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Alatrany AS, Khan W, Hussain A, Kolivand H, Al-Jumeily D. An explainable machine learning approach for Alzheimer's disease classification. Sci Rep 2024; 14:2637. [PMID: 38302557 PMCID: PMC10834965 DOI: 10.1038/s41598-024-51985-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 01/11/2024] [Indexed: 02/03/2024] Open
Abstract
The early diagnosis of Alzheimer's disease (AD) presents a significant challenge due to the subtle biomarker changes often overlooked. Machine learning (ML) models offer a promising tool for identifying individuals at risk of AD. However, current research tends to prioritize ML accuracy while neglecting the crucial aspect of model explainability. The diverse nature of AD data and the limited dataset size introduce additional challenges, primarily related to high dimensionality. In this study, we leveraged a dataset obtained from the National Alzheimer's Coordinating Center, comprising 169,408 records and 1024 features. After applying various steps to reduce the feature space. Notably, support vector machine (SVM) models trained on the selected features exhibited high performance when tested on an external dataset. SVM achieved a high F1 score of 98.9% for binary classification (distinguishing between NC and AD) and 90.7% for multiclass classification. Furthermore, SVM was able to predict AD progression over a 4-year period, with F1 scores reached 88% for binary task and 72.8% for multiclass task. To enhance model explainability, we employed two rule-extraction approaches: class rule mining and stable and interpretable rule set for classification model. These approaches generated human-understandable rules to assist domain experts in comprehending the key factors involved in AD development. We further validated these rules using SHAP and LIME models, underscoring the significance of factors such as MEMORY, JUDGMENT, COMMUN, and ORIENT in determining AD risk. Our experimental outcomes also shed light on the crucial role of the Clinical Dementia Rating tool in predicting AD.
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Affiliation(s)
- Abbas Saad Alatrany
- School of Computer Science and Mathematics, Liverpool John Moores University, Liverpool, UK.
- University of Information Technology and Communications, Baghdad, Iraq.
- Imam Ja'afar Al-Sadiq University, Baghdad, Iraq.
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK.
| | - Wasiq Khan
- School of Computer Science and Mathematics, Liverpool John Moores University, Liverpool, UK
| | - Abir Hussain
- School of Computer Science and Mathematics, Liverpool John Moores University, Liverpool, UK.
- Department of Electrical Engineering, University of Sharjah, Sharjah, United Arab Emirates.
| | - Hoshang Kolivand
- School of Computer Science and Mathematics, Liverpool John Moores University, Liverpool, UK
| | - Dhiya Al-Jumeily
- School of Computer Science and Mathematics, Liverpool John Moores University, Liverpool, UK
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Rhodes JS, Aumon A, Morin S, Girard M, Larochelle C, Brunet-Ratnasingham E, Pagliuzza A, Marchitto L, Zhang W, Cutler A, Grand'Maison F, Zhou A, Finzi A, Chomont N, Kaufmann DE, Zandee S, Prat A, Wolf G, Moon KR. Gaining Biological Insights through Supervised Data Visualization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.22.568384. [PMID: 38293135 PMCID: PMC10827133 DOI: 10.1101/2023.11.22.568384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Dimensionality reduction-based data visualization is pivotal in comprehending complex biological data. The most common methods, such as PHATE, t-SNE, and UMAP, are unsupervised and therefore reflect the dominant structure in the data, which may be independent of expert-provided labels. Here we introduce a supervised data visualization method called RF-PHATE, which integrates expert knowledge for further exploration of the data. RF-PHATE leverages random forests to capture intricate featurelabel relationships. Extracting information from the forest, RF-PHATE generates low-dimensional visualizations that highlight relevant data relationships while disregarding extraneous features. This approach scales to large datasets and applies to classification and regression. We illustrate RF-PHATE's prowess through three case studies. In a multiple sclerosis study using longitudinal clinical and imaging data, RF-PHATE unveils a sub-group of patients with non-benign relapsingremitting Multiple Sclerosis, demonstrating its aptitude for time-series data. In the context of Raman spectral data, RF-PHATE effectively showcases the impact of antioxidants on diesel exhaust-exposed lung cells, highlighting its proficiency in noisy environments. Furthermore, RF-PHATE aligns established geometric structures with COVID-19 patient outcomes, enriching interpretability in a hierarchical manner. RF-PHATE bridges expert insights and visualizations, promising knowledge generation. Its adaptability, scalability, and noise tolerance underscore its potential for widespread adoption.
