BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.

The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHackathons hosted in Japan for the past five years. Here we provide a review of the activities and outcomes from the BioHackathons held in 2011 in Kyoto and 2012 in Toyama. In order to efficiently implement semantic technologies in the life sciences, participants formed various sub-groups and worked on the following topics: Resource Description Framework (RDF) models for specific domains, text mining of the literature, ontology development, essential metadata for biological databases, platforms to enable efficient Semantic Web technology development and interoperability, and the development of applications for Semantic Web data. In this review, we briefly introduce the themes covered by these sub-groups. The observations made, conclusions drawn, and software development projects that emerged from these activities are discussed.

A blackboard architecture for a hybrid CBR system for scientific software

This paper describes the use of a blackboard architecture for building a hybrid case based reasoning (CBR) system. The Smartfire fire field modelling package has been built using this architecture and includes a CBR component. It allows the integration into the system of qualitative spatial reasoning knowledge from domain experts. The system can be used for the automatic set-up of fire field models. This enables fire safety practitioners who are not expert in modelling techniques to use a fire modelling tool. The paper discusses the integrating powers of the architecture, which is based on a common knowledge representation comprising a metric diagram and place vocabulary and mechanisms for adaptation and conflict resolution built on the Blackboard.

Incremental learning from stream data

Recent years have witnessed an incredibly increasing interest in the topic of incremental learning. Unlike conventional machine learning situations, data flow targeted by incremental learning becomes available continuously over time. Accordingly, it is desirable to be able to abandon the traditional assumption of the availability of representative training data during the training period to develop decision boundaries. Under scenarios of continuous data flow, the challenge is how to transform the vast amount of stream raw data into information and knowledge representation, and accumulate experience over time to support future decision-making process. In this paper, we propose a general adaptive incremental learning framework named ADAIN that is capable of learning from continuous raw data, accumulating experience over time, and using such knowledge to improve future learning and prediction performance. Detailed system level architecture and design strategies are presented in this paper. Simulation results over several real-world data sets are used to validate the effectiveness of this method.

Communicating open systems

Just as conventional institutions are organisational structures for coordinating the activities of multiple interacting individuals, electronic institutions provide a computational analogue for coordinating the activities of multiple interacting software agents. In this paper, we argue that open multi-agent systems can be effectively designed and implemented as electronic institutions, for which we provide a comprehensive computational model. More specifically, the paper provides an operational semantics for electronic institutions, specifying the essential data structures, the state representation and the key operations necessary to implement them. We specify the agent workflow structure that is the core component of such electronic institutions and particular instantiations of knowledge representation languages that support the institutional model. In so doing, we provide the first formal account of the electronic institution concept in a rigorous and unambiguous way.

Assembling a consistent set of sentences in relational probabilistic logic with stochastic independence

We examine the representation of judgements of stochastic independence in probabilistic logics. We focus on a relational logic where (i) judgements of stochastic independence are encoded by directed acyclic graphs, and (ii) probabilistic assessments are flexible in the sense that they are not required to specify a single probability measure. We discuss issues of knowledge representation and inference that arise from our particular combination of graphs, stochastic independence, logical formulas and probabilistic assessments.

Revising Partial Pre-Orders with Partial Pre-Orders: A Unit-Based Revision Framework

Belief revision studies strategies about how agents revise their belief states when receiving new evidence. Both in classical belief revision and in epistemic revision, a new input is either in the form of a (weighted) propositional formula or a total
pre-order (where the total pre-order is considered as a whole).
However, in some real-world applications, a new input can be a partial pre-order where each unit that constitutes the partial pre-order is important and should be considered individually. To address this issue, in this paper, we study how a partial preorder representing the prior epistemic state can be revised by another partial pre-order (the new input) from a different perspective, where the revision is conducted recursively on the individual units of partial pre-orders. We propose different revision operators (rules), dubbed the extension, match, inner and outer revision operators, from different revision points of view. We also analyze several properties for these operators.

Exact and heuristic methods for solving Boolean games

Boolean games are a framework for reasoning about the rational behavior of agents whose goals are formalized using propositional formulas. Compared to normal form games, a well-studied and related game framework, Boolean games allow for an intuitive and more compact representation of the agents’ goals. So far, Boolean games have been mainly studied in the literature from the Knowledge Representation perspective, and less attention has been paid on the algorithmic issues underlying the computation of solution concepts. Although some suggestions for solving specific classes of Boolean games have been made in the literature, there is currently no work available on the practical performance. In this paper, we propose the first technique to solve general Boolean games that does not require an exponential translation to normal-form games. Our method is based on disjunctive answer set programming and computes solutions (equilibria) of arbitrary Boolean games. It can be applied to a wide variety of solution concepts, and can naturally deal with extensions of Boolean games such as constraints and costs. We present detailed experimental results in which we compare the proposed method against a number of existing methods for solving specific classes of Boolean games, as well as adaptations of methods that were initially designed for normal-form games. We found that the heuristic methods that do not require all payoff matrix entries performed well for smaller Boolean games, while our ASP based technique is faster when the problem instances have a higher number of agents or action variables.

