We describe a hierarchy of motif-based kernels for multiple alignments of biological sequences, particularly suitable to process regulatory regions of genes. The kernels incorporate progressively more information, with the most complex kernel accounting for a multiple alignment of orthologous regions, the phylogenetic tree relating the species, and the prior knowledge that relevant sequence patterns occur in conserved motif blocks. These kernels can be used in the presence of a library of known transcription factor binding sites, or de novo by iterating over all k-mers of a given length. In the latter mode, a discriminative classifier built from such a kernel not only recognizes a given class of promoter regions, but as a side effect simultaneously identifies a collection of relevant, discriminative sequence motifs. We demonstrate the utility of the motif-based multiple alignment kernels by using a collection of aligned promoter regions from five yeast species to recognize classes of cell-cycle regulated genes.

We present a generalization of temporal-difference networks to include temporally abstract options on the links of the question network. Temporal-difference (TD) networks have been proposed as a way of representing and learning a wide variety of predictions about the interaction between an agent and its environment. These predictions are compositional in that their targets are defined in terms of other predictions, and subjunctive in that that they are about what would happen if an action or sequence of actions were taken. In conventional TD networks, the interrelated predictions are at successive time steps and contingent on a single action; here we generalize them to accommodate extended time intervals and contingency on whole ways of behaving. Our generalization is based on the options framework for temporal abstraction. The primary contribution of this paper is to introduce a new algorithm for intra-option learning in TD networks with function approximation and eligibility traces.

We present a new Gaussian process (GP) regression model whose covariance is parameterized by the the locations of M pseudo-input points, which we learn by a gradient based optimization.

When trying to understand the brain, it is of fundamental importance to analyse (e.g. from EEG/MEG measurements) what parts of the cortex interact with each other in order to infer more accurate models of brain activity. Common techniques like Blind Source Separation (BSS) can estimate brain sources and single out artifacts by using the underlying assumption of source signal independence. However, physiologically interesting brain sources typically interact, so BSS will--by construction-- fail to characterize them properly. Noting that there are truly interacting sources and signals that only seemingly interact due to effects of volume conduction, this work aims to contribute by distinguishing these effects. For this a new BSS technique is proposed that uses anti-symmetrized cross-correlation matrices and subsequent diagonalization. The resulting decomposition consists of the truly interacting brain sources and suppresses any spurious interaction stemming from volume conduction. Our new concept of interacting source analysis (ISA) is successfully demonstrated on MEG data.

We argue that when objects are characterized by many attributes, clustering them on the basis of a relatively small random subset of these attributes can capture information on the unobserved attributes as well. Moreover, we show that under mild technical conditions, clustering the objects on the basis of such a random subset performs almost as well as clustering with the full attribute set. We prove a finite sample generalization theorems for this novel learning scheme that extends analogous results from the supervised learning setting. The scheme is demonstrated for collaborative filtering of users with movies rating as attributes.

We investigate the problem of automatically constructing efficient representations or basis functions for approximating value functions based on analyzing the structure and topology of the state space. In particular, two novel approaches to value function approximation are explored based on automatically constructing basis functions on state spaces that can be represented as graphs or manifolds: one approach uses the eigenfunctions of the Laplacian, in effect performing a global Fourier analysis on the graph; the second approach is based on diffusion wavelets, which generalize classical wavelets to graphs using multiscale dilations induced by powers of a diffusion operator or random walk on the graph. Together, these approaches form the foundation of a new generation of methods for solving large Markov decision processes, in which the underlying representation and policies are simultaneously learned.

We propose efficient algorithms for learning ranking functions from order constraints between sets--i.e.

Spectral clustering enjoys its success in both data clustering and semisupervised learning. But, most spectral clustering algorithms cannot handle multi-class clustering problems directly. Additional strategies are needed to extend spectral clustering algorithms to multi-class clustering problems. Furthermore, most spectral clustering algorithms employ hard cluster membership, which is likely to be trapped by the local optimum. In this paper, we present a new spectral clustering algorithm, named "Soft Cut". It improves the normalized cut algorithm by introducing soft membership, and can be efficiently computed using a bound optimization algorithm. Our experiments with a variety of datasets have shown the promising performance of the proposed clustering algorithm.

Survival in the natural world demands the selection of relevant visual cues to rapidly and reliably guide attention towards prey and predators in cluttered environments. We investigate whether our visual system selects cues that guide search in an optimal manner. We formally obtain the optimal cue selection strategy by maximizing the signal to noise ratio (SN R) between a search target and surrounding distractors. This optimal strategy successfully accounts for several phenomena in visual search behavior, including the effect of target-distractor discriminability, uncertainty in target's features, distractor heterogeneity, and linear separability. Furthermore, the theory generates a new prediction, which we verify through psychophysical experiments with human subjects. Our results provide direct experimental evidence that humans select visual cues so as to maximize SN R between the targets and surrounding clutter.

Linear text classification algorithms work by computing an inner product between a test document vector and a parameter vector. In many such algorithms, including naive Bayes and most TFIDF variants, the parameters are determined by some simple, closed-form, function of training set statistics; we call this mapping mapping from statistics to parameters, the parameter function. Much research in text classification over the last few decades has consisted of manual efforts to identify better parameter functions. In this paper, we propose an algorithm for automatically learning this function from related classification problems. The parameter function found by our algorithm then defines a new learning algorithm for text classification, which we can apply to novel classification tasks. We find that our learned classifier outperforms existing methods on a variety of multiclass text classification tasks.