• Journal of Korean Library and Information Science Society
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• v.47 no.4
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• pp.289-307
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• 2016

This paper introduces a software system and process model for constructing domain-specific relation extraction datasets semi-automatically. The system uses a set of terms such as genes, proteins diseases and so forth as inputs and then by exploiting massive biological interaction database, generates a set of term pairs which are utilized as queries for retrieving sentences containing the pairs from scientific databases. To assess the usefulness of the proposed system, this paper applies it into constructing a genic interaction dataset related to Alzheimer's disease domain, which extracts 3,510 interaction-related sentences by using 140 gene names in the area. In conclusion, the resulting outputs of the case study performed in this paper indicate the fact that the system and process could highly boost the efficiency of the dataset construction in various subfields of biomedical research.

• Journal of Ecology and Environment
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• v.45 no.4
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• pp.313-327
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• 2021

Background: Citizen science is becoming a mainstream approach of baseline data collection to monitor biodiversity and climate change. Dragonflies (Odonata) have been ranked as the highest priority group in biodiversity monitoring for global warming. Ischnura senegalensis Rambur has been designated a biological indicator of climate change and is being monitored by the citizen science project "Korean Biodiversity Observation Network." This study has been performed to understand changes in the distribution range of I. senegalensis in response to climate change using citizen science data in South Korea. Results: We constructed a dataset of 397 distribution records for I. senegalensis, ranging from 1980 to 2020. The number of records sharply increased over time and space, and in particular, citizen science monitoring data accounted for the greatest proportion (58.7%) and covered the widest geographical range. This species was only distributed in the southern provinces until 2010 but was recorded in the higher latitudes such as Gangwon-do, Incheon, Seoul, and Gyeonggi-do (max. Paju-si, 37.70° latitude) by 2020. A species distribution model showed that the annual mean temperature (Bio1; 63.2%) and the maximum temperature of the warmest month (Bio5; 16.7%) were the most critical factors influencing its distribution. Future climate change scenarios have predicted an increase in suitable habitats for this species. Conclusions: This study is the first to show the northward expansion in the distribution range of I. senegalensis in response to climate warming in South Korea over the past 40 years. In particular, citizen science was crucial in supplying critical baseline data to detect the distribution change toward higher latitudes. Our results provide new insights on the value of citizen science as a tool for detecting the impact of climate change on ecosystems in South Korea.

• Journal of Biomedical Engineering Research
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• v.43 no.1
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• pp.19-26
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• 2022

The Comprehensive in vitro Proarrhythmic Assay(CiPA) project was launched for solving the hERG assay problem of being classified as high-risk groups even though they are low-risk drugs due to their high sensitivity. CiPA presented a protocol to predict drug toxicity using physiological data calculated based on the in-silico model. in this study, features calculated through the in-silico model are analyzed for correlation of changing action potential in the near future, and features are verified through predictive performance according to drug datasets. Using the O'Hara Rudy model modified by Dutta et al., Pearson correlation analysis was performed between 13 features(dVm/dtmax, APpeak, APresting, APD90, APD50, APDtri, Ca_peak, Ca_resting, CaD90, CaD50, CaDtri, qNet, qInward) calculated at 100 pacing, and between dVm/d_{tmax_repol} calculated at 1,000 pacing, and linear regression analysis was performed on each of the 12 training drugs, 16 verification drugs, and 28 drugs. Indicators showing high coefficient of determination(R²) in the training drug dataset were qNet 0.93, AP resting 0.83, APDtri 0.78, Ca resting 0.76, dVm/dt_max 0.63, and APD90 0.61. The indicators showing high determinants in the validated drug dataset were APDtri 0.94, APD90 0.92, APD50 0.85, CaD50 0.84, qNet 0.76, and CaD90 0.64. Indicators with high coefficients of determination for all 28 drugs are qNet 0.78, APD90 0.74, and qInward 0.59. The indicators vary in predictive performance depending on the drug dataset, and qNet showed the same high performance of 0.7 or more on the training drug dataset, the verified drug dataset, and the entire drug dataset.

