EMT/BSSE: Biological networks as a communication model for entities with complex interactions

生物网络显示了生物化学实体之间的复杂相互作用，这些实体往往对有机体的生存至关重要。这些实体相互通信，以协作和执行它们无法单独完成的复杂功能。许多应用遵循一种类似于生物网络的交互模式。无线网络、传感器网络和国土安全只是这些应用的几个例子。利用生物网络对这些应用中的通信模式进行建模是非常有前途的，因为生物网络具有健壮性和灵活性。生物网络能够有效地适应基因或蛋白质的变化，通过寻找其他可能的方法来保持网络的稳定，从而最大限度地减少对网络造成的损害。生物网络分析以及许多其他复杂通信网络应用中的关键问题之一是寻找它们之间的相似之处。为了解决这个问题，有必要找到输入路径的交互实体的对齐。两个网络的对准是它们的节点(即实体)的子集之间的一对一映射。这项研究开发了一个通用框架，使基因相互作用和代谢网络的两个网络能够有效地对齐。这两个网络涵盖了从布尔模型到化学计量模型的广泛范围的通信模型。与现有的网络对齐方法不同，该方法除了考虑结构和拓扑上的相似性外，还考虑了相互作用实体的功能相似性。这项研究还开发了索引网络数据库的新方法。这些索引结构允许在网络数据库上高效地回答范围和TOP-K查询。

Biological networks show the complex interactions between bio-chemical entities that are often vital for the survival of organisms. The entities communicate with each other to collaborate and perform complex functions that they can not do individually. Numerous applications follow an interaction pattern that resembles biological networks. Wireless networks, sensor networks and homeland security are just a few examples to these applications. Employing biological networks to model the communication patterns in these applications is very promising as the biological networks are robust and flexible. The biological networks efficiently adapt to the alterations in genes or proteins to minimize the damage done to the network by finding alternative ways to keep the network stable whenever it is possible.One of the critical problems in analysis of biological networks as well as many other applications with complex communication networks is finding similarities between them. To solve this problem, it is necessary to find an alignment of the interacting entities of the input pathways. An alignment of two networks is a one-to-one mapping between a subset of their nodes (i.e., entities). This research develops a generic framework that enables efficient alignment of two networks for gene interaction and metabolic networks. These two networks cover a broad spectrum of communication models ranging from Boolean to stoichiometric models. Unlike existing network alignment methods, this proposal considers the functional similarities of the interacting entities in addition to their structural and topological similarities. This research also develops new methods for indexing network databases. These index structures allow answering range and top-k queries efficiently over a network database.