Study of dynamic characteristics of scale-free spiking neural networks based on synaptic plasticity / 生物医学工程学杂志

Biological neural networks have dual properties of small-world attributes and scale-free attributes. Most of the current researches on neural networks are based on small-world networks or scale-free networks with lower clustering coefficient, however, the real brain network is a scale-free network with small-world attributes. In this paper, a scale-free spiking neural network with high clustering coefficient and small-world attribute was constructed. The dynamic evolution process was analyzed from three aspects: synaptic regulation process, firing characteristics and complex network characteristics. The experimental results show that, as time goes by, the synaptic strength gradually decreases and tends to be stable. As a result, the connection strength of the network decreases and tends to be stable; the firing rate of neurons gradually decreases and tends to be stable, and the synchronization becomes worse; the local information transmission efficiency is stable, the global information transmission efficiency is reduced and tends to be stable, and the small-world attributes are relatively stable. The dynamic characteristics vary with time and interact with each other. The regulation of synapses is based on the firing time of neurons, and the regulation of synapses will affect the firing of neurons and complex characteristics of networks. In this paper, a scale-free spiking neural network was constructed, which has biological authenticity. It lays a foundation for the research of artificial neural network and its engineering application.

Study on Traditional Chinese Medicine Medication Rules in the Treatment of Gastric Cancer based on Scale-free Network Analysis / 世界科学技术-中医药现代化

This article was aimed to study medication rules of traditional Chinese medicine (TCM) in the treatment of gastric cancer. The history information of 111 hospitalized cases from 2008 to 2011 was collected from the Department of Oncology of Guang'anmen Hospital with the clinical collection system. The medication rules in the treatment of gastric cancer by TCM were explored by the scale-free network analysis from several aspects, such as effects, classifications and compatibility relations of Chinese medicine. The analysis result of 111 gastric cancer cases showed that strengthening the body resistance was the main treatment principle. Liujunzi decoction was the most frequently used prescription. In TCM compatibility, deficiency-nourishing herbs were the main ingredients, especiallyqi-supplementing herbs which take the first place in the prescription. And the heat-reducing herbs, dampness-eliminating herbs, blood-activating and stasis-eliminating herbs, food stagnation resolving herbs and qi regulation herbs were also used in the combination. Core herbs in the prescription for the treatment of gastric cancer were Tuckahoe, Codonopsis pilosula, Astragalus root, Pericarpium Citri Reticulatae, Fructus Aurantii, Nidus Vespae and etc. TCM treatment, syndrome differentiation and medication are varied according to different therapeutic stages and disease stages. The result showed that scale-free network analysis had certain significance in the understanding of medication rules of TCM treatment of gastric cancer.

Preliminary Study on Traditional Chinese Medicine Treatment Characteristics of Intestinal Cancer based on Scale-free Network Analysis Method / 世界科学技术-中医药现代化

This article was aimed to study the characteristics of intestinal cancer by traditional Chinese medicine (TCM) based on the scale-free network analysis method. History information of 145 hospitalized cases from 2008 to 2011 was collected from the Oncology Department, Guang A nmen Hospital, in the clinical collection system. The rule of medication in the treatment of intestinal cancer by TCM was explored by scale-free network analysis method from several aspects, such as effects, classification and compatibility relations. The analysis results of 145 intestinal cancer cases showed that strengthening the body resistance was the main treatment principle. Si-Jun-Zi (SJZ) decoc-tion was used with the highest frequency. In the prescription design, qi-supplementing herbs were the most. The heat-clearing, dampness-eliminating, qi-regulating, blood-activating and stasis-removing, food stagnation removing and phlegm-removing herbs were also used frequently. The TCM treatment and syndrome differentiation will be changed due to the treatment and disease stages. It was concluded that scale-free network analysis method is able to relatively show the TCM treatment rule of intestinal cancer quantificationally and intuitively.

J2dpathway: A Global Metabolic Pathway Viewer with Node-Abstracting Features

The static approach of representing metabolic pathway diagrams offers no flexibility. Thus, many systems adopt automatic graph layout techniques to visualize the topological architecture of pathways. There are weaknesses, however, because automatically drawn figures are generally difficult to understand. The problem becomes even more serious when we attempt to visualize all of the information in a single, big picture, which usually results in a confusing diagram. To provide a partial solution to this thorny issue, we propose J2dpathway, a metabolic pathway atlas viewer that has node-abstracting features.

Parsing KEGG XML Files to Find Shared and Duplicate Compounds Contained in Metabolic Pathway Maps: A Graph-Theoretical Perspective

The basic graph layout technique, one of many visualization techniques, deals with the problem of positioning vertices in a way to maximize some measure of desirability in a graph. The technique is becoming critically important for further development of the field of systems biology. However, applying the appropriate automatic graph layout techniques to the genomic scale flow of metabolism requires an understanding of the characteristics and patterns of duplicate and shared vertices, which is crucial for bioinformatics software developers. In this paper, we provide the results of parsing KEGG XML files from a graph-theoretical perspective, for future research in the area of automatic layout techniques in biological pathway domains.

A Metabolic Pathway Drawing Algorithm for Reducing the Number of Edge Crossings

For the direct understanding of flow, pathway data are usually represented as directed graphs in biological journals and texts. Databases of metabolic pathways or signal transduction pathways inevitably contain these kinds of graphs to show the flow. KEGG, one of the representative pathway databases, uses the manually drawn figure which can not be easily maintained. Graph layout algorithms are applied for visualizing metabolic pathways in some databases, such as EcoCyc. Although these can express any changes of data in the real time, it exponentially increases the edge crossings according to the increase of nodes. For the understanding of genome scale flow of metabolism, it is very important to reduce the unnecessary edge crossings which exist in the automatic graph layout. We propose a metabolic pathway drawing algorithm for reducing the number of edge crossings by considering the fact that metabolic pathway graph is scale-free network. The experimental results show that the number of edge crossings is reduced about 37~40% by the consideration of scale-free network in contrast with non-considering scale-free network. And also we found that the increase of nodes do not always mean that there is an increase of edge crossings.