Abdillah, Abid Famasya
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Named Entity Recognition in Medical Domain: A systematic Literature Review Kusuma, Selvia Ferdiana; Wibowo, Prasetyo; Abdillah, Abid Famasya; Basuki, Setio
JOIV : International Journal on Informatics Visualization Vol 8, No 4 (2024)
Publisher : Society of Visual Informatics

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.62527/joiv.8.4.3111

Abstract

Biomedical Named Entity Recognition (BioNER) is essential to bioinformatics because it identifies and classifies biological entities in biomedical texts. With the increasing number of biomedical literature and the rapid progress of the BioNER approach, it is essential to conduct a systematic literature review (SLR) on BioNER. This SLR consolidates existing information and provides directions for future studies in the BioNER field. This review systematically explores scientific journals and conferences published from 2019 to 2024. This research uses PubMed and Scholar as reference search databases because of their affiliation with other well-known publishers such as IEEE, Elsevier, and Springer. The results show a transition from conventional machine learning to deep learning. Neural networks and transformers show better performance in deep learning methods. The datasets often used in BioNER development are BC2GM, BC5CDR, and NCBI-Disease. Precision, Recall, and F1-Score are used in most papers to evaluate model performance. The performance of these models mostly depends on the availability of big annotated datasets and significant computational tools. Therefore, it is vital for future research to address the issues of annotated data and resource availability to build accurate models. Researchers should investigate the creation of ideal designs that lower computing complexity without compromising performance. Overall, this SLR offers a thorough overview of the latest research on BioNER. It provides significant insights for academics and practitioners in bioinformatics and medical research, helping them understand the innovative aspects of BioNER research.
Pengenalan Entitas Biomedis dalam Teks Konsultasi Kesehatan Online Berbahasa Indonesia Berbasis Arsitektur Transformers Abdillah, Abid Famasya; Purwitasari, Diana; Juanita, Safitri; Purnomo, Mauridhi Hery
Jurnal Teknologi Informasi dan Ilmu Komputer Vol 10 No 1: Februari 2023
Publisher : Fakultas Ilmu Komputer, Universitas Brawijaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.25126/jtiik.2023106337

Abstract

Pengenalan entitas biomedis merupakan salah satu tahapan penting dalam ekstraksi informasi pada domain kesehatan. Untuk melakukannya, penelitian terkini banyak menggunakan model ekstraksi biomedis berbasis deep learning yang juga dikenal sebagai Biomedical NER (BioNER). Banyak penelitian menggunakan data sosial media sebagai basis data latih BioNER untuk memenuhi kebutuhan data yang besar. Di sisi lain, banyaknya topik bahasan pada sosial media membuat sumber data ini kurang representatif digunakan dalam pelatihan BioNER seiring dengan melimpahnya bias serta kurangnya data terkait biomedis. Oleh karena itu, penelitian ini mengusulkan suatu model BioNER yang telah dilatih pada situs konsultasi kesehatan online (KKO) agar memiliki representasi data medis lebih baik dibandingkan dengan  penelitian lain yang sejenis. Kontribusi utama penelitian ini adalah terbentuknya model BioNER yang dapat digunakan dalam metode ekstraksi informasi biomedis dalam Bahasa Indonesia. Model ini dibangun menggunakan arsitektur state-of-the-art Transformers sehingga mendapatkan hasil evaluasi F1 score sebesar 0.7691, mengungguli model LSTM sebesar 0.03 poin. Hasil simulasi terhadap data riil juga menunjukkan bahwa model BioNER mampu mengenali entitas biomedis secara umum meskipun dilatih pada data yang terbatas. Selain itu, dengan digunakannya model berbasis XLM-R, maka model juga memiliki kemampuan pengenalan multibahasa sehingga potensi implementasinya tidak terbatas pada entitas Bahasa Indonesia saja. Untuk mendukung penelitian lanjutan, model pengenalan entitas biomedis ini juga dapat diakses secara publik untuk di https://huggingface.co/abid/indonesia-bioner. AbstractBiomedical entity recognition is one of the important stage in the information extraction, particularly in the health domain. Recent research uses a deep learning-based biomedical extraction model known as Biomedical NER (BioNER). Due to extensive data requirement, many studies still use social media data as a BioNER training data. On the other hand, social media data is less representative because it contains a lot of bias and lack of medical representation terms as the impact of many topics discussed. Therefore, this study proposes a BioNER model that has trained on an online health consultation platform to gain a better representation of biomedical data. This model also built using the state-of-the-art Transformers architecture. Hence, its evaluation results show that this model is able to achieve an F1 score of 0.7691, outperforming the LSTM model by 0.03. Simulation results on the real data also indicate that the BioNER model is able to recognize biomedical entities in general cases despite only trained on limited data. In addition, by using an XLM-R-based model, the recognition model also has multilingual recognition capabilities. Therefore, there is a potential implementation to apply the our BioNER model beyond Indonesian biomedical entities. Our biomedical entity recognition model is also accessible at https://huggingface.co/abid/indonesia-bioner.