The formation of disulphide bridges among cysteines is an important feature of protein structures. Here we develop new methods for the prediction of disulphide bond connectivity. We first build a large curated data set of proteins containing disulphide bridges and then use 2-Dimensional Recursive Neural Networks to predict bonding probabilities between cysteine pairs. These probabilities in turn lead to a weighted graph matching problem that can be addressed efficiently. We show how the method consistently achieves better results than previous approaches on the same validation data. In addition, the method can easily cope with chains with arbitrary numbers of bonded cysteines. Therefore, it overcomes one of the major limitations of previous approaches restricting predictions to chains containing no more than 10 oxidized cysteines. The method can be applied both to situations where the bonded state of each cysteine is known or unknown, in which case bonded state can be predicted with 85% precision and 90% recall. The method also yields an estimate for the total number of disulphide bridges in each chain.

In this paper we show that it is possible to model sensory impressions of consumers about beef meat. This is not a straightforward task; the reason is that when we are aiming to induce a function that maps object descriptions into ratings, we must consider that consumers' ratings are just a way to express their preferences about the products presented in the same testing session. Therefore, we had to use a special purpose SVM polynomial kernel. The training data set used collects the ratings of panels of experts and consumers; the meat was provided by 103 bovines of 7 Spanish breeds with different carcass weights and aging periods. Additionally, to gain insight into consumer preferences, we used feature subset selection tools. The result is that aging is the most important trait for improving consumers' appreciation of beef meat.

The problem of learning a sparse conic combination of kernel functions or kernel matrices for classification or regression can be achieved via the regularization by a block 1-norm [1]. In this paper, we present an algorithm that computes the entire regularization path for these problems. The path is obtained by using numerical continuation techniques, and involves a running time complexity that is a constant times the complexity of solving the problem for one value of the regularization parameter. Working in the setting of kernel linear regression and kernel logistic regression, we show empirically that the effect of the block 1-norm regularization differs notably from the (non-block) 1-norm regularization commonly used for variable selection, and that the regularization path is of particular value in the block case.

We introduce a new algorithm based on linear programming that approximates the differential value function of an average-cost Markov decision process via a linear combination of pre-selected basis functions. The algorithm carries out a form of cost shaping and minimizes a version of Bellman error. We establish an error bound that scales gracefully with the number of states without imposing the (strong) Lyapunov condition required by its counterpart in [6]. We propose a path-following method that automates selection of important algorithm parameters which represent counterparts to the "state-relevance weights" studied in [6].

A new distance measure between probability density functions (pdfs) is introduced, which we refer to as the Laplacian pdf distance. The Laplacian pdf distance exhibits a remarkable connection to Mercer kernel based learning theory via the Parzen window technique for density estimation. In a kernel feature space defined by the eigenspectrum of the Laplacian data matrix, this pdf distance is shown to measure the cosine of the angle between cluster mean vectors. The Laplacian data matrix, and hence its eigenspec-trum, can be obtained automatically based on the data at hand, by optimal Parzen window selection. We show that the Laplacian pdf distance has an interesting interpretation as a risk function connected to the probability of error.

The representation of acoustic signals at the cochlear nerve must serve a wide range of auditory tasks that require exquisite sensitivity in both time and frequency. Lewicki (2002) demonstrated that many of the filtering properties of the cochlea could be explained in terms of efficient coding of natural sounds. This model, however, did not account for properties such as phase-locking or how sound could be encoded in terms of action potentials. Here, we extend this theoretical approach with algorithm for learning efficient auditory codes using a spiking population code. Here, we propose an algorithm for learning efficient auditory codes using a theoretical model for coding sound in terms of spikes.

Clustering and prediction of sets of curves is an important problem in many areas of science and engineering. It is often the case that curves tend to be misaligned from each other in a continuous manner, either in space (across the measurements) or in time. We develop a probabilistic framework that allows for joint clustering and continuous alignment of sets of curves in curve space (as opposed to a fixed-dimensional featurevector space). The proposed methodology integrates new probabilistic alignment models with model-based curve clustering algorithms. The probabilistic approach allows for the derivation of consistent EM learning algorithms for the joint clustering-alignment problem. Experimental results are shown for alignment of human growth data, and joint clustering and alignment of gene expression time-course data.

We present an algorithm to perform blind, one-microphone speech separation.

We use unsupervised probabilistic machine learning ideas to try to explain the kinds of learning observed in real neurons, the goal being to connect abstract principles of self-organisation to known biophysical processes. For example, we would like to explain Spike Timing-Dependent Plasticity (see [5,6] and Figure 3A), in terms of information theory. Starting out, we explore the optimisation of a network sensitivity measure related to maximising the mutual information between input spike timings and output spike timings. Our derivations are analogous to those in ICA, except that the sensitivity of output timings to input timings is maximised, rather than the sensitivity of output'firing rates' to inputs. ICA and related approaches have been successful in explaining the learning of many properties of early visual receptive fields in rate coding models, and we are hoping for similar gains in understanding of spike coding in networks, and how this is supported, in principled probabilistic ways, by cellular biophysical processes. For now, in our initial simulations, we show that our derived rule can learn synaptic weights which can unmix, or demultiplex, mixed spike trains. That is, it can recover independent point processes embedded in distributed correlated input spike trains, using an adaptive single-layer feedforward spiking network.

We propose to selectively remove examples from the training set using probabilistic estimates related to editing algorithms (Devijver and Kittler, 1982). This heuristic procedure aims at creating a separable distribution of training examples with minimal impact on the position of the decision boundary. It breaks the linear dependency between the number of SVs and the number of training examples, and sharply reduces the complexity of SVMs during both the training and prediction stages.