Structure-activity relationships derived by machine learning: the use of atoms and their bond connectivities to predict mutagenicity by inductive logic programming.

We present a general approach to forming structure-activity relationships (SARs). This approach is based on representing chemical structure by atoms and their bond connectivities in combination with the inductive logic programming (ILP) algorithm PROGOL. Existing SAR methods describe chemical structure by using attributes which are general properties of an object. It is not possible to map chemical structure directly to attribute-based descriptions, as such descriptions have no internal organization. A more natural and general way to describe chemical structure is to use a relational description, where the internal construction of the description maps that of the object described. Our atom and bond connectivities representation is a relational description. ILP algorithms can form SARs with relational descriptions. We have tested the relational approach by investigating the SARs of 230 aromatic and heteroaromatic nitro compounds. These compounds had been split previously into two subsets, 188 compounds that were amenable to regression and 42 that were not. For the 188 compounds, a SAR was found that was as accurate as the best statistical or neural network-generated SARs. The PROGOL SAR has the advantages that it did not need the use of any indicator variables handcrafted by an expert, and the generated rules were easily comprehensible. For the 42 compounds, PROGOL formed a SAR that was significantly (P < 0.025) more accurate than linear regression, quadratic regression, and back-propagation. This SAR is based on an automatically generated structural alert for mutagenicity.

Synthesis of optimal double-rail logic networks using NOR-OR gates by integer programming.

"Supported in part by ... Grant no. NSF GJ-503."

Embedding defeasible logic into logic programming

Defeasible reasoning is a simple but efficient approach to nonmonotonic reasoning that has recently attracted considerable interest and that has found various applications. Defeasible logic and its variants are an important family of defeasible reasoning methods. So far no relationship has been established between defeasible logic and mainstream nonmonotonic reasoning approaches. In this paper we establish close links to known semantics of logic programs. In particular, we give a translation of a defeasible theory D into a meta-program P(D). We show that under a condition of decisiveness, the defeasible consequences of D correspond exactly to the sceptical conclusions of P(D) under the stable model semantics. Without decisiveness, the result holds only in one direction (all defeasible consequences of D are included in all stable models of P(D)). If we wish a complete embedding for the general case, we need to use the Kunen semantics of P(D), instead.

On the Equivalence between Assumption-Based Argumentation and Logic Programming

Postprint

Constraint-Informed Information Systems in Space Management Utilization

Declarative techniques such as Constraint Programming can be very effective in modeling and assisting management decisions. We present a method for managing university classrooms which extends the previous design of a Constraint-Informed Information System to generate the timetables while dealing with spatial resource optimization issues. We seek to maximize space utilization along two dimensions: classroom use and occupancy rates. While we want to maximize the room use rate, we still need to satisfy the soft constraints which model students’ and lecturers’ preferences. We present a constraint logic programming-based local search method which relies on an evaluation function that combines room utilization and timetable soft preferences. Based on this, we developed a tool which we applied to the improvement of classroom allocation in a University. Comparing the results to the current timetables obtained without optimizing space utilization, the initial versions of our tool manages to reach a 30% improvement in space utilization, while preserving the quality of the timetable, both for students and lecturers.

Rough Notes on Programming AVR Microcontrollers in C

These notes follow on from the material that you studied in CSSE1000 Introduction to Computer Systems. There you studied details of logic gates, binary numbers and instruction set architectures using the Atmel AVR microcontroller family as an example. In your present course (METR2800 Team Project I), you need to get on to designing and building an application which will include such a microcontroller. These notes focus on programming an AVR microcontroller in C and provide a number of example programs to illustrate the use of some of the AVR peripheral devices.

DR-NEGOTIATE - A system for automated agent negotiation with defeasible logic-based strategies

This paper reports on a system for automated agent negotiation, based on a formal and executable approach to capture the behavior of parties involved in a negotiation. It uses the JADE agent framework, and its major distinctive feature is the use of declarative negotiation strategies. The negotiation strategies are expressed in a declarative rules language, defeasible logic, and are applied using the implemented system DR-DEVICE. The key ideas and the overall system architecture are described, and a particular negotiation case is presented in detail.

Scheduling maintenance activities of electric power transmission networks using an hybrid constraint method

In this paper we present a Constraint Logic Programming (CLP) based model, and hybrid solving method for the Scheduling of Maintenance Activities in the Power Transmission Network. The model distinguishes from others not only because of its completeness but also by the way it models and solves the Electric Constraints. Specifically we present a efficient filtering algorithm for the Electrical Constraints. Furthermore, the solving method improves the pure CLP methods efficiency by integrating a type of Local Search technique with CLP. To test the approach we compare the method results with another method using a 24 bus network, which considerers 42 tasks and 24 maintenance periods.

Group decision making and Quality-of-information in e-Health systems

Knowledge is central to the modern economy and society. Indeed, the knowledge society has transformed the concept of knowledge and is more and more aware of the need to overcome the lack of knowledge when has to make options or address its problems and dilemmas. One’s knowledge is less based on exact facts and more on hypotheses, perceptions or indications. Even when we use new computational artefacts and novel methodologies for problem solving, like the use of Group Decision Support Systems (GDSSs), the question of incomplete information is in most of the situations marginalized. On the other hand, common sense tells us that when a decision is made it is impossible to have a perception of all the information involved and the nature of its intrinsic quality. Therefore, something has to be made in terms of the information available and the process of its evaluation. It is under this framework that a Multi-valued Extended Logic Programming language will be used for knowledge representation and reasoning, leading to a model that embodies the Quality-of-Information (QoI) and its quantification, along the several stages of the decision-making process. In this way, it is possible to provide a measure of the value of the QoI that supports the decision itself. This model will be here presented in the context of a GDSS for VirtualECare, a system aimed at sustaining online healthcare services.

