Comparing Dissimilarity Metrics for Clustering Gene into Functional Modules using Machine Learning

2020 ◽  
Author(s):  
Xin Yan ◽  
Dantong Lyu
Keyword(s):  
Machine Learning ◽  
Functional Modules

scholarly journals Using a Machine Learning Approach to Identify Key Prognostic Molecules for Esophageal Squamous Cell Carcinoma

2021 ◽  
Author(s):  
Meng-Xiang Li ◽  
Xiao-Meng Sun ◽  
Wei-Gang Cheng ◽  
Hao-Jie Ruan ◽  
Ke Liu ◽  
...  
Keyword(s):  
Machine Learning ◽  
Squamous Cell Carcinoma ◽  
Feature Selection ◽  
Esophageal Squamous Cell Carcinoma ◽  
Molecular Interaction ◽  
Prognostic Biomarker ◽  
Interaction Network ◽  
Machine Learning Algorithms ◽  
Functional Modules ◽  
Molecular Interaction Network

Abstract ObjectiveA plethora of prognostic biomarkers for esophageal squamous cell carcinoma (ESCC) that have hitherto been reported are challenged with low reproducibility due to high molecular heterogeneity of ESCC. The purpose of this study is to identify the optimal biomarkers for ESCC using machine learning algorithms.MethodsBiomarkers related to clinical survival, recurrence or therapeutic response of patients with ESCC were determined through literature database searching. Forty-eight biomarkers linked to prognosis of ESCC were used to construct a molecular interaction network based on NetBox and then to identify the functional modules. Publicably available mRNA transcriptome data of ESCC downloaded from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) datasets included GSE53625 and TCGA-ESCC. Five machine learning algorithms, including logical regression (LR), support vector machine (SVM), artificial neural network (ANN), random forest (RF) and XGBoost, were used to develop classifiers for prognostic classification for feature selection. The area under ROC curve (AUC) was used to evaluate the performance of the prognostic classifiers. The importances of these 17 molecules were ranked by their occurrence frequencies in the prognostic classifiers. Kaplan-Meier survival analysis and log-rank test were performed to determine the statistical significance of overall survival.ResultsA total of 48 clinical proven molecules associated with ESCC progression were used to construct a molecular interaction network with 3 functional modules comprising 17 component molecules. The 131071 prognostic classifiers using these 17 molecules were built for each machine learning algorithm. Using the occurrence frequencies in the prognostic classifiers with AUCs greater than the mean value of all 131,071 AUCs to rank importances of these 17 molecules, stratifin encoded by SFN was identified as the optimal prognostic biomarker for ESCC, whose performance was further validated in another 2 independent cohorts.ConclusionThe occurrence frequencies across various feature selection approaches reflect the degree of clinical importance and stratifin is an optimal prognostic biomarker for ESCC.

scholarly journals Integrative Systems Biology Analysis Elucidates Mastitis Disease Underlying Functional Modules in Dairy Cattle

2021 ◽  
Vol 12 ◽  
Author(s):  
Nooshin Ghahramani ◽  
Jalil Shodja ◽  
Seyed Abbas Rafat ◽  
Bahman Panahi ◽  
Karim Hasanpur
Keyword(s):  
Machine Learning ◽  
Systems Biology ◽  
Dairy Cattle ◽  
Candidate Genes ◽  
Signaling Pathway ◽  
Machine Learning Algorithms ◽  
Functional Modules ◽  
Rna Seq ◽  
Hub Genes ◽  
E Coli

Background: Mastitis is the most prevalent disease in dairy cattle and one of the most significant bovine pathologies affecting milk production, animal health, and reproduction. In addition, mastitis is the most common, expensive, and contagious infection in the dairy industry.Methods: A meta-analysis of microarray and RNA-seq data was conducted to identify candidate genes and functional modules associated with mastitis disease. The results were then applied to systems biology analysis via weighted gene coexpression network analysis (WGCNA), Gene Ontology, enrichment analysis for the Kyoto Encyclopedia of Genes and Genomes (KEGG), and modeling using machine-learning algorithms.Results: Microarray and RNA-seq datasets were generated for 2,089 and 2,794 meta-genes, respectively. Between microarray and RNA-seq datasets, a total of 360 meta-genes were found that were significantly enriched as “peroxisome,” “NOD-like receptor signaling pathway,” “IL-17 signaling pathway,” and “TNF signaling pathway” KEGG pathways. The turquoise module (n = 214 genes) and the brown module (n = 57 genes) were identified as critical functional modules associated with mastitis through WGCNA. PRDX5, RAB5C, ACTN4, SLC25A16, MAPK6, CD53, NCKAP1L, ARHGEF2, COL9A1, and PTPRC genes were detected as hub genes in identified functional modules. Finally, using attribute weighting and machine-learning methods, hub genes that are sufficiently informative in Escherichia coli mastitis were used to optimize predictive models. The constructed model proposed the optimal approach for the meta-genes and validated several high-ranked genes as biomarkers for E. coli mastitis using the decision tree (DT) method.Conclusion: The candidate genes and pathways proposed in this study may shed new light on the underlying molecular mechanisms of mastitis disease and suggest new approaches for diagnosing and treating E. coli mastitis in dairy cattle.

