Online convex programming has recently emerged as a powerful primitive for designing machine learning algorithms. For example, OCP can be used for learning a linear classifier, dynamically rebalancing a binary search tree, finding the shortest path in a graph with unknown edge lengths, solving a structured classification problem, or finding a good strategy in an extensive-form game. Several researchers have designed no-regret algorithms for OCP. But, compared to algorithms for special cases of OCP such as learning from expert advice, these algorithms are not very numerous or flexible. In learning from expert advice, one tool which has proved particularly valuable is the correspondence between no-regret algorithms and convex potential functions: by reasoning about these potential functions, researchers have designed algorithms with a wide variety of useful guarantees such as good performance when the target hypothesis is sparse. Until now, there has been no such recipe for the more general OCP problem, and therefore no ability to tune OCP algorithms to take advantage of properties of the problem or data. In this paper we derive a new class of no-regret learning algorithms for OCP. These Lagrangian Hedging algorithms are based on a general class of potential functions, and are a direct generalization of known learning rules like weighted majority and external-regret matching. In addition to proving regret bounds, we demonstrate our algorithms learning to play one-card poker.

We present a probabilistic model applied to the fMRI video rating prediction task of the Pittsburgh Brain Activity Interpretation Competition (PBAIC) [2]. Our goal is to predict a time series of subjective, semantic ratings of a movie given functional MRI data acquired during viewing by three subjects. Our method uses conditionally trained Gaussian Markov random fields, which model both the relationships between the subjects' fMRI voxel measurements and the ratings, as well as the dependencies of the ratings across time steps and between subjects. We also employed nontraditional methods for feature selection and regularization that exploit the spatial structure of voxel activity in the brain. The model displayed good performance in predicting the scored ratings for the three subjects in test data sets, and a variant of this model was the third place entrant to the 2006 PBAIC.

We describe Hidden Semi-Markov Support Vector Machines (SHM SVMs), an extension of HM SVMs to semi-Markov chains. This allows us to predict segmentations of sequences based on segment-based features measuring properties such as the length of the segment. We propose a novel technique to partition the problem into sub-problems. The independently obtained partial solutions can then be recombined in an efficient way, which allows us to solve label sequence learning problems with several thousands of labeled sequences. We have tested our algorithm for predicting gene structures, an important problem in computational biology. Results on a well-known model organism illustrate the great potential of SHM SVMs in computational biology.

Active learning refers to algorithmic frameworks aimed at selecting training data points in order to reduce the number of required training data points and/or improve the generalization performance of a learning method. In this paper, we present an asymptotic analysis of active learning for generalized linear models. Our analysis holds under the common practical situation of model misspecification, and is based on realistic assumptions regarding the nature of the sampling distributions, which are usually neither independent nor identical. We derive unbiased estimators of generalization performance, as well as estimators of expected reduction in generalization error after adding a new training data point, that allow us to optimize its sampling distribution through a convex optimization problem. Our analysis naturally leads to an algorithm for sequential active learning which is applicable for all tasks supported by generalized linear models (e.g., binary classification, multi-class classification, regression) and can be applied in nonlinear settings through the use of Mercer kernels.

We consider the problem of inferring the structure of a network from cooccurrence data: observations that indicate which nodes occur in a signaling pathway but do not directly reveal node order within the pathway. This problem is motivated by network inference problems arising in computational biology and communication systems, in which it is difficult or impossible to obtain precise time ordering information. Without order information, every permutation of the activated nodes leads to a different feasible solution, resulting in combinatorial explosion of the feasible set. However, physical principles underlying most networked systems suggest that not all feasible solutions are equally likely. Intuitively, nodes that cooccur more frequently are probably more closely connected. Building on this intuition, we model path co-occurrences as randomly shuffled samples of a random walk on the network. We derive a computationally efficient network inference algorithm and, via novel concentration inequalities for importance sampling estimators, prove that a polynomial complexity Monte Carlo version of the algorithm converges with high probability.

The performance of EEGbased Brain-Computer-Interfaces (BCIs) critically depends on the extraction of features from the EEG carrying information relevant for the classification of different mental states. For BCIs employing imaginary movements of different limbs, the method of Common Spatial Patterns (CSP) has been shown to achieve excellent classification results. The CSP-algorithm however suffers from a lack of robustness, requiring training data without artifacts for good performance. To overcome this lack of robustness, we propose an adaptive spatial filter that replaces the training data in the CSP approach by a-priori information. More specifically, we design an adaptive spatial filter that maximizes the ratio of the variance of the electric field originating in a predefined region of interest (ROI) and the overall variance of the measured EEG. Since it is known that the component of the EEG used for discriminating imaginary movements originates in the motor cortex, we design two adaptive spatial filters with the ROIs centered in the hand areas of the left and right motor cortex. We then use these to classify EEG data recorded during imaginary movements of the right and left hand of three subjects, and show that the adaptive spatial filters outperform the CSP-algorithm, enabling classification rates of up to 94.7 % without artifact rejection.

The increasingly popular independent component analysis (ICA) may only be applied to data following the generative ICA model in order to guarantee algorithmindependent and theoretically valid results. Subspace ICA models generalize the assumption of component independence to independence between groups of components. They are attractive candidates for dimensionality reduction methods, however are currently limited by the assumption of equal group sizes or less general semi-parametric models. By introducing the concept of irreducible independent subspaces or components, we present a generalization to a parameter-free mixture model. Moreover, we relieve the condition of at-most-one-Gaussian by including previous results on non-Gaussian component analysis. After introducing this general model, we discuss joint block diagonalization with unknown block sizes, on which we base a simple extension of JADE to algorithmically perform the subspace analysis. Simulations confirm the feasibility of the algorithm.

Modelling the dynamics of transcriptional processes in the cell requires the knowledge of a number of key biological quantities. While some of them are relatively easy to measure, such as mRNA decay rates and mRNA abundance levels, it is still very hard to measure the active concentration levels of the transcription factor proteins that drive the process and the sensitivity of target genes to these concentrations. In this paper we show how these quantities for a given transcription factor can be inferred from gene expression levels of a set of known target genes. We treat the protein concentration as a latent function with a Gaussian process prior, and include the sensitivities, mRNA decay rates and baseline expression levels as hyperparameters. We apply this procedure to a human leukemia dataset, focusing on the tumour repressor p53 and obtaining results in good accordance with recent biological studies.

Parsing and translating natural languages can be viewed as problems of predicting tree structures. For machine learning approaches to these predictions, the diversity and high dimensionality of the structures involved mandate very large training sets. This paper presents a purely discriminative learning method that scales up well to problems of this size. Its accuracy was at least as good as other comparable methods on a standard parsing task. To our knowledge, it is the first purely discriminative learning algorithm for translation with treestructured models. Unlike other popular methods, this method does not require a great deal of feature engineering a priori, because it performs feature selection over a compound feature space as it learns. Experiments demonstrate the method's versatility, accuracy, and efficiency. Relevant software is freely available at http://nlp.cs.nyu.edu/parser and http://nlp.cs.nyu.edu/GenPar.

In previous studies, quadratic modelling of natural images has resulted in cell models that react strongly to edges and bars. Here we apply quadratic Independent Component Analysis to natural image patches, and show that up to a small approximation error, the estimated components are computing conjunctions of two linear features. These conjunctive features appear to represent not only edges and bars, but also inherently two-dimensional stimuli, such as corners. In addition, we show that for many of the components, the underlying linear features have essentially V1 simple cell receptive field characteristics. Our results indicate that the development of the V2 cells preferring angles and corners may be partly explainable by the principle of unsupervised sparse coding of natural images.