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Bai L, Wu Y, Li G, Zhang W, Zhang H, Su J. AI-enabled organoids: Construction, analysis, and application. Bioact Mater 2024; 31:525-548. [PMID: 37746662 PMCID: PMC10511344 DOI: 10.1016/j.bioactmat.2023.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 09/09/2023] [Accepted: 09/09/2023] [Indexed: 09/26/2023] Open
Abstract
Organoids, miniature and simplified in vitro model systems that mimic the structure and function of organs, have attracted considerable interest due to their promising applications in disease modeling, drug screening, personalized medicine, and tissue engineering. Despite the substantial success in cultivating physiologically relevant organoids, challenges remain concerning the complexities of their assembly and the difficulties associated with data analysis. The advent of AI-Enabled Organoids, which interfaces with artificial intelligence (AI), holds the potential to revolutionize the field by offering novel insights and methodologies that can expedite the development and clinical application of organoids. This review succinctly delineates the fundamental concepts and mechanisms underlying AI-Enabled Organoids, summarizing the prospective applications on rapid screening of construction strategies, cost-effective extraction of multiscale image features, streamlined analysis of multi-omics data, and precise preclinical evaluation and application. We also explore the challenges and limitations of interfacing organoids with AI, and discuss the future direction of the field. Taken together, the AI-Enabled Organoids hold significant promise for advancing our understanding of organ development and disease progression, ultimately laying the groundwork for clinical application.
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Affiliation(s)
- Long Bai
- Department of Orthopedics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
- Organoid Research Center, Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
- National Center for Translational Medicine (Shanghai) SHU Branch, Shanghai University, Shanghai, 200444, China
- Wenzhou Institute of Shanghai University, Wenzhou, 325000, China
| | - Yan Wu
- Department of Orthopedics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
- Organoid Research Center, Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
- National Center for Translational Medicine (Shanghai) SHU Branch, Shanghai University, Shanghai, 200444, China
| | - Guangfeng Li
- Organoid Research Center, Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
- National Center for Translational Medicine (Shanghai) SHU Branch, Shanghai University, Shanghai, 200444, China
- Department of Orthopedics, Shanghai Zhongye Hospital, Shanghai, 201941, China
| | - Wencai Zhang
- Department of Orthopedics, First Affiliated Hospital, Jinan University, Guangzhou, 510632, China
| | - Hao Zhang
- Department of Orthopedics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
- Organoid Research Center, Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
- National Center for Translational Medicine (Shanghai) SHU Branch, Shanghai University, Shanghai, 200444, China
| | - Jiacan Su
- Department of Orthopedics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
- Organoid Research Center, Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
- National Center for Translational Medicine (Shanghai) SHU Branch, Shanghai University, Shanghai, 200444, China
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Li F, Bi Z, Xu H, Shi Y, Duan N, Li Z. Design and implementation of a smart Internet of Things chest pain center based on deep learning. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:18987-19011. [PMID: 38052586 DOI: 10.3934/mbe.2023840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
The data input process for most chest pain centers is not intelligent, requiring a lot of staff to manually input patient information. This leads to problems such as long processing times, high potential for errors, an inability to access patient data in a timely manner and an increasing workload. To address the challenge, an Internet of Things (IoT)-driven chest pain center is designed, which crosses the sensing layer, network layer and application layer. The system enables the construction of intelligent chest pain management through a pre-hospital app, Ultra-Wideband (UWB) positioning, and in-hospital treatment. The pre-hospital app is provided to emergency medical services (EMS) centers, which allows them to record patient information in advance and keep it synchronized with the hospital's database, reducing the time needed for treatment. UWB positioning obtains the patient's hospital information through the zero-dimensional base station and the corresponding calculation engine, and in-hospital treatment involves automatic acquisition of patient information through web and mobile applications. The system also introduces the Bidirectional Long Short-Term Memory (BiLSTM)-Conditional Random Field (CRF)-based algorithm to train electronic medical record information for chest pain patients, extracting the patient's chest pain clinical symptoms. The resulting data are saved in the chest pain patient database and uploaded to the national chest pain center. The system has been used in Liaoning Provincial People's Hospital, and its subsequent assistance to doctors and nurses in collaborative treatment, data feedback and analysis is of great significance.
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Affiliation(s)
- Feng Li
- School of Information and Electronic Engineering, Zhejiang Gongshang University, Hangzhou 310018, China
- School of Computer Science and Engineering, Nanyang Technological University, 639798, Singapore
| | - Zhongao Bi
- School of Information and Electronic Engineering, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Hongzeng Xu
- Department of Cardiology, The People's Hospital of Liaoning Province, Liaoning, Shenyang 110011, China
| | - Yunqi Shi
- Department of Cardiology, The People's Hospital of Liaoning Province, Liaoning, Shenyang 110011, China
| | - Na Duan
- Department of Cardiology, The People's Hospital of Liaoning Province, Liaoning, Shenyang 110011, China
| | - Zhaoyu Li
- Department of Cardiology, The Second Affiliated Hospital Zhejiang University School of Medicine, Hangzhou 310000, China
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Rao C, Huang Q, Chen L, Goh M, Hu Z. Forecasting the carbon emissions in Hubei Province under the background of carbon neutrality: a novel STIRPAT extended model with ridge regression and scenario analysis. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:57460-57480. [PMID: 36964474 PMCID: PMC10038777 DOI: 10.1007/s11356-023-26599-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 03/17/2023] [Indexed: 05/07/2023]
Abstract
The impact of global greenhouse gas emissions is increasingly serious, and the development of green low-carbon circular economy has become an inevitable trend for the development of all countries in the world. To achieve emission peak and carbon neutrality is the primary goal of energy conservation and emission reduction. As the core province in central China, Hubei Province is under prominent pressure of carbon emission reduction. In this paper, the future development trend of carbon emissions is analyzed, and the emission peak value and carbon peak time in Hubei Province is predicted. Firstly, the generalized Divisia index method (GDIM) model is proposed to determine the main influencing factors of carbon emissions in Hubei Province. Secondly, based on the main influencing factors identified, a novel STIRPAT (Stochastic Impacts by Regression on Population, Affluence, and Technology) extended model with ridge regression is established to predict carbon emissions. Thirdly, the scenario analysis method is used to set the variables of the STIRPAT extended model and to predict the emission peak value and carbon peak time in Hubei Province. The results show that Hubei Province's carbon emissions peaked first in 2025, with a peak value of 361.81 million tons. Finally, according to the prediction results, the corresponding suggestions on carbon emission reduction are provided in three aspects of industrial structure, energy structure, and urbanization, so as to help government establish a green, low-carbon, and circular development economic system and achieve the industry's cleaner production and sustainable development of society.
