An ensemble approach to accurately detect somatic mutations using SomaticSeq

SomaticSeq is an accurate somatic mutation detection pipeline implementing a stochastic boosting algorithm to produce highly accurate somatic mutation calls for both single nucleotide variants and small insertions and deletions. The workflow currently incorporates five state-of-the-art somatic mutation callers, and extracts over 70 individual genomic and sequencing features for each candidate site. A training set is provided to an adaptively boosted decision tree learner to create a classifier for predicting mutation statuses. We validate our results with both synthetic and real data. We report that SomaticSeq is able to achieve better overall accuracy than any individual tool incorporated. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-015-0758-2) contains supplementary material, which is available to authorized users

Reducing Overfitting in Process Model Induction

In this paper, we review the paradigm of inductive process modeling, which uses background knowledge about possible component processes to construct quantitative models of dynamical systems. We note that previous methods for this task tend to overfit the training data, which suggests ensemble learning as a likely response. However, such techniques combine models in ways that reduce comprehensibility, making their output much less accessible to domain scientists. As an alternative, we introduce a new approach that induces a set of process models from di#erent samples of the training data and uses them to guide a final search through the space of model structures. Experiments with synthetic and natural data suggest this method reduces error and decreases the chance of including unnecessary processes in the model