Hierarchically-coupled hidden Markov models for learning kinetic rates from single-molecule data

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.Comment: 9 pages, 5 figure

Exemplar Based Deep Discriminative and Shareable Feature Learning for Scene Image Classification

In order to encode the class correlation and class specific information in image representation, we propose a new local feature learning approach named Deep Discriminative and Shareable Feature Learning (DDSFL). DDSFL aims to hierarchically learn feature transformation filter banks to transform raw pixel image patches to features. The learned filter banks are expected to: (1) encode common visual patterns of a flexible number of categories; (2) encode discriminative information; and (3) hierarchically extract patterns at different visual levels. Particularly, in each single layer of DDSFL, shareable filters are jointly learned for classes which share the similar patterns. Discriminative power of the filters is achieved by enforcing the features from the same category to be close, while features from different categories to be far away from each other. Furthermore, we also propose two exemplar selection methods to iteratively select training data for more efficient and effective learning. Based on the experimental results, DDSFL can achieve very promising performance, and it also shows great complementary effect to the state-of-the-art Caffe features.Comment: Pattern Recognition, Elsevier, 201