"Life" shaped by genes that depend on their surrounds

Never was dogmatic reductionism helpful in conceiving the phenomenon of life. The post-genomic era has made it clear that genes alone cannot explain the functioning of whole organisms. Already each cell represents a unique, non-recurring individual. Recent progress in developmental biology has conveyed new perspectives both on the makings of individual organisms (ontogeny), as on evolutionary change (Evo-Devo). The genome (the entirety of all genes) of an animal remains constant from fertilization onwards in each cell. The realization of genes requires molecular environments, in particular pertinent to the cytoplasm of the unfertilized egg. Individuality of an organism therefore is not only determined by its genome, but is shaped through developmental processes (it needs time!). Organisms can only exist through mutual interplays with their respective (molecular and cellular) environments at all levels of organization. Thus, life can be conceived of as endless networks of communication, e.g. as a mutual continuum, connecting all individuals, all species and all generations within their given environments. Evolutionarily, nature does not select fitting genes, but rather viable traits. The presented concepts render it unlikely that it was genes that founded our living world, but rather that distinct environments shaped “genes” (of whatever chemical nature) which proved to be “life-suitable”

A Backtracking-Based Algorithm for Computing Hypertree-Decompositions

Hypertree decompositions of hypergraphs are a generalization of tree decompositions of graphs. The corresponding hypertree-width is a measure for the cyclicity and therefore tractability of the encoded computation problem. Many NP-hard decision and computation problems are known to be tractable on instances whose structure corresponds to hypergraphs of bounded hypertree-width. Intuitively, the smaller the hypertree-width, the faster the computation problem can be solved. In this paper, we present the new backtracking-based algorithm det-k-decomp for computing hypertree decompositions of small width. Our benchmark evaluations have shown that det-k-decomp significantly outperforms opt-k-decomp, the only exact hypertree decomposition algorithm so far. Even compared to the best heuristic algorithm, we obtained competitive results as long as the hypergraphs are not too large.Comment: 19 pages, 6 figures, 3 table

The Vadalog System: Datalog-based Reasoning for Knowledge Graphs

Over the past years, there has been a resurgence of Datalog-based systems in the database community as well as in industry. In this context, it has been recognized that to handle the complex knowl\-edge-based scenarios encountered today, such as reasoning over large knowledge graphs, Datalog has to be extended with features such as existential quantification. Yet, Datalog-based reasoning in the presence of existential quantification is in general undecidable. Many efforts have been made to define decidable fragments. Warded Datalog+/- is a very promising one, as it captures PTIME complexity while allowing ontological reasoning. Yet so far, no implementation of Warded Datalog+/- was available. In this paper we present the Vadalog system, a Datalog-based system for performing complex logic reasoning tasks, such as those required in advanced knowledge graphs. The Vadalog system is Oxford's contribution to the VADA research programme, a joint effort of the universities of Oxford, Manchester and Edinburgh and around 20 industrial partners. As the main contribution of this paper, we illustrate the first implementation of Warded Datalog+/-, a high-performance Datalog+/- system utilizing an aggressive termination control strategy. We also provide a comprehensive experimental evaluation.Comment: Extended version of VLDB paper <https://doi.org/10.14778/3213880.3213888

Pure Nash Equilibria: Hard and Easy Games

We investigate complexity issues related to pure Nash equilibria of strategic games. We show that, even in very restrictive settings, determining whether a game has a pure Nash Equilibrium is NP-hard, while deciding whether a game has a strong Nash equilibrium is SigmaP2-complete. We then study practically relevant restrictions that lower the complexity. In particular, we are interested in quantitative and qualitative restrictions of the way each players payoff depends on moves of other players. We say that a game has small neighborhood if the utility function for each player depends only on (the actions of) a logarithmically small number of other players. The dependency structure of a game G can be expressed by a graph DG(G) or by a hypergraph H(G). By relating Nash equilibrium problems to constraint satisfaction problems (CSPs), we show that if G has small neighborhood and if H(G) has bounded hypertree width (or if DG(G) has bounded treewidth), then finding pure Nash and Pareto equilibria is feasible in polynomial time. If the game is graphical, then these problems are LOGCFL-complete and thus in the class NC2 of highly parallelizable problems

Complexity of Nested Circumscription and Nested Abnormality Theories

The need for a circumscriptive formalism that allows for simple yet elegant modular problem representation has led Lifschitz (AIJ, 1995) to introduce nested abnormality theories (NATs) as a tool for modular knowledge representation, tailored for applying circumscription to minimize exceptional circumstances. Abstracting from this particular objective, we propose L_{CIRC}, which is an extension of generic propositional circumscription by allowing propositional combinations and nesting of circumscriptive theories. As shown, NATs are naturally embedded into this language, and are in fact of equal expressive capability. We then analyze the complexity of L_{CIRC} and NATs, and in particular the effect of nesting. The latter is found to be a source of complexity, which climbs the Polynomial Hierarchy as the nesting depth increases and reaches PSPACE-completeness in the general case. We also identify meaningful syntactic fragments of NATs which have lower complexity. In particular, we show that the generalization of Horn circumscription in the NAT framework remains CONP-complete, and that Horn NATs without fixed letters can be efficiently transformed into an equivalent Horn CNF, which implies polynomial solvability of principal reasoning tasks. Finally, we also study extensions of NATs and briefly address the complexity in the first-order case. Our results give insight into the ``cost'' of using L_{CIRC} (resp. NATs) as a host language for expressing other formalisms such as action theories, narratives, or spatial theories.Comment: A preliminary abstract of this paper appeared in Proc. Seventeenth International Joint Conference on Artificial Intelligence (IJCAI-01), pages 169--174. Morgan Kaufmann, 200

Tractable Optimization Problems through Hypergraph-Based Structural Restrictions

Several variants of the Constraint Satisfaction Problem have been proposed and investigated in the literature for modelling those scenarios where solutions are associated with some given costs. Within these frameworks computing an optimal solution is an NP-hard problem in general; yet, when restricted over classes of instances whose constraint interactions can be modelled via (nearly-)acyclic graphs, this problem is known to be solvable in polynomial time. In this paper, larger classes of tractable instances are singled out, by discussing solution approaches based on exploiting hypergraph acyclicity and, more generally, structural decomposition methods, such as (hyper)tree decompositions

Querying the Guarded Fragment

Evaluating a Boolean conjunctive query Q against a guarded first-order theory F is equivalent to checking whether "F and not Q" is unsatisfiable. This problem is relevant to the areas of database theory and description logic. Since Q may not be guarded, well known results about the decidability, complexity, and finite-model property of the guarded fragment do not obviously carry over to conjunctive query answering over guarded theories, and had been left open in general. By investigating finite guarded bisimilar covers of hypergraphs and relational structures, and by substantially generalising Rosati's finite chase, we prove for guarded theories F and (unions of) conjunctive queries Q that (i) Q is true in each model of F iff Q is true in each finite model of F and (ii) determining whether F implies Q is 2EXPTIME-complete. We further show the following results: (iii) the existence of polynomial-size conformal covers of arbitrary hypergraphs; (iv) a new proof of the finite model property of the clique-guarded fragment; (v) the small model property of the guarded fragment with optimal bounds; (vi) a polynomial-time solution to the canonisation problem modulo guarded bisimulation, which yields (vii) a capturing result for guarded bisimulation invariant PTIME.Comment: This is an improved and extended version of the paper of the same title presented at LICS 201