Bagging ensemble selection for regression

Bagging ensemble selection (BES) is a relatively new ensemble learning strategy. The strategy can be seen as an ensemble of the ensemble selection from libraries of models (ES) strategy. Previous experimental results on binary classification problems have shown that using random trees as base classifiers, BES-OOB (the most successful variant of BES) is competitive with (and in many cases, superior to) other ensemble learning strategies, for instance, the original ES algorithm, stacking with linear regression, random forests or boosting. Motivated by the promising results in classification, this paper examines the predictive performance of the BES-OOB strategy for regression problems. Our results show that the BES-OOB strategy outperforms Stochastic Gradient Boosting and Bagging when using regression trees as the base learners. Our results also suggest that the advantage of using a diverse model library becomes clear when the model library size is relatively large. We also present encouraging results indicating that the non negative least squares algorithm is a viable approach for pruning an ensemble of ensembles

Gene set based ensemble methods for cancer classification

Diagnosis of cancer very often depends on conclusions drawn after both clinical and microscopic examinations of tissues to study the manifestation of the disease in order to place tumors in known categories. One factor which determines the categorization of cancer is the tissue from which the tumor originates. Information gathered from clinical exams may be partial or not completely predictive of a specific category of cancer. Further complicating the problem of categorizing various tumors is that the histological classification of the cancer tissue and description of its course of development may be atypical. Gene expression data gleaned from micro-array analysis provides tremendous promise for more accurate cancer diagnosis. One hurdle in the classification of tumors based on gene expression data is that the data space is ultra-dimensional with relatively few points; that is, there are a small number of examples with a large number of genes. A second hurdle is expression bias caused by the correlation of genes. Analysis of subsets of genes, known as gene set analysis, provides a mechanism by which groups of differentially expressed genes can be identified. We propose an ensemble of classifiers whose base classifiers are ℓ1-regularized logistic regression models with restriction of the feature space to biologically relevant genes. Some researchers have already explored the use of ensemble classifiers to classify cancer but the effect of the underlying base classifiers in conjunction with biologically-derived gene sets on cancer classification has not been explored

CREATE: Clinical Record Analysis Technology Ensemble

In this thesis, we describe an approach that won a psychiatric symptom severity prediction challenge. The challenge was to correctly predict the severity of psychiatric symptoms on a 4-point scale. Our winning submission uses a novel stacked machine learning architecture in which (i) a base data ingestion/cleaning step was followed by the (ii) derivation of a base set of features defined using text analytics, after which (iii) association rule learning was used in a novel way to generate new features, followed by a (iv) feature selection step to eliminate irrelevant features, followed by a (v) classifier training algorithm in which a total of 22 classifiers including new classifier variants of AdaBoost and RandomForest were trained on seven different data views, and (vi) finally an ensemble learning step, in which ensembles of best learners were used to improve on the accuracy of individual learners. All of this was tested via standard 10-fold cross-validation on training data provided by the N-GRID challenge organizers, of which the three best ensembles were selected for submission to N-GRID\u27s blind testing. The best of our submitted solutions garnered an overall final score of 0.863 according to the organizer\u27s measure. All 3 of our submissions placed within the top 10 out of the 65 total submissions. The challenge constituted Track 2 of the 2016 Centers of Excellence in Genomic Science (CEGS) Neuropsychiatric Genome-Scale and RDOC Individualized Domains (N-GRID) Shared Task in Clinical Natural Language Processing

Using rule extraction to improve the comprehensibility of predictive models.

Whereas newer machine learning techniques, like artifficial neural net-works and support vector machines, have shown superior performance in various benchmarking studies, the application of these techniques remains largely restricted to research environments. A more widespread adoption of these techniques is foiled by their lack of explanation capability which is required in some application areas, like medical diagnosis or credit scoring. To overcome this restriction, various algorithms have been proposed to extract a meaningful description of the underlying `blackbox' models. These algorithms' dual goal is to mimic the behavior of the black box as closely as possible while at the same time they have to ensure that the extracted description is maximally comprehensible. In this research report, we first develop a formal definition of`rule extraction and comment on the inherent trade-off between accuracy and comprehensibility. Afterwards, we develop a taxonomy by which rule extraction algorithms can be classiffied and discuss some criteria by which these algorithms can be evaluated. Finally, an in-depth review of the most important algorithms is given.This report is concluded by pointing out some general shortcomings of existing techniques and opportunities for future research.Models; Model; Algorithms; Criteria; Opportunities; Research; Learning; Neural networks; Networks; Performance; Benchmarking; Studies; Area; Credit; Credit scoring; Behavior; Time;