Markov jump processes play an important role in a large number of application domains. However, realistic systems are analytically intractable and they have traditionally been analysed using simulation based techniques, which do not provide a framework for statistical inference. We propose a mean field approximation to perform posterior inference and parameter estimation. The approximation allows a practical solution to the inference problem, {while still retaining a good degree of accuracy.} We illustrate our approach on two biologically motivated systems.

We present a nonparametric Bayesian method of estimating variable order Markov processes up to a theoretically infinite order. By extending a stick-breaking prior, which is usually defined on a unit interval, "vertically" to the trees of infinite depth associated with a hierarchical Chinese restaurant process, our model directly infers the hidden orders of Markov dependencies from which each symbol originated. Experiments on character and word sequences in natural language showed that the model has a comparative performance with an exponentially large full-order model, while computationally much efficient in both time and space. We expect that this basic model will also extend to the variable order hierarchical clustering of general data.

We address the problem of adaptive sensor control in dynamic resource-constrained sensor networks. We focus on a meteorological sensing network comprising radars that can perform sector scanning rather than always scanning 360 degrees. We compare three sector scanning strategies. The sit-and-spin strategy always scans 360 degrees. The limited lookahead strategy additionally uses the expected environmental state K decision epochs in the future, as predicted from Kalman filters, in its decision-making. The full lookahead strategy uses all expected future states by casting the problem as a Markov decision process and using reinforcement learning to estimate the optimal scan strategy. We show that the main benefits of using a lookahead strategy are when there are multiple meteorological phenomena in the environment, and when the maximum radius of any phenomenon is sufficiently smaller than the radius of the radars. We also show that there is a trade-off between the average quality with which a phenomenon is scanned and the number of decision epochs before which a phenomenon is rescanned.

In many structured prediction problems, the highest-scoring labeling is hard to compute exactly, leading to the use of approximate inference methods. However, when inference is used in a learning algorithm, a good approximation of the score may not be sufficient. We show in particular that learning can fail even with an approximate inference method with rigorous approximation guarantees. There are two reasons for this. First, approximate methods can effectively reduce the expressivity ofan underlying model by making it impossible to choose parameters that reliably give good predictions. Second, approximations can respond to parameter changes in such a way that standard learning algorithms are misled. In contrast, we give two positive results in the form of learning bounds for the use of LPrelaxed inference in structured perceptron and empirical risk minimization settings. We argue that without understanding combinations of inference and learning, such as these, that are appropriately compatible, learning performance under approximate inference cannot be guaranteed.

The model is based on a construction of tree-structured copulas -- multivariate distributions with uniform on [07 1] marginals.

A method is proposed for semiparametric estimation where parametric and nonparametric criteria are exploited in density estimation and unsupervised learning.

It is known that determinining whether a DEC-POMDP, namely, a cooperative partially observable stochastic game (POSG), has a cooperative strategy with positive expected reward is complete for NEXP. It was not known until now how cooperation affected that complexity. We show that, for competitive POSGs, the complexity of determining whether one team has a positive-expected-reward strategy is complete for the class NEXP with an oracle for NP.

Much of this work, however, uses various approximations, which severely restrict the domain of applicability of these implementations.

We combine two threads of research on approximate dynamic programming: random sampling of states and using local trajectory optimizers to globally optimize a policy and associated value function. This combination allows us to replace a dense multidimensional grid with a much sparser adaptive sampling of states. Our focus is on finding steady state policies for the deterministic time invariant discrete time control problems with continuous states and actions often found in robotics. In this paper we show that we can now solve problems we couldn't solve previously with regular grid-based approaches.

Motivation: Profile hidden Markov Models (pHMMs) are a popular and very useful tool in the detection of the remote homologue protein families. Unfortunately, their performance is not always satisfactory when proteins are in the 'twilight zone'. We present HMMER-STRUCT, a model construction algorithm and tool that tries to improve pHMM performance by using structural information while training pHMMs. As a first step, HMMER-STRUCT constructs a set of pHMMs. Each pHMM is constructed by weighting each residue in an aligned protein according to a specific structural property of the residue. Properties used were primary, secondary and tertiary structures, accessibility and packing. HMMER-STRUCT then prioritizes the results by voting. Results: We used the SCOP database to perform our experiments. Throughout, we apply leave-one-family-out cross-validation over protein superfamilies. First, we used the MAMMOTH-mult structural aligner to align the training set proteins. Then, we performed two sets of experiments. In a first experiment, we compared structure weighted models against standard pHMMs and against each other. In a second experiment, we compared the voting model against individual pHMMs. We compare method performance through ROC curves and through Precision/Recall curves, and assess significance through the paired two tailed t-test. Our results show significant performance improvements of all structurally weighted models over default HMMER, and a significant improvement in sensitivity of the combined models over both the original model and the structurally weighted models.