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.

Co-training is a method for combining labeled and unlabeled data when examples can be thought of as containing two distinct sets of features. It has had a number of practical successes, yet previous theoretical analyses have needed very strong assumptions on the data that are unlikely to be satisfied in practice. In this paper, we propose a much weaker "expansion" assumption on the underlying data distribution, that we prove is sufficient for iterative cotraining to succeed given appropriately strong PAClearning algorithms on each feature set, and that to some extent is necessary as well. This expansion assumption in fact motivates the iterative nature of the original co-training algorithm, unlike stronger assumptions (such as independence given the label) that allow a simpler one-shot co-training to succeed. We also heuristically analyze the effect on performance of noise in the data. Predicted behavior is qualitatively matched in synthetic experiments on expander graphs.

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.

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

We give a fast rejection scheme that is based on image segments and demonstrate it on the canonical example of face detection. However, instead of focusing on the detection step we focus on the rejection step and show that our method is simple and fast to be learned, thus making it an excellent pre-processing step to accelerate standard machine learning classifiers, such as neural-networks, Bayes classifiers or SVM. We decompose a collection of face images into regions of pixels with similar behavior over the image set. The relationships between the mean and variance of image segments are used to form a cascade of rejectors that can reject over 99.8% of image patches, thus only a small fraction of the image patches must be passed to a full-scale classifier. Moreover, the training time for our method is much less than an hour, on a standard PC.

Survey propagation is a powerful technique from statistical physics that has been applied to solve the 3-SAT problem both in principle and in practice. We give, using only probability arguments, a common derivation of survey propagation, belief propagation and several interesting hybrid methods. We then present numerical experiments which use WSAT (a widely used random-walk based SAT solver) to quantify the complexity of the 3-SAT formulae as a function of their parameters, both as randomly generated and after simpli£cation, guided by survey propagation. Some properties of WSAT which have not previously been reported make it an ideal tool for this purpose - its mean cost is proportional to the number of variables in the formula (at a £xed ratio of clauses to variables) in the easy-SAT regime and slightly beyond, and its behavior in the hard-SAT regime appears to re¤ect the underlying structure of the solution space that has been predicted by replica symmetry-breaking arguments. An analysis of the tradeoffs between the various methods of search for satisfying assignments shows WSAT to be far more powerful than has been appreciated, and suggests some interesting new directions for practical algorithm development.

We examine the problem of approximating, in the Frobenius-norm sense, a positive, semidefinite symmetric matrix by a rank-one matrix, with an upper bound on the cardinality of its eigenvector. The problem arises in the decomposition of a covariance matrix into sparse factors, and has wide applications ranging from biology to finance. We use a modification of the classical variational representation of the largest eigenvalue of a symmetric matrix, where cardinality is constrained, and derive a semidefinite programming based relaxation for our problem.

Many interesting multiclass problems can be cast in the general framework of label ranking defined on a given set of classes. The evaluation for such a ranking is generally given in terms of the number of violated order constraints between classes. In this paper, we propose the Preference Learning Model as a unifying framework to model and solve a large class of multiclass problems in a large margin perspective. In addition, an original kernel-based method is proposed and evaluated on a ranking dataset with state-of-the-art results.

The area under the ROC curve (AUC) has been advocated as an evaluation criterion for the bipartite ranking problem. We study large deviation properties of the AUC; in particular, we derive a distribution-free large deviation bound for the AUC which serves to bound the expected accuracy of a ranking function in terms of its empirical AUC on an independent test sequence. A comparison of our result with a corresponding large deviation result for the classification error rate suggests that the test sample size required to obtain an ɛ-accurate estimate of the expected accuracy of a ranking function with δ-confidence is larger than that required to obtain an ɛ-accurate estimate of the expected error rate of a classification function with the same confidence. A simple application of the union bound allows the large deviation bound to be extended to learned ranking functions chosen from finite function classes.