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Kim HS, Seo HG, Jhee JH, Park CH, Lee HW, Park B, Kim BG. Machine Learning-assisted Quantitative Mapping of Intracortical Axonal Plasticity Following a Focal Cortical Stroke in Rodents. Exp Neurobiol 2023; 32:170-180. [PMID: 37403225 DOI: 10.5607/en23016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 06/04/2023] [Accepted: 06/22/2023] [Indexed: 07/06/2023] Open
Abstract
Stroke destroys neurons and their connections leading to focal neurological deficits. Although limited, many patients exhibit a certain degree of spontaneous functional recovery. Structural remodeling of the intracortical axonal connections is implicated in the reorganization of cortical motor representation maps, which is considered to be an underlying mechanism of the improvement in motor function. Therefore, an accurate assessment of intracortical axonal plasticity would be necessary to develop strategies to facilitate functional recovery following a stroke. The present study developed a machine learning-assisted image analysis tool based on multi-voxel pattern analysis in fMRI imaging. Intracortical axons originating from the rostral forelimb area (RFA) were anterogradely traced using biotinylated dextran amine (BDA) following a photothrombotic stroke in the mouse motor cortex. BDA-traced axons were visualized in tangentially sectioned cortical tissues, digitally marked, and converted to pixelated axon density maps. Application of the machine learning algorithm enabled sensitive comparison of the quantitative differences and the precise spatial mapping of the post-stroke axonal reorganization even in the regions with dense axonal projections. Using this method, we observed a substantial extent of the axonal sprouting from the RFA to the premotor cortex and the peri-infarct region caudal to the RFA. Therefore, the machine learningassisted quantitative axonal mapping developed in this study can be utilized to discover intracortical axonal plasticity that may mediate functional restoration following stroke.
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Affiliation(s)
- Hyung Soon Kim
- Department of Brain Science, Ajou University School of Medicine, Suwon 16499, Korea
- Neuroscience Graduate Program, Department of Biomedical Science, Ajou University Graduate School of Medicine, Suwon 16499, Korea
| | - Hyo Gyeong Seo
- Department of Brain Science, Ajou University School of Medicine, Suwon 16499, Korea
- Neuroscience Graduate Program, Department of Biomedical Science, Ajou University Graduate School of Medicine, Suwon 16499, Korea
| | - Jong Ho Jhee
- Center for KIURI Bio-Artificial Intelligence, Ajou University School of Medicine, Suwon 16499, Korea
| | - Chang Hyun Park
- Division of Artificial Intelligence and Software, College of Engineering, Ewha Womans University, Seoul 03760, Korea
| | - Hyang Woon Lee
- Department of Neurology and Medical Science, Ewha Womans University School of Medicine and Ewha Medical Research Institute, Seoul 03760, Korea
- Computational Medicine, Graduate Programs in System Health Science & Engineering and Artificial Intelligence Convergence, Ewha Womans University, Seoul 03760, Korea
| | - Bumhee Park
- Department of Biomedical Informatics, Ajou University School of Medicine, Suwon 16499, Korea
- Office of Biostatistics, Medical Research Collaborating Center, Ajou Research Institute for Innovative Medicine, Ajou University Medical Center, Suwon 16499, Korea
| | - Byung Gon Kim
- Department of Brain Science, Ajou University School of Medicine, Suwon 16499, Korea
- Neuroscience Graduate Program, Department of Biomedical Science, Ajou University Graduate School of Medicine, Suwon 16499, Korea
- Department of Neurology, Ajou University School of Medicine, Suwon 16499, Korea
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Bang S, Jhee JH, Shin H. Polypharmacy side-effect prediction with enhanced interpretability based on graph feature attention network. Bioinformatics 2021; 37:2955-2962. [PMID: 33714994 DOI: 10.1093/bioinformatics/btab174] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 03/02/2021] [Accepted: 03/12/2021] [Indexed: 02/02/2023] Open
Abstract
MOTIVATION Polypharmacy side effects should be carefully considered for new drug development. However, considering all the complex drug-drug interactions that cause polypharmacy side effects is challenging. Recently, graph neural network (GNN) models have handled these complex interactions successfully and shown great predictive performance. Nevertheless, the GNN models have difficulty providing intelligible factors of the prediction for biomedical and pharmaceutical domain experts. METHOD A novel approach, graph feature attention network (GFAN), is presented for interpretable prediction of polypharmacy side effects by emphasizing target genes differently. To artificially simulate polypharmacy situations, where two different drugs are taken together, we formulated a node classification problem by using the concept of line graph in graph theory. RESULTS Experiments with benchmark datasets validated interpretability of the GFAN and demonstrated competitive performance with the graph attention network in a previous work. And the specific cases in the polypharmacy side-effect prediction experiments showed that the GFAN model is capable of very sensitively extracting the target genes for each side-effect prediction. AVAILABILITY AND IMPLEMENTATION https://github.com/SunjooBang/Polypharmacy-side-effect-prediction.
