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Logical modeling has been widely used to understand and expand the knowledge about protein interactions among different pathways. Realizing this, the caspo-ts system has been proposed recently to learn logical models from time series data. It uses Answer Set Programming to enumerate Boolean Networks (BNs) given prior knowledge networks and phosphoproteomic time series data. In the resulting sequence of solutions, similar BNs are typically clustered together. This can be problematic for large scale problems where we cannot explore the whole solution space in reasonable time. Our approach extends the caspo-ts system to cope with the important use case of finding diverse solutions of a problem with a large number of solutions. We first present the algorithm for finding diverse solutions and then we demonstrate the results of the proposed approach on two different benchmark scenarios in systems biology: (1) an artificial dataset to model TCR signaling and (2) the HPN-DREAM challenge dataset to model breast cancer cell lines.
We present a system-level synthesis approach for heterogeneous multi-processor on chip, based on Answer Set Programming(ASP). Starting with a high-level description of an application, its timing constraints and the physical constraints of the target device, our goal is to produce the optimal computing infrastructure made of heterogeneous processors, peripherals, memories and communication components. Optimization aims at maximizing speed, while minimizing chip area. Also, a scheduler must be produced that fulfills the real-time requirements of the application. Even though our approach will work for application specific integrated circuits, we have chosen FPGA as target device in this work because of their reconfiguration capabilities which makes it possible to explore several design alternatives. This paper addresses the bottleneck of problem representation size by providing a direct and compact ASP encoding for automatic synthesis that is semantically equivalent to previously established ILP and ASP models. We describe a use-case in which designers specify their applications in C/C++ from which optimum systems can be derived. We demonstrate the superiority of our approach toward existing heuristics and exact methods with synthesis results on a set of realistic case studies. (C) 2018 Elsevier Inc. All rights reserved.
teaspoon
(2018)
Answer Set Programming (ASP) is an approach to declarative problem solving, combining a rich yet simple modeling language with high performance solving capacities. We here develop an ASP-based approach to curriculum-based course timetabling (CB-CTT), one of the most widely studied course timetabling problems. The resulting teaspoon system reads a CB-CTT instance of a standard input format and converts it into a set of ASP facts. In turn, these facts are combined with a first-order encoding for CB-CTT solving, which can subsequently be solved by any off-the-shelf ASP systems. We establish the competitiveness of our approach by empirically contrasting it to the best known bounds obtained so far via dedicated implementations. Furthermore, we extend the teaspoon system to multi-objective course timetabling and consider minimal perturbation problems.