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

A variational model for data fitting on manifolds by minimizing the acceleration of a B\'ezier curve

We derive a variational model to fit a composite B\'ezier curve to a set of data points on a Riemannian manifold. The resulting curve is obtained in such a way that its mean squared acceleration is minimal in addition to remaining close the data points. We approximate the acceleration by discretizing the squared second order derivative along the curve. We derive a closed-form, numerically stable and efficient algorithm to compute the gradient of a B\'ezier curve on manifolds with respect to its control points, expressed as a concatenation of so-called adjoint Jacobi fields. Several examples illustrate the capabilites and validity of this approach both for interpolation and approximation. The examples also illustrate that the approach outperforms previous works tackling this problem

Interior Point Decoding for Linear Vector Channels

In this paper, a novel decoding algorithm for low-density parity-check (LDPC) codes based on convex optimization is presented. The decoding algorithm, called interior point decoding, is designed for linear vector channels. The linear vector channels include many practically important channels such as inter symbol interference channels and partial response channels. It is shown that the maximum likelihood decoding (MLD) rule for a linear vector channel can be relaxed to a convex optimization problem, which is called a relaxed MLD problem. The proposed decoding algorithm is based on a numerical optimization technique so called interior point method with barrier function. Approximate variations of the gradient descent and the Newton methods are used to solve the convex optimization problem. In a decoding process of the proposed algorithm, a search point always lies in the fundamental polytope defined based on a low-density parity-check matrix. Compared with a convectional joint message passing decoder, the proposed decoding algorithm achieves better BER performance with less complexity in the case of partial response channels in many cases.Comment: 18 pages, 17 figures, The paper has been submitted to IEEE Transaction on Information Theor

Importance mixing: Improving sample reuse in evolutionary policy search methods

Deep neuroevolution, that is evolutionary policy search methods based on deep neural networks, have recently emerged as a competitor to deep reinforcement learning algorithms due to their better parallelization capabilities. However, these methods still suffer from a far worse sample efficiency. In this paper we investigate whether a mechanism known as "importance mixing" can significantly improve their sample efficiency. We provide a didactic presentation of importance mixing and we explain how it can be extended to reuse more samples. Then, from an empirical comparison based on a simple benchmark, we show that, though it actually provides better sample efficiency, it is still far from the sample efficiency of deep reinforcement learning, though it is more stable