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Building biological models by inferring functional dependencies from experimental data is an important issue in Molecular Biology. To relieve the biologist from this traditionally manual process, various approaches have been proposed to increase the degree of automation. However, available approaches often yield a single model only, rely on specific assumptions, and/or use dedicated, heuristic algorithms that are intolerant to changing circumstances or requirements in the view of the rapid progress made in Biotechnology. Our aim is to provide a declarative solution to the problem by appeal to Answer Set Programming (ASP) overcoming these difficulties. We build upon an existing approach to Automatic Network Reconstruction proposed by part of the authors. This approach has firm mathematical foundations and is well suited for ASP due to its combinatorial flavor providing a characterization of all models explaining a set of experiments. The usage of ASP has several benefits over the existing heuristic algorithms. First, it is declarative and thus transparent for biological experts. Second, it is elaboration tolerant and thus allows for an easy exploration and incorporation of biological constraints. Third, it allows for exploring the entire space of possible models. Finally, our approach offers an excellent performance, matching existing, special-purpose systems.
Boolean networks (and more general logic models) are useful frameworks to study signal transduction across multiple pathways. Logic models can be learned from a prior knowledge network structure and multiplex phosphoproteomics data. However, most efficient and scalable training methods focus on the comparison of two time-points and assume that the system has reached an early steady state. In this paper, we generalize such a learning procedure to take into account the time series traces of phosphoproteomics data in order to discriminate Boolean networks according to their transient dynamics. To that end, we identify a necessary condition that must be satisfied by the dynamics of a Boolean network to be consistent with a discretized time series trace. Based on this condition, we use Answer Set Programming to compute an over-approximation of the set of Boolean networks which fit best with experimental data and provide the corresponding encodings. Combined with model-checking approaches, we end up with a global learning algorithm. Our approach is able to learn logic models with a true positive rate higher than 78% in two case studies of mammalian signaling networks; for a larger case study, our method provides optimal answers after 7 min of computation. We quantified the gain in our method predictions precision compared to learning approaches based on static data. Finally, as an application, our method proposes erroneous time-points in the time series data with respect to the optimal learned logic models. (C) 2016 Elsevier Ireland Ltd. All rights reserved.
Circumscribing inconsistency
(1997)
claspfolio 2
(2014)
Building on the award-winning, portfolio-based ASP solver claspfolio, we present claspfolio 2, a modular and open solver architecture that integrates several different portfolio-based algorithm selection approaches and techniques. The claspfolio 2 solver framework supports various feature generators, solver selection approaches, solver portfolios, as well as solver-schedule-based pre-solving techniques. The default configuration of claspfolio 2 relies on a light-weight version of the ASP solver clasp to generate static and dynamic instance features. The flexible open design of claspfolio 2 is a distinguishing factor even beyond ASP. As such, it provides a unique framework for comparing and combining existing portfolio-based algorithm selection approaches and techniques in a single, unified framework. Taking advantage of this, we conducted an extensive experimental study to assess the impact of different feature sets, selection approaches and base solver portfolios. In addition to gaining substantial insights into the utility of the various approaches and techniques, we identified a default configuration of claspfolio 2 that achieves substantial performance gains not only over clasp's default configuration and the earlier version of claspfolio, but also over manually tuned configurations of clasp.
claspfolio 2
(2014)
Building on the award-winning, portfolio-based ASP solver claspfolio, we present claspfolio 2, a modular and open solver architecture that integrates several different portfolio-based algorithm selection approaches and techniques. The claspfolio 2 solver framework supports various feature generators, solver selection approaches, solver portfolios, as well as solver-schedule-based pre-solving techniques. The default configuration of claspfolio 2 relies on a light-weight version of the ASP solver clasp to generate static and dynamic instance features. The flexible open design of claspfolio 2 is a distinguishing factor even beyond ASP. As such, it provides a unique framework for comparing and combining existing portfolio-based algorithm selection approaches and techniques in a single, unified framework. Taking advantage of this, we conducted an extensive experimental study to assess the impact of different feature sets, selection approaches and base solver portfolios. In addition to gaining substantial insights into the utility of the various approaches and techniques, we identified a default configuration of claspfolio 2 that achieves substantial performance gains not only over clasp's default configuration and the earlier version of claspfolio, but also over manually tuned configurations of clasp.
The recent series 5 of the Answer Set Programming (ASP) system clingo provides generic means to enhance basic ASP with theory reasoning capabilities. We instantiate this framework with different forms of linear constraints and elaborate upon its formal properties. Given this, we discuss the respective implementations, and present techniques for using these constraints in a reactive context. More precisely, we introduce extensions to clingo with difference and linear constraints over integers and reals, respectively, and realize them in complementary ways. Finally, we empirically evaluate the resulting clingo derivatives clingo[dl] and clingo[lp] on common language fragments and contrast them to related ASP systems.
