Related papers: Designer Gene Networks: Towards Fundamental Cellul…
Tumorigenic transformation of human epithelial cells in vitro has been described experimentally as the potential result of a process known as spontaneous immortalization. In this process a generic series of cell state transitions occur in…
Designing networks with specified collective properties is useful in a variety of application areas, enabling the study of how given properties affect the behavior of network models, the downscaling of empirical networks to workable sizes,…
Metabolic networks consist of linked functional components, or modules. The mechanism underlying metabolic network modularity is of great interest not only to researchers of basic science but also to those in fields of engineering. Previous…
Recent developments in neural networks have led to the advance in data-to-text generation. However, the lack of ability of neural models to control the structure of generated output can be limiting in certain real-world applications. In…
Program synthesis is the task of automatically generating a program consistent with a given specification. A natural way to specify programs is to provide examples of desired input-output behavior, and many current program synthesis…
We review a recent trend in computational systems biology which aims at using pattern recognition algorithms to infer the structure of large-scale biological networks from heterogeneous genomic data. We present several strategies that have…
Networks coming from protein-protein interactions, transcriptional regulation, signaling, or metabolism may appear to have "unusual" properties. To quantify this, it is appropriate to randomize the network and test the hypothesis that the…
The fields of neural computation and artificial neural networks have developed much in the last decades. Most of the works in these fields focus on implementing and/or learning discrete functions or behavior. However, technical, physical,…
Directed acyclic graphs are a fundamental class of networks that includes citation networks, food webs, and family trees, among others. Here we define a random graph model for directed acyclic graphs and give solutions for a number of the…
Based on a non-equilibrium mechanism for spatial pattern formation we study how position information can be controlled by locally coupled discrete dynamical networks, similar to gene regulation networks of cells in a developing…
By linking conceptual theories with observed data, generative models can support reasoning in complex situations. They have come to play a central role both within and beyond statistics, providing the basis for power analysis in molecular…
The design of novel protein sequences with targeted functionalities underpins a central theme in protein engineering, impacting diverse fields such as drug discovery and enzymatic engineering. However, navigating this vast combinatorial…
Essentially, motive behind using control system is to generate suitable control signal for yielding desired response of a physical process. Control of synchronous generator has always remained very critical in power system operation and…
The generation of synthetic data is an essential tool to study complex systems, allowing for example to test models of these in precisely controlled settings, or to parametrize simulation models when data is missing. This paper focuses on…
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…
Symmetries in a network regulate its organization into functional clustered states. Given a generic ensemble of nodes and a desirable cluster (or group of clusters), we exploit the direct connection between the elements of the eigenvector…
Gene Regulatory Network (GRN) plays an important role in knowing insight of cellular life cycle. It gives information about at which different environmental conditions genes of particular interest get over expressed or under expressed.…
Emergence is a phenomenon taken for granted in science but also still not well understood. We have developed a model of artificial genetic evolution intended to allow for emergence on genetic, population and social levels. We present the…
This paper deals with controllability of dynamical networks. It is often unfeasible or unnecessary to fully control large-scale networks, which motivates the control of a prescribed subset of agents of the network. This specific form of…
Generative modeling of anatomical structures plays a crucial role in virtual imaging trials, which allow researchers to perform studies without the costs and constraints inherent to in vivo and phantom studies. For clinical relevance,…