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Wang H, Shi J, Yang Y, Ma K, Xue Y. Machine learning methods predict recurrence of pN3b gastric cancer after radical resection. Transl Cancer Res 2024; 13:1519-1532. [PMID: 38617507 PMCID: PMC11009806 DOI: 10.21037/tcr-23-1367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 01/16/2024] [Indexed: 04/16/2024]
Abstract
Background The incidence of stage pN3b gastric cancer (GC) is low, and the clinical prognosis is poor, with a high rate of postoperative recurrence. Machine learning (ML) methods can predict the recurrence of GC after surgery. However, the prognostic significance for pN3b remains unclear. Therefore, we aimed to predict the recurrence of pN3b through ML models. Methods This retrospective study included 336 patients with pN3b GC who underwent radical surgery. A 3-fold cross-validation was used to partition the participants into training and test cohorts. Linear combinations of new variable features were constructed using principal component analysis (PCA). Various ML algorithms, including random forest, support vector machine (SVM), logistic regression, multilayer perceptron (MLP), extreme gradient boosting (XGBoost), and Gaussian naive Bayes (GNB), were utilized to establish a recurrence prediction model. Model performance was evaluated using the receiver operating characteristic (ROC) curve and the area under the curve (AUC). Python was used for the analysis of ML algorithms. Results Nine principal components with a cumulative variance interpretation rate of 90.71% were identified. The output results of the test set showed that random forests had the highest AUC (0.927) for predicting overall recurrence with an accuracy rate of 80.5%. Random forests had the highest AUC (0.940) for predicting regional recurrence with an accuracy of 89.7%. For predicting distant recurrence, random forests had the highest AUC (0.896) with an accuracy of 84.3%. For peritoneal recurrence, random forests had the highest AUC (0.923) with an accuracy of 83.3%. Conclusions ML can personalize the prediction of postoperative recurrence in patients with GC with stage pN3b.
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Affiliation(s)
- Hao Wang
- Department of Gastrointestinal Surgery, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, China
| | - Jianting Shi
- School of Computer and Information Engineering, Heilongjiang University of Science and Technology, Harbin, China
| | - Yuhang Yang
- School of Computer and Information Engineering, Heilongjiang University of Science and Technology, Harbin, China
| | - Keru Ma
- Department of Thoracic Surgery, Esophagus and Mediastinum, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yingwei Xue
- Department of Gastrointestinal Surgery, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, China
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Jiang Y, Wang C, Zhou S. Artificial intelligence-based risk stratification, accurate diagnosis and treatment prediction in gynecologic oncology. Semin Cancer Biol 2023; 96:82-99. [PMID: 37783319 DOI: 10.1016/j.semcancer.2023.09.005] [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: 12/17/2022] [Revised: 08/27/2023] [Accepted: 09/25/2023] [Indexed: 10/04/2023]
Abstract
As data-driven science, artificial intelligence (AI) has paved a promising path toward an evolving health system teeming with thrilling opportunities for precision oncology. Notwithstanding the tremendous success of oncological AI in such fields as lung carcinoma, breast tumor and brain malignancy, less attention has been devoted to investigating the influence of AI on gynecologic oncology. Hereby, this review sheds light on the ever-increasing contribution of state-of-the-art AI techniques to the refined risk stratification and whole-course management of patients with gynecologic tumors, in particular, cervical, ovarian and endometrial cancer, centering on information and features extracted from clinical data (electronic health records), cancer imaging including radiological imaging, colposcopic images, cytological and histopathological digital images, and molecular profiling (genomics, transcriptomics, metabolomics and so forth). However, there are still noteworthy challenges beyond performance validation. Thus, this work further describes the limitations and challenges faced in the real-word implementation of AI models, as well as potential solutions to address these issues.
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Affiliation(s)
- Yuting Jiang
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan 610041, China; Department of Pulmonary and Critical Care Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Chengdi Wang
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan 610041, China; Department of Pulmonary and Critical Care Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Shengtao Zhou
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan 610041, China; Department of Pulmonary and Critical Care Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
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Fu XY, Mao XL, Wu HW, Lin JY, Ma ZQ, Liu ZC, Cai Y, Yan LL, Sun Y, Ye LP, Li SW. Development and validation of LightGBM algorithm for optimizing of Helicobacter pylori antibody during the minimum living guarantee crowd based gastric cancer screening program in Taizhou, China. Prev Med 2023; 174:107605. [PMID: 37419420 DOI: 10.1016/j.ypmed.2023.107605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 06/22/2023] [Accepted: 07/02/2023] [Indexed: 07/09/2023]
Abstract
Gastric cancer continues to be a significant health concern in China, with a high incidence rate. To mitigate its impact, early detection and treatment is key. However, conducting large-scale endoscopic gastric cancer screening is not feasible in China. Instead, a more appropriate approach would be to initially screen high-risk groups and follow up with endoscopic testing as needed. We conducted a study on 25,622 asymptomatic participants aged 45-70 years from a free gastric cancer screening program in the Taizhou city government's Minimum Living Guarantee Crowd (MLGC) initiative. Participants completed questionnaires, blood tests, and underwent gastrin-17 (G-17), pepsinogen I and II (PGI and PGII), and H. pylori IgG antibody (IgG) assessments. Using the light gradient boosting machine (lightGBM) algorithm, we developed a predictive model for gastric cancer risk. In the full model, F1 score was 2.66%, precision was 1.36%, and recall was 58.14%. In the high-risk model, F1 score was 2.51%, precision was 1.27%, and recall was 94.55%. Excluding IgG, the F1 score was 2.73%, precision was 1.40%, and recall was 68.62%. We conclude that H. pylori IgG appears to be able to be excluded from the prediction model without significantly affecting its performance, which is important from a health economic point of view. It suggests that screening indicators can be optimized, and expenditures reduced. These findings can have important implications for policymakers, as we can focus resources on other important aspects of gastric cancer prevention and control.
