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Chapter
Interpretability of Machine Learning Models
Machine Learning (ML) or Artificial Intelligence (AI) models have become a common tool in business and research over the past years. Models, for example, assist our decisions on which hotel to book or set the ...
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Article
Open AccessA multiscale signalling network map of innate immune response in cancer reveals cell heterogeneity signatures
The lack of integrated resources depicting the complexity of the innate immune response in cancer represents a bottleneck for high-throughput data interpretation. To address this challenge, we perform a system...
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Article
Open AccessDeconvolution of transcriptomes and miRNomes by independent component analysis provides insights into biological processes and clinical outcomes of melanoma patients
The amount of publicly available cancer-related “omics” data is constantly growing and can potentially be used to gain insights into the tumour biology of new cancer patients, their diagnosis and suitable trea...
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Article
Adjustment of dendritic cells to the breast-cancer microenvironment is subset specific
The functions and transcriptional profiles of dendritic cells (DCs) result from the interplay between ontogeny and tissue imprinting. How tumors shape human DCs is unknown. Here we used RNA-based next-generati...
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Chapter and Conference Paper
Application of Independent Component Analysis to Tumor Transcriptomes Reveals Specific and Reproducible Immune-Related Signals
Independent Component Analysis (ICA) can be used to model gene expression data as an action of a set of statistically independent hidden factors. The ICA analysis with a downstream component analysis was succe...
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Article
Open AccessDetermining the optimal number of independent components for reproducible transcriptomic data analysis
Independent Component Analysis (ICA) is a method that models gene expression data as an action of a set of statistically independent hidden factors. The output of ICA depends on a fundamental parameter: the nu...
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Article
Open AccessDeDaL: Cytoscape 3 app for producing and morphing data-driven and structure-driven network layouts
Visualization and analysis of molecular profiling data together with biological networks are able to provide new mechanistic insights into biological functions. Currently, it is possible to visualize high-thro...
