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Yayın Soft decision trees(IEEE, 2012) İrsoy, Ozan; Yıldız, Olcay Taner; Alpaydın, Ahmet İbrahim EthemWe discuss a novel decision tree architecture with soft decisions at the internal nodes where we choose both children with probabilities given by a sigmoid gating function. Our algorithm is incremental where new nodes are added when needed and parameters are learned using gradient-descent. We visualize the soft tree fit on a toy data set and then compare it with the canonical, hard decision tree over ten regression and classification data sets. Our proposed model has significantly higher accuracy using fewer nodes.Yayın Budding trees(IEEE Computer Soc, 2014-08-24) İrsoy, Ozan; Yıldız, Olcay Taner; Alpaydın, Ahmet İbrahim EthemWe propose a new decision tree model, named the budding tree, where a node can be both a leaf and an internal decision node. Each bud node starts as a leaf node, can then grow children, but then later on, if necessary, its children can be pruned. This contrasts with traditional tree construction algorithms that only grows the tree during the training phase, and prunes it in a separate pruning phase. We use a soft tree architecture and show that the tree and its parameters can be trained using gradient-descent. Our experimental results on regression, binary classification, and multi-class classification data sets indicate that our newly proposed model has better performance than traditional trees in terms of accuracy while inducing trees of comparable size.Yayın Design and analysis of classifier learning experiments in bioinformatics: survey and case studies(IEEE Computer Soc, 2012-12) İrsoy, Ozan; Yıldız, Olcay Taner; Alpaydın, Ahmet İbrahim EthemIn many bioinformatics applications, it is important to assess and compare the performances of algorithms trained from data, to be able to draw conclusions unaffected by chance and are therefore significant. Both the design of such experiments and the analysis of the resulting data using statistical tests should be done carefully for the results to carry significance. In this paper, we first review the performance measures used in classification, the basics of experiment design and statistical tests. We then give the results of our survey over 1,500 papers published in the last two years in three bioinformatics journals (including this one). Although the basics of experiment design are well understood, such as resampling instead of using a single training set and the use of different performance metrics instead of error, only 21 percent of the papers use any statistical test for comparison. In the third part, we analyze four different scenarios which we encounter frequently in the bioinformatics literature, discussing the proper statistical methodology as well as showing an example case study for each. With the supplementary software, we hope that the guidelines we discuss will play an important role in future studies.Yayın Bagging soft decision trees(Springer Verlag, 2016) Yıldız, Olcay Taner; İrsoy, Ozan; Alpaydın, Ahmet İbrahim EthemThe decision tree is one of the earliest predictive models in machine learning. In the soft decision tree, based on the hierarchical mixture of experts model, internal binary nodes take soft decisions and choose both children with probabilities given by a sigmoid gating function. Hence for an input, all the paths to all the leaves are traversed and all those leaves contribute to the final decision but with different probabilities, as given by the gating values on the path. Tree induction is incremental and the tree grows when needed by replacing leaves with subtrees and the parameters of the newly-added nodes are learned using gradient-descent. We have previously shown that such soft trees generalize better than hard trees; here, we propose to bag such soft decision trees for higher accuracy. On 27 two-class classification data sets (ten of which are from the medical domain), and 26 regression data sets, we show that the bagged soft trees generalize better than single soft trees and bagged hard trees. This contribution falls in the scope of research track 2 listed in the editorial, namely, machine learning algorithms.
