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Guo S, Zhang R, Wang T, Wang J. Comparative study of machine-and deep-learning based classification algorithms for biomedical Raman spectroscopy (RS): case study of RS based pathogenic microbe identification. ANAL SCI 2024; 40:2101-2109. [PMID: 39207655 DOI: 10.1007/s44211-024-00645-0] [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: 04/22/2024] [Accepted: 08/01/2024] [Indexed: 09/04/2024]
Abstract
One key aspect pushing the frontiers of biomedical RS is dedicated machine- or deep- learning (ML or DL) algorithms. Yet, systematic comparative study between ML and DL algorithms has not been conducted for biomedical RS, largely due to the limited availability of open-source and large Raman spectra dataset. Therefore we compared typical ML partial least square-discriminant analysis (PLS-DA) and DL one dimensional convolution neural network (1D-CNN) based pathogenic microbe identification on 12,000 Raman spectra from six species of microbe (i.e., K. aerogenes (Klebsiella aerogenes), C. albicans (Candida albicans), C. glabrata (Candida glabrata), Group A Strep. (Group A Streptococcus), E. coli1 (Escherichia coli1), E. coli2 (Escherichia coli2)) when 100%, 75%, 50% and 25% of the 12,000 Raman spectra were retained. The total Raman dataset was analyzed with 80% split for training and 20% for testing. The 100% retained testing dataset accuracy, area under curve (AUC) of the receiver operating characteristic (ROC) curve were 95.25% and 0.997 for 1D-CNN, which are higher than those (89.42% and 0.979) of PLS-DA. Yet, PLS-DA outperforms 1D-CNN for 75%, 50% and 25% retained testing dataset. The resultant accuracies and AUCs demonstrated the performance reliance of PLS-DA and 1D-CNN on Raman spectra number. Besides, both loadings on the latent variables of PLS-DA and the saliency maps of 1D-CNN largely captured Raman peaks arising from DNA and proteins with comparable interpretability. The results of the current work indicated that both ML and DL algorithms should be explored for application-wise Raman spectra identification to select whichever with higher accuracies and AUCs.
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Affiliation(s)
- Sisi Guo
- Key Laboratory of Photoelectronic Imaging Technology and System of Ministry of Education of China, School of Optics and Photonics, Beijing Institute of Technology, Beijing, 100081, China
| | - Ruoyu Zhang
- School of Medical Technology, Beijing Institute of Technology, Beijing, 100081, China
| | - Tao Wang
- Department of Gastroenterology, the First Medical Center of PLA General Hospital, Beijing, 100853, China.
| | - Jianfeng Wang
- Key Laboratory of Photoelectronic Imaging Technology and System of Ministry of Education of China, School of Optics and Photonics, Beijing Institute of Technology, Beijing, 100081, China.
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Duan Y, Wang R, Huang Z, Chen H, Tang M, Zhou J, Hu Z, Hu W, Chen Z, Qian Q, Wang H. Intelligent diagnosis of Kawasaki disease from real-world data using interpretable machine learning models. Hellenic J Cardiol 2024:S1109-9666(24)00170-2. [PMID: 39128707 DOI: 10.1016/j.hjc.2024.08.003] [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: 03/06/2024] [Revised: 07/14/2024] [Accepted: 08/04/2024] [Indexed: 08/13/2024] Open
Abstract
OBJECTIVE This study aimed to leverage real-world electronic medical record data to develop interpretable machine learning models for diagnosis of Kawasaki disease while also exploring and prioritizing the significant risk factors. METHODS A comprehensive study was conducted on 4087 pediatric patients at the Children's Hospital of Chongqing, China. The study collected demographic data, physical examination results, and laboratory findings. Statistical analyses were performed using IBM SPSS Statistics, Version 26.0. The optimal feature subset was used to develop intelligent diagnostic prediction models based on the Light Gradient Boosting Machine, Explainable Boosting Machine (EBM), Gradient Boosting Classifier (GBC), Fast Interpretable Greedy-Tree Sums, Decision Tree, AdaBoost Classifier, and Logistic Regression. Model performance was evaluated in three dimensions: discriminative ability via receiver operating characteristic curves, calibration accuracy using calibration curves, and interpretability through SHAP (SHapley Additive exPlanations) and LIME (Local Interpretable Model-Agnostic Explanations). RESULTS In this study, Kawasaki disease was diagnosed in 2971 participants. Analysis was conducted on 31 indicators, including red blood cell distribution width and erythrocyte sedimentation rate. The EBM model demonstrated superior performance relative to other models, with an area under the curve of 0.97, second only to the GBC model. Furthermore, the EBM model exhibited the highest calibration accuracy and maintained its interpretability without relying on external analytical tools such as SHAP and LIME, thus reducing interpretation biases. Platelet distribution width, total protein, and erythrocyte sedimentation rate were identified by the model as significant predictors for the diagnosis of Kawasaki disease. CONCLUSION This study used diverse machine learning models for early diagnosis of Kawasaki disease. The findings demonstrated that interpretable models such as EBM outperformed traditional machine learning models in terms of both interpretability and performance. Ensuring consistency between predictive models and clinical evidence is crucial for the successful integration of artificial intelligence into real-world clinical practice.
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Affiliation(s)
- Yifan Duan
- Institute of Medical Information, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100020, PR China
| | - Ruiqi Wang
- College of Medical Informatics, Chongqing Medical University, Chongqing 400016, PR China
| | - Zhilin Huang
- Children's Hospital of Chongqing Medical University, Chongqing 400014, PR China
| | - Haoran Chen
- Institute of Medical Information, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100020, PR China
| | - Mingkun Tang
- Institute of Medical Information, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100020, PR China
| | - Jiayin Zhou
- Institute of Medical Information, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100020, PR China
| | - Zhengyong Hu
- Institute of Medical Information, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100020, PR China
| | - Wanfei Hu
- Institute of Medical Information, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100020, PR China
| | - Zhenli Chen
- Institute of Medical Information, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100020, PR China
| | - Qing Qian
- Institute of Medical Information, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100020, PR China.
| | - Haolin Wang
- College of Medical Informatics, Chongqing Medical University, Chongqing 400016, PR China.
