Learning accurate and interpretable models based on regularized random forests regression.

BACKGROUND: Many biology related research works combine data from multiple sources in an effort to understand the underlying problems. It is important to find and interpret the most important information from these sources. Thus it will be beneficial to have an effective algorithm that can simultaneously extract decision rules and select critical features for good interpretation while preserving the prediction performance. METHODS: In this study, we focus on regression problems for biological data where target outcomes are continuous. In general, models constructed from linear regression approaches are relatively easy to interpret. However, many practical biological applications are nonlinear in essence where we can hardly find a direct linear relationship between input and output. Nonlinear regression techniques can reveal nonlinear relationship of data, but are generally hard for human to interpret. We propose a rule based regression algorithm that uses 1-norm regularized random forests. The proposed approach simultaneously extracts a small number of rules from generated random forests and eliminates unimportant features. RESULTS: We tested the approach on some biological data sets. The proposed approach is able to construct a significantly smaller set of regression rules using a subset of attributes while achieving prediction performance comparable to that of random forests regression. CONCLUSION: It demonstrates high potential in aiding prediction and interpretation of nonlinear relationships of the subject being studied.

Novel extraction of volatile biomarkers from canine breath for gas chromatography-mass spectrometry.

Here we describe an effective, reproducible, non-invasive volatile organic compound collection and analysis method for exhaled breath gas samples designed specifically for use with dogs. Conditions of the method were optimized, using a range of standard chemicals. This method utilizes a canine mask, two-way non-re-breathing valve, teflon connector, tubing and bag for sample collection. Collection is followed by condensation and headspace solid phase microextraction for sample concentration and gas chromatography-mass spectrometry for analysis. Custom-made glassware, designed to hold the SPME fiber assembly, was cooled to -10 °C and used for the collection of the condensate followed by 2 h of headspace extraction at 37 °C. Standards show LOD of 0.6-16.8 ppbv, LOQ between 2.1-55.8 ppbv, and good linearity with R(2) between 0.996-0.999 (RSD% 10-19). The method was verified with preliminary results from three dogs demonstrating that this technique is capable of collecting, identifying and quantifying volatile organic chemical constituents in different breath samples.