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Affiliation(s)
- Sunjoo Bang
- Department of Industrial Engineering, Ajou University, Suwon 443-749, South Korea
| | - Jong Ho Jhee
- Department of Industrial Engineering, Ajou University, Suwon 443-749, South Korea
| | - Hyunjung Shin
- Department of Industrial Engineering, Ajou University, Suwon 443-749, South Korea
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Jhee JH, Bang S, Lee DG, Shin H. Corrections to "Comorbidity Scoring With Causal Disease Networks". IEEE/ACM Trans Comput Biol Bioinform 2020; 17:2196. [PMID: 33290207 DOI: 10.1109/tcbb.2020.3000846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
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Abstract
In recent years, there has been numerous studies constructing a disease network with diverse sources of data. Many researchers attempted to extend the usage of the disease network by employing machine learning algorithms on various problems such as prediction of comorbidity. The relations between diseases can further be specified into causal relations. When causality is laid on the edges in the network, prediction for comorbid diseases can be more improved. However, not many machine learning algorithms have been developed to concern causality. In this study, we exploit a network based machine learning algorithm that generates comorbidity scores from a causal disease network. In order to find comorbid diseases, semi-supervised scoring for causal networks is proposed. It computes scores of entire nodes in the network when a specific node is labeled. Each score is calculated one at a time and affects to the others along causal edges. The algorithm iterates until it converges. We compared the scoring results of the causal disease network and those of simple association network. As a gold standard, we referenced the values of relative risk from prevalence database, HuDiNe. Scoring by the proposed method provides clearer distinguishability between the top-ranked diseases in the comorbidity list. This is a benefit because it allows the choosing of the most significant ones on an easier fashion. To present typical use of the resulting list, comorbid diseases of Huntington disease and pnuemonia are validated via PubMed literature, respectively.