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Koyun OC, Keser RK, Şahin SO, Bulut D, Yorulmaz M, Yücesoy V, Töreyin BU. RamanFormer: A Transformer-Based Quantification Approach for Raman Mixture Components. ACS OMEGA 2024; 9:23241-23251. [PMID: 38854537 PMCID: PMC11154961 DOI: 10.1021/acsomega.3c09247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 05/03/2024] [Accepted: 05/10/2024] [Indexed: 06/11/2024]
Abstract
Raman spectroscopy is a noninvasive technique to identify materials by their unique molecular vibrational fingerprints. However, distinguishing and quantifying components in mixtures present challenges due to overlapping spectra, especially when components share similar features. This study presents "RamanFormer", a transformer-based model designed to enhance the analysis of Raman spectroscopy data. By effectively managing sequential data and integrating self-attention mechanisms, RamanFormer identifies and quantifies components in chemical mixtures with high precision, achieving a mean absolute error of 1.4% and a root mean squared error of 1.6%, significantly outperforming traditional methods such as least squares, MLP, VGG11, and ResNet50. Tested extensively on binary and ternary mixtures under varying conditions, including noise levels with a signal-to-noise ratio of up to 10 dB, RamanFormer proves to be a robust tool, improving the reliability of material identification and broadening the application of Raman spectroscopy in fields, such as material science, forensics, and biomedical diagnostics.
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Affiliation(s)
- Onur Can Koyun
- Signal
Processing for Computational Intelligence Research Group (SP4CING),
Informatics Institute, Istanbul Technical
University, 34469 Istanbul, Turkey
| | - Reyhan Kevser Keser
- Signal
Processing for Computational Intelligence Research Group (SP4CING),
Informatics Institute, Istanbul Technical
University, 34469 Istanbul, Turkey
| | | | - Damla Bulut
- ASELSAN
Inc, Yenimahalle, 06200 Ankara, Turkey
| | | | | | - Behçet Uğur Töreyin
- Signal
Processing for Computational Intelligence Research Group (SP4CING),
Informatics Institute, Istanbul Technical
University, 34469 Istanbul, Turkey
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Zhuang Y, Ouyang Y, Ding L, Xu M, Shi F, Shan D, Cao D, Cao X. Source Tracing of Kidney Injury via the Multispectral Fingerprint Identified by Machine Learning-Driven Surface-Enhanced Raman Spectroscopic Analysis. ACS Sens 2024; 9:2622-2633. [PMID: 38700898 DOI: 10.1021/acssensors.4c00407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Early diagnosis of drug-induced kidney injury (DIKI) is essential for clinical treatment and intervention. However, developing a reliable method to trace kidney injury origins through retrospective studies remains a challenge. In this study, we designed ordered fried-bun-shaped Au nanocone arrays (FBS NCAs) to create microarray chips as a surface-enhanced Raman scattering (SERS) analysis platform. Subsequently, the principal component analysis (PCA)-two-layer nearest neighbor (TLNN) model was constructed to identify and analyze the SERS spectra of exosomes from renal injury induced by cisplatin and gentamycin. The established PCA-TLNN model successfully differentiated the SERS spectra of exosomes from renal injury at different stages and causes, capturing the most significant spectral features for distinguishing these variations. For the SERS spectra of exosomes from renal injury at different induction times, the accuracy of PCA-TLNN reached 97.8% (cisplatin) and 93.3% (gentamicin). For the SERS spectra of exosomes from renal injury caused by different agents, the accuracy of PCA-TLNN reached 100% (7 days) and 96.7% (14 days). This study demonstrates that the combination of label-free exosome SERS and machine learning could serve as an innovative strategy for medical diagnosis and therapeutic intervention.
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Affiliation(s)
- Yanwen Zhuang
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou 225001, P. R. China
| | - Yu Ouyang
- Department of Clinical Laboratory, The Affiliated Taizhou Second People's Hospital of Yangzhou University, Taizhou 225300, P. R. China
| | - Li Ding
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou 225001, P. R. China
| | - Miaowen Xu
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou 225001, P. R. China
| | - Fanfeng Shi
- Yangzhou Polytechnic Institute, Yangzhou 225002, P. R. China
| | - Dan Shan
- School of Information Engineering/Carbon Based Low Dimensional Semiconductor Materials and Device Engineering Research Center of Jiangsu Province, Yangzhou Polytechnic Institute, Yangzhou 225127, P. R. China
| | - Dawei Cao
- Yangzhou Polytechnic Institute, Yangzhou 225002, P. R. China
- School of Information Engineering/Carbon Based Low Dimensional Semiconductor Materials and Device Engineering Research Center of Jiangsu Province, Yangzhou Polytechnic Institute, Yangzhou 225127, P. R. China
| | - Xiaowei Cao
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou 225001, P. R. China
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Medical College, Yangzhou University, Yangzhou 225001, P. R. China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Medical College, Yangzhou University, Yangzhou 225001, P. R. China
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Chheda J, Fang Y, Deriu C, Ezzat AA, Fabris L. Discrimination of Genetic Biomarkers of Disease through Machine-Learning-Based Hypothesis Testing of Direct SERS Spectra of DNA and RNA. ACS Sens 2024; 9:2488-2498. [PMID: 38684231 DOI: 10.1021/acssensors.4c00166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Cancer is globally a leading cause of death that would benefit from diagnostic approaches detecting it in its early stages. However, despite much research and investment, cancer early diagnosis is still underdeveloped. Owing to its high sensitivity, surface-enhanced Raman spectroscopy (SERS)-based detection of biomarkers has attracted growing interest in this area. Oligonucleotides are an important type of genetic biomarkers as their alterations can be linked to the disease prior to symptom onset. We propose a machine-learning (ML)-enabled framework to analyze complex direct SERS spectra of short, single-stranded DNA and RNA targets to identify relevant mutations occurring in genetic biomarkers, which are key disease indicators. First, by employing ad hoc-synthesized colloidal silver nanoparticles as SERS substrates, we analyze single-base mutations in ssDNA and RNA sequences using a direct SERS-sensing approach. Then, an ML-based hypothesis test is proposed to identify these changes and differentiate the mutated sequences from the corresponding native ones. Rooted in "functional data analysis," this ML approach fully leverages the rich information and dependencies within SERS spectral data for improved modeling and detection capability. Tested on a large set of DNA and RNA SERS data, including from miR-21 (a known cancer miRNA biomarker), our approach is shown to accurately differentiate SERS spectra obtained from different oligonucleotides, outperforming various data-driven methods across several performance metrics, including accuracy, sensitivity, specificity, and F1-scores. Hence, this work represents a step forward in the development of the combined use of SERS and ML as effective methods for disease diagnosis with real applicability in the clinic.
