Multivariate multi-way modelling of multiple high-dimensional data sources

Ilkka Huopaniemi

    Research output: ThesisDoctoral ThesisCollection of Articles


    A widely employed strategy in current biomedical research is to study samples from patients using high-throughput measurement techniques, such as transcriptomics, proteomics, and metabolomics. In contrast to the static information obtained from the DNA sequence, these techniques deliver a "dynamic fingerprint" describing the phenotypic status of the patient in the form of absolute or relative concentrations of hundreds, or even tens of thousands of molecules: mRNA, proteins, metabolites and lipids. The huge number of variables measured opens up new possibilities for biomedical research; harnessing the information contained in such 'omics' data requires advanced data analysis methods. The standard setup in biomedical research is comparing case (diseased) and control (healthy) samples and determining differentially expressed molecules that are then considered potential bio-markers for disease. In modern biomedical experiments, more complicated research questions are common. For instance, diet or drug treatments, gender and age play central roles in many case-control experiments and the measurements are often in the form of a time-series. Due to these additional covariates, the experimental setting becomes a multi-way experimental design, but few tools for proper data-analysis of high-dimensional data with such a design exist. Moreover, the task of integrating multiple data sources with different variables is nowadays often encountered in two classes of biomedical experiments: (i) Multiple omics types or samples from several tissues are measured from each patient (paired samples), (ii) Translating biomarkers between human studies and model organisms (no paired samples). These data integration tasks usually additionally involve a multi-way experimental design. In this dissertation, a novel Bayesian machine learning model for multi-way modelling of data from such multi-way, single-source or multi-source setups is presented, covering the majority of situations commonly encountered in statistical analysis of omics data coming from current biomedical research. The problem of high dimensionality is solved by assuming that the data can be described as highly correlated groups of variables. The Bayesian modelling approach involves training a single, unified, interpretable model to explain all the data. This approach can overcome the main difficulties in omics analysis: small sample-size and high dimensionality, multicollinearity of data, and the problem of multiple testing. This approach also enables rigorous uncertainty estimation, dimensionality reduction and easy interpretability of results from a complex setup involving multiple covariates and multiple data sources.
    Translated title of the contributionUsean korkeaulotteisen datalähteen analyysi monisuuntaisessa koeasetelmassa
    Original languageEnglish
    QualificationDoctor's degree
    Awarding Institution
    • Aalto University
    • Kaski, Samuel, Supervising Professor
    Print ISBNs978-952-60-4782-9
    Electronic ISBNs978-952-60-4783-6
    Publication statusPublished - 2012
    MoE publication typeG5 Doctoral dissertation (article)


    • Bayesian methods
    • data integration
    • machine learning
    • multi-way ANOVA
    • small sample-size

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