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Tang Y, Zhang Y, Li J. A time series driven model for early sepsis prediction based on transformer module. BMC Med Res Methodol 2024; 24:23. [PMID: 38273257 PMCID: PMC10809699 DOI: 10.1186/s12874-023-02138-6] [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: 09/10/2023] [Accepted: 12/27/2023] [Indexed: 01/27/2024] Open
Abstract
Sepsis remains a critical concern in intensive care units due to its high mortality rate. Early identification and intervention are paramount to improving patient outcomes. In this study, we have proposed predictive models for early sepsis prediction based on time-series data, utilizing both CNN-Transformer and LSTM-Transformer architectures. By collecting time-series data from patients at 4, 8, and 12 h prior to sepsis diagnosis and subjecting it to various network models for analysis and comparison. In contrast to traditional recurrent neural networks, our model exhibited a substantial improvement of approximately 20%. On average, our model demonstrated an accuracy of 0.964 (± 0.018), a precision of 0.956 (± 0.012), a recall of 0.967 (± 0.012), and an F1 score of 0.959 (± 0.014). Furthermore, by adjusting the time window, it was observed that the Transformer-based model demonstrated exceptional predictive capabilities, particularly within the earlier time window (i.e., 12 h before onset), thus holding significant promise for early clinical diagnosis and intervention. Besides, we employed the SHAP algorithm to visualize the weight distribution of different features, enhancing the interpretability of our model and facilitating early clinical diagnosis and intervention.
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Affiliation(s)
- Yan Tang
- Department of Clinical Laboratory Medicine, Jinniu Maternity and Child Health Hospital of Chengdu, Chengdu, China
| | - Yu Zhang
- Information Center, West China Hospital, Sichuan University, Chengdu, China
| | - Jiaxi Li
- Department of Clinical Laboratory Medicine, Jinniu Maternity and Child Health Hospital of Chengdu, Chengdu, China.
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Singh Aditya M, Rasipuram S, Chattopadhyay S, Maitra A, Sanjoy P, Maziyar BP, Roy D, Dey S. Early-warning of Cardiac Condition through Detection of Murmur in Heart Sound - A Case Study. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2023; 2023:1-6. [PMID: 38083243 DOI: 10.1109/embc40787.2023.10340924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Cardiovascular disease, particularly Rheumatic Heart Disease (RHD), is one of the leading causes of death in many developing countries. RHD is manageable and treatable with early detection. However, multiple countries across the globe suffer from a scarcity of experienced physicians who can perform screening at large scales. Advancements in machine learning and signal processing have paved way for Phonocardiogram (PCG)-based automatic heart sound classification. The direct implication of such methods is that it is possible to enable a person without specialized training to detect potential cardiac conditions with just a digital stethoscope. Hospitalization or life-threatening situations can be dramatically reduced via such early screenings. Towards this, we conducted a case study amongst a population from a particular geography using machine learning and deep learning methods for the detection of murmur in heart sounds. The methodology consists of first pre-processing and identifying normal vs. abnormal heart sound signals using 3 state-of-the-art methods. The second step further identifies the murmur to be systolic or diastolic by capturing the auscultation location. Abnormal findings are then sent for early attention of clinicians for proper diagnosis. The case study investigates the efficacy of the automated method employed for early screening of potential RHD and initial encouraging results of the study are presented.
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An efficient and robust Phonocardiography (PCG)-based Valvular Heart Diseases (VHD) detection framework using Vision Transformer (ViT). Comput Biol Med 2023; 158:106734. [PMID: 36989745 DOI: 10.1016/j.compbiomed.2023.106734] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 01/31/2023] [Accepted: 02/28/2023] [Indexed: 03/05/2023]
Abstract
BACKGROUND AND OBJECTIVES Valvular heart diseases (VHDs) are one of the dominant causes of cardiovascular abnormalities that have been associated with high mortality rates globally. Rapid and accurate diagnosis of the early stage of VHD based on cardiac phonocardiogram (PCG) signal is critical that allows for optimum medication and reduction of mortality rate. METHODS To this end, the current study proposes novel deep learning (DL)-based high-performance VHD detection frameworks that are relatively simpler in terms of network structures, yet effective for accurately detecting multiple VHDs. We present three different frameworks considering both 1D and 2D PCG raw signals. For 1D PCG, Mel frequency cepstral coefficients (MFCC) and linear prediction cepstral coefficients (LPCC) features, whereas, for 2D PCG, various deep convolutional neural networks (D-CNNs) features are extracted. Additionally, nature/bio-inspired algorithms (NIA/BIA) including particle swarm optimization (PSO) and genetic algorithm (GA) have been utilized for automatic and efficient feature selection directly from the raw PCG signal. To further improve the performance of the classifier, vision transformer (ViT) has been implemented levering the self-attention mechanism on the time frequency representation (TFR) of 2D PCG signal. Our extensive study presents a comparative performance analysis and the scope of enhancement for the combination of different descriptors, classifiers, and feature selection algorithms. MAIN RESULTS Among all classifiers, ViT provides the best performance by achieving mean average accuracy Acc of 99.90 % and F1-score of 99.95 % outperforming current state-of-the-art VHD classification models. CONCLUSIONS The present research provides a robust and efficient DL-based end-to-end PCG signal classification framework for designing a automated high-performance VHD diagnosis system.
