Conditional random fields for the prediction of signal peptide cleavage sites

Correct prediction of signal peptide cleavage sites has a significant impact on drug design. State-of-the-art approaches to cleavage site prediction typically use generative models (such as HMMs) to represent the statistics of amino acid sequences or use neural networks to detect the changes in short amino-acid segments along a query sequence. By formulating cleavage site prediction as a sequence labeling problem, this paper demonstrates how conditional random fields (CRFs) can be applied to cleavage site prediction. The paper also demonstrates how amino acid properties can be exploited and incorporated into the CRFs to boost prediction performance. Results show that the performance of CRFs is comparable to that of a state-of-the-art predictor (SignalP V3.0). Further performance improvement was observed when the decisions of SignalP and the CRF-based predictor are fused. Index Terms — Conditional random fields, discriminative models, signal peptides, cleavage sites, protein sequences

Privacy Enhancing Machine Learning via Removal of Unwanted Dependencies

The rapid rise of IoT and Big Data has facilitated copious data driven applications to enhance our quality of life. However, the omnipresent and all-encompassing nature of the data collection can generate privacy concerns. Hence, there is a strong need to develop techniques that ensure the data serve only the intended purposes, giving users control over the information they share. To this end, this paper studies new variants of supervised and adversarial learning methods, which remove the sensitive information in the data before they are sent out for a particular application. The explored methods optimize privacy preserving feature mappings and predictive models simultaneously in an end-to-end fashion. Additionally, the models are built with an emphasis on placing little computational burden on the user side so that the data can be desensitized on device in a cheap manner. Experimental results on mobile sensing and face datasets demonstrate that our models can successfully maintain the utility performances of predictive models while causing sensitive predictions to perform poorly.Comment: 15 pages, 5 figures, submitted to IEEE Transactions on Neural Networks and Learning System