We propose a generic algorithm for computation of similarity measures for sequential data. The algorithm uses generalized suffix trees for efficient calculation of various kernel, distance and non-metric similarity functions. Its worst-case run-time is linear in the length of sequences and independent of the underlying embedding language, which can cover words, k-grams or all contained subsequences. Experiments with network intrusion detection, DNA analysis and text processing applications demonstrate the utility of distances and similarity coefficients for sequences as alternatives to classical kernel functions.

Princeton Center for Theoretical Physics, Princeton University, Princeton, New Jersey 08544 USA (Dated: December 13, 2021) We consider words as a network of interacting letters, and approximate the probability distribution of states taken on by this network. Despite the intuition that the rules of English spelling are highly combinatorial (and arbitrary), we find that maximum entropy models consistent with pairwise correlations among letters provide a surprisingly good approximation to the full statistics of four letter words, capturing 92% of the multi-information among letters and even'discovering' real words that were not represented in the data from which the pairwise correlations were estimated. The maximum entropy model defines an energy landscape on the space of possible words, and local minima in this landscape account for nearly two-thirds of words used in written English. Many complex systems convey an impression of order into these controversies about language in the broad that is not so easily captured by the traditional tools of sense, but rather to test the power of pairwise interactions theoretical physics. Thus, it is not clear what sort of to capture seemingly complex structure.

Multinomial logistic regression provides the standard penalised maximumlikelihood solution to multi-class pattern recognition problems. More recently, the development of sparse multinomial logistic regression models has found application in text processing and microarray classification, where explicit identification of the most informative features is of value. In this paper, we propose a sparse multinomial logistic regression method, in which the sparsity arises from the use of a Laplace prior, but where the usual regularisation parameter is integrated out analytically. Evaluation over a range of benchmark datasets reveals this approach results in similar generalisation performance to that obtained using cross-validation, but at greatly reduced computational expense.

Many recent studies analyze how data from different modalities can be combined. Often this is modeled as a system that optimally combines several sources of information about the same variable. However, it has long been realized that this information combining depends on the interpretation of the data. Two cues that are perceived by different modalities can have different causal relationships: (1) They can both have the same cause, in this case we should fully integrate both cues into a joint estimate.

Gaussian data is pervasive and many learning algorithms (e.g., k-means) model their inputs as a single sample drawn from a multivariate Gaussian. However, in many real-life settings, each input object is best described by multiple samples drawn from a multivariate Gaussian. Such data can arise, for example, in a movie review database where each movie is rated by several users, or in time-series domains such as sensor networks. Here, each input can be naturally described by both a mean vector and covariance matrix which parameterize the Gaussian distribution. In this paper, we consider the problem of clustering such input objects, each represented as a multivariate Gaussian. We formulate the problem using an information theoretic approach and draw several interesting theoretical connections to Bregman divergences and also Bregman matrix divergences. We evaluate our method across several domains, including synthetic data, sensor network data, and a statistical debugging application.

We present a method for binary online classification of triggered but temporally blurred events that are embedded in noisy time series in the context of online discrimination between left and right imaginary hand-movement. In particular the goal of the binary classification problem is to obtain the decision, as fast and as reliably as possible from the recorded EEG single trials. To provide a probabilistic decision at every time-point t the presented method gathers information from two distinct sequences of features across time. In order to incorporate decisions from prior time-points we suggest an appropriate weighting scheme, that emphasizes time instances, providing a higher discriminatory power between the instantaneous class distributions of each feature, where the discriminatory power is quantified in terms of the Bayes error of misclassification. The effectiveness of this procedure is verified by its successful application in the 3rd BCI competition. Disclosure of the data after the competition revealed this approach to be superior with single trial error rates as low as 10.7, 11.5 and 16.7% for the three different subjects under study.

Stress and genetic background regulate different aspects of behavioral learning through the action of stress hormones and neuromodulators.

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.