Bounded Coordinate-Descent for Biological Sequence Classification in High Dimensional Predictor Space

We present a framework for discriminative sequence classification where the learner works directly in the high dimensional predictor space of all subsequences in the training set. This is possible by employing a new coordinate-descent algorithm coupled with bounding the magnitude of the gradient for selecting discriminative subsequences fast. We characterize the loss functions for which our generic learning algorithm can be applied and present concrete implementations for logistic regression (binomial log-likelihood loss) and support vector machines (squared hinge loss). Application of our algorithm to protein remote homology detection and remote fold recognition results in performance comparable to that of state-of-the-art methods (e.g., kernel support vector machines). Unlike state-of-the-art classifiers, the resulting classification models are simply lists of weighted discriminative subsequences and can thus be interpreted and related to the biological problem

Large Margin GMM for discriminative speaker verifi cation

International audienceGaussian mixture models (GMM), trained using the generative cri- terion of maximum likelihood estimation, have been the most popular ap- proach in speaker recognition during the last decades. This approach is also widely used in many other classi cation tasks and applications. Generative learning in not however the optimal way to address classi cation problems. In this paper we rst present a new algorithm for discriminative learning of diagonal GMM under a large margin criterion. This algorithm has the ma- jor advantage of being highly e cient, which allow fast discriminative GMM training using large scale databases. We then evaluate its performances on a full NIST speaker veri cation task using NIST-SRE'2006 data. In particular, we use the popular Symmetrical Factor Analysis (SFA) for session variability compensation. The results show that our system outperforms the state-of-the- art approaches of GMM-SFA and the SVM-based one, GSL-NAP. Relative reductions of the Equal Error Rate of about 9.33% and 14.88% are respec- tively achieved over these systems