DynASP2.5: Dynamic Programming on Tree Decompositions in Action

Efficient, exact parameterized algorithms are a vibrant theoretical research area. Recent solving competitions, such as the PACE challenge, show that there is also increasing practical interest in the parameterized algorithms community. An important research question is whether such algorithms can be built to efficiently solve specific problems in practice, that is, to be competitive with established solving systems. In this paper, we consider Answer Set Programming (ASP), a logic-based declarative modeling and problem solving framework. State-of-the-art ASP solvers generally rely on SAT-based algorithms. In addition, DynASP2, an ASP solver that is based on a classical dynamic programming on tree decompositions, has recently been introduced. DynASP2 outperforms modern ASP solvers when the goal is to count the number of solutions of programs that have small treewidth. However, for quickly finding one solutions, DynASP2 proved uncompetitive. In this paper, we present a new algorithm and implementation, called DynASP2.5, that shows competitive behavior compared to state-of-the-art ASP solvers on problems like Steiner tree for low-treewidth graphs, even when the task is to find just one solution. Our implementation is based on a novel approach that we call multi-pass dynamic programming

Stable Model Semantics for Tuple-Generating Dependencies Revisited

Normal tuple-generating dependencies (NTGDs) are TGDs enriched with default negation, a.k.a. negation as failure. Query answering under NTGDs, where negation is interpreted according to the stable model semantics, is an intriguing new problem that gave rise to flourishing research activity in the database and KR communities. So far, all the existing works that investigate this problem, except for one recent paper that adopts an operational semantics based on the chase, follow the so-called logic programming (LP) approach. According to the LP approach, the existentially quantified variables are first eliminated via Skolemization, which leads to a normal logic program, and then the standard stable model semantics for normal logic programs is applied. However, as we discuss in the paper, Skolemization is not appropriate in the presence of default negation since it fails to capture the intended meaning of NTGDs, while the operational semantics mentioned above fails to overcome the limitations of the LP approach. This reveals the need to adopt an alternative approach to stable model semantics that is directly applicable to NTGDs with existentially quantified variables. We propose such an approach based on a recent characterization of stable models in terms of second-order logic, which indeed overcomes the limitations of the LP approach. We then perform an in-depth complexity analysis of query answering under prominent classes of NTGDs based on the main decidability paradigms for TGDs, namely weak-acyclicity, guardedness and stickiness. Interestingly, weakly-acyclic NTGDs give rise to robust and highly expressive query languages that allow us to solve in a declarative way problems in the second level of the polynomial hierarchy

Estimating sea surface temperature measurement methods using characteristic differences in the diurnal cycle

Lack of reliable observational metadata represents a key barrier to understanding sea surface temperature (SST) measurement biases, a large contributor to uncertainty in the global surface record. We present a method to identify SST measurement practice by comparing the observed SST diurnal cycle from individual ships with a reference from drifting buoys under similar conditions of wind and solar radiation. Compared to existing estimates, we found a larger number of engine room-intake (ERI) reports post War World II and in the period 1960 – 1980. Differences in the inferred mixture of observations lead to a systematic warmer shift of the bias adjusted SST anomalies from 1980 compared to previous estimates, while reducing the ensemble spread. Changes in mean field differences between bucket and ERI SST anomalies in the Northern Hemisphere over the period 1955 – 1995 could be as large as 0.5 °C and are not well reproduced by current bias adjustment models

The impact of disjunction on reasoning under existential rules

Ontological database management systems are a powerful tool that combine traditional database techniques with ontological reasoning methods. In this setting, a classical extensional database is enriched with an ontology, or a set of logical assertions, that describe how new, intensional knowledge can be derived from the extensional data. Conjunctive queries are therefore answered against this combined knowledge base of extensional and intensional data. Many languages that represent ontologies have been introduced in the literature. In this thesis we will focus on existential rules (also called tuple-generating dependencies or Datalog± rules), and three established languages in this area, namely guarded-based rules, sticky rules and weakly-acyclic rules. The main goal of the thesis is to enrich these languages with non-deterministic constructs (i.e. disjunctions) and investigate the complexity of the answering conjunctive queries under these extended languages. As is common in the literature, we will distinguish between combined complexity, where the database, the ontology and the query are considered as input, and data complexity, where only the database is considered as input. The latter case is relevant in practice, as usually the ontology and the query can be considered as fixed, and are usually much smaller than the database itself. After giving appropriate definitions to extend the considered languages to disjunctive existential rules, we establish a series of complexity results, completing the complexity picture for each of the above languages, and four different query languages: arbitrary conjunctive queries, bounded (hyper-)treewidth queries, acyclic queries and atomic queries. For the guarded-based languages, we show a strong 2EXPTIME lower bound for general queries that holds even for fixed ontologies, and establishes 2EXPTIME-completeness of the query answering problem in this case. For acyclic queries, the complexity can be reduced to EXPTIME, if the predicate arity is bounded, and the problem even becomes tractable for certain restricted languages, if only atomic queries are used. For ontologies represented by sticky disjunctive rules, we show that the problem becomes undecidable, even in the case of data complexity and atomic queries. Finally, for weakly-acyclic rules, we show that the complexity increases from 2EXPTIME to coN2EXPTIME in general, and from tractable to coNP in case of the data complexity, independent of which query language is used. After answering the open complexity questions, we investigate applications and relevant consequences of our results for description logics and give two generic complexity statements, respectively, for acyclic and general conjunctive query answering over description logic knowledge bases. These generic results allow for an easy determination of the complexity of this reasoning task, based on the expressivity of the considered description logic

Association between TAS2R38 gene polymorphisms and colorectal cancer risk

Molecular sensing in the lingual mucosa and in the gastro-intestinal tract play a role in the detection of ingested harmful drugs and toxins. Therefore, genetic polymorphisms affecting the capability of initiating these responses may be critical for the subsequent efficiency of avoiding and/or eliminating possible threats to the organism. By using a tagging approach in the region of Taste Receptor 2R38 (TAS2R38) gene, we investigated all the common genetic variation of this gene region in relation to colorectal cancer risk with a case-control study in a German population (709 controls and 602 cases) and in a Czech population (623 controls and 601 cases). We found that there were no significant associations between individual SNPs of the TAS2R38 gene and colorectal cancer in the Czech or in the German population, nor in the joint analysis. However, when we analyzed the diplotypes and the phenotypes we found that the non-taster group had an increased risk of colorectal cancer in comparison to the taster group. This association was borderline significant in the Czech population, (OR = 1.28, 95% CI 0.99-1.67; P(value) = 0.058) and statistically significant in the German population (OR = 1.36, 95% CI 1.06-1.75; P(value) = 0.016) and in the joint analysis (OR = 1.34, 95% CI 1.12-1.61; P(value) = 0.001). In conclusion, we found a suggestive association between the human bitter tasting phenotype and the risk of CRC in two different populations of Caucasian origin