5,740 research outputs found
Predicting Genetic Regulatory Response Using Classification
We present a novel classification-based method for learning to predict gene
regulatory response. Our approach is motivated by the hypothesis that in simple
organisms such as Saccharomyces cerevisiae, we can learn a decision rule for
predicting whether a gene is up- or down-regulated in a particular experiment
based on (1) the presence of binding site subsequences (``motifs'') in the
gene's regulatory region and (2) the expression levels of regulators such as
transcription factors in the experiment (``parents''). Thus our learning task
integrates two qualitatively different data sources: genome-wide cDNA
microarray data across multiple perturbation and mutant experiments along with
motif profile data from regulatory sequences. We convert the regression task of
predicting real-valued gene expression measurement to a classification task of
predicting +1 and -1 labels, corresponding to up- and down-regulation beyond
the levels of biological and measurement noise in microarray measurements. The
learning algorithm employed is boosting with a margin-based generalization of
decision trees, alternating decision trees. This large-margin classifier is
sufficiently flexible to allow complex logical functions, yet sufficiently
simple to give insight into the combinatorial mechanisms of gene regulation. We
observe encouraging prediction accuracy on experiments based on the Gasch S.
cerevisiae dataset, and we show that we can accurately predict up- and
down-regulation on held-out experiments. Our method thus provides predictive
hypotheses, suggests biological experiments, and provides interpretable insight
into the structure of genetic regulatory networks.Comment: 8 pages, 4 figures, presented at Twelfth International Conference on
Intelligent Systems for Molecular Biology (ISMB 2004), supplemental website:
http://www.cs.columbia.edu/compbio/geneclas
Popular Ensemble Methods: An Empirical Study
An ensemble consists of a set of individually trained classifiers (such as
neural networks or decision trees) whose predictions are combined when
classifying novel instances. Previous research has shown that an ensemble is
often more accurate than any of the single classifiers in the ensemble. Bagging
(Breiman, 1996c) and Boosting (Freund and Shapire, 1996; Shapire, 1990) are two
relatively new but popular methods for producing ensembles. In this paper we
evaluate these methods on 23 data sets using both neural networks and decision
trees as our classification algorithm. Our results clearly indicate a number of
conclusions. First, while Bagging is almost always more accurate than a single
classifier, it is sometimes much less accurate than Boosting. On the other
hand, Boosting can create ensembles that are less accurate than a single
classifier -- especially when using neural networks. Analysis indicates that
the performance of the Boosting methods is dependent on the characteristics of
the data set being examined. In fact, further results show that Boosting
ensembles may overfit noisy data sets, thus decreasing its performance.
Finally, consistent with previous studies, our work suggests that most of the
gain in an ensemble's performance comes in the first few classifiers combined;
however, relatively large gains can be seen up to 25 classifiers when Boosting
decision trees
On PAC-Bayesian Bounds for Random Forests
Existing guarantees in terms of rigorous upper bounds on the generalization
error for the original random forest algorithm, one of the most frequently used
machine learning methods, are unsatisfying. We discuss and evaluate various
PAC-Bayesian approaches to derive such bounds. The bounds do not require
additional hold-out data, because the out-of-bag samples from the bagging in
the training process can be exploited. A random forest predicts by taking a
majority vote of an ensemble of decision trees. The first approach is to bound
the error of the vote by twice the error of the corresponding Gibbs classifier
(classifying with a single member of the ensemble selected at random). However,
this approach does not take into account the effect of averaging out of errors
of individual classifiers when taking the majority vote. This effect provides a
significant boost in performance when the errors are independent or negatively
correlated, but when the correlations are strong the advantage from taking the
majority vote is small. The second approach based on PAC-Bayesian C-bounds
takes dependencies between ensemble members into account, but it requires
estimating correlations between the errors of the individual classifiers. When
the correlations are high or the estimation is poor, the bounds degrade. In our
experiments, we compute generalization bounds for random forests on various
benchmark data sets. Because the individual decision trees already perform
well, their predictions are highly correlated and the C-bounds do not lead to
satisfactory results. For the same reason, the bounds based on the analysis of
Gibbs classifiers are typically superior and often reasonably tight. Bounds
based on a validation set coming at the cost of a smaller training set gave
better performance guarantees, but worse performance in most experiments
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