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Affiliation(s)
- Congjun Rao
- School of Science, Wuhan University of Technology, Wuhan, 430070, People's Republic of China
| | - Qifan Huang
- School of Science, Wuhan University of Technology, Wuhan, 430070, People's Republic of China
| | - Lin Chen
- School of Management, Wuhan Institute of Technology, Wuhan, 430205, People's Republic of China
| | - Mark Goh
- NUS Business School & The Logistics Institute-Asia Pacific, National University of Singapore, Singapore, 119623, Singapore
| | - Zhuo Hu
- School of Automation, Wuhan University of Technology, Wuhan, 430070, People's Republic of China.
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Trigka M, Dritsas E. Long-Term Coronary Artery Disease Risk Prediction with Machine Learning Models. SENSORS (BASEL, SWITZERLAND) 2023; 23:1193. [PMID: 36772237 PMCID: PMC9920214 DOI: 10.3390/s23031193] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
The heart is the most vital organ of the human body; thus, its improper functioning has a significant impact on human life. Coronary artery disease (CAD) is a disease of the coronary arteries through which the heart is nourished and oxygenated. It is due to the formation of atherosclerotic plaques on the wall of the epicardial coronary arteries, resulting in the narrowing of their lumen and the obstruction of blood flow through them. Coronary artery disease can be delayed or even prevented with lifestyle changes and medical intervention. Long-term risk prediction of coronary artery disease will be the area of interest in this work. In this specific research paper, we experimented with various machine learning (ML) models after the use or non-use of the synthetic minority oversampling technique (SMOTE), evaluating and comparing them in terms of accuracy, precision, recall and an area under the curve (AUC). The results showed that the stacking ensemble model after the SMOTE with 10-fold cross-validation prevailed over the other models, achieving an accuracy of 90.9 %, a precision of 96.7%, a recall of 87.6% and an AUC equal to 96.1%.
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Rao C, Gao M, Goh M, Xiao X. Green Supplier Selection Mechanism Based on Information Environment of Z-Numbers. Cognit Comput 2022. [DOI: 10.1007/s12559-022-10055-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Rao C, Liu Y, Goh M. Credit risk assessment mechanism of personal auto loan based on PSO-XGBoost Model. COMPLEX INTELL SYST 2022. [DOI: 10.1007/s40747-022-00854-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AbstractAs online P2P loans in automotive financing grows, there is a need to manage and control the credit risk of the personal auto loans. In this paper, the personal auto loans data sets on the Kaggle platform are used on a machine learning based credit risk assessment mechanism for personal auto loans. An integrated Smote-Tomek Link algorithm is proposed to convert the data set into a balanced data set. Then, an improved Filter-Wrapper feature selection method is presented to select credit risk assessment indexes for the loans. Combining Particle Swarm Optimization (PSO) with the eXtreme Gradient Boosting (XGBoost) model, a PSO-XGBoost model is formed to assess the credit risk of the loans. The PSO-XGBoost model is compared against the XGBoost, Random Forest, and Logistic Regression models on the standard performance evaluation indexes of accuracy, precision, ROC curve, and AUC value. The PSO-XGBoost model is found to be superior on classification performance and classification effect.
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Peng JJ, Chen XG, Tian C, Zhang ZQ, Song HY, Dong F. Picture fuzzy large-scale group decision-making in a trust- relationship-based social network environment. Inf Sci (N Y) 2022. [DOI: 10.1016/j.ins.2022.07.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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A Boundedly Rational Decision-Making Model Based on Weakly Consistent Preference Relations. Symmetry (Basel) 2022. [DOI: 10.3390/sym14050918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Completeness is one of the basic assumptions about the rational preference relation in classical decision theory. Strongly and weakly consistent preferences are presented by abandoning the completeness of the rational preference relation. Some expansion and contraction conditions are proposed and the relationships between these conditions of rationality are discussed. The relationships between the conditions of rationality and boundedly rational choice behavior based on strongly and weakly consistent preferences are analyzed and discussed. Furthermore, an example about the choices of chocolates with interval ordinal numbers is given to explain some of the main conclusions in this paper. The results can be used as references for the study of boundedly rational decisions.
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