)

Recommendations

• Topological analysis of gene expression arrays identifies high risk molecular subtypes in breast cancer
• Discovering Combinations of Genomic Aberrations Associated With Cancer
• Identification of differential aberrations in multiple-sample array CGH studies
• Bayesian random segmentation models to identify shared copy number aberrations for array CGH data
• A latent class model with hidden Markov dependence for array CGH data

Cites work

• Applications of computational homology to the analysis of treatment response in breast cancer patients
• Hidden Markov models approach to the analysis of array CGH data
• Morse theory for filtrations and efficient computation of persistent homology
• Persistent homology -- a survey
• Simplicial models and topological inference in biological systems
• Statistical topological data analysis using persistence landscapes
• The Group Lasso for Logistic Regression

Cited in

(5)

• What Are Higher-Order Networks?
• Topological analysis of gene expression arrays identifies high risk molecular subtypes in breast cancer
• Learning Oncogenic Pathways from Binary Genomic Instability Data
• Prediction of metastasis in advanced colorectal carcinomas using CGH data
• Multi-target QPDR classification model for human breast and colon cancer-related proteins using star graph topological indices

Describes a project that uses

Uses Software

• R
• Gudhi
• Perseus
• jPlex
• Eirene
• Ripser
• KCsmart
• GitHub

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