Automatic Segmentation of Fluorescence Lifetime Microscopy Images of Cells Using Multi-Resolution Community Detection

We have developed an automatic method for segmenting fluorescence lifetime (FLT) imaging microscopy (FLIM) images of cells inspired by a multi-resolution community detection (MCD) based network segmentation method. The image processing problem is framed as identifying segments with respective average FLTs against a background in FLIM images. The proposed method segments a FLIM image for a given resolution of the network composed using image pixels as the nodes and similarity between the pixels as the edges. In the resulting segmentation, low network resolution leads to larger segments and high network resolution leads to smaller segments. Further, the mean-square error (MSE) in estimating the FLT segments in a FLIM image using the proposed method was found to be consistently decreasing with increasing resolution of the corresponding network. The proposed MCD method outperformed a popular spectral clustering based method in performing FLIM image segmentation. The spectral segmentation method introduced noisy segments in its output at high resolution. It was unable to offer a consistent decrease in MSE with increasing resolution.Comment: 21 pages, 6 figure

Entropy-scaling search of massive biological data

Many datasets exhibit a well-defined structure that can be exploited to design faster search tools, but it is not always clear when such acceleration is possible. Here, we introduce a framework for similarity search based on characterizing a dataset's entropy and fractal dimension. We prove that searching scales in time with metric entropy (number of covering hyperspheres), if the fractal dimension of the dataset is low, and scales in space with the sum of metric entropy and information-theoretic entropy (randomness of the data). Using these ideas, we present accelerated versions of standard tools, with no loss in specificity and little loss in sensitivity, for use in three domains---high-throughput drug screening (Ammolite, 150x speedup), metagenomics (MICA, 3.5x speedup of DIAMOND [3,700x BLASTX]), and protein structure search (esFragBag, 10x speedup of FragBag). Our framework can be used to achieve "compressive omics," and the general theory can be readily applied to data science problems outside of biology.Comment: Including supplement: 41 pages, 6 figures, 4 tables, 1 bo

Analysis of Software Binaries for Reengineering-Driven Product Line Architecture\^aAn Industrial Case Study

This paper describes a method for the recovering of software architectures from a set of similar (but unrelated) software products in binary form. One intention is to drive refactoring into software product lines and combine architecture recovery with run time binary analysis and existing clustering methods. Using our runtime binary analysis, we create graphs that capture the dependencies between different software parts. These are clustered into smaller component graphs, that group software parts with high interactions into larger entities. The component graphs serve as a basis for further software product line work. In this paper, we concentrate on the analysis part of the method and the graph clustering. We apply the graph clustering method to a real application in the context of automation / robot configuration software tools.Comment: In Proceedings FMSPLE 2015, arXiv:1504.0301

A temporal precedence based clustering method for gene expression microarray data

Background: Time-course microarray experiments can produce useful data which can help in understanding the underlying dynamics of the system. Clustering is an important stage in microarray data analysis where the data is grouped together according to certain characteristics. The majority of clustering techniques are based on distance or visual similarity measures which may not be suitable for clustering of temporal microarray data where the sequential nature of time is important. We present a Granger causality based technique to cluster temporal microarray gene expression data, which measures the interdependence between two time-series by statistically testing if one time-series can be used for forecasting the other time-series or not. Results: A gene-association matrix is constructed by testing temporal relationships between pairs of genes using the Granger causality test. The association matrix is further analyzed using a graph-theoretic technique to detect highly connected components representing interesting biological modules. We test our approach on synthesized datasets and real biological datasets obtained for Arabidopsis thaliana. We show the effectiveness of our approach by analyzing the results using the existing biological literature. We also report interesting structural properties of the association network commonly desired in any biological system. Conclusions: Our experiments on synthesized and real microarray datasets show that our approach produces encouraging results. The method is simple in implementation and is statistically traceable at each step. The method can produce sets of functionally related genes which can be further used for reverse-engineering of gene circuits

Node-attribute graph layout for small-world networks

Small-world networks are a very commonly occurring type of graph in the real-world, which exhibit a clustered structure that is not well represented by current graph layout algorithms. In many cases we also have information about the nodes in such graphs, which are typically depicted on the graph as node colour, shape or size. Here we demonstrate that these attributes can instead be used to layout the graph in high-dimensional data space. Then using a dimension reduction technique, targeted projection pursuit, the graph layout can be optimised for displaying clustering. The technique out-performs force-directed layout methods in cluster separation when applied to a sample, artificially generated, small-world network

Flow-based Influence Graph Visual Summarization

Visually mining a large influence graph is appealing yet challenging. People are amazed by pictures of newscasting graph on Twitter, engaged by hidden citation networks in academics, nevertheless often troubled by the unpleasant readability of the underlying visualization. Existing summarization methods enhance the graph visualization with blocked views, but have adverse effect on the latent influence structure. How can we visually summarize a large graph to maximize influence flows? In particular, how can we illustrate the impact of an individual node through the summarization? Can we maintain the appealing graph metaphor while preserving both the overall influence pattern and fine readability? To answer these questions, we first formally define the influence graph summarization problem. Second, we propose an end-to-end framework to solve the new problem. Our method can not only highlight the flow-based influence patterns in the visual summarization, but also inherently support rich graph attributes. Last, we present a theoretic analysis and report our experiment results. Both evidences demonstrate that our framework can effectively approximate the proposed influence graph summarization objective while outperforming previous methods in a typical scenario of visually mining academic citation networks.Comment: to appear in IEEE International Conference on Data Mining (ICDM), Shen Zhen, China, December 201