• International Journal of Fuzzy Logic and Intelligent Systems
• /
• v.15 no.2
• /
• pp.111-120
• /
• 2015

Protein named entity identification is one of the most essential and fundamental predecessor for extracting information about protein-protein interactions from biomedical literature. In this paper, we explore the use of abstracts of biomedical literature in MEDLINE for protein name identification and present the results of the conducted experiments. We present a robust and effective approach to classify biomedical named entities into protein and non-protein classes, based on a rich set of features: orthographic, keyword, morphological and newly introduced Protein-Score features. Our procedure shows significant performance in the experiments on GENIA corpus using Random Forest, achieving the highest values of precision 92.7%, recall 91.7%, and F-measure 92.2% for protein identification, while reducing the training and testing time significantly.

• Journal of Information Processing Systems
• /
• v.8 no.4
• /
• pp.575-588
• /
• 2012

Exploiting unlabeled text data with a relatively small labeled corpus has been an active and challenging research topic in text mining, due to the recent growth of the amount of biomedical literature. Biomedical named-entity recognition is an essential prerequisite task before effective text mining of biomedical literature can begin. This paper proposes an Active Co-Training (ACT) algorithm for biomedical named-entity recognition. ACT is a semi-supervised learning method in which two classifiers based on two different feature sets iteratively learn from informative examples that have been queried from the unlabeled data. We design a new classification problem to measure the informativeness of an example in unlabeled data. In this classification problem, the examples are classified based on a joint view of a feature set to be informative/non-informative to both classifiers. To form the training data for the classification problem, we adopt a query-by-committee method. Therefore, in the ACT, both classifiers are considered to be one committee, which is used on the labeled data to give the informativeness label to each example. The ACT method outperforms the traditional co-training algorithm in terms of f-measure as well as the number of training iterations performed to build a good classification model. The proposed method tends to efficiently exploit a large amount of unlabeled data by selecting a small number of examples having not only useful information but also a comprehensive pattern.

• Genomics & Informatics
• /
• v.19 no.3
• /
• pp.22.1-22.5
• /
• 2021

Automatic document classification for highly interrelated classes is a demanding task that becomes more challenging when there is little labeled data for training. Such is the case of the coronavirus disease 2019 (COVID-19) clinical repository-a repository of classified and translated academic articles related to COVID-19 and relevant to the clinical practice-where a 3-way classification scheme is being applied to COVID-19 literature. During the 7th Biomedical Linked Annotation Hackathon (BLAH7) hackathon, we performed experiments to explore the use of named-entity-recognition (NER) to improve the classification. We processed the literature with OntoGene's Biomedical Entity Recogniser (OGER) and used the resulting identified Named Entities (NE) and their links to major biological databases as extra input features for the classifier. We compared the results with a baseline model without the OGER extracted features. In these proof-of-concept experiments, we observed a clear gain on COVID-19 literature classification. In particular, NE's origin was useful to classify document types and NE's type for clinical specialties. Due to the limitations of the small dataset, we can only conclude that our results suggests that NER would benefit this classification task. In order to accurately estimate this benefit, further experiments with a larger dataset would be needed.

• The Journal of the Korea institute of electronic communication sciences
• /
• v.19 no.4
• /
• pp.701-708
• /
• 2024

The advent of transformer architectures in deep learning has been a major breakthrough in natural language processing research. Object name recognition is a branch of natural language processing and is an important research area for tasks such as information retrieval. It is also important in the biomedical field, but the lack of Korean biomedical corpora for training has limited the development of Korean clinical research using AI. In this study, we built a new biomedical corpus for Korean biomedical entity name recognition and selected language models pre-trained on a large Korean corpus for transfer learning. We compared the name recognition performance of the selected language models by F1-score and the recognition rate by tag, and analyzed the errors. In terms of recognition performance, KlueRoBERTa showed relatively good performance. The error analysis of the tagging process shows that the recognition performance of Disease is excellent, but Body and Treatment are relatively low. This is due to over-segmentation and under-segmentation that fails to properly categorize entity names based on context, and it will be necessary to build a more precise morphological analyzer and a rich lexicon to compensate for the incorrect tagging.

• Journal of the Korean Society for Library and Information Science
• /
• v.51 no.4
• /
• pp.227-248
• /
• 2017

This paper introduces an integrated model for systematically constructing a linguistic resource database that can be used by machine learning-based biomedical information extraction systems. The proposed method suggests an orderly process of collecting and constructing dictionaries and training sets for both named-entity recognition and relation extraction. Multiple heterogeneous structures for the resources which are collected from diverse sources are analyzed to derive essential items and fields for constructing the integrated database. All the collected resources are converted and refined to build an integrated linguistic resource storage. In this paper, we constructed entity dictionaries of gene, protein, disease and drug, which are considered core linguistic elements or core named entities in the biomedical domains and conducted verification tests to measure their acceptability.