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Affiliation(s)
- Jinisha Chheda
- Department of Materials Science and Engineering, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Yating Fang
- Department of Industrial and Systems Engineering, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Chiara Deriu
- Department of Applied Science and Technology, Politecnico di Torino, 10129 Torino, Italy
| | - Ahmed Aziz Ezzat
- Department of Industrial and Systems Engineering, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Laura Fabris
- Department of Applied Science and Technology, Politecnico di Torino, 10129 Torino, Italy
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Sha P, Zhu C, Wang T, Dong P, Wu X. Detection and Identification of Pesticides in Fruits Coupling to an Au-Au Nanorod Array SERS Substrate and RF-1D-CNN Model Analysis. NANOMATERIALS (BASEL, SWITZERLAND) 2024; 14:717. [PMID: 38668211 PMCID: PMC11053652 DOI: 10.3390/nano14080717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/03/2024] [Accepted: 04/17/2024] [Indexed: 04/29/2024]
Abstract
In this research, a method was developed for fabricating Au-Au nanorod array substrates through the deposition of large-area Au nanostructures on an Au nanorod array using a galvanic cell reaction. The incorporation of a granular structure enhanced both the number and intensity of surface-enhanced Raman scattering (SERS) hot spots on the substrate, thereby elevating the SERS performance beyond that of substrates composed solely of an Au nanorod. Calculations using the finite difference time domain method confirmed the generation of a strong electromagnetic field around the nanoparticles. Motivated by the electromotive force, Au ions in the chloroauric acid solution were reduced to form nanostructures on the nanorod array. The size and distribution density of these granular nanostructures could be modulated by varying the reaction time and the concentration of chloroauric acid. The resulting Au-Au nanorod array substrate exhibited an active, uniform, and reproducible SERS effect. With 1,2-bis(4-pyridyl)ethylene as the probe molecule, the detection sensitivity of the Au-Au nanorod array substrate was enhanced to 10-11 M, improving by five orders of magnitude over the substrate consisting only of an Au nanorod array. For a practical application, this substrate was utilized for the detection of pesticides, including thiram, thiabendazole, carbendazim, and phosmet, within the concentration range of 10-4 to 5 × 10-7 M. An analytical model combining a random forest and a one-dimensional convolutional neural network, referring to the important variable-one-dimensional convolutional neural network model, was developed for the precise identification of thiram. This approach demonstrated significant potential for biochemical sensing and rapid on-site identification.
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Affiliation(s)
| | | | | | - Peitao Dong
- Colleage of Intelligence Science and Technology, National University of Defense Technology, Changsha 410073, China
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Yang T, Yang H, Liu Y, Liu X, Ding YJ, Li R, Mao AQ, Huang Y, Li XL, Zhang Y, Yu FX. Postoperative delirium prediction after cardiac surgery using machine learning models. Comput Biol Med 2024; 169:107818. [PMID: 38134752 DOI: 10.1016/j.compbiomed.2023.107818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 11/03/2023] [Accepted: 12/03/2023] [Indexed: 12/24/2023]
Abstract
OBJECTIVE Postoperative delirium (POD) is a common postoperative complication in elderly patients, especially those undergoing cardiac surgery, which seriously affects the short- and long-term prognosis of patients. Early identification of risk factors for the development of POD can help improve the perioperative management of surgical patients. In the present study, five machine learning models were developed to predict patients at high risk of delirium after cardiac surgery and their performance was compared. METHODS A total of 367 patients who underwent cardiac surgery were retrospectively included in this study. Using single-factor analysis, 21 risk factors for POD were selected for inclusion in machine learning. The dataset was divided using 10-fold cross-validation for model training and testing. Five machine learning models (random forest (RF), support vector machine (SVM), radial based kernel neural network (RBFNN), K-nearest neighbour (KNN), and Kernel ridge regression (KRR)) were compared using area under the receiver operating characteristic curve (AUC-ROC), accuracy (ACC), sensitivity (SN), specificity (SPE), and Matthews coefficient (MCC). RESULTS Among 367 patients, 105 patients developed POD, the incidence of delirium was 28.6 %. Among the five ML models, RF had the best performance in ACC (87.99 %), SN (69.27 %), SPE (95.38 %), MCC (70.00 %) and AUC (0.9202), which was far superior to the other four models. CONCLUSION Delirium is common in patients after cardiac surgery. This analysis confirms the importance of the computational ML models in predicting the occurrence of delirium after cardiac surgery, especially the outstanding performance of the RF model, which has practical clinical applications for early identification of patients at risk of developing POD.
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Affiliation(s)
- Tan Yang
- Department of Cardiovascular Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Hai Yang
- Department of Anesthesiology, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Yan Liu
- Department of Anesthesiology, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Xiao Liu
- Department of Anesthesiology, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Yi-Jie Ding
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, 324000 Quzhou, Zhejiang, China
| | - Run Li
- Department of Anesthesiology, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - An-Qiong Mao
- Department of Anesthesiology, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Yue Huang
- Department of Anesthesiology, Zigong First People's Hospital, Zi Gong, 644099, Sichuan, China
| | - Xiao-Liang Li
- Department of Cardiothoracic Surgery, First Peoples Hospital of Neijiang, Nei Jiang, 641000, Sichuan, China
| | - Ying Zhang
- Department of Anesthesiology, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China.
| | - Feng-Xu Yu
- Department of Cardiovascular Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China.
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Chang M, He C, Du Y, Qiu Y, Wang L, Chen H. RaT: Raman Transformer for highly accurate melanoma detection with critical features visualization. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 305:123475. [PMID: 37806238 DOI: 10.1016/j.saa.2023.123475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 10/10/2023]
Abstract
Melanoma is an important cause of death from skin cancer. Early and accurate diagnosis can effectively reduce mortality. But the current diagnosis relies on the experience of pathologists, increasing the rate of misdiagnosis. In this paper, Raman Transformer (RaT) model is proposed by combining Raman spectroscopy and a Transformer encoder to distinguish the Raman spectra of melanoma and normal tissue. To make the spectral data more suitable for the Transformer encoder, we split the Raman spectrum into segments and map them into block vectors, which are then input into the Transformer encoder and classified using the multi-head self-attention mechanism and the Multilayer Perceptron (MLP). The RaT model achieves 99.69% accuracy, 99.61% sensitivity, and 99.82% specificity, which is higher than the classical principal component analysis with the neural network (PCA + NNET) method. In addition, we visualize and explain the fingerprint peaks found by the RaT model and their corresponding biological information. Our proposed RaT model provides a novel and reliable method for processing Raman spectral data, which is expected to help distinguish melanoma from normal cells, diagnose other diseases, and save human lives.
