Faculty of Computer Science and Engineering

Permanent URI for this communityhttps://repository.ukim.mk/handle/20.500.12188/5

The Faculty of Computer Science and Engineering (FCSE) within UKIM is the largest and most prestigious faculty in the field of computer science and technologies in Macedonia, and among the largest faculties in that field in the region. The FCSE teaching staff consists of 50 professors and 30 associates. These include many “best in field” personnel, such as the most referenced scientists in Macedonia and the most influential professors in the ICT industry in the Republic of Macedonia.

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    Item type:Publication,
    Review of Natural Language Processing in Pharmacology
    (American Society for Pharmacology & Experimental Therapeutics (ASPET), 2023-07)
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    Trajkovski, Vangel
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    Dimitrieva, Makedonka
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    Dobreva, Jovana
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    Natural language processing (NLP) is an area of artificial intelligence that applies information technologies to process the human language, understand it to a certain degree, and use it in various applications. This area has rapidly developed in the past few years and now employs modern variants of deep neural networks to extract relevant patterns from large text corpora. The main objective of this work is to survey the recent use of NLP in the field of pharmacology. As our work shows, NLP is a highly relevant information extraction and processing approach for pharmacology. It has been used extensively, from intelligent searches through thousands of medical documents to finding traces of adversarial drug interactions in social media. We split our coverage into five categories to survey modern NLP: methodology, commonly addressed tasks, relevant textual data, knowledge bases, and useful programming libraries. We split each of the five categories into appropriate subcategories, describe their main properties and ideas, and summarize them in a tabular form. The resulting survey presents a comprehensive overview of the area, useful to practitioners and interested observers. SIGNIFICANCE STATEMENT: The main objective of this work is to survey the recent use of NLP in the field of pharmacology in order to provide a comprehensive overview of the current state in the area after the rapid developments that occurred in the past few years. The resulting survey will be useful to practitioners and interested observers in the domain.
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    Learning Robust Food Ontology Alignment
    (IEEE, 2022-12-17)
    Mijalcheva, Viktorija
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    Davcheva, Ana
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    In today’s knowledge society, large number of information systems use many different individual schemes to represent data. Ontologies are a promising approach for formal knowledge representation and their number is growing rapidly. The semantic linking of these ontologies is a necessary prerequisite for establishing interoperability between the large number of services that structure the data with these ontologies. Consequently, the alignment of ontologies becomes a central issue when building a worldwide Semantic Web. There is a need to develop automatic or at least semi-automatic techniques to reduce the burden of manually creating and maintaining alignments. Ontologies are seen as a solution to data heterogeneity on the Web. However, the available ontologies are themselves a source of heterogeneity. On the Web, there are multiple ontologies that refer to the same domain, and with that comes the challenge of a given graph-based system using multiple ontologies whose taxonomy is different, but the semantics are the same. This can be overcome by aligning the ontologies or by finding the correspondence between their components.In this paper, we propose a method for indexing ontologies as a support to a solution for ontology alignment based on a neural network. In this process, for each semantic resource we combine the graph based representations from the RDF2vec model, together with the text representation from the BERT model in order to capture the semantic and structural features. This methodology is evaluated using the FoodOn and OntoFood ontologies, based on the Food Onto Map alignment dataset, which contains 155 unique and validly aligned resources. Using these limited resources, we managed to obtain accuracy of 74% and F1 score of 75% on the test set, which is a promising result that can be further improved in future. Furthermore, the methodology presented in this paper is both robust and ontology-agnostic. It can be applied to any ontology, regardless of the domain.