De novo Sequencing of peptides is a challenging task in proteome research. Whilethere exist reliable DNAsequencing methods, the highthroughput denovo sequencing of proteins by mass spectrometry is still an open problem. Current approaches suffer from a lack in precision to detect mass peaks in the spectrograms. In this paper we present a novel method for de novo peptide sequencing based on a hidden Markov model. Experiments effectively demonstrate that this new method significantly outperformsstandard approaches in matching quality.

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 tothe "state-relevance weights" studied in [6].

Many works have shown that strong connections relate learning from examples toregularization techniques for ill-posed inverse problems. Nevertheless bynow there was no formal evidence neither that learning from examples could be seen as an inverse problem nor that theoretical results in learning theory could be independently derived using tools from regularization theory.In this paper we provide a positive answer to both questions. Indeed, considering the square loss, we translate the learning problem in the language of regularization theory and show that consistency resultsand optimal regularization parameter choice can be derived by the discretization of the corresponding inverse problem.

We show that anomaly detection can be interpreted as a binary classification problem.Using this interpretation we propose a support vector machine (SVM) for anomaly detection. We then present some theoretical resultswhich include consistency and learning rates. Finally, we experimentally compare our SVM with the standard one-class SVM.

We present a discriminative part-based approach for the recognition of object classes from unsegmented cluttered scenes. Objects are modeled as flexible constellations of parts conditioned on local observations found by an interest operator. For each object class the probability of a given assignment of parts to local features is modeled by a Conditional Random Field(CRF). We propose an extension of the CRF framework that incorporates hidden variables and combines class conditional CRFs into a unified framework for part-based object recognition. The parameters of the CRF are estimated in a maximum likelihood framework and recognition proceedsby finding the most likely class under our model. The main advantage of the proposed CRF framework is that it allows us to relax the assumption of conditional independence of the observed data (i.e.

Learning in a multiagent system is a challenging problem due to two key factors. First, if other agents are simultaneously learning then the environment isno longer stationary, thus undermining convergence guarantees. Second, learning is often susceptible to deception, where the other agents may be able to exploit a learner's particular dynamics. In the worst case, this could result in poorer performance than if the agent was not learning at all. These challenges are identifiable in the two most common evaluationcriteria for multiagent learning algorithms: convergence and regret. Algorithms focusing on convergence or regret in isolation are numerous. In this paper, we seek to address both criteria in a single algorithm by introducing GIGA-WoLF, a learning algorithm for normalform games.We prove the algorithm guarantees at most zero average regret, while demonstrating the algorithm converges in many situations of self-play. We prove convergence in a limited setting and give empirical resultsin a wider variety of situations. These results also suggest a third new learning criterion combining convergence and regret, which we call negative non-convergence regret (NNR).

Semantic taxonomies such as WordNet provide a rich source of knowledge fornatural language processing applications, but are expensive to build, maintain, and extend. Motivated by the problem of automatically constructing and extending such taxonomies, in this paper we present a new algorithm for automatically learning hypernym (is-a) relations from text. Our method generalizes earlier work that had relied on using small numbers of handcrafted regular expression patterns to identify hypernym pairs.Using "dependency path" features extracted from parse trees, we introduce a general-purpose formalization and generalization of these patterns. Given a training set of text containing known hypernym pairs, our algorithm automatically extracts useful dependency paths and applies them to new corpora to identify novel pairs. On our evaluation task (determining whethertwo nouns in a news article participate in a hypernym relationship), our automatically extracted database of hypernyms attains both higher precision and higher recall than WordNet.

In this setting, TD learning is often simpler and more data-efficient than other methods.

We provide a method for mass meta-analysis in a neuroinformatics database containing stereotaxic Talairach coordinates from neuroimaging experiments.Database labels are used to group the individual experiments, e.g., according to cognitive function, and the consistent pattern of the experiments within the groups are determined.

We propose a family of kernels based on the Binet-Cauchy theorem and its extension toFredholm operators. This includes as special cases all currently known kernels derived from the behavioral framework, diffusion processes, marginalized kernels, kernels on graphs, and the kernels on sets arising from the subspace angle approach. Many of these kernels can be seen as the extrema of a new continuum of kernel functions, which leads to numerous new special cases. As an application, we apply the new class of kernels to the problem of clustering of video sequences with encouraging results.