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Affiliation(s)
- Min Chang
- Key Laboratory of Optical Technology and Instrument for Medicine, Ministry of Education, University of Shanghai for Science and Technology, Shanghai 200093, China.
| | - Chen He
- Key Laboratory of Optical Technology and Instrument for Medicine, Ministry of Education, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Yi Du
- Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Yemin Qiu
- Key Laboratory of Optical Technology and Instrument for Medicine, Ministry of Education, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Luyao Wang
- Key Laboratory of Optical Technology and Instrument for Medicine, Ministry of Education, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Hui Chen
- Key Laboratory of Optical Technology and Instrument for Medicine, Ministry of Education, University of Shanghai for Science and Technology, Shanghai 200093, China
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Chen SL, Chin SC, Chan KC, Ho CY. A Machine Learning Approach to Assess Patients with Deep Neck Infection Progression to Descending Mediastinitis: Preliminary Results. Diagnostics (Basel) 2023; 13:2736. [PMID: 37685275 PMCID: PMC10486957 DOI: 10.3390/diagnostics13172736] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/25/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
BACKGROUND Deep neck infection (DNI) is a serious infectious disease, and descending mediastinitis is a fatal infection of the mediastinum. However, no study has applied artificial intelligence to assess progression to descending mediastinitis in DNI patients. Thus, we developed a model to assess the possible progression of DNI to descending mediastinitis. METHODS Between August 2017 and December 2022, 380 patients with DNI were enrolled; 75% of patients (n = 285) were assigned to the training group for validation, whereas the remaining 25% (n = 95) were assigned to the test group to determine the accuracy. The patients' clinical and computed tomography (CT) parameters were analyzed via the k-nearest neighbor method. The predicted and actual progression of DNI patients to descending mediastinitis were compared. RESULTS In the training and test groups, there was no statistical significance (all p > 0.05) noted at clinical variables (age, gender, chief complaint period, white blood cells, C-reactive protein, diabetes mellitus, and blood sugar), deep neck space (parapharyngeal, submandibular, retropharyngeal, and multiple spaces involved, ≥3), tracheostomy performance, imaging parameters (maximum diameter of abscess and nearest distance from abscess to level of sternum notch), or progression to mediastinitis. The model had a predictive accuracy of 82.11% (78/95 patients), with sensitivity and specificity of 41.67% and 87.95%, respectively. CONCLUSIONS Our model can assess the progression of DNI to descending mediastinitis depending on clinical and imaging parameters. It can be used to identify DNI patients who will benefit from prompt treatment.
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Affiliation(s)
- Shih-Lung Chen
- Department of Otorhinolaryngology & Head and Neck Surgery, Chang Gung Memorial Hospital, New Taipei City 333, Taiwan
- School of Medicine, Chang Gung University, Taoyuan 333, Taiwan
| | - Shy-Chyi Chin
- School of Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Department of Medical Imaging and Intervention, Chang Gung Memorial Hospital, New Taipei City 333, Taiwan
| | - Kai-Chieh Chan
- Department of Otorhinolaryngology & Head and Neck Surgery, Chang Gung Memorial Hospital, New Taipei City 333, Taiwan
- School of Medicine, Chang Gung University, Taoyuan 333, Taiwan
| | - Chia-Ying Ho
- School of Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Division of Chinese Internal Medicine, Center for Traditional Chinese Medicine, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
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Li Q, Zhang Z, Ma Z. Raman spectral pattern recognition of breast cancer: A machine learning strategy based on feature fusion and adaptive hyperparameter optimization. Heliyon 2023; 9:e18148. [PMID: 37501962 PMCID: PMC10368853 DOI: 10.1016/j.heliyon.2023.e18148] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 07/08/2023] [Accepted: 07/10/2023] [Indexed: 07/29/2023] Open
Abstract
Raman spectroscopy, as a kind of molecular vibration spectroscopy, provides abundant information for measuring components and molecular structure in the early detection and diagnosis of breast cancer. Currently, portable Raman spectrometers have simplified and made equipment application more affordable, albeit at the cost of sacrificing the signal-to-noise ratio (SNR). Consequently, this necessitates a higher recognition rate from pattern recognition algorithms. Our study employs a feature fusion strategy to reduce the dimensionality of high-dimensional Raman spectra and enhance the discriminative information between normal tissues and tumors. In the conducted random experiment, the classifier achieved a performance of over 96% for all three average metrics: accuracy, sensitivity, and specificity. Additionally, we propose a multi-parameter serial encoding evolutionary algorithm (MSEA) and integrate it into the Adaptive Local Hyperplane K-nearest Neighbor classification algorithm (ALHK) for adaptive hyperparameter optimization. The implementation of serial encoding tackles the predicament of parallel optimization in multi-hyperparameter vector problems. To bolster the convergence of the optimization algorithm towards a global optimal solution, an exponential viability function is devised for nonlinear processing. Moreover, an improved elitist strategy is employed for individual selection, effectively eliminating the influence of probability factors on the robustness of the optimization algorithm. This study further optimizes the hyperparameter space through sensitivity analysis of hyperparameters and cross-validation experiments, leading to superior performance compared to the ALHK algorithm with manual hyperparameter configuration.
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Affiliation(s)
- Qingbo Li
- School of Instrumentation and Optoelectronic Engineering, Precision Opto-Mechatronics Technology Key Laboratory of Education Ministry, Beihang University, Xueyuan Road No. 37, Haidian District, Beijing, 100191, China
| | - Zhixiang Zhang
- School of Instrumentation and Optoelectronic Engineering, Precision Opto-Mechatronics Technology Key Laboratory of Education Ministry, Beihang University, Xueyuan Road No. 37, Haidian District, Beijing, 100191, China
| | - Zhenhe Ma
- Hebei Key Laboratory of Micro-Nano Precision Optical Sensing and Detection Technology, Northeastern University, Qinhuangdao Campus, Qinhuangdao, 066004, China
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Zhao B, Zhai H, Shao H, Bi K, Zhu L. Potential of vibrational spectroscopy coupled with machine learning as a non-invasive diagnostic method for COVID-19. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2023; 229:107295. [PMID: 36706562 PMCID: PMC9711896 DOI: 10.1016/j.cmpb.2022.107295] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/10/2022] [Accepted: 11/29/2022] [Indexed: 06/18/2023]
Abstract
BACKGROUND AND OBJECTIVE Efforts to alleviate the ongoing coronavirus disease 2019 (COVID-19) crisis showed that rapid, sensitive, and large-scale screening is critical for controlling the current infection and that of ongoing pandemics. METHODS Here, we explored the potential of vibrational spectroscopy coupled with machine learning to screen COVID-19 patients in its initial stage. Herein presented is a hybrid classification model called grey wolf optimized support vector machine (GWO-SVM). The proposed model was tested and comprehensively compared with other machine learning models via vibrational spectroscopic fingerprinting including saliva FTIR spectra dataset and serum Raman scattering spectra dataset. RESULTS For the unknown vibrational spectra, the presented GWO-SVM model provided an accuracy, specificity and F1_score value of 0.9825, 0.9714 and 0.9778 for saliva FTIR spectra dataset, respectively, while an overall accuracy, specificity and F1_score value of 0.9085, 0.9552 and 0.9036 for serum Raman scattering spectra dataset, respectively, which showed superiority than those of state-of-the-art models, thereby suggesting the suitability of the GWO-SVM model to be adopted in a clinical setting for initial screening of COVID-19 patients. CONCLUSIONS Prospectively, the presented vibrational spectroscopy based GWO-SVM model can facilitate in screening of COVID-19 patients and alleviate the medical service burden. Therefore, herein proof-of-concept results showed the chance of vibrational spectroscopy coupled with GWO-SVM model to help COVID-19 diagnosis and have the potential be further used for early screening of other infectious diseases.
