Study On Article Exchange Model And Its Applications To Biological Regulation Networks

Looking over many examples in the world, you can find many interesting phenomena taking on a variety of circular regulating relations. Then what are the circular regulating relations? In the following paragraphs, we will introduce the details.First, we give some examples. In the medical fields, there are the circular interactions between the vital organs of the human body. These organs are mutually dependent and interact with each other. From the point of Mathematics, There are also a lot of repeating infinite decimals and the repeating relationships between the decimal fractions. From a musical standpoint, the internal time bar is a circular rhythm. From the angle of the Instruments, Pythagoras, a Greek philosopher and mathematician, found the Music Number : 3, 4 and 6. He proved that if the ration of the chord length is 3:4:6, the sound of the Chinese fiddle or the three stringed instruments is fine, which could be taken as a kind of circular relationships. On the economic side, there is also a circular of loan-borrowing relationship among customers, banks and enterprises. From the view of the commercial activity on the internet, the fiduciary relationship is more important than others, and it is a circular among the buyer, the seller and the Third Party.Off course, the Article Exchange Sites (AESs) help the persons on the internet to get the article they want by exchanging their owns. So the online exchange relation is also circular among them. Besides these examples, the Traveling Salesman Problem (TSP) is a typical optimization problem in graph theory, which belongs to a large family of NP-complete problems. The essential point of TSP is how to find the shortest circular path. From simple to complex, the relationships refer to the collaborative network of thousands of scientists, social networks, internet networks, and so on. Just under such a social background, it inspires the idea of this paper.Taking the article exchange on the internet for an example, we propose a novel model to solve the article exchanging problems. Meanwhile, we apply the proposed model to some complex networks in bioinformatics. However, the proposed model could be applied more wide fields, not limited to the problems investigated in this paper.For instance, the application on banking can solve the loan-borrowing relationship between the bank and the client. It also can solve the problems of the urban planning, some circular problems relating to the TSP, regulation networks problems and so on. We believe that the solutions of these problems will bring us a lot of practical benefits and significance. In this paper, we take the protein-protein interaction networks and gene regulatory network of bioinformatics as examples to demonstrate the application of the proposed model. Heretofore, we didn t find any related work about the circular relationship.By analyzing the relationship between the online articles exchange activities, we use the computer technology methods and adopting the relevant knowledge of graph theory to establish a new combinatorial optimization model, named Article Exchange Model (AEM). On the windows platform, we use the c++ programming language to code our algorithm in Microsoft Visual Studio 2008. By numerical simulation experiments, we have verified the effectiveness of the proposed algorithm on time complexity and space complexity to solve the problems of the online articles exchange. The experimental and analytical results show that it can simplify complex networks containing tens of thousands of nodes and billions of relations. At the same time, to extend the application, we combine the AEM with the complex network algorithms. We adopt the fast algorithm, named FN , for detecting community structure in network and apply the hybrid algorithm to the regulation of gene expression network of Arabidopsis and human protein reference network (HPRD) in bioinformatics. By the tools of the Osprey and Cytoscape in bioinformatics we analyze and discuss the results of the experiment.By analysis, we know that the circular and regulatory relations also exist in the networks of bioinformatics, and the proposed model makes complex biological networks simplified. In the paper, we analyze the protein regulation circles and find out that the proteins of the circle have the similar function and action. It explains that the protein circuits are valuable. This provides the useful information for the further study.So far, there are many models for studying the gene networks and protein reference networks, but which search the networks from the micro sense, such as the Boolean Network Model, Linear Combination Model, the weighted matrix model, Bayesian network model, differential equation models. These models deal with the gene networks from microarray data by biological experiments. However, the proposed AEM model not only solves the problems of the online article exchange but also can deal with other problems of the above-mentioned networks.Through the overall arrangement of the paper structure, the paper expounds and proves the AEM model clearly and solves the online article exchange. In the meantime, we apply it to the biological regulation networks and illustrate the practical significance of the AEM model. Be compared with other models, some defects maybe exits. But we have the different starting points and solve the problems from the different angles. In addition to these, it can be used in the different application areas.We believe that more value and significance of the AEM model will be found when it is applied to other fields, such as urban planning, bank loan and borrowing, and so on. We will also continue to work and explore in the future research.