We address the problem of analyzing sets of noisy time-varying signals that all report on the same process but confound straightforward analyses due to complex inter-signal heterogeneities and measurement artifacts. In particular we consider single-molecule experiments which indirectly measure the distinct steps in a biomolecular process via observations of noisy time-dependent signals such as a fluorescence intensity or bead position. Straightforward hidden Markov model (HMM) analyses attempt to characterize such processes in terms of a set of conformational states, the transitions that can occur between these states, and the associated rates at which those transitions occur; but require ad-hoc post-processing steps to combine multiple signals. Here we develop a hierarchically coupled HMM that allows experimentalists to deal with inter-signal variability in a principled and automatic way. Our approach is a generalized expectation maximization hyperparameter point estimation procedure with variational Bayes at the level of individual time series that learns an single interpretable representation of the overall data generating process.

We propose an original model for inferring team strengths using a Markov Random Field, which can be used to generate historical estimates of the offensive and defensive strengths of a team over time. This model was designed to be applied to sports such as soccer or hockey, in which contest outcomes take value in a limited discrete space. We perform inference using a combination of Expectation Maximization and Loopy Belief Propagation. The challenges of working with a non-convex optimization problem and a high-dimensional parameter space are discussed. The performance of the model is demonstrated on professional soccer data from the English Premier League.

Understanding human activities and object affordances are two very important skills, especially for personal robots which operate in human environments. In this work, we consider the problem of extracting a descriptive labeling of the sequence of sub-activities being performed by a human, and more importantly, of their interactions with the objects in the form of associated affordances. Given a RGB-D video, we jointly model the human activities and object affordances as a Markov random field where the nodes represent objects and sub-activities, and the edges represent the relationships between object affordances, their relations with sub-activities, and their evolution over time. We formulate the learning problem using a structural support vector machine (SSVM) approach, where labelings over various alternate temporal segmentations are considered as latent variables. We tested our method on a challenging dataset comprising 120 activity videos collected from 4 subjects, and obtained an accuracy of 79.4% for affordance, 63.4% for sub-activity and 75.0% for high-level activity labeling. We then demonstrate the use of such descriptive labeling in performing assistive tasks by a PR2 robot.

We propose a new algorithm to do posterior sampling of Kingman's coalescent, based upon the Particle Markov Chain Monte Carlo methodology. Specifically, the algorithm is an instantiation of the Particle Gibbs Sampling method, which alternately samples coalescent times conditioned on coalescent tree structures, and tree structures conditioned on coalescent times via the conditional Sequential Monte Carlo procedure. We implement our algorithm as a C++ package, and demonstrate its utility via a parameter estimation task in population genetics on both single- and multiple-locus data. The experiment results show that the proposed algorithm performs comparable to or better than several well-developed methods.

We introduce a new method for training deep Boltzmann machines jointly. Prior methods of training DBMs require an initial learning pass that trains the model greedily, one layer at a time, or do not perform well on classification tasks. In our approach, we train all layers of the DBM simultaneously, using a novel training procedure called multi-prediction training. The resulting model can either be interpreted as a single generative model trained to maximize a variational approximation to the generalized pseudolikelihood, or as a family of recurrent networks that share parameters and may be approximately averaged together using a novel technique we call the multi-inference trick. We show that our approach performs competitively for classification and outperforms previous methods in terms of accuracy of approximate inference and classification with missing inputs.

The problem of clustering is considered, for the case when each data point is a sample generated by a stationary ergodic process. We propose a very natural asymptotic notion of consistency, and show that simple consistent algorithms exist, under most general non-parametric assumptions. The notion of consistency is as follows: two samples should be put into the same cluster if and only if they were generated by the same distribution. With this notion of consistency, clustering generalizes such classical statistical problems as homogeneity testing and process classification. We show that, for the case of a known number of clusters, consistency can be achieved under the only assumption that the joint distribution of the data is stationary ergodic (no parametric or Markovian assumptions, no assumptions of independence, neither between nor within the samples). If the number of clusters is unknown, consistency can be achieved under appropriate assumptions on the mixing rates of the processes. (again, no parametric or independence assumptions). In both cases we give examples of simple (at most quadratic in each argument) algorithms which are consistent.

We present a system for recognising human activity given a symbolic representation of video content. The input of our system is a set of time-stamped short-term activities (STA) detected on video frames. The output is a set of recognised long-term activities (LTA), which are pre-defined temporal combinations of STA. The constraints on the STA that, if satisfied, lead to the recognition of a LTA, have been expressed using a dialect of the Event Calculus. In order to handle the uncertainty that naturally occurs in human activity recognition, we adapted this dialect to a state-of-the-art probabilistic logic programming framework. We present a detailed evaluation and comparison of the crisp and probabilistic approaches through experimentation on a benchmark dataset of human surveillance videos.

Unsupervised feature learning has shown impressive results for a wide range of input modalities, in particular for object classification tasks in computer vision. Using a large amount of unlabeled data, unsupervised feature learning methods are utilized to construct high-level representations that are discriminative enough for subsequently trained supervised classification algorithms. However, it has never been \emph{quantitatively} investigated yet how well unsupervised learning methods can find \emph{low-level representations} for image patches without any additional supervision. In this paper we examine the performance of pure unsupervised methods on a low-level correspondence task, a problem that is central to many Computer Vision applications. We find that a special type of Restricted Boltzmann Machines (RBMs) performs comparably to hand-crafted descriptors. Additionally, a simple binarization scheme produces compact representations that perform better than several state-of-the-art descriptors.

Probabilistic logic programs are logic programs in which some of the facts are annotated with probabilities. This paper investigates how classical inference and learning tasks known from the graphical model community can be tackled for probabilistic logic programs. Several such tasks such as computing the marginals given evidence and learning from (partial) interpretations have not really been addressed for probabilistic logic programs before. The first contribution of this paper is a suite of efficient algorithms for various inference tasks. It is based on a conversion of the program and the queries and evidence to a weighted Boolean formula. This allows us to reduce the inference tasks to well-studied tasks such as weighted model counting, which can be solved using state-of-the-art methods known from the graphical model and knowledge compilation literature. The second contribution is an algorithm for parameter estimation in the learning from interpretations setting. The algorithm employs Expectation Maximization, and is built on top of the developed inference algorithms. The proposed approach is experimentally evaluated. The results show that the inference algorithms improve upon the state-of-the-art in probabilistic logic programming and that it is indeed possible to learn the parameters of a probabilistic logic program from interpretations.

The problem of structure estimation in graphical models with latent variables is considered. We characterize conditions for tractable graph estimation and develop efficient methods with provable guarantees. We consider models where the underlying Markov graph is locally tree-like, and the model is in the regime of correlation decay. For the special case of the Ising model, the number of samples $n$ required for structural consistency of our method scales as $n=\Omega(\theta_{\min}^{-\delta\eta(\eta+1)-2}\log p)$, where p is the number of variables, $\theta_{\min}$ is the minimum edge potential, $\delta$ is the depth (i.e., distance from a hidden node to the nearest observed nodes), and $\eta$ is a parameter which depends on the bounds on node and edge potentials in the Ising model. Necessary conditions for structural consistency under any algorithm are derived and our method nearly matches the lower bound on sample requirements. Further, the proposed method is practical to implement and provides flexibility to control the number of latent variables and the cycle lengths in the output graph.