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, PharmKE: Knowledge Extraction Platform for Pharmaceutical Texts Using Transfer Learning(MDPI, 2023-01-09); ; ; Even though named entity recognition (NER) has seen tremendous development in recent years, some domain-specific use-cases still require tagging of unique entities, which is not well handled by pre-trained models. Solutions based on enhancing pre-trained models or creating new ones are efficient, but creating reliable labeled training for them to learn on is still challenging. In this paper, we introduce PharmKE, a text analysis platform tailored to the pharmaceutical industry that uses deep learning at several stages to perform an in-depth semantic analysis of relevant publications. The proposed methodology is used to produce reliably labeled datasets leveraging cutting-edge transfer learning, which are later used to train models for specific entity labeling tasks. By building models for the well-known text-processing libraries spaCy and AllenNLP, this technique is used to find Pharmaceutical Organizations and Drugs in texts from the pharmaceutical domain. The PharmKE platform also incorporates the NER findings to resolve co-references of entities and examine the semantic linkages in each phrase, creating a foundation for further text analysis tasks, such as fact extraction and question answering. Additionally, the knowledge graph created by DBpedia Spotlight for a specific pharmaceutical text is expanded using the identified entities. The obtained results with the proposed methodology result in about a 96% F1-score on the NER tasks, which is up to 2% better than those of the fine-tuned BERT and BioBERT models developed using the same dataset. The ultimate benefits of the platform are that pharmaceutical domain specialists may more easily identify the knowledge extracted from the input texts thanks to the platform’s visualization of the model findings. Likewise, the proposed techniques can be integrated into mobile and pervasive systems to give patients more relevant and comprehensive information from scanned medication guides. Similarly, it can provide preliminary insights to patients and even medical personnel on whether a drug from a different vendor is compatible with the patient’s prescription medication. - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Named Entity Recognition and Knowledge Extraction from Pharmaceutical Texts using Transfer Learning(Elsevier, 2022-01-01); ; ; The challenge of recognizing named entities in a given text has been a very dynamic field in recent years. This task is generally focused on tagging common entities, such as Person, Organization, Date, etc. However, many domain-specific use-cases exist which require tagging custom entities that are not part of the pre-trained models. This can be solved by fine-tuning the pre-trained models or training custom models. The main challenge lies in obtaining reliable labeled training and test datasets, and manual labeling would be a highly tedious task. This paper presents a text analysis platform focused on the pharmaceutical domain. We perform text classification using state-ofthe-art transfer learning models based on spaCy, AllenNLP, BERT, and BioBERT. We developed methodology that is used to create accurately labeled training and test datasets used for custom entity labeling model fine-tuning. Finally, this methodology is applied in the process of detecting Pharmaceutical Organizations and Drugs in texts from the pharmaceutical domain. The obtained F1 scores are 96.14% for the entities occuring in the training set, and 95.14% for the unseen entities, which is noteworthy compared to other state-of-the-art methods. The proposed approach implemented in the platform could be applied in mobile and pervasive systems since it can provide more relevant and understandable information to patients by allowing them to scan the medication guides of their drugs. Furthermore, the proposed methodology has a potential application in verifying whether another drug from another vendor is compatible with the patient’s prescription medicine. Such approaches are the future of patient empowerment. - Some of the metrics are blocked by yourconsent settings
Item type:Publication, PharmKE: Knowledge Extraction Platform for Pharmaceutical Texts using Transfer Learning(2021-02-25); ; ; The challenge of recognizing named entities in a given text has been a very dynamic field in recent years. This is due to the advances in neural network architectures, increase of computing power and the availability of diverse labeled datasets, which deliver pre-trained, highly accurate models. These tasks are generally focused on tagging common entities, but domain-specific use-cases require tagging custom entities which are not part of the pre-trained models. This can be solved by either fine-tuning the pre-trained models, or by training custom models. The main challenge lies in obtaining reliable labeled training and test datasets, and manual labeling would be a highly tedious task. In this paper we present PharmKE, a text analysis platform focused on the pharmaceutical domain, which applies deep learning through several stages for thorough semantic analysis of pharmaceutical articles. It performs text classification using state-of-the-art transfer learning models, and thoroughly integrates the results obtained through a proposed methodology. The methodology is used to create accurately labeled training and test datasets, which are then used to train models for custom entity labeling tasks, centered on the pharmaceutical domain. The obtained results are compared to the fine-tuned BERT and BioBERT models trained on the same dataset. Additionally, the PharmKE platform integrates the results obtained from named entity recognition tasks to resolve co-references of entities and analyze the semantic relations in every sentence, thus setting up a baseline for additional text analysis tasks, such as question answering and fact extraction. The recognized entities are also used to expand the knowledge graph generated by DBpedia Spotlight for a given pharmaceutical text. - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Named Entity Discovery for the Drug Domain(Ss. Cyril and Methodius University in Skopje, Faculty of Computer Science and Engineering, Republic of North Macedonia, 2019-05); Medical datasets that contain data relating to drugs and chemical substances, in general tend to contain multiple variations of a generic name which denotes the same drug or a drug product. This ambiguity lies in the fact that a single drug, referenced by a unique code, has an active substance which can be known under different chemical names in different countries, thus forming an obstacle during the process for extracting relevant and useful information. To overcome the issues presented by this ambiguity, we developed a scalable, term frequency based data cleaning algorithm, that solely uses the data available in the dataset to infer the correct generic name for each drug based on text similarities, thus forming the roots for building a model that would be able to predict generic names for related and previously unseen drug records with high accuracy. This paper describes the application of the algorithm towards the cleaning and standardization process of an already populated drug products availability dataset, by representing all of the variations of a substance under a single generic name, thus eliminating ambiguity. Our proposed algorithm is also evaluated against a Linked Data approach for detecting related drug products in the dataset. - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Improving NER Performance by Applying Text Summarization on Pharmaceutical Articles(Springer International Publishing, 2020-10-30); Analyzing long text articles in the pharmaceutical domain, for the purpose of knowledge extraction and recognizing entities of interest, is a tedious task. In our previous research efforts, we were able to develop a platform which successfully extracts entities and facts from pharmaceutical texts and populates a knowledge graph with the extracted knowledge. However, one drawback of our approach was the processing time; the analysis of a single text source was not interactive enough, and the batch processing of entire article datasets took too long. In this paper, we propose a modified pipeline where the texts are summarized before the analysis begins. With this, the source articles is reduced significantly, to a compact version which contains only the most commonly encountered entities. We show that by reducing the text size, we get knowledge extraction results comparable to the full text analysis approach and, at the same time, we significantly reduce the processing time, which is essential for getting both real-time results on single text sources, and faster results when analyzing entire batches of collected articles from the domain.