Non-parametric Bayesian modelling of digital gene expression data

Next-generation sequencing technologies provide a revolutionary tool for generating gene expression data. Starting with a fixed RNA sample, they construct a library of millions of differentially abundant short sequence tags or "reads", which constitute a fundamentally discrete measure of the level of gene expression. A common limitation in experiments using these technologies is the low number or even absence of biological replicates, which complicates the statistical analysis of digital gene expression data. Analysis of this type of data has often been based on modified tests originally devised for analysing microarrays; both these and even de novo methods for the analysis of RNA-seq data are plagued by the common problem of low replication. We propose a novel, non-parametric Bayesian approach for the analysis of digital gene expression data. We begin with a hierarchical model for modelling over-dispersed count data and a blocked Gibbs sampling algorithm for inferring the posterior distribution of model parameters conditional on these counts. The algorithm compensates for the problem of low numbers of biological replicates by clustering together genes with tag counts that are likely sampled from a common distribution and using this augmented sample for estimating the parameters of this distribution. The number of clusters is not decided a priori, but it is inferred along with the remaining model parameters. We demonstrate the ability of this approach to model biological data with high fidelity by applying the algorithm on a public dataset obtained from cancerous and non-cancerous neural tissues

Clear Visual Separation of Temporal Event Sequences

Extracting and visualizing informative insights from temporal event sequences becomes increasingly difficult when data volume and variety increase. Besides dealing with high event type cardinality and many distinct sequences, it can be difficult to tell whether it is appropriate to combine multiple events into one or utilize additional information about event attributes. Existing approaches often make use of frequent sequential patterns extracted from the dataset, however, these patterns are limited in terms of interpretability and utility. In addition, it is difficult to assess the role of absolute and relative time when using pattern mining techniques. In this paper, we present methods that addresses these challenges by automatically learning composite events which enables better aggregation of multiple event sequences. By leveraging event sequence outcomes, we present appropriate linked visualizations that allow domain experts to identify critical flows, to assess validity and to understand the role of time. Furthermore, we explore information gain and visual complexity metrics to identify the most relevant visual patterns. We compare composite event learning with two approaches for extracting event patterns using real world company event data from an ongoing project with the Danish Business Authority.Comment: In Proceedings of the 3rd IEEE Symposium on Visualization in Data Science (VDS), 201

Element-centric clustering comparison unifies overlaps and hierarchy

Clustering is one of the most universal approaches for understanding complex data. A pivotal aspect of clustering analysis is quantitatively comparing clusterings; clustering comparison is the basis for many tasks such as clustering evaluation, consensus clustering, and tracking the temporal evolution of clusters. In particular, the extrinsic evaluation of clustering methods requires comparing the uncovered clusterings to planted clusterings or known metadata. Yet, as we demonstrate, existing clustering comparison measures have critical biases which undermine their usefulness, and no measure accommodates both overlapping and hierarchical clusterings. Here we unify the comparison of disjoint, overlapping, and hierarchically structured clusterings by proposing a new element-centric framework: elements are compared based on the relationships induced by the cluster structure, as opposed to the traditional cluster-centric philosophy. We demonstrate that, in contrast to standard clustering similarity measures, our framework does not suffer from critical biases and naturally provides unique insights into how the clusterings differ. We illustrate the strengths of our framework by revealing new insights into the organization of clusters in two applications: the improved classification of schizophrenia based on the overlapping and hierarchical community structure of fMRI brain networks, and the disentanglement of various social homophily factors in Facebook social networks. The universality of clustering suggests far-reaching impact of our framework throughout all areas of science