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Affiliation(s)
- Bingqiang Zhao
- College of Chemistry & Chemical Engineering, Lanzhou University; South Tianshui Road 222, Lanzhou, Gansu 730000, PR China
| | - Honglin Zhai
- College of Chemistry & Chemical Engineering, Lanzhou University; South Tianshui Road 222, Lanzhou, Gansu 730000, PR China.
| | - Haiping Shao
- College of Chemistry & Chemical Engineering, Lanzhou University; South Tianshui Road 222, Lanzhou, Gansu 730000, PR China
| | - Kexin Bi
- College of Chemistry & Chemical Engineering, Lanzhou University; South Tianshui Road 222, Lanzhou, Gansu 730000, PR China
| | - Ling Zhu
- College of Chemistry & Chemical Engineering, Lanzhou University; South Tianshui Road 222, Lanzhou, Gansu 730000, PR China
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12
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Cheng Z, Li H, Chen C, Lv X, Zuo E, Han S, Li Z, Liu P, Li H, Chen C. Application of serum SERS technology based on thermally annealed silver nanoparticle composite substrate in breast cancer. Photodiagnosis Photodyn Ther 2023; 41:103284. [PMID: 36646366 DOI: 10.1016/j.pdpdt.2023.103284] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/24/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023]
Abstract
Liquid biopsy is currently a non-destructive and convenient method of cancer screening, due to human blood containing a variety of cancer-related biomolecules. Therefore, the development of an accurate and rapid breast cancer screening technique combined with breast cancer serum is crucial for the treatment and prognosis of breast cancer patients. In this study, the surface enhanced Raman spectroscopy (SERS) technique is used to enhance the Raman spectroscopy (RS) signal of serum based on a high sensitivity thermally annealed silver nanoparticle/porous silicon bragg mirror (AgNPs/PSB) composite substrate. Compared with RS, SERS reflects more and stronger spectral peak information, which is beneficial to discover new biomarkers of breast cancer. At the same time, to further explore the diagnostic ability of SERS technology for breast cancer. In this study, the raw spectral data are processed by baseline correction, polynomial smoothing, and normalization. Then, the relevant feature information of SERS and RS is extracted by principal component analysis (PCA), and five classification models are established to compare the diagnostic performance of SERS and RS models respectively. The experimental results show that the breast cancer diagnosis model based on the improved SERS substrate combined with the machine learning algorithm can be used to distinguish breast cancer patients from controls. The accuracy, sensitivity, specificity and AUC values of the SVM model are 100%, 100%, 100% and 100%, respectively, as well as the training time of 4ms. The above experimental results show that the SERS technology based on AgNPs/PSB composite substrate, combined with machine learning methods, has great potential in the rapid and accurate identification of breast cancer patients.
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Affiliation(s)
- Zhiyuan Cheng
- College of Software, Xinjiang University, Urumqi 830046, China
| | - Hongyi Li
- Guangzhou Panyu Polytechnic, No. 1342 Shiliang Road, Guangzhou Panyu 511483, Guangdong, China
| | - Chen Chen
- College of Information Science, Engineering Xinjiang University, Urumqi 830046, China
| | - Xiaoyi Lv
- College of Software, Xinjiang University, Urumqi 830046, China
| | - EnGuang Zuo
- College of Information Science, Engineering Xinjiang University, Urumqi 830046, China
| | - Shibin Han
- School of Physical Science and Technology, Xinjiang University, Urumqi 830046, China
| | - Zhongyuan Li
- College of Information Science, Engineering Xinjiang University, Urumqi 830046, China
| | - Pei Liu
- College of Information Science, Engineering Xinjiang University, Urumqi 830046, China
| | - Hongtao Li
- Xinjiang Medical University Affiliated Tumor Hospital, Urumqi 830054, China.
| | - Cheng Chen
- College of Software, Xinjiang University, Urumqi 830046, China.
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13
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Cao D, Lin H, Liu Z, Gu Y, Hua W, Cao X, Qian Y, Xu H, Zhu X. Serum-based surface-enhanced Raman spectroscopy combined with PCA-RCKNCN for rapid and accurate identification of lung cancer. Anal Chim Acta 2022; 1236:340574. [DOI: 10.1016/j.aca.2022.340574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 10/15/2022] [Accepted: 10/29/2022] [Indexed: 11/05/2022]
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14
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Wang MH, Liu X, Wang Q, Zhang HW. Diagnosis accuracy of Raman spectroscopy in the diagnosis of breast cancer: a meta-analysis. Anal Bioanal Chem 2022; 414:7911-7922. [PMID: 36138121 DOI: 10.1007/s00216-022-04326-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/31/2022] [Accepted: 09/05/2022] [Indexed: 11/25/2022]
Abstract
To investigate the diagnostic efficiency of Raman spectroscopy for the diagnosis of breast cancer, we searched PubMed, Web of Science, Cochrane Library, and Embase for articles published from the database establishment to May 20, 2022. Pooled sensitivity, specificity, diagnostic odds ratio, and area under the receiver pooled operating characteristic curve were derived for the included studies as outcome measures. The methodological quality was assessed according to the questionnaires and criteria suggested by the Diagnostic Accuracy Research Quality Assessment-2 tool. Sixteen studies were included in this meta-analysis. The pooled sensitivity and specificity of Raman spectroscopy for breast cancer diagnosis were 0.97 (95% CI, [0.92-0.99]) and 0.96 (95% CI, [0.91-0.98]). The diagnostic odds ratio was 720.89 (95% CI, [135.73-3828.88]) and the area under the curve of summary receiver operating characteristic curves was 0.99 (95% CI, [0.98-1]). Subgroup analysis revealed that all subgroup types in our analysis, including different races, sample types, diagnostic algorithms, number of spectra, instrument types, and laser wavelengths, turned out to have a sensitivity and specificity greater than 0.9. Significant heterogeneity was found between studies. Deeks' funnel plot demonstrated that publication bias was acceptable. This meta-analysis suggests that Raman spectroscopy may be an effective and accurate tool to differentiate breast cancer from normal breast tissue, which will help us diagnose and treat breast cancer.
