Biological data mining with neural networks: implementation and application of a flexible decision tree extraction algorithm to genomic problem domains

Proteochemometric modeling as a tool to design selective compounds and for extrapolating to novel targets

Proteochemometric modeling is founded on the principles of QSAR but is able to benefit from additional information in model training due to the inclusion of target information.

Prediction of glycosylation sites using random forests

BACKGROUND

Post translational modifications (PTMs) occur in the vast majority of proteins and are essential for function. Prediction of the sequence location of PTMs enhances the functional characterisation of proteins. Glycosylation is one type of PTM, and is implicated in protein folding, transport and function.

RESULTS

We use the random forest algorithm and pairwise patterns to predict glycosylation sites. We identify pairwise patterns surrounding glycosylation sites and use an odds ratio to weight their propensity of association with modified residues. Our prediction program, GPP (glycosylation prediction program), predicts glycosylation sites with an accuracy of 90.8% for Ser sites, 92.0% for Thr sites and 92.8% for Asn sites. This is significantly better than current glycosylation predictors. We use the trepan algorithm to extract a set of comprehensible rules from GPP, which provide biological insight into all three major glycosylation types.

CONCLUSION

We have created an accurate predictor of glycosylation sites and used this to extract comprehensible rules about the glycosylation process. GPP is available online at http://comp.chem.nottingham.ac.uk/glyco/.

Logistic model tree extraction from artificial neural networks

Artificial neural networks (ANNs) are a powerful and widely used pattern recognition technique. However, they remain "black boxes" giving no explanation for the decisions they make. This paper presents a new algorithm for extracting a logistic model tree (LMT) from a neural network, which gives a symbolic representation of the knowledge hidden within the ANN. Landwehr's LMTs are based on standard decision trees, but the terminal nodes are replaced with logistic regression functions. This paper reports the results of an empirical evaluation that compares the new decision tree extraction algorithm with Quinlan's C4.5 and ExTree. The evaluation used 12 standard benchmark datasets from the University of California, Irvine machine-learning repository. The results of this evaluation demonstrate that the new algorithm produces decision trees that have higher accuracy and higher fidelity than decision trees created by both C4.5 and ExTree.