Informatica

The Gene Ontology (GO) knowledge base provides a standardized vocabulary of GO terms for describing gene functions and attributes. It consists of three directed acyclic graphs which represent the hierarchical structure of relationships between GO terms. GO terms enable the organization of genes based on their functional attributes by annotating genes to specific GO terms. We propose an information-retrieval derived distance between genes by using their annotations. Four gene sets with causal associations were examined by employing our proposed methodology. As a result, the discovered homogeneous subsets of these gene sets are semantically related, in contrast to comparable works. The relevance of the found clusters can be described with the help of ChatGPT by asking for their biological meaning. The R package BIDistances, readily available on CRAN, empowers researchers to effortlessly calculate the distance for any given gene set.

The paper deals with the causality perspective of the Enterprise Architecture (EA) frameworks. The analysis showed that there is a gap between the capabilities of EA frameworks and the behavioural characteristics of the real world domain (enterprise management activities). The contribution of research is bridging the gap between enterprise domain knowledge and EA framework content by the integration of meta-models as part of EA structures. Meta-models that cover not only simple process flows, but also business behaviour, i.e. causality of the domain, have been developed. Meta-models enable to create a layer of knowledge in the EA framework, which ensures smart EA development, allows validation of developer decisions. Two levels of the enterprise causal modelling were obtained. The first level uses the Management Transaction (MT) framework. At the second level, deep knowledge was revealed using a framework called the Elementary Management Cycle (EMC). These two causal frameworks were applied here to justify the causal meta-models of the EA. The new concepts Collapsed Capability, Capability Type and Capability Role which meaningfully complement MODAF with causal knowledge are introduced. Strategic Viewpoint (StV) modelling using causal meta-models is described in detail and illustrated in the case study. The example provided shows a principled way that causal knowledge supports the verification and validation of EA solutions. The presented method provides an opportunity to move the EA development to smart platforms.

The paper deals with the causality driven modelling method applied for the domain deep knowledge elicitation. This method is suitable for discovering causal relationships in domains that are characterized by internal circular causality, e.g. control and management, regulatory processes, self-regulation and renewal. Such domains are organizational systems (i.e. enterprise) or cyber-social systems, also biological systems, ecological systems, and other complex systems. Subject domain may be of different nature: real-world activities or documented content. A causality driven approach is applied here for the learning content analysis and normalization of the knowledge structures. This method was used in the field of education, and a case study of learning content renewal is provided. The domain here is a real world area – a learning content is about. The paper is on how to align the existing learning content and current (new) knowledge of the domain using the same causality driven viewpoint and the described models (frameworks). Two levels of the domain causal modelling are obtained. The first level is the discovery of the causality of the domain using the Management Transaction (MT) framework. Secondly, a deep knowledge structure of MT is revealed through a more detailed framework called the Elementary Management Cycle (EMC). The algorithms for updating the LO content in two steps are presented. Traceability matrix indicates the mismatch of the LO content (old knowledge) and new domain knowledge. Classification of the content discrepancies and an example of the study program content analysis is presented. The main outcome of the causality driven modelling approach is the effectiveness of discovering the deep knowledge when the relevant domain causality frameworks are applicable.

The paper deals with the intelligent functional model for optimizing the product design and its manufacturing process in hybrid manufacturing systems consisting of people, machines and computers. The knowledge‐based framework of an intelligent functional model has been developed. It furnishes the possibility for a product designer and manufacturer to find an optimal production plan in the early stage of the product design. The mathematical model formalization is provided. A consecutive optimization scheme has been applied for selecting an optimal alternative of a product design and its production plan. The proposed model is being implemented both in industry and university education process.

The paper presents a technique that defines creation of ESTELLE/Ag specifications using knowledge bases (KB). Application KB is created using the knowledge acquisition technique joined with a piece‐linear aggregate model. The production rules of the application KB are transformed to decision tables, and the static properties of the KB are checked in PROLOGA system. Further, the application KB is combined with the defined KB of validated properties and validation method, and application KB dynamic properties are checked in the expert system in CLIPS. A validated application KB is used defining a framework of ESTELLE/Ag specification using PRAXIS editor and supplementing PRAXIS generated framework with the application functional description. The technique is illustrated with an example of a single channel queuing system.