Preference handling and optimization are indispensable means for addressing nontrivial applications in Answer Set Programming (ASP). However, their implementation becomes difficult whenever they bring about a significant increase in computational complexity. As a consequence, existing ASP systems do not offer complex optimization capacities, supporting, for instance, inclusion-based minimization or Pareto efficiency. Rather, such complex criteria are typically addressed by resorting to dedicated modeling techniques, like saturation. Unlike the ease of common ASP modeling, however, these techniques are rather involved and hardly usable by ASP laymen. We address this problem by developing a general implementation technique by means of meta-prpogramming, thus reusing existing ASP systems to capture various forms of qualitative preferences among answer sets. In this way, complex preferences and optimization capacities become readily available for ASP applications.
Preference handling and optimization are indispensable means for addressing nontrivial applications in Answer Set Programming (ASP). However, their implementation becomes difficult whenever they bring about a significant increase in computational complexity. As a consequence, existing ASP systems do not offer complex optimization capacities, supporting, for instance, inclusion-based minimization or Pareto efficiency. Rather, such complex criteria are typically addressed by resorting to dedicated modeling techniques, like saturation. Unlike the ease of common ASP modeling, however, these techniques are rather involved and hardly usable by ASP laymen. We address this problem by developing a general implementation technique by means of meta-prpogramming, thus reusing existing ASP systems to capture various forms of qualitative preferences among answer sets. In this way, complex preferences and optimization capacities become readily available for ASP applications.
Compressions and extensions
(1998)
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 introduce an approach to computing answer sets of logic programs, based on concepts successfully applied in Satisfiability (SAT) checking. The idea is to view inferences in Answer Set Programming (ASP) as unit propagation on nogoods. This provides us with a uniform constraint-based framework capturing diverse inferences encountered in ASP solving. Moreover, our approach allows us to apply advanced solving techniques from the area of SAT. As a result, we present the first full-fledged algorithmic framework for native conflict-driven ASP solving. Our approach is implemented in the ASP solver clasp that has demonstrated its competitiveness and versatility by winning first places at various solver contests.
The aim of our project design space exploration with answer set programming is to develop a general framework based on Answer Set Programming (ASP) that finds valid solutions to the system design problem and simultaneously performs Design Space Exploration (DSE) to find the most favorable alternatives. We leverage recent developments in ASP solving that allow for tight integration of background theories to create a holistic framework for effective DSE.
We introduce an approach to detecting inconsistencies in large biological networks by using answer set programming. To this end, we build upon a recently proposed notion of consistency between biochemical/genetic reactions and high-throughput profiles of cell activity. We then present an approach based on answer set programming to check the consistency of large-scale data sets. Moreover, we extend this methodology to provide explanations for inconsistencies by determining minimal representations of conflicts. In practice, this can be used to identify unreliable data or to indicate missing reactions.
We introduce an approach to detecting inconsistencies in large biological networks by using answer set programming. To this end, we build upon a recently proposed notion of consistency between biochemical/genetic reactions and high-throughput profiles of cell activity. We then present an approach based on answer set programming to check the consistency of large-scale data sets. Moreover, we extend this methodology to provide explanations for inconsistencies by determining minimal representations of conflicts. In practice, this can be used to identify unreliable data or to indicate missing reactions.
Eclingo
(2020)
We describe eclingo, a solver for epistemic logic programs under Gelfond 1991 semantics built upon the Answer Set Programming system clingo. The input language of eclingo uses the syntax extension capabilities of clingo to define subjective literals that, as usual in epistemic logic programs, allow for checking the truth of a regular literal in all or in some of the answer sets of a program. The eclingo solving process follows a guess and check strategy. It first generates potential truth values for subjective literals and, in a second step, it checks the obtained result with respect to the cautious and brave consequences of the program. This process is implemented using the multi-shot functionalities of clingo. We have also implemented some optimisations, aiming at reducing the search space and, therefore, increasing eclingo 's efficiency in some scenarios. Finally, we compare the efficiency of eclingo with two state-of-the-art solvers for epistemic logic programs on a pair of benchmark scenarios and show that eclingo generally outperforms their obtained results.
The design of embedded systems is becoming continuously more complex such that efficient system-level design methods are becoming crucial. Recently, combined Answer Set Programming (ASP) and Quantifier Free Integer Difference Logic (QF-IDL) solving has been shown to be a promising approach in system synthesis. However, this approach still has several restrictions limiting its applicability. In the paper at hand, we propose a novel ASP modulo Theories (ASPmT) system synthesis approach, which (i) supports more sophisticated system models, (ii) tightly integrates the QF-IDL solving into the ASP solving, and (iii) makes use of partial assignment checking. As a result, more realistic systems are considered and an early exclusion of infeasible solutions improves the entire system synthesis.
An efficient Design Space Exploration (DSE) is imperative for the design of modern, highly complex embedded systems in order to steer the development towards optimal design points. The early evaluation of design decisions at system-level abstraction layer helps to find promising regions for subsequent development steps in lower abstraction levels by diminishing the complexity of the search problem. In recent works, symbolic techniques, especially Answer Set Programming (ASP) modulo Theories (ASPmT), have been shown to find feasible solutions of highly complex system-level synthesis problems with non-linear constraints very efficiently. In this paper, we present a novel approach to a holistic system-level DSE based on ASPmT. To this end, we include additional background theories that concurrently guarantee compliance with hard constraints and perform the simultaneous optimization of several design objectives. We implement and compare our approach with a state-of-the-art preference handling framework for ASP. Experimental results indicate that our proposed method produces better solutions with respect to both diversity and convergence to the true Pareto front.
