Dealing with Biology Systems in the Framework of Answer Set Programming
Tarek Khaled, Belaïd Benhamou · Procedia Computer Science · 2020
Reasoning about gene networks is essential from various perspectives, such as predicting side effects of drugs or explaining unusual cellular behavior. Because of the massive size of these gene networks, a biologist can only work on a small part of the network. Thus, there is an essential requirement for logical representations and automated reasoning on such networks to help biologists to understand genetic interactions. However, the knowledge about gene networks is always incomplete and sometimes not accurate. Hence, knowledge has to be continuously revised and extended. In this work, we propose an approach based on non-monotonic logic programming, and the framework of Answer Set Programming(ASP), to represent and handle gene networks. We show how to model reasoning, predict events, and explain observations in gene networks. Finally, we show how our approach is applied to represent and resolve the DNA double-strand breaks, which is one of the most severe genomic lesions.