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PCG signal classification using a hybrid multi round transfer learning classifier. Biocybern Biomed Eng 2023. [DOI: 10.1016/j.bbe.2023.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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A Computer-Aided Heart Valve Disease Diagnosis System Based on Machine Learning. JOURNAL OF HEALTHCARE ENGINEERING 2023; 2023:7382316. [PMID: 36726774 PMCID: PMC9886464 DOI: 10.1155/2023/7382316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/24/2023]
Abstract
Cardiac auscultation is a noninvasive, convenient, and low-cost diagnostic method for heart valvular disease, and it can diagnose the abnormality of the heart valve at an early stage. However, the accuracy of auscultation relies on the professionalism of cardiologists. Doctors in remote areas may lack the experience to diagnose correctly. Therefore, it is necessary to design a system to assist with the diagnosis. This study proposed a computer-aided heart valve disease diagnosis system, including a heart sound acquisition module, a trained model for diagnosis, and software, which can diagnose four kinds of heart valve diseases. In this study, a training dataset containing five categories of heart sounds was collected, including normal, mitral stenosis, mitral regurgitation, and aortic stenosis heart sound. A convolutional neural network GoogLeNet and weighted KNN are used to train the models separately. For the model trained by the convolutional neural network, time series heart sound signals are converted into time-frequency scalograms based on continuous wavelet transform to adapt to the architecture of GoogLeNet. For the model trained by weighted KNN, features from the time domain and time-frequency domain are extracted manually. Then feature selection based on the chi-square test is performed to get a better group of features. Moreover, we designed software that lets doctors upload heart sounds, visualize the heart sound waveform, and use the model to get the diagnosis. Model assessments using accuracy, sensitivity, specificity, and F1 score indicators are done on two trained models. The results showed that the model trained by modified GoogLeNet outperformed others, with an overall accuracy of 97.5%. The average accuracy, sensitivity, specificity, and F1 score for diagnosing four kinds of heart valve diseases are 98.75%, 96.88%, 99.22%, and 97.99%, respectively. The computer-aided diagnosis system, with a heart sound acquisition module, a diagnostic model, and software, can visualize the heart sound waveform and show the reference diagnostic results. This can assist in the diagnosis of heart valve diseases, especially in remote areas, which lack skilled doctors.
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Chen Q, Li R, Lin C, Lai C, Chen D, Qu H, Huang Y, Lu W, Tang Y, Li L. Transferability and interpretability of the sepsis prediction models in the intensive care unit. BMC Med Inform Decis Mak 2022; 22:343. [PMID: 36581881 PMCID: PMC9798724 DOI: 10.1186/s12911-022-02090-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 12/16/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND We aimed to develop an early warning system for real-time sepsis prediction in the ICU by machine learning methods, with tools for interpretative analysis of the predictions. In particular, we focus on the deployment of the system in a target medical center with small historical samples. METHODS Light Gradient Boosting Machine (LightGBM) and multilayer perceptron (MLP) were trained on Medical Information Mart for Intensive Care (MIMIC-III) dataset and then finetuned on the private Historical Database of local Ruijin Hospital (HDRJH) using transfer learning technique. The Shapley Additive Explanations (SHAP) analysis was employed to characterize the feature importance in the prediction inference. Ultimately, the performance of the sepsis prediction system was further evaluated in the real-world study in the ICU of the target Ruijin Hospital. RESULTS The datasets comprised 6891 patients from MIMIC-III, 453 from HDRJH, and 67 from Ruijin real-world data. The area under the receiver operating characteristic curves (AUCs) for LightGBM and MLP models derived from MIMIC-III were 0.98 - 0.98 and 0.95 - 0.96 respectively on MIMIC-III dataset, and, in comparison, 0.82 - 0.86 and 0.84 - 0.87 respectively on HDRJH, from 1 to 5 h preceding. After transfer learning and ensemble learning, the AUCs of the final ensemble model were enhanced to 0.94 - 0.94 on HDRJH and to 0.86 - 0.9 in the real-world study in the ICU of the target Ruijin Hospital. In addition, the SHAP analysis illustrated the importance of age, antibiotics, net balance, and ventilation for sepsis prediction, making the model interpretable. CONCLUSIONS Our machine learning model allows accurate real-time prediction of sepsis within 5-h preceding. Transfer learning can effectively improve the feasibility to deploy the prediction model in the target cohort, and ameliorate the model performance for external validation. SHAP analysis indicates that the role of antibiotic usage and fluid management needs further investigation. We argue that our system and methodology have the potential to improve ICU management by helping medical practitioners identify at-sepsis-risk patients and prepare for timely diagnosis and intervention. TRIAL REGISTRATION NCT05088850 (retrospectively registered).