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Nam Y, Jhee JH, Cho J, Lee JH, Shin H. Disease gene identification based on generic and disease-specific genome networks. Bioinformatics 2018; 35:1923-1930. [DOI: 10.1093/bioinformatics/bty882] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 10/11/2018] [Accepted: 10/17/2018] [Indexed: 01/11/2023] Open
Affiliation(s)
- Yonghyun Nam
- Department of Industrial Engineering, Ajou University, Yeongtong-gu, Suwon, South Korea
| | - Jong Ho Jhee
- Department of Industrial Engineering, Ajou University, Yeongtong-gu, Suwon, South Korea
| | - Junhee Cho
- Department of Industrial Engineering, Ajou University, Yeongtong-gu, Suwon, South Korea
| | - Ji-Hyun Lee
- DR. Noah Biotech, Yeongtong-gu, Suwon, South Korea
| | - Hyunjung Shin
- Department of Industrial Engineering, Ajou University, Yeongtong-gu, Suwon, South Korea
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Kim H, Lee M, Cha MU, Nam KH, An SY, Park S, Jhee JH, Yun HR, Kee YK, Park JT, Yoo TH, Kang SW, Han SH. Microscopic hematuria is a risk factor of incident chronic kidney disease in the Korean general population: a community-based prospective cohort study. QJM 2018; 111:389-397. [PMID: 29554373 DOI: 10.1093/qjmed/hcy054] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Although asymptomatic microscopic hematuria (MH) is a common finding in clinical practice, its long-term outcome remains unknown. AIM This study evaluated the clinical implication of MH in the general population using a large-scale long-term longitudinal cohort database. METHODS This study included 8719 participants from the Korean Genome and Epidemiology Study between 2001 and 2014. MH was defined as ≥5 red blood cells per high-power field in random urinalysis without evidence of pyuria. The primary study outcome measure was incident chronic kidney disease (CKD), defined as estimated glomerular filtration rate <60 ml min-1⋅1.73⋅m-2. RESULTS During a median follow-up of 11.7 years, CKD occurred in 677 (7.8%) subjects. In Cox regression after adjustment for multiple confounders, subjects with MH had a significantly higher risk of incident CKD than those without [hazard ratio (HR) 1.45, 95% confidence interval (CI) 1.12-1.87; P = 0.005]. Isolated MH without proteinuria was also a risk factor of incident CKD (HR 1.37, 95% CI 1.04-1.79; P = 0.023) and the risk was further increased in MH with concomitant proteinuria (HR 5.41, 95% CI 2.54-11.49; P < 0.001). In propensity score matching analysis after excluding subjects with proteinuria, multi-variable stratified Cox regression analysis revealed that subjects with isolated MH had a significantly higher risk of incident CKD than those without (HR 1.83, 95% CI 1.14-2.94; P = 0.012). CONCLUSION The presence of MH is associated with an increased risk of incident CKD in the general population. Therefore, attentive follow-up is warranted in persons with MH for early detection of CKD.
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Affiliation(s)
- H Kim
- Department of Internal Medicine, College of Medicine, Institute of Kidney Disease Research, Yonsei University, Seoul, Korea
- Division of Nephrology, Soonchunhyang University Hospital, Seoul, Korea
| | - M Lee
- Department of Internal Medicine, College of Medicine, Institute of Kidney Disease Research, Yonsei University, Seoul, Korea
| | - M-U Cha
- Department of Internal Medicine, College of Medicine, Institute of Kidney Disease Research, Yonsei University, Seoul, Korea
| | - K H Nam
- Department of Internal Medicine, College of Medicine, Institute of Kidney Disease Research, Yonsei University, Seoul, Korea
| | - S Y An
- Department of Internal Medicine, College of Medicine, Institute of Kidney Disease Research, Yonsei University, Seoul, Korea
| | - S Park
- Department of Internal Medicine, College of Medicine, Institute of Kidney Disease Research, Yonsei University, Seoul, Korea
| | - J H Jhee
- Department of Internal Medicine, College of Medicine, Institute of Kidney Disease Research, Yonsei University, Seoul, Korea
| | - H-R Yun
- Department of Internal Medicine, College of Medicine, Institute of Kidney Disease Research, Yonsei University, Seoul, Korea
| | - Y K Kee
- Department of Internal Medicine, Hangang Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Korea
| | - J T Park
- Department of Internal Medicine, College of Medicine, Institute of Kidney Disease Research, Yonsei University, Seoul, Korea
| | - T-H Yoo
- Department of Internal Medicine, College of Medicine, Institute of Kidney Disease Research, Yonsei University, Seoul, Korea
| | - S-W Kang
- Department of Internal Medicine, College of Medicine, Institute of Kidney Disease Research, Yonsei University, Seoul, Korea
| | - S H Han
- Department of Internal Medicine, College of Medicine, Institute of Kidney Disease Research, Yonsei University, Seoul, Korea
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