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Affiliation(s)
- Mei-Huan Wang
- Department of Ultrasound, Shandong Provincial Hospital affiliated to Shandong First Medical University, No. 324 Jing 5 Rd, Shandong Provincial Hospital, Jinan, Shandong, 250021, People's Republic of China
| | - Xiao Liu
- Department of Ultrasound, Shandong Provincial Hospital affiliated to Shandong First Medical University, No. 324 Jing 5 Rd, Shandong Provincial Hospital, Jinan, Shandong, 250021, People's Republic of China
| | - Qian Wang
- Department of Ultrasound, Shandong Provincial Hospital affiliated to Shandong First Medical University, No. 324 Jing 5 Rd, Shandong Provincial Hospital, Jinan, Shandong, 250021, People's Republic of China.
- Department of Ultrasound, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, Shandong, China.
| | - Hua-Wei Zhang
- Department of Ultrasound, Shandong Provincial Hospital affiliated to Shandong First Medical University, No. 324 Jing 5 Rd, Shandong Provincial Hospital, Jinan, Shandong, 250021, People's Republic of China.
- Department of Ultrasound, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, Shandong, China.
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15
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Li Q, Shen J, Zhou Y. Diagnosis of Glioma Using Raman Spectroscopy and the Entropy Weight Fuzzy-Rough Nearest Neighbor (EFRNN) Algorithm on Fresh Tissue. ANAL LETT 2022. [DOI: 10.1080/00032719.2022.2107660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Qingbo Li
- School of Instrumentation and Optoelectronic Engineering, Precision Opto-Mechatronics Technology Key Laboratory of Education Ministry, Beihang University, Beijing, China
| | - Jiaqi Shen
- School of Instrumentation and Optoelectronic Engineering, Precision Opto-Mechatronics Technology Key Laboratory of Education Ministry, Beihang University, Beijing, China
| | - Yan Zhou
- Department of Neurosurgery, PLA Air Force Medical Center, Beijing, China
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16
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Raman spectroscopy: current applications in breast cancer diagnosis, challenges and future prospects. Br J Cancer 2022; 126:1125-1139. [PMID: 34893761 PMCID: PMC8661339 DOI: 10.1038/s41416-021-01659-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 11/11/2021] [Accepted: 11/25/2021] [Indexed: 12/26/2022] Open
Abstract
Despite significant improvements in the way breast cancer is managed and treated, it continues to persist as a leading cause of death worldwide. If detected and diagnosed early, when tumours are small and localised, there is a considerably higher chance of survival. However, current methods for detection and diagnosis lack the required sensitivity and specificity for identifying breast cancer at the asymptomatic or very early stages. Thus, there is a need to develop more rapid and reliable methods, capable of detecting disease earlier, for improved disease management and patient outcome. Raman spectroscopy is a non-destructive analytical technique that can rapidly provide highly specific information on the biochemical composition and molecular structure of samples. In cancer, it has the capacity to probe very early biochemical changes that accompany malignant transformation, even prior to the onset of morphological changes, to produce a fingerprint of disease. This review explores the application of Raman spectroscopy in breast cancer, including discussion on its capabilities in analysing both ex-vivo tissue and liquid biopsy samples, and its potential in vivo applications. The review also addresses current challenges and potential future uses of this technology in cancer research and translational clinical application.
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17
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Kouri MA, Spyratou E, Karnachoriti M, Kalatzis D, Danias N, Arkadopoulos N, Seimenis I, Raptis YS, Kontos AG, Efstathopoulos EP. Raman Spectroscopy: A Personalized Decision-Making Tool on Clinicians' Hands for In Situ Cancer Diagnosis and Surgery Guidance. Cancers (Basel) 2022; 14:1144. [PMID: 35267451 PMCID: PMC8909093 DOI: 10.3390/cancers14051144] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 12/23/2022] Open
Abstract
Accurate in situ diagnosis and optimal surgical removal of a malignancy constitute key elements in reducing cancer-related morbidity and mortality. In surgical oncology, the accurate discrimination between healthy and cancerous tissues is critical for the postoperative care of the patient. Conventional imaging techniques have attempted to serve as adjuvant tools for in situ biopsy and surgery guidance. However, no single imaging modality has been proven sufficient in terms of specificity, sensitivity, multiplexing capacity, spatial and temporal resolution. Moreover, most techniques are unable to provide information regarding the molecular tissue composition. In this review, we highlight the potential of Raman spectroscopy as a spectroscopic technique with high detection sensitivity and spatial resolution for distinguishing healthy from malignant margins in microscopic scale and in real time. A Raman spectrum constitutes an intrinsic "molecular finger-print" of the tissue and any biochemical alteration related to inflammatory or cancerous tissue state is reflected on its Raman spectral fingerprint. Nowadays, advanced Raman systems coupled with modern instrumentation devices and machine learning methods are entering the clinical arena as adjunct tools towards personalized and optimized efficacy in surgical oncology.
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Affiliation(s)
- Maria Anthi Kouri
- Department of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.A.K.); (E.S.); (M.K.)
- 2nd Department of Radiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece;
- Medical Physics Program, Department of Physics and Applied Physics, Kennedy College of Sciences, University of Massachusetts Lowell, 265 Riverside Street, Lowell, MA 01854, USA
| | - Ellas Spyratou
- Department of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.A.K.); (E.S.); (M.K.)
- Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens, Iroon Politechniou 9, 15780 Athens, Greece; (Y.S.R.); (A.G.K.)
| | - Maria Karnachoriti
- Department of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.A.K.); (E.S.); (M.K.)
- Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens, Iroon Politechniou 9, 15780 Athens, Greece; (Y.S.R.); (A.G.K.)
| | - Dimitris Kalatzis
- 2nd Department of Radiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Nikolaos Danias
- 4th Department of Surgery, School of Medicine, Attikon University Hospital, University of Athens, 1 Rimini Street, 12462 Athens, Greece; (N.D.); (N.A.)
| | - Nikolaos Arkadopoulos
- 4th Department of Surgery, School of Medicine, Attikon University Hospital, University of Athens, 1 Rimini Street, 12462 Athens, Greece; (N.D.); (N.A.)
| | - Ioannis Seimenis
- Medical School, National and Kapodistrian University of Athens, 75 Mikras Assias Street, 11527 Athens, Greece;
| | - Yannis S. Raptis
- Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens, Iroon Politechniou 9, 15780 Athens, Greece; (Y.S.R.); (A.G.K.)
| | - Athanassios G. Kontos
- Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens, Iroon Politechniou 9, 15780 Athens, Greece; (Y.S.R.); (A.G.K.)
| | - Efstathios P. Efstathopoulos
- 2nd Department of Radiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece;
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18
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Zhang L, Li C, Peng D, Yi X, He S, Liu F, Zheng X, Huang WE, Zhao L, Huang X. Raman spectroscopy and machine learning for the classification of breast cancers. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 264:120300. [PMID: 34455388 DOI: 10.1016/j.saa.2021.120300] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 07/26/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
Breast cancer is a major health threat for women. The drug responses associated with different breast cancer subtypes have obvious effects on therapeutic outcomes; therefore, the accurate classification of breast cancer subtypes is critical. Breast cancer subtype classification has recently been examined using various methods, and Raman spectroscopy has emerged as an effective technique that can be used for noninvasive breast cancer analysis. However, the accurate and rapid classification of breast cancer subtypes currently requires a great deal of effort and experience with the processing and analysis of Raman spectra data. Here, we adopted Raman spectroscopy and machine learning techniques to simplify and accelerate the process used to distinguish normal from breast cancer cells and classify breast cancer subtypes. Raman spectra were obtained from cultured breast cancer cell lines, and the data were analyzed by two machine learning algorithms: principal component analysis (PCA)-discriminant function analysis (DFA) and PCA-support vector machine (SVM). The accuracies with which these two algorithms were able to distinguish normal breast cells from breast cancer cells were both greater than 97%, and the accuracies of breast cancer subtype classification for both algorithms were both greater than 92%. Moreover, our results showed evidence to support the use of characteristic Raman spectral features as cancer cell biomarkers, such as the intensity of intrinsic Raman bands, which increased in cancer cells. Raman spectroscopy combined with machine learning techniques provides a rapid method for breast cancer analysis able to reveal differences in intracellular compositions and molecular structures among subtypes.
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Affiliation(s)
- Lihao Zhang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Keling Road, Suzhou, Jiangsu Province, 215163, China
| | - Chengjian Li
- Department of Pharmacy, Shanghai Baoshan Luodian Hospital, Baoshan District, Shanghai, 201908, China; Luodian Clinical Drug Research Center, Institute for Translational Medicine Research, Shanghai University, Shanghai, 200444, China
| | - Di Peng
- Shanghai D-band Medical Instrument Co., Ltd, Huyi Highway, Jiading District, Shanghai, 201800, China
| | - Xiaofei Yi
- Shanghai D-band Medical Instrument Co., Ltd, Huyi Highway, Jiading District, Shanghai, 201800, China
| | - Shuai He
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Keling Road, Suzhou, Jiangsu Province, 215163, China
| | - Fengxiang Liu
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Keling Road, Suzhou, Jiangsu Province, 215163, China
| | - Xiangtai Zheng
- Luodian Clinical Drug Research Center, Institute for Translational Medicine Research, Shanghai University, Shanghai, 200444, China
| | - Wei E Huang
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK
| | - Liang Zhao
- Department of Pharmacy, Shanghai Baoshan Luodian Hospital, Baoshan District, Shanghai, 201908, China; Luodian Clinical Drug Research Center, Institute for Translational Medicine Research, Shanghai University, Shanghai, 200444, China.
| | - Xia Huang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Keling Road, Suzhou, Jiangsu Province, 215163, China; Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China.
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19
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Alkhathlan L, Saudagar AKJ. Predicting and Classifying Breast Cancer Using Machine Learning. J Comput Biol 2021; 29:497-514. [PMID: 34883032 DOI: 10.1089/cmb.2021.0236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The proposed research work aims to develop a method to predict and classify breast cancer (BC) at an early stage. In this research, three models are developed, and their performance is compared against each other. The first model was built using one of the machine learning algorithms called support vector machine (SVM), the second model was built using a deep learning algorithm called convolutional neural networks (CNNs), and the third model combines CNNs with a transfer learning technique for delivering better results. The data set is provided by the BC Histopathological Image Classification (BreakHis). All models are trained on the training set with two main categories: benign tumor and malignant tumor. The malignant tumor category is divided into subsets of invasive carcinoma tumors and in situ carcinoma tumors. Furthermore, invasive carcinoma tumors are classified into grade 1, grade 2, or grade 3, where grade 3 is the highest and is more aggressive. The results show that the accuracies of biopsy image classification using SVM are 92%, the accuracy of CNN is 94%, and the accuracy of CNN using the transfer learning technique is 97%. The results of this research will be beneficial in the early diagnosis of BC and help doctors in making better decisions and medical interventions.
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Affiliation(s)
- Lina Alkhathlan
- Information Systems Department, College of Computer and Information Sciences, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Abdul Khader Jilani Saudagar
- Information Systems Department, College of Computer and Information Sciences, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
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20
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Guan H, Huang C, Lu D, Chen G, Lin J, Hu J, He Y, Huang Z. Label-free Raman spectroscopy: A potential tool for early diagnosis of diabetic keratopathy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 256:119731. [PMID: 33819764 DOI: 10.1016/j.saa.2021.119731] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 06/12/2023]
Abstract
Diabetes has become a major public health problem worldwide, and the incidence of diabetes has been increasing progressively. Diabetes is prone to cause various complications, among which diabetic keratopathy (DK) emphasizes the significant impact on the cornea. The current diagnosis of DK lacks biochemical markers that can be used for early and non-invasive screening and detection. In contrast, in this study, Raman spectroscopy, which demonstrates non-destructive, label-free features, especially the unique advantage of providing molecular fingerprint information for target substances, were utilized to interrogate the intrinsic information of the corneal tissues from normal and diabetic mouse models, respectively. Visually, the Raman spectral response derived from the biochemical components and biochemical differences between the two groups were compared. Moreover, multivariate analysis methods such as principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) were carried out for advanced statistical analysis. PCA yields a diagnostic results of 57.4% sensitivity, 89.2% specificity, 74.8% accuracy between the diabetic group and control group; Moreover, PLS-DA was employed to enhance the diagnostic ability, showing 76.1% sensitivity, 86.1% specificity, and 87.6% accuracy between the diabetic group and control group. Our proof-of-concept results show the potential of Raman spectroscopy-based techniques to help explore the underlying pathogenesis of DK disease and thus be further expanded for potential applications in the early screening of diabetic diseases.
