The Pathways Domain [Y. Dimopoulos, A. Gerevini, A. Saetti] =========================================================== This domain is inspired by the field of molecular biology, and specifically biochemical pathways. "A pathway is a sequence of chemical reactions in a biological organism. Such pathways specify mechanisms that explain how cells carry out their major functions by means of molecules and reactions that produce regular changes. Many diseases can be explained by defects in pathways, and new treatments often involve finding drugs that correct those defects" [1]. We can model parts of the functioning of a pathway as a planning problem by simply representing chemical reactions as actions. The biochemical pathway domain of the competition is based on the pathway of the Mammalian Cell Cycle Control as it described in [2] and modelled in [3]. There are 3 different kinds of basic actions corresponding to the different kinds of reactions that appear in the pathway. Propositional ------------- This is a simple qualitative encoding of the reactions of the pathway. The domain has five different actions: an action for choosing the initial substrates, an action for increasing the quantity of a chosen substrate (in the propositional version, quantity coincides with presence, and it is modeled through a predicate indicating if a substrate is available or not), an action modeling biochemical association reactions, an action modeling biochemical association reactions requiring catalysts, and an action modeling biochemical synthesis reactions. Also, there is an additional set of dummy actions representing the disjunctive problem goals. The goals refer to substances that must be synthesized by the pathway, and are disjunctive with two disjuncts each. Furthermore, there is a limit on the number of input substrates that can be used in the pathway. Note that each problem file has its own domain file (e.g., domain_p01.pddl for p01.pddl). Moreover, for this domain variant we give an (equivalent) compiled STRIPS version. Simple Preferences ------------------ This is similar to the propositional version, with the difference that both the products that must be synthesized by the pathway and the number of the input substrates that are used by the network are turned into preferences. The challenge here is finding plans that achieve a good tradeoff between the different kinds of preferences. Metric Temporal --------------- In this version of the domain, reactions have different durations. The reactions can happen if their input substrates reach some concentration level. On the other hand, reactions generate their products in specific quantities. The goals in this version are summations of substance concentrations that must be generated by the pathway. The plan metric minimizes some linear combination of the number of input substrates and the plan duration. Complex Preferences ------------------- This is an extension of the Metric Temporal version with different preferences concerning the concentration of substances in the pathway, the order in which substances appear in the pathway, etc. The metric is a combination of these preferences. References ---------- [1] P. Thagard. "Pathways to Biomedical Discovery". Philosophy of Science, volume 70 (2003). [2]. K. Kohn. "Molecular Interaction Map of the Mammalian Cell Cycle Control and DNA Repair Systems", Mol Biol Cell. 10(8), 1999. [3] http://contraintes.inria.fr/BIOCHAM/EXAMPLES/cell_cycle/cell_cycle.bc