Attribute Exploration of Gene Regulatory Processes

This thesis aims at the logical analysis of discrete processes, in particular of such generated by gene regulatory networks. States, transitions and operators from temporal logics are expressed in the language of Formal Concept Analysis. By the attribute exploration algorithm, an expert or a computer program is enabled to validate a minimal and complete set of implications, e.g. by comparison of predictions derived from literature with observed data. Here, these rules represent temporal dependencies within gene regulatory networks including coexpression of genes, reachability of states, invariants or possible causal relationships. This new approach is embedded into the theory of universal coalgebras, particularly automata, Kripke structures and Labelled Transition Systems. A comparison with the temporal expressivity of Description Logics is made. The main theoretical results concern the integration of background knowledge into the successive exploration of the defined data structures (formal contexts). Applying the method a Boolean network from literature modelling sporulation of Bacillus subtilis is examined. Finally, we developed an asynchronous Boolean network for extracellular matrix formation and destruction in the context of rheumatoid arthritis.Comment: 111 pages, 9 figures, file size 2.1 MB, PhD thesis University of Jena, Germany, Faculty of Mathematics and Computer Science, 2011. Online available at http://www.db-thueringen.de/servlets/DocumentServlet?id=1960

Obtaining Formal Models through Non-Monotonic Refinement

When designing a model for formal verification, we want to\ud be certain that what we proved about the model also holds for the system we modelled. This raises the question of whether our model represents the system, and what makes us confident about this. By performing so called, non-monotonic refinement in the modelling process, we make the steps and decisions explicit. This helps us to (1) increase the confidence that the model represents the system, (2) structure and organize the communication with domain experts and the problem owner, and (3) identify rational steps made while modelling. We focus on embedded control systems

Conceptual graph-based knowledge representation for supporting reasoning in African traditional medicine

Although African patients use both conventional or modern and traditional healthcare simultaneously, it has been proven that 80% of people rely on African traditional medicine (ATM). ATM includes medical activities stemming from practices, customs and traditions which were integral to the distinctive African cultures. It is based mainly on the oral transfer of knowledge, with the risk of losing critical knowledge. Moreover, practices differ according to the regions and the availability of medicinal plants. Therefore, it is necessary to compile tacit, disseminated and complex knowledge from various Tradi-Practitioners (TP) in order to determine interesting patterns for treating a given disease. Knowledge engineering methods for traditional medicine are useful to model suitably complex information needs, formalize knowledge of domain experts and highlight the effective practices for their integration to conventional medicine. The work described in this paper presents an approach which addresses two issues. First it aims at proposing a formal representation model of ATM knowledge and practices to facilitate their sharing and reusing. Then, it aims at providing a visual reasoning mechanism for selecting best available procedures and medicinal plants to treat diseases. The approach is based on the use of the Delphi method for capturing knowledge from various experts which necessitate reaching a consensus. Conceptual graph formalism is used to model ATM knowledge with visual reasoning capabilities and processes. The nested conceptual graphs are used to visually express the semantic meaning of Computational Tree Logic (CTL) constructs that are useful for formal specification of temporal properties of ATM domain knowledge. Our approach presents the advantage of mitigating knowledge loss with conceptual development assistance to improve the quality of ATM care (medical diagnosis and therapeutics), but also patient safety (drug monitoring)

The VEX-93 environment as a hybrid tool for developing knowledge systems with different problem solving techniques

The paper describes VEX-93 as a hybrid environment for developing knowledge-based and problem solver systems. It integrates methods and techniques from artificial intelligence, image and signal processing and data analysis, which can be mixed. Two hierarchical levels of reasoning contains an intelligent toolbox with one upper strategic inference engine and four lower ones containing specific reasoning models: truth-functional (rule-based), probabilistic (causal networks), fuzzy (rule-based) and case-based (frames). There are image/signal processing-analysis capabilities in the form of programming languages with more than one hundred primitive functions. User-made programs are embeddable within knowledge basis, allowing the combination of perception and reasoning. The data analyzer toolbox contains a collection of numerical classification, pattern recognition and ordination methods, with neural network tools and a data base query language at inference engines's disposal. VEX-93 is an open system able to communicate with external computer programs relevant to a particular application. Metaknowledge can be used for elaborate conclusions, and man-machine interaction includes, besides windows and graphical interfaces, acceptance of voice commands and production of speech output. The system was conceived for real-world applications in general domains, but an example of a concrete medical diagnostic support system at present under completion as a cuban-spanish project is mentioned. Present version of VEX-93 is a huge system composed by about one and half millions of lines of C code and runs in microcomputers under Windows 3.1.Postprint (published version

