11,455 research outputs found
Optimal classifier selection and negative bias in error rate estimation: An empirical study on high-dimensional prediction
In biometric practice, researchers often apply a large number of different methods in a "trial-and-error" strategy to get as much as possible out of their data and, due to publication pressure or pressure from the consulting customer, present only the most favorable results. This strategy may induce a substantial optimistic bias in prediction error estimation, which is quantitatively assessed in the present manuscript. The focus of our work is on class prediction based on high-dimensional data (e.g. microarray data), since such analyses are particularly exposed to this kind of bias.
In our study we consider a total of 124 variants of classifiers (possibly including variable selection or tuning steps) within a cross-validation evaluation scheme. The classifiers are applied to original and modified real microarray data sets, some of which are obtained by randomly permuting the class labels to mimic non-informative predictors while preserving their correlation structure. We then assess the minimal misclassification rate over the different variants of classifiers in order to quantify the bias arising when the optimal classifier is selected a posteriori in a data-driven manner. The bias resulting from the parameter tuning (including gene selection parameters as a special case) and the bias resulting from the choice of the classification method are examined both separately and jointly.
We conclude that the strategy to present only the optimal result is not acceptable, and suggest alternative approaches for properly reporting classification accuracy
Efficient Benchmarking of Algorithm Configuration Procedures via Model-Based Surrogates
The optimization of algorithm (hyper-)parameters is crucial for achieving
peak performance across a wide range of domains, ranging from deep neural
networks to solvers for hard combinatorial problems. The resulting algorithm
configuration (AC) problem has attracted much attention from the machine
learning community. However, the proper evaluation of new AC procedures is
hindered by two key hurdles. First, AC benchmarks are hard to set up. Second
and even more significantly, they are computationally expensive: a single run
of an AC procedure involves many costly runs of the target algorithm whose
performance is to be optimized in a given AC benchmark scenario. One common
workaround is to optimize cheap-to-evaluate artificial benchmark functions
(e.g., Branin) instead of actual algorithms; however, these have different
properties than realistic AC problems. Here, we propose an alternative
benchmarking approach that is similarly cheap to evaluate but much closer to
the original AC problem: replacing expensive benchmarks by surrogate benchmarks
constructed from AC benchmarks. These surrogate benchmarks approximate the
response surface corresponding to true target algorithm performance using a
regression model, and the original and surrogate benchmark share the same
(hyper-)parameter space. In our experiments, we construct and evaluate
surrogate benchmarks for hyperparameter optimization as well as for AC problems
that involve performance optimization of solvers for hard combinatorial
problems, drawing training data from the runs of existing AC procedures. We
show that our surrogate benchmarks capture overall important characteristics of
the AC scenarios, such as high- and low-performing regions, from which they
were derived, while being much easier to use and orders of magnitude cheaper to
evaluate
Markov Network Structure Learning via Ensemble-of-Forests Models
Real world systems typically feature a variety of different dependency types
and topologies that complicate model selection for probabilistic graphical
models. We introduce the ensemble-of-forests model, a generalization of the
ensemble-of-trees model. Our model enables structure learning of Markov random
fields (MRF) with multiple connected components and arbitrary potentials. We
present two approximate inference techniques for this model and demonstrate
their performance on synthetic data. Our results suggest that the
ensemble-of-forests approach can accurately recover sparse, possibly
disconnected MRF topologies, even in presence of non-Gaussian dependencies
and/or low sample size. We applied the ensemble-of-forests model to learn the
structure of perturbed signaling networks of immune cells and found that these
frequently exhibit non-Gaussian dependencies with disconnected MRF topologies.
In summary, we expect that the ensemble-of-forests model will enable MRF
structure learning in other high dimensional real world settings that are
governed by non-trivial dependencies.Comment: 13 pages, 6 figure
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