Nicholas A. Heard

A Quantitative Study of Gene Regulation Involved in the Immune Response of Anopheline Mosquitoes: An Application of Bayesian Hierarchical Clustering of Curves

Malaria represents one of the major worldwide challenges to public health. A recent breakthrough in the study of the disease follows the annotation of the genome of the malaria parasite Plasmodium falciparum and the mosquito vector (an organism that spreads an infectious disease)Anopheles. Of particular interest is the molecular biology underlying the immune response system of Anopheles, which actively fights against Plasmodium infection. This article reports a statistical analysis of gene expression time profiles from mosquitoes that have been infected with a bacterial agent. Specifically, we introduce a Bayesian model-based hierarchical clustering algorithm for curve data to investigate mechanisms of regulation in the genes concerned; that is, we aim to cluster genes having similar expression profiles. Genes displaying similar, interesting profiles can then be highlighted for further investigation by the experimenter. We show how our approach reveals structure within the data not captured by other approaches. One of the most pertinent features of the data is the sample size, which records the expression levels of 2,771 genes at 6 time points. Additionally, the time points are unequally spaced, and there is expected nonstationary behavior in the gene profiles. We demonstrate our approach to be readily implementable under these conditions, and highlight some crucial computational savings that can be made in the context of a fully Bayesian analysis.

Bayesian anomaly detection methods for social networks

Learning the network structure of a large graph is computationally demanding, and dynamically monitoring the network over time for any changes in structure threatens to be more challenging still. This paper presents a two-stage method for anomaly detection in dynamic graphs: the first stage uses simple, conjugate Bayesian models for discrete time counting processes to track the pairwise links of all nodes in the graph to assess normality of behavior; the second stage applies standard network inference tools on a greatly reduced subset of potentially anomalous nodes. The utility of the method is demonstrated on simulated and real data sets.

Bayesian cluster identification in single-molecule localization microscopy data.

Single-molecule localization-based super-resolution microscopy techniques such as photoactivated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM) produce pointillist data sets of molecular coordinates. Although many algorithms exist for the identification and localization of molecules from raw image data, methods for analyzing the resulting point patterns for properties such as clustering have remained relatively under-studied. Here we present a model-based Bayesian approach to evaluate molecular cluster assignment proposals, generated in this study by analysis based on Ripleys K function. The method takes full account of the individual localization precisions calculated for each emitter. We validate the approach using simulated data, as well as experimental data on the clustering behavior of CD3ζ, a subunit of the CD3 T cell receptor complex, in resting and activated primary human T cells.

Finding groups in gene expression data

The vast potential of the genomic insight offered by microarray technologies has led to their widespread use since they were introduced a decade ago. Application areas include gene function discovery, disease diagnosis, and inferring regulatory networks. Microarray experiments enable large-scale, high-throughput investigations of gene activity and have thus provided the data analyst with a distinctive, high-dimensional field of study. Many questions in this field relate to finding subgroups of data profiles which are very similar. A popular type of exploratory tool for finding subgroups is cluster analysis, and many different flavors of algorithms have been used and indeed tailored for microarray data. Cluster analysis, however, implies a partitioning of the entire data set, and this does not always match the objective. Sometimes pattern discovery or bump hunting tools are more appropriate. This paper reviews these various tools for finding interesting subgroups.

Dissecting the fission yeast regulatory network reveals phase-specific control elements of its cell cycle

BackgroundFission yeast Schizosaccharomyces pombe and budding yeast Saccharomyces cerevisiae are among the original model organisms in the study of the cell-division cycle. Unlike budding yeast, no large-scale regulatory network has been constructed for fission yeast. It has only been partially characterized. As a result, important regulatory cascades in budding yeast have no known or complete counterpart in fission yeast.ResultsBy integrating genome-wide data from multiple time course cell cycle microarray experiments we reconstructed a gene regulatory network. Based on the network, we discovered in addition to previously known regulatory hubs in M phase, a new putative regulatory hub in the form of the HMG box transcription factor SPBC19G7.04. Further, we inferred periodic activities of several less known transcription factors over the course of the cell cycle, identified over 500 putative regulatory targets and detected many new phase-specific and conserved cis-regulatory motifs. In particular, we show that SPBC19G7.04 has highly significant periodic activity that peaks in early M phase, which is coordinated with the late G2 activity of the forkhead transcription factor fkh2. Finally, using an enhanced Bayesian algorithm to co-cluster the expression data, we obtained 31 clusters of co-regulated genes 1) which constitute regulatory modules from different phases of the cell cycle, 2) whose phase order is coherent across the 10 time course experiments, and 3) which lead to identification of phase-specific control elements at both the transcriptional and post-transcriptional levels in S. pombe. In particular, the ribosome biogenesis clusters expressed in G2 phase reveal new, highly conserved RNA motifs.ConclusionUsing a systems-level analysis of the phase-specific nature of the S. pombe cell cycle gene regulation, we have provided new testable evidence for post-transcriptional regulation in the G2 phase of the fission yeast cell cycle. Based on this comprehensive gene regulatory network, we demonstrated how one can generate and investigate plausible hypotheses on fission yeast cell cycle regulation which can potentially be explored experimentally.

