Optimizing Wrapper-Based Feature Selection for Use on Bioinformatics Data

AAAI Conferences

High dimensionality (having a large number of independent attributes) is a major problem for bioinformatics datasets such as gene microarray datasets. Feature selection algorithms are necessary to remove the irrelevant (not useful) and redundant (contain duplicate information) features. One approach to handle this problem is wrapper-based subset evaluation, which builds classification models on different feature subsets to discover which performs best. Although the computational complexity of this technique has led to it being rarely used for bioinformatics, its ability to find the features which give the best model make it important in this domain. However, when using wrapper-based feature selection, it is not obvious whether the learner used within the wrapper should match the learner used for building the final classification model. Furthermore, this question may depend on other properties of the dataset, such as difficulty of learning (general performance without feature selection) and dataset balance (ratio of minority and majority instances). To study this, we use nine datasets with varying levels of difficulty and balance. We find that across all datasets, the best strategy is to use one learner (Na¨ıve Bayes) inside the wrapper regardless of the learner which will be used outside. However, when broken down by difficulty and balance levels, our results show that the more balanced and less difficult datasets work best when the learners inside and outside the wrapper match. Thus, the answer to this question will depend on properties of the dataset.


Robust and Parallel Bayesian Model Selection

arXiv.org Machine Learning

Effective and accurate model selection is an important problem in modern data analysis. One of the major challenges is the computational burden required to handle large data sets that cannot be stored or processed on one machine. Another challenge one may encounter is the presence of outliers and contaminations that damage the inference quality. The parallel "divide and conquer" model selection strategy divides the observations of the full data set into roughly equal subsets and perform inference and model selection independently on each subset. After local subset inference, this method aggregates the posterior model probabilities or other model/variable selection criteria to obtain a final model by using the notion of geometric median. This approach leads to improved concentration in finding the "correct" model and model parameters and also is provably robust to outliers and data contamination.


Bayesian model selection consistency and oracle inequality with intractable marginal likelihood

arXiv.org Machine Learning

In this article, we investigate large sample properties of model selection procedures in a general Bayesian framework when a closed form expression of the marginal likelihood function is not available or a local asymptotic quadratic approximation of the log-likelihood function does not exist. Under appropriate identifiability assumptions on the true model, we provide sufficient conditions for a Bayesian model selection procedure to be consistent and obey the Occam's razor phenomenon, i.e., the probability of selecting the "smallest" model that contains the truth tends to one as the sample size goes to infinity. In order to show that a Bayesian model selection procedure selects the smallest model containing the truth, we impose a prior anti-concentration condition, requiring the prior mass assigned by large models to a neighborhood of the truth to be sufficiently small. In a more general setting where the strong model identifiability assumption may not hold, we introduce the notion of local Bayesian complexity and develop oracle inequalities for Bayesian model selection procedures. Our Bayesian oracle inequality characterizes a trade-off between the approximation error and a Bayesian characterization of the local complexity of the model, illustrating the adaptive nature of averaging-based Bayesian procedures towards achieving an optimal rate of posterior convergence. Specific applications of the model selection theory are discussed in the context of high-dimensional nonparametric regression and density regression where the regression function or the conditional density is assumed to depend on a fixed subset of predictors. As a result of independent interest, we propose a general technique for obtaining upper bounds of certain small ball probability of stationary Gaussian processes.


Variational Bayes under Model Misspecification

arXiv.org Machine Learning

Variational Bayes (VB) is a scalable alternative to Markov chain Monte Carlo (MCMC) for Bayesian posterior inference. Though popular, VB comes with few theoretical guarantees, most of which focus on well-specified models. However, models are rarely well-specified in practice. In this work, we study VB under model misspecification. We prove the VB posterior is asymptotically normal and centers at the value that minimizes the Kullback-Leibler (KL) divergence to the true data-generating distribution. Moreover, the VB posterior mean centers at the same value and is also asymptotically normal. These results generalize the variational Bernstein--von Mises theorem [29] to misspecified models. As a consequence of these results, we find that the model misspecification error dominates the variational approximation error in VB posterior predictive distributions. It explains the widely observed phenomenon that VB achieves comparable predictive accuracy with MCMC even though VB uses an approximating family. As illustrations, we study VB under three forms of model misspecification, ranging from model over-/under-dispersion to latent dimensionality misspecification. We conduct two simulation studies that demonstrate the theoretical results.


On the consistency between model selection and link prediction in networks

arXiv.org Machine Learning

A principled approach to understand network structures is to formulate generative models. Given a collection of models, however, an outstanding key task is to determine which one provides a more accurate description of the network at hand, discounting statistical fluctuations. This problem can be approached using two principled criteria that at first may seem equivalent: selecting the most plausible model in terms of its posterior probability; or selecting the model with the highest predictive performance in terms of identifying missing links. Here we show that while these two approaches yield consistent results in most of cases, there are also notable instances where they do not, that is, where the most plausible model is not the most predictive. We show that in the latter case the improvement of predictive performance can in fact lead to overfitting both in artificial and empirical settings. Furthermore, we show that, in general, the predictive performance is higher when we average over collections of models that are individually less plausible, than when we consider only the single most plausible model.