Complex networks approach to gene expression driven phenotype imaging

Evaluating the role of community detection in improving influence maximization heuristics

Both community detection and influence maximization are well-researched fields of network science. Here, we investigate how several popular community detection algorithms can be used as part of a heuristic approach to influence maximization. The heuristic is based on the community value, a node-based metric defined on the outputs of overlapping community detection algorithms. This metric is used to select nodes as high influence candidates for expanding the set of influential nodes. Our aim in this paper is twofold. First, we evaluate the performance of eight frequently used overlapping community detection algorithms on this specific task to show how much improvement can be gained compared to the originally proposed method of Kempe et al. Second, selecting the community detection algorithm(s) with the best performance, we propose a variant of the influence maximization heuristic with significantly reduced runtime, at the cost of slightly reduced quality of the output. We use both artificial benchmarks and real-life networks to evaluate the performance of our approach.

Pattern recognition with weighted complex networks

In this paper we introduce a weighted complex networks model to investigate and recognize structures of patterns. The regular treating in pattern recognition models is to describe each pattern as a high-dimensional vector which however is insufficient to express the structural information. Thus, a number of methods are developed to extract the structural information, such as different feature extraction algorithms used in pre-processing steps, or the local receptive fields in convolutional networks. In our model, each pattern is attributed to a weighted complex network, whose topology represents the structure of that pattern. Based upon the training samples, we get several prototypal complex networks which could stand for the general structural characteristics of patterns in different categories. We use these prototypal networks to recognize the unknown patterns. It is an attempt to use complex networks in pattern recognition, and our result shows the potential for real-world pattern recognition. A spatial parameter is introduced to get the optimal recognition accuracy, and it remains constant insensitive to the amount of training samples. We have discussed the interesting properties of the prototypal networks. An approximate linear relation is found between the strength and color of vertexes, in which we could compare the structural difference between each category. We have visualized these prototypal networks to show that their topology indeed represents the common characteristics of patterns. We have also shown that the asymmetric strength distribution in these prototypal networks brings high robustness for recognition. Our study may cast a light on understanding the mechanism of the biologic neuronal systems in object recognition as well.

Pipeline for acquisition of quantitative data on segmentation gene expression from confocal images

We describe a data pipeline developed to extract the quantitative data on segmentation gene expression from confocal images of gene expression patterns in Drosophila. The pipeline consists of five steps: image segmentation, background removal, temporal characterization of an embryo, data registration and data averaging. This pipeline was successfully applied to obtain quantitative gene expression data at cellular resolution in space and at the 6.5-minute resolution in time, as well as to construct a spatiotemporal atlas of segmentation gene expression. Each data pipeline step can be easily adapted to process a wide range of images of gene expression patterns.

A new method for quantifying three-dimensional interactions between biological structures

In this paper we examine a new distance-based method for identifying and characterizing possible interactions between biological structures and objects, with respect to the initial developmental stages of Echinococcus granulosus. By adopting the surface of the foramen as the distance reference, several interesting results have been identified, including the fact that the cell nuclei tend to be organized with respect to the foramen surface as well as the stability of the spatial distribution of these nuclei along the development stages.