Inference of Temporally Varying Bayesian Networks

When analysing gene expression time series data an often overlooked but crucial aspect of the model is that the regulatory network structure may change over time. Whilst some approaches have addressed this problem previously in the literature, many are not well suited to the sequential nature of the data. Here we present a method that allows us to infer regulatory network structures that may vary between time points, utilising a set of hidden states that describe the network structure at a given time point. To model the distribution of the hidden states we have applied the Hierarchical Dirichlet Process Hideen Markov Model, a nonparametric extension of the traditional Hidden Markov Model, that does not require us to fix the number of hidden states in advance. We apply our method to exisiting microarray expression data as well as demonstrating is efficacy on simulated test data

Parallels in the sequential organization of birdsong and human speech.

Human speech possesses a rich hierarchical structure that allows for meaning to be altered by words spaced far apart in time. Conversely, the sequential structure of nonhuman communication is thought to follow non-hierarchical Markovian dynamics operating over only short distances. Here, we show that human speech and birdsong share a similar sequential structure indicative of both hierarchical and Markovian organization. We analyze the sequential dynamics of song from multiple songbird species and speech from multiple languages by modeling the information content of signals as a function of the sequential distance between vocal elements. Across short sequence-distances, an exponential decay dominates the information in speech and birdsong, consistent with underlying Markovian processes. At longer sequence-distances, the decay in information follows a power law, consistent with underlying hierarchical processes. Thus, the sequential organization of acoustic elements in two learned vocal communication signals (speech and birdsong) shows functionally equivalent dynamics, governed by similar processes

Deterministic Consistency: A Programming Model for Shared Memory Parallelism

The difficulty of developing reliable parallel software is generating interest in deterministic environments, where a given program and input can yield only one possible result. Languages or type systems can enforce determinism in new code, and runtime systems can impose synthetic schedules on legacy parallel code. To parallelize existing serial code, however, we would like a programming model that is naturally deterministic without language restrictions or artificial scheduling. We propose "deterministic consistency", a parallel programming model as easy to understand as the "parallel assignment" construct in sequential languages such as Perl and JavaScript, where concurrent threads always read their inputs before writing shared outputs. DC supports common data- and task-parallel synchronization abstractions such as fork/join and barriers, as well as non-hierarchical structures such as producer/consumer pipelines and futures. A preliminary prototype suggests that software-only implementations of DC can run applications written for popular parallel environments such as OpenMP with low (<10%) overhead for some applications.Comment: 7 pages, 3 figure

Unsupervised morphological segmentation for images

This paper deals with a morphological approach to unsupervised image segmentation. The proposed technique relies on a multiscale Top-Down approach allowing a hierarchical processing of the data ranging from the most global scale to the most detailed one. At each scale, the algorithm consists of four steps: image simplification, feature extraction, contour localization and quality estimation. The main emphasis of this paper is to discuss the selection of a simplification filter for segmentation. Morphological filters based on reconstruction proved to be very efficient for this purpose. The resulting unsupervised algorithm is very robust and can deal with very different type of images.Peer ReviewedPostprint (published version

Streaming, Distributed Variational Inference for Bayesian Nonparametrics

This paper presents a methodology for creating streaming, distributed inference algorithms for Bayesian nonparametric (BNP) models. In the proposed framework, processing nodes receive a sequence of data minibatches, compute a variational posterior for each, and make asynchronous streaming updates to a central model. In contrast to previous algorithms, the proposed framework is truly streaming, distributed, asynchronous, learning-rate-free, and truncation-free. The key challenge in developing the framework, arising from the fact that BNP models do not impose an inherent ordering on their components, is finding the correspondence between minibatch and central BNP posterior components before performing each update. To address this, the paper develops a combinatorial optimization problem over component correspondences, and provides an efficient solution technique. The paper concludes with an application of the methodology to the DP mixture model, with experimental results demonstrating its practical scalability and performance.Comment: This paper was presented at NIPS 2015. Please use the following BibTeX citation: @inproceedings{Campbell15_NIPS, Author = {Trevor Campbell and Julian Straub and John W. {Fisher III} and Jonathan P. How}, Title = {Streaming, Distributed Variational Inference for Bayesian Nonparametrics}, Booktitle = {Advances in Neural Information Processing Systems (NIPS)}, Year = {2015}