Showing papers by "Frank R. Burden published in 2015"

Sparse feature selection methods identify unexpected global cellular response to strontium-containing materials

Abstract: Despite the increasing sophistication of biomaterials design and functional characterization studies, little is known regarding cells’ global response to biomaterials. Here, we combined nontargeted holistic biological and physical science techniques to evaluate how simple strontium ion incorporation within the well-described biomaterial 45S5 bioactive glass (BG) influences the global response of human mesenchymal stem cells. Our objective analyses of whole gene-expression profiles, confirmed by standard molecular biology techniques, revealed that strontium-substituted BG up-regulated the isoprenoid pathway, suggesting an influence on both sterol metabolite synthesis and protein prenylation processes. This up-regulation was accompanied by increases in cellular and membrane cholesterol and lipid raft contents as determined by Raman spectroscopy mapping and total internal reflection fluorescence microscopy analyses and by an increase in cellular content of phosphorylated myosin II light chain. Our unexpected findings of this strong metabolic pathway regulation as a response to biomaterial composition highlight the benefits of discovery-driven nonreductionist approaches to gain a deeper understanding of global cell–material interactions and suggest alternative research routes for evaluating biomaterials to improve their design.

Relevance Vector Machines: Sparse Classification Methods for QSAR

Abstract: Sparse machine learning methods have provided substantial benefits to quantitative structure property modeling, as they make model interpretation simpler and generate models with improved predictivity. Sparsity is usually induced via Bayesian regularization using sparsity-inducing priors and by the use of expectation maximization algorithms with sparse priors. The focus to date has been on using sparse methods to model continuous data and to carry out sparse feature selection. We describe the relevance vector machine (RVM), a sparse version of the support vector machine (SVM) that is one of the most widely used classification machine learning methods in QSAR and QSPR. We illustrate the superior properties of the RVM by modeling eight data sets using SVM, RVM, and another sparse Bayesian machine learning method, the Bayesian regularized artificial neural network with Laplacian prior (BRANNLP). We show that RVM models are substantially sparser than the SVM models and have similar or superior performance to ...