Logic-based schedulability analysis for compositional hard real-time embedded systems

Over the past decades several approaches for schedulability analysis have been proposed for both uni-processor and multi-processor real-time systems. Although different techniques are employed, very little has been put forward in using formal specifications, with the consequent possibility for mis-interpretations or ambiguities in the problem statement. Using a logic based approach to schedulability analysis in the design of hard real-time systems eases the synthesis of correct-by-construction procedures for both static and dynamic verification processes. In this paper we propose a novel approach to schedulability analysis based on a timed temporal logic with time durations. Our approach subsumes classical methods for uni-processor scheduling analysis over compositional resource models by providing the developer with counter-examples, and by ruling out schedules that cause unsafe violations on the system. We also provide an example showing the effectiveness of our proposal.

Constraint-based verification of imperative programs

work presented in the context of the European Master’s program in Computational Logic, as the partial requirement for obtaining Master of Science degree in Computational Logic

A bio-inspired agent-based programming environment for pervasive platforms

Abstract in English : Ubiquitous Computing is the emerging trend in computing systems. Based on this observation this thesis proposes an analysis of the hardware and environmental constraints that rule pervasive platforms. These constraints have a strong impact on the programming of such platforms. Therefore solutions are proposed to facilitate this programming both at the platform and node levels. The first contribution presented in this document proposes a combination of agentoriented programming with the principles of bio-inspiration (Phylogenesys, Ontogenesys and Epigenesys) to program pervasive platforms such as the PERvasive computing framework for modeling comPLEX virtually Unbounded Systems platform. The second contribution proposes a method to program efficiently parallelizable applications on each computing node of this platform. Résumé en Français : Basée sur le constat que les calculs ubiquitaires vont devenir le paradigme de programmation dans les années à venir, cette thèse propose une analyse des contraintes matérielles et environnementale auxquelles sont soumises les plateformes pervasives. Ces contraintes ayant un impact fort sur la programmation des plateformes. Des solutions sont donc proposées pour faciliter cette programmation tant au niveau de l'ensemble des noeuds qu'au niveau de chacun des noeuds de la plateforme. La première contribution présentée dans ce document propose d'utiliser une alliance de programmation orientée agent avec les grands principes de la bio-inspiration (Phylogénèse, Ontogénèse et Épigénèse). Ceci pour répondres aux contraintes de programmation de plateformes pervasives comme la plateforme PERvasive computing framework for modeling comPLEX virtually Unbounded Systems . La seconde contribution propose quant à elle une méthode permettant de programmer efficacement des applications parallélisable sur chaque noeud de calcul de la plateforme

Modeling small-scale dairy farms in central Mexico using multi-criteria programming

Milk supply from Mexican dairy farms does not meet demand and small-scale farms can contribute toward closing the gap. Two multi-criteria programming techniques, goal programming and compromise programming, were used in a study of small-scale dairy farms in central Mexico. To build the goal and compromise programming models, 4 ordinary linear programming models were also developed, which had objective functions to maximize metabolizable energy for milk production, to maximize margin of income over feed costs, to maximize metabolizable protein for milk production, and to minimize purchased feedstuffs. Neither multicriteria approach was significantly better than the other; however, by applying both models it was possible to perform a more comprehensive analysis of these small-scale dairy systems. The multi-criteria programming models affirm findings from previous work and suggest that a forage strategy based on alfalfa, rye-grass, and corn silage would meet nutrient requirements of the herd. Both models suggested that there is an economic advantage in rescheduling the calving season to the second and third calendar quarters to better synchronize higher demand for nutrients with the period of high forage availability.

Web-based occupant feedback for building energy management systems using fuzzy logic

This paper describes the development and validation of a novel web-based interface for the gathering of feedback from building occupants about their environmental discomfort including signs of Sick Building Syndrome (SBS). The gathering of such feedback may enable better targeting of environmental discomfort down to the individual as well as the early detection and subsequently resolution by building services of more complex issues such as SBS. The occupant's discomfort is interpreted and converted to air-conditioning system set points using Fuzzy Logic. Experimental results from a multi-zone air-conditioning test rig have been included in this paper.

Using adaptive automata in a multi-paradigm programming environment

In this paper the architecture of an experimental multiparadigmatic programming environment is sketched, showing how its parts combine together with application modules in order to perform the integration of program modules written in different programming languages and paradigms. Adaptive automata are special self-modifying formal state machines used as a design and implementation tool in the representation of complex systems. Adaptive automata have been proven to have the same formal power as Turing Machines. Therefore, at least in theory, arbitrarily complex systems may be modeled with adaptive automata. The present work briefly introduces such formal tool and presents case studies showing how to use them in two very different situations: the first one, in the name management module of a multi-paradigmatic and multi-language programming environment, and the second one, in an application program implementing an adaptive automaton that accepts a context-sensitive language.