Ilkka Huopaniemi

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MOTIVATION Analysis of variance (ANOVA)-type methods are the default tool for the analysis of data with multiple covariates. These tools have been generalized to the multivariate analysis of high-throughput biological datasets, where the main challenge is the problem of small sample size and high dimensionality. However, the existing multi-way analysis(More)
Ilkka Huopaniemi Two-way analysis of high-dimensional collinear data Introduction: Two-way experimental setups Bayesian Multi-way model Results Conclusions Outline Introduction: Two-way experimental setups Bayesian Multi-way model Factor analysis Solving small n, large p problem by clustering approach Two-way covariate information as population priors(More)
In a recent FIELD study the fenofibrate therapy surprisingly failed to achieve significant benefit over placebo in the primary endpoint of coronary heart disease events. Increased levels of atherogenic homocysteine were observed in some patients assigned to fenofibrate therapy but the molecular mechanisms behind this are poorly understood. Herein we(More)
We investigate the dynamics of polymer translocation through a nanopore under an externally applied field using the 2D fluctuating bond model with single-segment Monte Carlo moves. We concentrate on the influence of the field strength E, length of the chain N, and length of the pore L on forced translocation. As our main result, we find a crossover scaling(More)
Multivariate multi-way ANOVA-type models are the default tools for analyzing experimental data with multiple independent covari-ates. However, formulating standard multi-way models is not possible when the data comes from different sources or in cases where some co-variates have (partly) unknown structure, such as time with unknown alignment. The " small n,(More)
We investigate polymer translocation through a nanopore under a pulling force using Langevin dynamics simulations. We concentrate on the influence of the chain length N and the pulling force F on the translocation time tau . The distribution of tau is symmetric and narrow for strong F . We find that tau approximately N{2} and translocation velocity v(More)
We extend multi-way, multivariate ANOVA-type analysis to cases where one covariate is the view, with features of each view coming from different, high-dimensional domains. The different views are assumed to be connected by having paired samples; this is common in our main application, biological experiments integrating data from different sources. Such(More)
Electronic medical records (EMR) contain a longitudinal collection of laboratory data that contains valuable phenotypic information on disease progression of a large collection of patients. These data can be potentially used in medical research or patient care; finding disease progression subtypes is a particularly important application. There are, however,(More)
We determine the scaling exponents of polymer translocation (PT) through a nanopore by extensive computer simulations of various microscopic models for chain lengths extending up to N=800 in some cases. We focus on the scaling of the average PT time tau approximately Nalpha and the mean-square change of the PT coordinate, <s2(t)> approximately tbeta. We(More)
We present a Bayesian translational model for matching patterns in data sets which have neither co-occurring samples nor variables, but only a similar experiment design dividing the samples into two or more categories. The model estimates covariate effects related to this design and separates the factors that are shared across the data sets from those(More)