Using Answer Set Programming for Solving Boolean Games

Boolean games are a framework for reasoning about the rational behaviour of agents, whose goals are formalized using propositional formulas. They offer an attractive alternative to normal-form games, because they allow for a more intuitive and more compact encoding. Unfortunately, however, there is currently no general, tailor-made method available to compute the equilibria of Boolean games. In this paper, we introduce a method for finding the pure Nash equilibria based on disjunctive answer set programming. Our method is furthermore capable of finding the core elements and the Pareto optimal equilibria, and can easily be modified to support other forms of optimality, thanks to the declarative nature of disjunctive answer set programming. Experimental results clearly demonstrate the effectiveness of the proposed method.

Logic Programming and Artificial Neural Networks in Pharmacological Screening of Schinus Essential Oils

Some plants of genus Schinus have been used in the folk medicine as topical antiseptic, digestive, purgative, diuretic, analgesic or antidepressant, and also for respiratory and urinary infections. Chemical composition of essential oils of S. molle and S. terebinthifolius had been evaluated and presented high variability according with the part of the plant studied and with the geographic and climatic regions. The pharmacological properties, namely antimicrobial, anti-tumoural and anti-inflammatory activities are conditioned by chemical composition of essential oils. Taking into account the difficulty to infer the pharmacological properties of Schinus essential oils without hard experimental approach, this work will focus on the development of a decision support system, in terms of its knowledge representation and reasoning procedures, under a formal framework based on Logic Programming, complemented with an approach to computing centered on Artificial Neural Networks and the respective Degree-of-Confidence that one has on such an occurrence.

Terminologia e ontologias : metodologias para representação do conhecimento

Discute-se na presente dissertação as metodologias de representação do conhecimento que podem ser utilizadas em terminologia na construção de ontologias. Através da análise de duas abordagens terminológicas – semasiologia e onomasiologia – observa-se o estatuto do texto de especialidade sob um ponto de vista teórico e prático, questionando-se a sua importância e o contributo do terminólogo e do especialista na captura de conhecimento enquanto especificação informal de uma conceptualização.

Training control centers' operators in incident diagnosis and power restoration using intelligent tutoring systems

The activity of Control Center operators is important to guarantee the effective performance of Power Systems. Operators’ actions are crucial to deal with incidents, especially severe faults like blackouts. In this paper, we present an Intelligent Tutoring approach for training Portuguese Control Center operators in tasks like incident analysis and diagnosis, and service restoration of Power Systems. Intelligent Tutoring System (ITS) approach is used in the training of the operators, having into account context awareness and the unobtrusive integration in the working environment. Several Artificial Intelligence techniques were criteriously used and combined together to obtain an effective Intelligent Tutoring environment, namely Multiagent Systems, Neural Networks, Constraint-based Modeling, Intelligent Planning, Knowledge Representation, Expert Systems, User Modeling, and Intelligent User Interfaces.

Attribute exploration with background implications and exceptions

Implications between attributes can represent knowledge about objects in a specified context. This knowledge representation is especially useful when it is not possible to list all specified objects. Attribute exploration is a tool of formal concept analysis that supports the acquisition of this knowledge. For a specified context this interactive procedure determines a miminal list of valid implications between attributes of this context together with a list of objects which are counterexamples for all implications not valid in the context. This paper describes how the exploration can be modified such that it determines a mimimal set of implications that fills the gap between previously given implications (called background implications) and all valid implications. The list of implications can be simplified further if exceptions are allowed for the implications.

Intelligent structuring and reducing of association rules with formal concept analysis

Association rules are used to investigate large databases. The analyst is usually confronted with large lists of such rules and has to find the most relevant ones for his purpose. Based on results about knowledge representation within the theoretical framework of Formal Concept Analysis, we present relatively small bases for association rules from which all rules can be deduced. We also provide algorithms for their calculation.

Off to new shores

In the last years, the main orientation of Formal Concept Analysis (FCA) has turned from mathematics towards computer science. This article provides a review of this new orientation and analyzes why and how FCA and computer science attracted each other. It discusses FCA as a knowledge representation formalism using five knowledge representation principles provided by Davis, Shrobe, and Szolovits [DSS93]. It then studies how and why mathematics-based researchers got attracted by computer science. We will argue for continuing this trend by integrating the two research areas FCA and Ontology Engineering. The second part of the article discusses three lines of research which witness the new orientation of Formal Concept Analysis: FCA as a conceptual clustering technique and its application for supporting the merging of ontologies; the efficient computation of association rules and the structuring of the results; and the visualization and management of conceptual hierarchies and ontologies including its application in an email management system.

Automated Reasoning About Classical Mechanics

In recent years, researchers in artificial intelligence have become interested in replicating human physical reasoning talents in computers. One of the most important skills in this area is predicting how physical systems will behave. This thesis discusses an implemented program that generates algebraic descriptions of how systems of rigid bodies evolve over time. Discussion about the design of this program identifies a physical reasoning paradigm and knowledge representation approach based on mathematical model construction and algebraic reasoning. This paradigm offers several advantages over methods that have become popular in the field, and seems promising for reasoning about a wide variety of classical mechanics problems.