• Proceedings of the Korean Society of Fisheries Technology Conference
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• 2003.05a
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• pp.377-377
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• 2003

We investigated the biogeography of Asian Corbicula using mitochondrial gene sequence variation for Corbicula members sampled from 24 localities of 8 Asian regions. A total of 210 individuals were genetically characterized by examining sequence variations of a 614 bp fragment of the mitochondrial cytochrome oxidase I (COI) gene. Phylogenetic analyses of the COI dataset revealed that Corbicula members are subdivided into two well-supported clades: estuarine and freshwater. (omitted)

• Proceedings of the KOSOMBE Conference
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• v.1995 no.05
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• pp.233-234
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• 1995

Tri-planar interpolation of the orthogonal digital brain Atlas is proposed to achieve a higher resolution of a volume-metric atlas. With these expanded dataset, the brain mapping will be accomplished with fewer registration errors.

• Journal of Conservation Science
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• v.32 no.3
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• pp.437-448
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• 2016

Studies on vulnerability of cultural heritage and adaptation strategy to worldwide climate change have been actively carried out in advanced countries since the late 20th century, and this established a valid research methodology and piled up climate and deterioration dataset in the field of climate change. Meanwhile, we still have tasks to acquire related scientific data despite referencing political researches in Korea. Applying Korean future climate to impact analysis, deterioration of Korean stone heritage is likely prospected to change into complexity in terms of physical, chemical and biological weathering that may bring impacts on conservation business and administrative field of cultural heritage. Further studies will ensure detailed implication of climate change impact on Korean stone heritage by means of down-scaling analysis of areas to local scale and dataset frequency to an hour. It is important to sort out capability and vulnerability of the stone heritage to future environment, and to make an adaption and prevention strategies.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2004.11a
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• pp.124-130
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• 2004

Microarray expression datasets are incessantly cumulated with the aid of recent technological advances. One of the first steps for analyzing these data under various experimental conditions is determining differentially expressed genes (DEGs) in each condition. Reasonable choices of thresholds for determining differentially expressed genes are used for the next -step-analysis with suitable statistical significances. We present a model for identifying DEGs using pathway information based on the global connectivity structure. Pathway information can be regarded as a collection of biological knowledge, thus we are tying to determine the optimal threshold so that the consequential connectivity structure can be the most compatible with the existing pathway information. The significant feature of our model is that it uses established knowledge as a reference to determine the direction of analyzing microarray dataset. In the most of previous work, only intrinsic information in the miroarray is used for the identifying DEGs. We hope that our proposed method could contribute to construct biologically meaningful network structure from microarray datasets.

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

• Journal of Biomedical Engineering Research
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• v.43 no.5
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• pp.299-307
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• 2022

In this paper, we propose a pre-processing method that converts to Spider Chart image data for classification of gripping movement using EMG (electromyography) sensors and Convolution Neural Networks (CNN) deep learning. First, raw data for six hand gestures are extracted from five test subjects using an 8-channel armband and converted into Spider Chart data of octagonal shapes, which are divided into several sliding windows and are learned. In classifying six hand gestures, the classification performance is compared with the proposed pre-processing method and the existing methods. Deep learning was performed on the dataset by dividing 70% of the total into training, 15% as testing, and 15% as validation. For system performance evaluation, five cross-validations were applied by dividing 80% of the entire dataset by training and 20% by testing. The proposed method generates 97% and 94.54% in cross-validation and general tests, respectively, using the Spider Chart preprocessing, which was better results than the conventional methods.

• Proceedings of the Korean Institute of Information and Commucation Sciences Conference
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• 2022.10a
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• pp.150-152
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• 2022

In this work, we propose a model that considers the behavior and synaptic plasticity of sensory neurons based on Liquid Time-constant Network (LTC). The neuron connection structure was experimented with four types: the increasing number of neurons, the decreasing number, the decreasing number, and the decreasing number. In this study, we experimented using a time series prediction dataset to see if the performance of the changed model improved compared to LTC. Experimental results show that the application of modeling of sensory neurons does not always bring about performance improvements, but improves performance through proper selection of learning rules depending on the type of dataset. In addition, the connective structure of neurons showed improved performance when it was less than four layers.