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Feature selection is commonly used in bioinformatics applications, such as gene selection from DNA micro array data. Recently, wrapper methods have been proposed as an improvement over traditionally used filter based feature selection methods. In wrapper methods, the goodness of a feature set is often measured using the cross-validation performance of a machine learning method trained with the features...
We propose novel computational short-cuts for constructing sparse linear predictors with regularized least-squares (RLS), also known as the least-squares support vector machine or ridge regression. The short-cuts make it possible to accelerate the search in the power set of features with leave-one-out criterion as a search heuristic. Our first short-cut finds the optimal search direction in the power...
Algorithm visualization tools can potentially be used to help novices to learn the abstract concepts of algorithms and data structures. Still, the methods of using such tools must be carefully considered. We conducted a study to find out if the TRAKLA2 algorithm visualization tool can be used to teach these concepts effectively. Moreover, we wanted to find out if there is a difference in learning...
Fluent patient information flow is a prerequisite for clinical decision making. Our purpose is to identify unmet information needs in the flow of Finnish intensive care narratives in order to focus the development of natural language processing methods for this domain. Our data set consists of 516 authentic electronic patient records. First, we assess statistically the amount of narratives. We find...
In a longitudinal medical study, various types of data and biomaterial samples are collected in frequent intervals, and are used to analyze factors and pathways leading to a defined disease or a group of diseases. Large volume of complex data consisting of medical history and biochemical analysis results are typically collected in such studies. Our research shows that if the appropriate data model...
Selecting a right programming language for introductory CS courses is not an easy task. The pressure to use a commercially successful language can easily be the most significant factor in choosing the language. However, several studies suggest that it is preferable to use a language specifically designed for teaching. These languages are usually some kind of pseudo languages, defined by the programming...
Hydropathy is a dominant force in protein folding and has been measured with numerous methods. Several hydropathy scales are widely used in sequence-based predictions, however, without knowledge about their reliability. We investigated the prediction accuracy of 56 hydropathy scales by correlating predicted values with the accessible surface area in known 3-D structures of proteins. The correlations...
We present an efficient algorithm for reverse engineering gene regulatory networks from microarray datasets using linear system of ordinary differential equations to deal with issues of underdetermined and ill-conditioned datasets. Our method was evaluated in in silico experiments. It was shown that the method can be readily applied to reconstruct the sparse network structure for a linear system with...
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