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Affiliation(s)
- Haohao Guan
- Key Laboratory of Opto-Electronic Science and Technology for Medicine of Ministry of Education, Fujian Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou, China
| | - Chunyan Huang
- Department of Ophthalmology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Dechan Lu
- Key Laboratory of Opto-Electronic Science and Technology for Medicine of Ministry of Education, Fujian Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou, China
| | - Guannan Chen
- Key Laboratory of Opto-Electronic Science and Technology for Medicine of Ministry of Education, Fujian Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou, China
| | - Juqiang Lin
- Key Laboratory of Opto-Electronic Science and Technology for Medicine of Ministry of Education, Fujian Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou, China
| | - Jianzhang Hu
- Department of Ophthalmology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Youwu He
- Key Laboratory of Opto-Electronic Science and Technology for Medicine of Ministry of Education, Fujian Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou, China
| | - Zufang Huang
- Key Laboratory of Opto-Electronic Science and Technology for Medicine of Ministry of Education, Fujian Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou, China.
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21
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Zhang Y, Yu H, Dong R, Ji X, Li F. Application Prospect of Artificial Intelligence in Rehabilitation and Management of Myasthenia Gravis. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5592472. [PMID: 33763475 PMCID: PMC7952150 DOI: 10.1155/2021/5592472] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/20/2021] [Accepted: 02/24/2021] [Indexed: 12/25/2022]
Abstract
Myasthenia gravis (MG) is a chronic autoimmune disease of the nervous system, which is still incurable. In recent years, with the progress of immunosuppressive and supportive treatment, the therapeutic effect of MG in the acute stage is satisfactory, and the mortality rate has been greatly reduced. However, there is still no consensus on how to conduct long-term management of stable MG, such as guiding patients to identify relapses, practice exercise, return to work and school, etc. In the international consensus guidance for management of myasthenia gravis published by the Myasthenia Gravis Foundation of America (MGFA) in 2020, for the first time, "the role of physical training/exercise in MG" was identified as the topic of discussion. Finally, due to a lack of high-quality evidence on physical training/exercise in patients with MG, the topic was excluded after the literature review. Therefore, this paper reviewed the current status of MG rehabilitation research and the difficulties faced by stable MG patients in self-management. It is suggested that we should take advantage of artificial intelligence (AI) and leverage it to develop the data-driven decision support platforms for MG management which can be used for adverse event monitoring, disease education, chronic management, and a wide variety of data collection and analysis.
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Affiliation(s)
- Ying Zhang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Hongmei Yu
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Rui Dong
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Xuan Ji
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Fujun Li
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
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22
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Zhang X, Liang B, Zhang J, Hao X, Xu X, Chang HM, Leung PCK, Tan J. Raman spectroscopy of follicular fluid and plasma with machine-learning algorithms for polycystic ovary syndrome screening. Mol Cell Endocrinol 2021; 523:111139. [PMID: 33359305 DOI: 10.1016/j.mce.2020.111139] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/04/2020] [Accepted: 12/18/2020] [Indexed: 10/22/2022]
Abstract
Polycystic ovary syndrome (PCOS) is the main cause of anovulatory infertility and affects women throughout their lives. The specific diagnostic method is still under investigation. In the present study, we aimed to identify the metabolic tracks of the follicular fluid and plasma samples from women with PCOS by performing Raman spectroscopy with principal component analysis and spectral classification models. Follicular fluid and plasma samples obtained from 50 healthy (non-PCOS) and 50 PCOS women were collected and measured by Raman spectroscopy. Multivariate statistical methods and different machine-learning algorithms based on the Raman spectra were established to analyze the results. The principal component analysis of the Raman spectra showed differences in the follicular fluid between the non-PCOS and PCOS groups. The stacking classification models based on the k-nearest-neighbor, random forests and extreme gradient boosting algorithms yielded a higher accuracy of 89.32% by using follicular fluid than the accuracy of 74.78% obtained with plasma samples in classifying the spectra from the two groups. In this regard, PCOS may lead to the changes of metabolic profiles that can be detected by Raman spectroscopy. As a novel, rapid and affordable method, Raman spectroscopy combined with advanced machine-learning algorithms have potential to analyze and characterize patients with PCOS.
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Affiliation(s)
- Xinyi Zhang
- Center of Reproductive Medicine, Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China; Key Laboratory of Reproductive Dysfunction Diseases and Fertility Remodeling of Liaoning Province, Shenyang, Liaoning, China
| | - Bo Liang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jun Zhang
- Basecare Medical Device Co., Jiangsu, China
| | - Xinyao Hao
- Center of Reproductive Medicine, Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China; Key Laboratory of Reproductive Dysfunction Diseases and Fertility Remodeling of Liaoning Province, Shenyang, Liaoning, China
| | - Xiaoyan Xu
- Center of Reproductive Medicine, Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China; Key Laboratory of Reproductive Dysfunction Diseases and Fertility Remodeling of Liaoning Province, Shenyang, Liaoning, China
| | - Hsun-Ming Chang
- Department of Obstetrics and Gynaecology, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Peter C K Leung
- Department of Obstetrics and Gynaecology, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Jichun Tan
- Center of Reproductive Medicine, Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China; Key Laboratory of Reproductive Dysfunction Diseases and Fertility Remodeling of Liaoning Province, Shenyang, Liaoning, China.
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Zhang W, Rhodes JS, Garg A, Takemoto JY, Qi X, Harihar S, Tom Chang CW, Moon KR, Zhou A. Label-free discrimination and quantitative analysis of oxidative stress induced cytotoxicity and potential protection of antioxidants using Raman micro-spectroscopy and machine learning. Anal Chim Acta 2020; 1128:221-230. [DOI: 10.1016/j.aca.2020.06.074] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 05/25/2020] [Accepted: 06/30/2020] [Indexed: 12/15/2022]
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Breast cancer diagnosis using a multi-verse optimizer-based gradient boosting decision tree. SN APPLIED SCIENCES 2020. [DOI: 10.1007/s42452-020-2575-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
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25
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Lussier F, Thibault V, Charron B, Wallace GQ, Masson JF. Deep learning and artificial intelligence methods for Raman and surface-enhanced Raman scattering. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.115796] [Citation(s) in RCA: 157] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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26
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Ralbovsky NM, Lednev IK. Towards development of a novel universal medical diagnostic method: Raman spectroscopy and machine learning. Chem Soc Rev 2020; 49:7428-7453. [DOI: 10.1039/d0cs01019g] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This review summarizes recent progress made using Raman spectroscopy and machine learning for potential universal medical diagnostic applications.
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Affiliation(s)
| | - Igor K. Lednev
- Department of Chemistry
- University at Albany
- SUNY
- Albany
- USA
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