scholarly journals Using a machine learning approach to identify key prognostic molecules for esophageal squamous cell carcinoma

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Meng-Xiang Li ◽  
Xiao-Meng Sun ◽  
Wei-Gang Cheng ◽  
Hao-Jie Ruan ◽  
Ke Liu ◽  
...  
Keyword(s):  
Machine Learning ◽  
Squamous Cell Carcinoma ◽  
Feature Selection ◽  
Esophageal Squamous Cell Carcinoma ◽  
Molecular Interaction ◽  
Prognostic Biomarker ◽  
Interaction Network ◽  
Machine Learning Algorithms ◽  
Functional Modules ◽  
Molecular Interaction Network

Abstract Background A plethora of prognostic biomarkers for esophageal squamous cell carcinoma (ESCC) that have hitherto been reported are challenged with low reproducibility due to high molecular heterogeneity of ESCC. The purpose of this study was to identify the optimal biomarkers for ESCC using machine learning algorithms. Methods Biomarkers related to clinical survival, recurrence or therapeutic response of patients with ESCC were determined through literature database searching. Forty-eight biomarkers linked to recurrence or prognosis of ESCC were used to construct a molecular interaction network based on NetBox and then to identify the functional modules. Publicably available mRNA transcriptome data of ESCC downloaded from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) datasets included GSE53625 and TCGA-ESCC. Five machine learning algorithms, including logical regression (LR), support vector machine (SVM), artificial neural network (ANN), random forest (RF) and XGBoost, were used to develop classifiers for prognostic classification for feature selection. The area under ROC curve (AUC) was used to evaluate the performance of the prognostic classifiers. The importances of identified molecules were ranked by their occurrence frequencies in the prognostic classifiers. Kaplan-Meier survival analysis and log-rank test were performed to determine the statistical significance of overall survival. Results A total of 48 clinically proven molecules associated with ESCC progression were used to construct a molecular interaction network with 3 functional modules comprising 17 component molecules. The 131,071 prognostic classifiers using these 17 molecules were built for each machine learning algorithm. Using the occurrence frequencies in the prognostic classifiers with AUCs greater than the mean value of all 131,071 AUCs to rank importances of these 17 molecules, stratifin encoded by SFN was identified as the optimal prognostic biomarker for ESCC, whose performance was further validated in another 2 independent cohorts. Conclusion The occurrence frequencies across various feature selection approaches reflect the degree of clinical importance and stratifin is an optimal prognostic biomarker for ESCC.

Mind wandering as data augmentation: How mental travel supports abstraction

2020 ◽  
Vol 43 ◽  
Author(s):  
Myrthe Faber
Keyword(s):  
Machine Learning ◽  
Data Augmentation ◽  
Mental Content ◽  
Mind Wandering ◽  
Theoretical Framework ◽  
Important Addition

Abstract Gilead et al. state that abstraction supports mental travel, and that mental travel critically relies on abstraction. I propose an important addition to this theoretical framework, namely that mental travel might also support abstraction. Specifically, I argue that spontaneous mental travel (mind wandering), much like data augmentation in machine learning, provides variability in mental content and context necessary for abstraction.

Data Mining and Machine Learning

2020 ◽  
Author(s):  
Mohammed J. Zaki ◽  
Wagner Meira, Jr
Keyword(s):  
Machine Learning ◽  
Data Mining

Mathematics for Machine Learning

2020 ◽  
Author(s):  
Marc Peter Deisenroth ◽  
A. Aldo Faisal ◽  
Cheng Soon Ong
Keyword(s):  
Machine Learning

Phase Transitions in Machine Learning

2009 ◽  
Author(s):  
Lorenza Saitta ◽  
Attilio Giordana ◽  
Antoine Cornuejols
Keyword(s):  
Machine Learning ◽  
Phase Transitions
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