A Bayesian cluster analysis method for single-molecule localization microscopy data

Cell function is regulated by the spatiotemporal organization of the signaling machinery, and a key facet of this is molecular clustering. Here, we present a protocol for the analysis of clustering in data generated by 2D single-molecule localization microscopy (SMLM)—for example, photoactivated localization microscopy (PALM) or stochastic optical reconstruction microscopy (STORM). Three features of such data can cause standard cluster analysis approaches to be ineffective: (i) the data take the form of a list of points rather than a pixel array; (ii) there is a non-negligible unclustered background density of points that must be accounted for; and (iii) each localization has an associated uncertainty in regard to its position. These issues are overcome using a Bayesian, model-based approach. Many possible cluster configurations are proposed and scored against a generative model, which assumes Gaussian clusters overlaid on a completely spatially random (CSR) background, before every point is scrambled by its localization precision. We present the process of generating simulated and experimental data that are suitable to our algorithm, the analysis itself, and the extraction and interpretation of key cluster descriptors such as the number of clusters, cluster radii and the number of localizations per cluster. Variations in these descriptors can be interpreted as arising from changes in the organization of the cellular nanoarchitecture. The protocol requires no specific programming ability, and the processing time for one data set, typically containing 30 regions of interest, is ∼18 h; user input takes ∼1 h.

Iterative Reclassification in Agglomerative Clustering

In model-based clustering of complex data, a probability model, typically a finite mixture probability model, forms the basis of the distance measure between any pair of clusters. The idea of model-based clustering was popularized by the framework and accompanying software of Fraley and Raftery (2002). In particular, model-based agglomerative hierarchical clustering is now a frequently used approach for probabilistic grouping of data, due to the speed and simplicity of implementation. This article investigates deficiencies in the clusterings proposed from this popular approach, and presents a review of small refinements and extensions to the procedure with differing performance gains and computational costs. The improvements are illustrated through application to simulated and real data examples, including the clustering of gene expression time profiles. Some of the proposed improvements to agglomerative clustering are, like the procedure itself in its usual form, deterministic; perhaps surprisingly though, the best overall results here are obtained via a stochasticized version of the entire procedure. While the focus of this article is probability model-based clustering, many of the schemes presented are equally applicable to agglomerative clustering under any distance measure. The simulated data from this article along with the C++ code used for implementing the algorithms for all of the examples can be obtained online from the Supplemental Material.

Poisson factorization for peer-based anomaly detection

Anomaly detection systems are a promising tool to identify compromised user credentials and malicious insiders in enterprise networks. Most existing approaches for modelling user behaviour rely on either independent observations for each user or on pre-defined user peer groups. A method is proposed based on recommender system algorithms to learn overlapping user peer groups and to use this learned structure to detect anomalous activity. Results analysing the authentication and process-running activities of thousands of users show that the proposed method can detect compromised user accounts during a red team exercise.

Network-wide anomaly detection via the Dirichlet process

Statistical anomaly detection techniques provide the next layer of cyber-security defences below traditional signature-based approaches. This article presents a scalable, principled, probability-based technique for detecting outlying connectivity behaviour within a directed interaction network such as a computer network. Independent Bayesian statistical models are fit to each message recipient in the network using the Dirichlet process, which provides a tractable, conjugate prior distribution for an unknown discrete probability distribution. The method is shown to successfully detect a red team attack in authentication data obtained from the enterprise network of Los Alamos National Laboratory.

Detecting Localised Anomalous Behaviour in a Computer Network

Temporal monitoring of computer network data for statistical anomalies provides a means for detecting malicious intruders. The high volumes of traffic typically flowing through these networks can make detecting important changes in structure extremely challenging. In this article, agile algorithms which readily scale to large networks are provided, assuming conditionally independent node and edge-based statistical models. As a first stage, changes in the data streams arising from edges (pairs of hosts) in the network are detected. A second stage analysis combines any anomalous edges to identify more general anomalous substructures in the network. The method is demonstrated on the entire internal computer network of Los Alamos National Laboratory, comprising approximately 50,000 hosts, using a data set which contains a real, sophisticated cyber attack. This attack is quickly identified from amongst the huge volume of data being processed.