• Genomics & Informatics
• /
• v.18 no.2
• /
• pp.15.1-15.6
• /
• 2020

Named entity recognition tools are used to identify mentions of biomedical entities in free text and are essential components of high-quality information retrieval and extraction systems. Without good entity recognition, methods will mislabel searched text and will miss important information or identify spurious text that will frustrate users. Most tools do not capture non-contiguous entities which are separate spans of text that together refer to an entity, e.g., the entity "type 1 diabetes" in the phrase "type 1 and type 2 diabetes." This type is commonly found in biomedical texts, especially in lists, where multiple biomedical entities are named in shortened form to avoid repeating words. Most text annotation systems, that enable users to view and edit entity annotations, do not support non-contiguous entities. Therefore, experts cannot even visualize non-contiguous entities, let alone annotate them to build valuable datasets for machine learning methods. To combat this problem and as part of the BLAH6 hackathon, we extended the TextAE platform to allow visualization and annotation of non-contiguous entities. This enables users to add new subspans to existing entities by selecting additional text. We integrate this new functionality with TextAE's existing editing functionality to allow easy changes to entity annotation and editing of relation annotations involving non-contiguous entities, with importing and exporting to the PubAnnotation format. Finally, we roughly quantify the problem across the entire accessible biomedical literature to highlight that there are a substantial number of non-contiguous entities that appear in lists that would be missed by most text mining systems.

• Genomics & Informatics
• /
• v.17 no.2
• /
• pp.17.1-17.3
• /
• 2019

Text mining has become an important research method in biology, with its original purpose to extract biological entities, such as genes, proteins and phenotypic traits, to extend knowledge from scientific papers. However, few thorough studies on text mining and application development, for plant molecular biology data, have been performed, especially for rice, resulting in a lack of datasets available to solve named-entity recognition tasks for this species. Since there are rare benchmarks available for rice, we faced various difficulties in exploiting advanced machine learning methods for accurate analysis of the rice literature. To evaluate several approaches to automatically extract information from gene/protein entities, we built a new dataset for rice as a benchmark. This dataset is composed of a set of titles and abstracts, extracted from scientific papers focusing on the rice species, and is downloaded from PubMed. During the 5th Biomedical Linked Annotation Hackathon, a portion of the dataset was uploaded to PubAnnotation for sharing. Our ultimate goal is to offer a shared task of rice gene/protein name recognition through the BioNLP Open Shared Tasks framework using the dataset, to facilitate an open comparison and evaluation of different approaches to the task.

• International Journal of Contents
• /
• v.17 no.4
• /
• pp.1-15
• /
• 2021

Named entity recognition (NER) is a crucial task for NLP, which aims to extract information from texts. To build NER systems, deep learning (DL) models are learned with dictionary features by mapping each word in the dataset to dictionary features and generating a unique index. However, this technique might generate noisy labels, which pose significant challenges for the NER task. In this paper, we proposed DL-dictionary features, and evaluated them on two datasets, including the OntoNotes 5.0 dataset and our new infectious disease outbreak dataset named GFID. We used (1) a Bidirectional Long Short-Term Memory (BiLSTM) character and (2) pre-trained embedding to concatenate with (3) our proposed features, named the Convolutional Neural Network (CNN), BiLSTM, and self-attention dictionaries, respectively. The combined features (1-3) were fed through BiLSTM - Conditional Random Field (CRF) to predict named entity classes as outputs. We compared these outputs with other predictions of the BiLSTM character, pre-trained embedding, and dictionary features from previous research, which used the exact matching and partial matching dictionary technique. The findings showed that the model employing our dictionary features outperformed other models that used existing dictionary features. We also computed the F1 score with the GFID dataset to apply this technique to extract medical or healthcare information.

• Genomics & Informatics
• /
• v.18 no.2
• /
• pp.13.1-13.6
• /
• 2020

The prototype version of the full-text corpus of Genomics & Informatics has recently been archived in a GitHub repository. The full-text publications of volumes 10 through 17 are also directly downloadable from PubMed Central (PMC) as XML files. During the Biomedical Linked Annotation Hackathon 6 (BLAH6), we experimented with converting, annotating, and updating 301 PMC full-text articles of Genomics & Informatics using PubAnnotation, a system that provides a convenient way to add PMC publications based on PMCID. Thus, this review aims to provide a tutorial overview of practicing the iterative task of named entity recognition with the PubAnnotation/PubDictionaries/TextAE ecosystem. We also describe developing a conversion tool between the Genia tagger output and the JSON format of PubAnnotation during the hackathon.

• The Journal of Korean Association of Computer Education
• /
• v.14 no.2
• /
• pp.83-94
• /
• 2011

In the biomedical domain, the longest matching method is frequently used for recognizing named entity written in the literature. This method uses a dictionary as a resource for named entity recognition. If there exist appropriated dictionary about target domain, the longest matching method has the advantage of being able to recognize the entities of target domain quickly and exactly. However, the longest matching method is difficult to recognize the enumerated named entities, because these entities are frequently expressed as being omitted some words. In order to resolve this problem, we propose the partial matching method using a dictionary. The proposed method makes several candidate entities on the assumption that the ellipses may be included. After that, the method selects the most valid one among candidate entities through the optimization algorithm. We tested the longest and partial matching method about HLA entities: HLA gene, antigen, and allele entities, which are frequently enumerated among biomedical entities. As preparing for named entity recognition, we built two new resource, extended dictionary and tag-based dictionary about HLA entities. And later, we performed the longest and partial matching method using each dictionary. According to our experiment result, the longest matching method was effective in recognizing HLA antigen entities, in which the ellipses are rare, and the partial matching method was effective in recognizing HLA gene and allele entities, in which the ellipses are frequent. Especially, the partial matching method had a high F-score 95.59% about HLA alleles.