Data mining in bioinformatics using Weka

The Weka machine learning workbench provides a general purpose environment for automatic classification, regression, clustering and feature selection-common data mining problems in bioinformatics research. It contains an extensive collection of machine learning algorithms and data exploration and the experimental comparison of different machine learning techniques on the same problem. Weka can process data given in the form of a single relational table. Its main objectives are to (a) assist users in extracting useful information from data and (b) enable them to easily identify a suitable algorithm for generating an accurate predictive model from it

Learning from the machine: interpreting machine learning algorithms for point- and extended- source classification

We investigate star-galaxy classification for astronomical surveys in the context of four methods enabling the interpretation of black-box machine learning systems. The first is outputting and exploring the decision boundaries as given by decision tree based methods, which enables the visualization of the classification categories. Secondly, we investigate how the Mutual Information based Transductive Feature Selection (MINT) algorithm can be used to perform feature pre-selection. If one would like to provide only a small number of input features to a machine learning classification algorithm, feature pre-selection provides a method to determine which of the many possible input properties should be selected. Third is the use of the tree-interpreter package to enable popular decision tree based ensemble methods to be opened, visualized, and understood. This is done by additional analysis of the tree based model, determining not only which features are important to the model, but how important a feature is for a particular classification given its value. Lastly, we use decision boundaries from the model to revise an already existing method of classification, essentially asking the tree based method where decision boundaries are best placed and defining a new classification method. We showcase these techniques by applying them to the problem of star-galaxy separation using data from the Sloan Digital Sky Survey (hereafter SDSS). We use the output of MINT and the ensemble methods to demonstrate how more complex decision boundaries improve star-galaxy classification accuracy over the standard SDSS frames approach (reducing misclassifications by up to $\approx33\%$). We then show how tree-interpreter can be used to explore how relevant each photometric feature is when making a classification on an object by object basis.Comment: 12 pages, 8 figures, 8 table

Using a unified measure function for heuristics, discretization, and rule quality evaluation in Ant-Miner

Ant-Miner is a classification rule discovery algorithm that is based on Ant Colony Optimization (ACO) meta-heuristic. cAnt-Miner is the extended version of the algorithm that handles continuous attributes on-the-fly during the rule construction process, while ?Ant-Miner is an extension of the algorithm that selects the rule class prior to its construction, and utilizes multiple pheromone types, one for each permitted rule class. In this paper, we combine these two algorithms to derive a new approach for learning classification rules using ACO. The proposed approach is based on using the measure function for 1) computing the heuristics for rule term selection, 2) a criteria for discretizing continuous attributes, and 3) evaluating the quality of the constructed rule for pheromone update as well. We explore the effect of using different measure functions for on the output model in terms of predictive accuracy and model size. Empirical evaluations found that hypothesis of different functions produce different results are acceptable according to Friedman’s statistical test