We introduce the asprilo1 framework to facilitate experimental studies of approaches addressing complex dynamic applications. For this purpose, we have chosen the domain of robotic intra-logistics. This domain is not only highly relevant in the context of today's fourth industrial revolution but it moreover combines a multitude of challenging issues within a single uniform framework. This includes multi-agent planning, reasoning about action, change, resources, strategies, etc. In return, asprilo allows users to study alternative solutions as regards effectiveness and scalability. Although asprilo relies on Answer Set Programming and Python, it is readily usable by any system complying with its fact-oriented interface format. This makes it attractive for benchmarking and teaching well beyond logic programming. More precisely, asprilo consists of a versatile benchmark generator, solution checker and visualizer as well as a bunch of reference encodings featuring various ASP techniques. Importantly, the visualizer's animation capabilities are indispensable for complex scenarios like intra-logistics in order to inspect valid as well as invalid solution candidates. Also, it allows for graphically editing benchmark layouts that can be used as a basis for generating benchmark suites.
Reiter's default logic is one of the best known and most studied of the approaches to nonmonotonic reasoning. Several variants of default logic have subsequently been proposed to give systems with properties differing from the original. In this paper, we examine the relationship between default logic and its major variants. We accomplish this by translating a default theory under a variant interpretation into a second default theory, under the original Reiter semantics, wherein the variant interpretation is respected. That is, in each case we show that, given an extension of a translated theory, one may extract an extension of the original variant default logic theory. We show how constrained, rational, justified, and cumulative default logic can be expressed in Reiter's default logic. As well, we show how Reiter's default logic can be expressed in rational default logic. From this, we suggest that any such variant can be similarly treated. Consequently, we provide a unification of default logics, showing how the original formulation of default logic may express its variants. Moreover, the translations clearly express the relationships between alternative approaches to default logic. The translations themselves are shown to generally have good properties. Thus, in at least a theoretical sense, we show that these variants are in a sense superfluous, in that for any of these variants of default logic, we can exactly mimic the behaviour of a variant in standard default logic. As well, the translations lend insight into means of classifying the expressive power of default logic variants; specifically we suggest that the property of semi-monotonicity represents a division with respect to expressibility, whereas regularity and cumulativity do not
Answer Set Programming (ASP) has become a popular and widespread paradigm for practical Knowledge Representation thanks to its expressiveness and the available enhancements of its input language. One of such enhancements is the use of aggregates, for which different semantic proposals have been made. In this paper, we show that any ASP aggregate interpreted under Gelfond and Zhang's (GZ) semantics can be replaced (under strong equivalence) by a propositional formula. Restricted to the original GZ syntax, the resulting formula is reducible to a disjunction of conjunctions of literals but the formulation is still applicable even when the syntax is extended to allow for arbitrary formulas (including nested aggregates) in the condition. Once GZ-aggregates are represented as formulas, we establish a formal comparison (in terms of the logic of Here-and-There) to Ferraris' (F) aggregates, which are defined by a different formula translation involving nested implications. In particular, we prove that if we replace an F-aggregate by a GZ-aggregate in a rule head, we do not lose answer sets (although more can be gained). This extends the previously known result that the opposite happens in rule bodies, i.e., replacing a GZ-aggregate by an F-aggregate in the body may yield more answer sets. Finally, we characterize a class of aggregates for which GZ- and F-semantics coincide.
We investigate the usage of rule dependency graphs and their colorings for characterizing and computing answer sets of logic programs. This approach provides us with insights into the interplay between rules when inducing answer sets. We start with different characterizations of answer sets in terms of totally colored dependency graphs that differ ill graph-theoretical aspects. We then develop a series of operational characterizations of answer sets in terms of operators on partial colorings. In analogy to the notion of a derivation in proof theory, our operational characterizations are expressed as (non-deterministically formed) sequences of colorings, turning an uncolored graph into a totally colored one. In this way, we obtain an operational framework in which different combinations of operators result in different formal properties. Among others, we identify the basic strategy employed by the noMoRe system and justify its algorithmic approach. Furthermore, we distinguish operations corresponding to Fitting's operator as well as to well-founded semantics
The integration of preferences into answer set programming constitutes an important practical device for distinguishing certain preferred answer sets from non-preferred ones. To this end, we elaborate upon rule dependency graphs and their colorings for characterizing different preference handling strategies found in the literature. We start from a characterization of (three types of) preferred answer sets in terms of totally colored dependency graphs. In particular, we demonstrate that this approach allows us to capture all three approaches to preferences in a uniform setting by means of the concept of a height function. In turn, we exemplarily develop an operational characterization of preferred answer sets in terms of operators on partial colorings for one particular strategy. In analogy to the notion of a derivation in proof theory, our operational characterization is expressed as a (non-deterministically formed) sequence of colorings, gradually turning an uncolored graph into a totally colored one