Continuous Improvement Through Knowledge-Guided Analysis in Experience Feedback

Continuous improvement in industrial processes is increasingly a key element of competitiveness for industrial systems. The management of experience feedback in this framework is designed to build, analyze and facilitate the knowledge sharing among problem solving practitioners of an organization in order to improve processes and products achievement. During Problem Solving Processes, the intellectual investment of experts is often considerable and the opportunities for expert knowledge exploitation are numerous: decision making, problem solving under uncertainty, and expert configuration. In this paper, our contribution relates to the structuring of a cognitive experience feedback framework, which allows a flexible exploitation of expert knowledge during Problem Solving Processes and a reuse such collected experience. To that purpose, the proposed approach uses the general principles of root cause analysis for identifying the root causes of problems or events, the conceptual graphs formalism for the semantic conceptualization of the domain vocabulary and the Transferable Belief Model for the fusion of information from different sources. The underlying formal reasoning mechanisms (logic-based semantics) in conceptual graphs enable intelligent information retrieval for the effective exploitation of lessons learned from past projects. An example will illustrate the application of the proposed approach of experience feedback processes formalization in the transport industry sector

Knowledge-based support in Non-Destructive Testing for health monitoring of aircraft structures

Maintenance manuals include general methods and procedures for industrial maintenance and they contain information about principles of maintenance methods. Particularly, Non-Destructive Testing (NDT) methods are important for the detection of aeronautical defects and they can be used for various kinds of material and in different environments. Conventional non-destructive evaluation inspections are done at periodic maintenance checks. Usually, the list of tools used in a maintenance program is simply located in the introduction of manuals, without any precision as regards to their characteristics, except for a short description of the manufacturer and tasks in which they are employed. Improving the identification concepts of the maintenance tools is needed to manage the set of equipments and establish a system of equivalence: it is necessary to have a consistent maintenance conceptualization, flexible enough to fit all current equipment, but also all those likely to be added/used in the future. Our contribution is related to the formal specification of the system of functional equivalences that can facilitate the maintenance activities with means to determine whether a tool can be substituted for another by observing their key parameters in the identified characteristics. Reasoning mechanisms of conceptual graphs constitute the baseline elements to measure the fit or unfit between an equipment model and a maintenance activity model. Graph operations are used for processing answers to a query and this graph-based approach to the search method is in-line with the logical view of information retrieval. The methodology described supports knowledge formalization and capitalization of experienced NDT practitioners. As a result, it enables the selection of a NDT technique and outlines its capabilities with acceptable alternatives

Knowledge formalization in experience feedback processes : an ontology-based approach

Because of the current trend of integration and interoperability of industrial systems, their size and complexity continue to grow making it more difficult to analyze, to understand and to solve the problems that happen in their organizations. Continuous improvement methodologies are powerful tools in order to understand and to solve problems, to control the effects of changes and finally to capitalize knowledge about changes and improvements. These tools involve suitably represent knowledge relating to the concerned system. Consequently, knowledge management (KM) is an increasingly important source of competitive advantage for organizations. Particularly, the capitalization and sharing of knowledge resulting from experience feedback are elements which play an essential role in the continuous improvement of industrial activities. In this paper, the contribution deals with semantic interoperability and relates to the structuring and the formalization of an experience feedback (EF) process aiming at transforming information or understanding gained by experience into explicit knowledge. The reuse of such knowledge has proved to have significant impact on achieving themissions of companies. However, the means of describing the knowledge objects of an experience generally remain informal. Based on an experience feedback process model and conceptual graphs, this paper takes domain ontology as a framework for the clarification of explicit knowledge and know-how, the aim of which is to get lessons learned descriptions that are significant, correct and applicable

Implementation of XpertMalTyph: An Expert System for Medical Diagnosis of the Complications of Malaria and Typhoid

The dearth of medical experts in the developing world has subjected a large percentage of its populace to preventable ailments and deaths. Also, because of the predominant rural communities, the few medical experts that are available always opt for practice in the few urban cities. This consequently puts the rural communities at a disadvantage with respect to access to quality health care services. In this work, we designed and implemented XpertMalTyph; a novel medical diagnostic expert system for the various kinds of malaria and typhoid complications. A medical diagnostic expert system uses computer(s) to simulate medical doctor skills in diagnosis of ailments and prescription of treatments, hence can be used to provide the same service in the absence of the experts. XpertMalTyph is based on JESS (Java Expert System Shell) programming because of its robust inference engine and rules for implementing expert system