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Stochastic spreading models defined on complex network topologies are used to mimic the diffusion of diseases, information, and opinions in real-world systems. Existing theoretical approaches to the characterization of the models in terms…
A system level view of cellular processes for human and several organisms can be cap- tured by analyzing molecular interaction networks. A molecular interaction network formed of differentially expressed genes and their interactions helps…
Heterogeneous, interconnected, systems-level, molecular data have become increasingly available and key in precision medicine. We need to utilize them to better stratify patients into risk groups, discover new biomarkers and targets,…
Neural network realizes multi-parameter optimization and control by simulating certain mechanisms of the human brain. It can be used in many fields such as signal processing, intelligent driving, optimal combination, vehicle abnormality…
The rapid advances in the field of optimization methods in many pure and applied science pose the difficulty of keeping track of the developments as well as selecting an appropriate technique that best suits the problem in-hand. From a…
A vast array of transformative technologies developed over the past decade has enabled measurement and perturbation at ever increasing scale, yet our understanding of many systems remains limited by experimental capacity. Overcoming this…
Composition is a powerful principle for systems biology, focused on the interfaces, interconnections, and orchestration of distributed processes to enable integrative multiscale simulations. Whereas traditional models focus on the structure…
Compositional Explanations is a method for identifying logical formulas of concepts that approximate the neurons' behavior. However, these explanations are linked to the small spectrum of neuron activations (i.e., the highest ones) used to…
The hematopoietic system has a highly regulated and complex structure in which cells are organized to successfully create and maintain new blood cells. Feedback regulation is crucial to tightly control this system, but the specific…
This dissertation is a study on the design and analysis of novel, optimal routing and rate control algorithms in wireless, mobile communication networks. Congestion control and routing algorithms upto now have been designed and optimized…
Reaction-diffusion systems offer a powerful framework for understanding self-organized patterns in biological systems, yet controlling these patterns remains a significant challenge. As a consequence, we present a rigorous framework of…
A typical goal of research in combinatorial optimization is to come up with fast algorithms that find optimal solutions to a computational problem. The process that takes a real-world problem and extracts a clean mathematical abstraction of…
As the development of distributed systems progresses, more and more challenges arise and the need for developing optimized systems and for optimizing existing systems from multiple perspectives becomes more stringent. In this paper I…
Metabolites, small molecules that are involved in cellular reactions, provide a direct functional signature of cellular state. Untargeted metabolomics experiments usually relies on tandem mass spectrometry to identify the thousands of…
Cancers are complex adaptive diseases regulated by the nonlinear feedback systems between genetic instabilities, environmental signals, cellular protein flows, and gene regulatory networks. Understanding the cybernetics of cancer requires…
Our ability to manipulate the behavior of complex networks depends on the design of efficient control algorithms and, critically, on the availability of an accurate and tractable model of the network dynamics. While the design of control…
Real-world problems are becoming highly complex and, therefore, have to be solved with combinatorial optimisation (CO) techniques. Motivated by the strong increase of publications on CO, 8,393 articles from this research field are subjected…
Network equilibrium models represent a versatile tool for the analysis of interconnected objects and their relationships. They have been widely employed in both science and engineering to study the behavior of complex systems under various…