Kernel methods in genomics and computational biology

Support vector machines and kernel methods are increasingly popular in genomics and computational biology, due to their good performance in real-world applications and strong modularity that makes them suitable to a wide range of problems, from the classification of tumors to the automatic annotation of proteins. Their ability to work in high dimension, to process non-vectorial data, and the natural framework they provide to integrate heterogeneous data are particularly relevant to various problems arising in computational biology. In this chapter we survey some of the most prominent applications published so far, highlighting the particular developments in kernel methods triggered by problems in biology, and mention a few promising research directions likely to expand in the future

Robot Introspection with Bayesian Nonparametric Vector Autoregressive Hidden Markov Models

Robot introspection, as opposed to anomaly detection typical in process monitoring, helps a robot understand what it is doing at all times. A robot should be able to identify its actions not only when failure or novelty occurs, but also as it executes any number of sub-tasks. As robots continue their quest of functioning in unstructured environments, it is imperative they understand what is it that they are actually doing to render them more robust. This work investigates the modeling ability of Bayesian nonparametric techniques on Markov Switching Process to learn complex dynamics typical in robot contact tasks. We study whether the Markov switching process, together with Bayesian priors can outperform the modeling ability of its counterparts: an HMM with Bayesian priors and without. The work was tested in a snap assembly task characterized by high elastic forces. The task consists of an insertion subtask with very complex dynamics. Our approach showed a stronger ability to generalize and was able to better model the subtask with complex dynamics in a computationally efficient way. The modeling technique is also used to learn a growing library of robot skills, one that when integrated with low-level control allows for robot online decision making.Comment: final version submitted to humanoids 201

Adversarial Speaker Adaptation

We propose a novel adversarial speaker adaptation (ASA) scheme, in which adversarial learning is applied to regularize the distribution of deep hidden features in a speaker-dependent (SD) deep neural network (DNN) acoustic model to be close to that of a fixed speaker-independent (SI) DNN acoustic model during adaptation. An additional discriminator network is introduced to distinguish the deep features generated by the SD model from those produced by the SI model. In ASA, with a fixed SI model as the reference, an SD model is jointly optimized with the discriminator network to minimize the senone classification loss, and simultaneously to mini-maximize the SI/SD discrimination loss on the adaptation data. With ASA, a senone-discriminative deep feature is learned in the SD model with a similar distribution to that of the SI model. With such a regularized and adapted deep feature, the SD model can perform improved automatic speech recognition on the target speaker's speech. Evaluated on the Microsoft short message dictation dataset, ASA achieves 14.4% and 7.9% relative word error rate improvements for supervised and unsupervised adaptation, respectively, over an SI model trained from 2600 hours data, with 200 adaptation utterances per speaker.Comment: 5 pages, 2 figures, ICASSP 201