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Affiliation(s)
- Qiyu Chen
- grid.8547.e0000 0001 0125 2443Department of Applied Mathematics, School of Mathematical Sciences, Fudan University, Shanghai, 200433 China
| | - Ranran Li
- grid.16821.3c0000 0004 0368 8293Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025 China
| | - ChihChe Lin
- grid.495525.a0000 0004 0552 4356Shanghai Electric Group Co., Ltd., Central Academe, Shanghai, China
| | - Chiming Lai
- grid.495525.a0000 0004 0552 4356Shanghai Electric Group Co., Ltd., Central Academe, Shanghai, China
| | - Dechang Chen
- grid.16821.3c0000 0004 0368 8293Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025 China
| | - Hongping Qu
- grid.16821.3c0000 0004 0368 8293Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025 China
| | - Yaling Huang
- grid.495525.a0000 0004 0552 4356Shanghai Electric Group Co., Ltd., Central Academe, Shanghai, China
| | - Wenlian Lu
- grid.8547.e0000 0001 0125 2443Department of Applied Mathematics, School of Mathematical Sciences, Fudan University, Shanghai, 200433 China
| | - Yaoqing Tang
- grid.16821.3c0000 0004 0368 8293Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025 China
| | - Lei Li
- grid.16821.3c0000 0004 0368 8293Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025 China
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An audio processing pipeline for acquiring diagnostic quality heart sounds via mobile phone. Comput Biol Med 2022; 145:105415. [PMID: 35366471 DOI: 10.1016/j.compbiomed.2022.105415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/22/2022] [Accepted: 03/14/2022] [Indexed: 11/27/2022]
Abstract
Recently, heart sound signals captured using mobile phones have been employed to develop data-driven heart disease detection systems. Such signals are generally captured in person by trained clinicians who can determine if the recorded heart sounds are of diagnosable quality. However, mobile phones have the potential to support heart health diagnostics, even where access to trained medical professionals is limited. To adopt mobile phones as self-diagnostic tools for the masses, we would need to have a mechanism to automatically establish that heart sounds recorded by non-expert users in uncontrolled conditions have the required quality for diagnostic purposes. This paper proposes a quality assessment and enhancement pipeline for heart sounds captured using mobile phones. The pipeline analyzes a heart sound and determines if it has the required quality for diagnostic tasks. Also, in cases where the quality of the captured signal is below the required threshold, the pipeline can improve the quality by applying quality enhancement algorithms. Using this pipeline, we can also provide feedback to users regarding the cause of low-quality signal capture and guide them towards a successful one. We conducted a survey of a group of thirteen clinicians with auscultation skills and experience. The results of this survey were used to inform and validate the proposed quality assessment and enhancement pipeline. We observed a high level of agreement between the survey results and fundamental design decisions within the proposed pipeline. Also, the results indicate that the proposed pipeline can reduce our dependency on trained clinicians for capture of diagnosable heart sounds.
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Ebbehoj A, Thunbo MØ, Andersen OE, Glindtvad MV, Hulman A. Transfer learning for non-image data in clinical research: A scoping review. PLOS DIGITAL HEALTH 2022; 1:e0000014. [PMID: 36812540 PMCID: PMC9931256 DOI: 10.1371/journal.pdig.0000014] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/15/2021] [Indexed: 01/14/2023]
Abstract
BACKGROUND Transfer learning is a form of machine learning where a pre-trained model trained on a specific task is reused as a starting point and tailored to another task in a different dataset. While transfer learning has garnered considerable attention in medical image analysis, its use for clinical non-image data is not well studied. Therefore, the objective of this scoping review was to explore the use of transfer learning for non-image data in the clinical literature. METHODS AND FINDINGS We systematically searched medical databases (PubMed, EMBASE, CINAHL) for peer-reviewed clinical studies that used transfer learning on human non-image data. We included 83 studies in the review. More than half of the studies (63%) were published within 12 months of the search. Transfer learning was most often applied to time series data (61%), followed by tabular data (18%), audio (12%) and text (8%). Thirty-three (40%) studies applied an image-based model to non-image data after transforming data into images (e.g. spectrograms). Twenty-nine (35%) studies did not have any authors with a health-related affiliation. Many studies used publicly available datasets (66%) and models (49%), but fewer shared their code (27%). CONCLUSIONS In this scoping review, we have described current trends in the use of transfer learning for non-image data in the clinical literature. We found that the use of transfer learning has grown rapidly within the last few years. We have identified studies and demonstrated the potential of transfer learning in clinical research in a wide range of medical specialties. More interdisciplinary collaborations and the wider adaption of reproducible research principles are needed to increase the impact of transfer learning in clinical research.
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Affiliation(s)
- Andreas Ebbehoj
- Department of Endocrinology and Internal Medicine, Aarhus University Hospital, Denmark
- Department of Clinical Medicine, Aarhus University, Denmark
| | | | | | | | - Adam Hulman
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Denmark
- * E-mail:
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Mazzu-Nascimento T, Evangelista DN, Abubakar O, Roscani MG, Aguilar RS, Chachá SGF, Rosa PRD, Silva DF. Smartphone-Based Screening for Cardiovascular Diseases: A Trend? INTERNATIONAL JOURNAL OF CARDIOVASCULAR SCIENCES 2021. [DOI: 10.36660/ijcs.20210096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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