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Affiliation(s)
- Xin-Yu Fu
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, Zhejiang, China
| | - Xin-Li Mao
- Key Laboratory of Minimally Invasive Techniques & Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Taizhou Hospital Affiliated to Wenzhou Medical University, Linhai, Zhejiang, China; Department of Gastroenterology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, Zhejiang, China; Institute of Digestive Disease, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, Zhejiang, China
| | - Hao-Wen Wu
- Department of Mathematics and Statistics, York University, Toronto, ON, Canada
| | - Jia-Ying Lin
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, Zhejiang, China
| | - Zong-Qing Ma
- Information center, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, Zhejiang, China
| | - Zhi-Cheng Liu
- Information center, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, Zhejiang, China
| | - Yue Cai
- Department of Gastroenterology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, Zhejiang, China
| | - Ling-Ling Yan
- Department of Gastroenterology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, Zhejiang, China
| | - Yi Sun
- Department of Neurology, Faculty of Medical, University of Toyama, Toyama, Toyama Ken, Japan.
| | - Li-Ping Ye
- Key Laboratory of Minimally Invasive Techniques & Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Taizhou Hospital Affiliated to Wenzhou Medical University, Linhai, Zhejiang, China; Department of Gastroenterology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, Zhejiang, China; Institute of Digestive Disease, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, Zhejiang, China.
| | - Shao-Wei Li
- Key Laboratory of Minimally Invasive Techniques & Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Taizhou Hospital Affiliated to Wenzhou Medical University, Linhai, Zhejiang, China; Department of Gastroenterology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, Zhejiang, China; Institute of Digestive Disease, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, Zhejiang, China.
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Ling D, Liu A, Sun J, Wang Y, Wang L, Song X, Zhao X. Integration of IDPC Clustering Analysis and Interpretable Machine Learning for Survival Risk Prediction of Patients with ESCC. Interdiscip Sci 2023:10.1007/s12539-023-00569-9. [PMID: 37248421 DOI: 10.1007/s12539-023-00569-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 04/26/2023] [Accepted: 04/26/2023] [Indexed: 05/31/2023]
Abstract
Precise forecasting of survival risk plays a pivotal role in comprehending and predicting the prognosis of patients afflicted with esophageal squamous cell carcinoma (ESCC). The existing methods have the problems of insufficient fitting ability and poor interpretability. To address this issue, this work proposes a novel interpretable survival risk prediction method for ESCC patients based on extreme gradient boosting improved by whale optimization algorithm (WOA-XGBoost) and shapley additive explanations (SHAP). Given the imbalanced nature of the data set, the adaptive synthetic sampling (ADASYN) is first used to generate the samples with high survival risk. Then, an improved clustering by fast search and find of density peaks (IDPC) algorithm based on cosine distance and K nearest neighbors is used to cluster the patients. Next, the prediction model for each cluster is obtained by WOA-XGBoost and the constructed model is visualized with SHAP to uncover the factors hidden in the structured model and improve the interpretability of the black-box model. Finally, the effectiveness of the proposed scheme is demonstrated by analyzing the data collected from the First Affiliated Hospital of Zhengzhou University. The results of the analysis reveal that the proposed methodology exhibits superior performance, as indicated by the area under the receiver operating characteristic curve (AUROC) of 0.918 and accuracy of 0.881.
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Affiliation(s)
- Dan Ling
- Henan Key Lab of Information-Based Electrical Appliances, Zhengzhou University of Light Industry, Zhengzhou, 450002, China
| | - Anhao Liu
- Henan Key Lab of Information-Based Electrical Appliances, Zhengzhou University of Light Industry, Zhengzhou, 450002, China
| | - Junwei Sun
- Henan Key Lab of Information-Based Electrical Appliances, Zhengzhou University of Light Industry, Zhengzhou, 450002, China
| | - Yanfeng Wang
- Henan Key Lab of Information-Based Electrical Appliances, Zhengzhou University of Light Industry, Zhengzhou, 450002, China.
| | - Lidong Wang
- State Key Laboratory of Esophageal Cancer Prevention and Treatment and Henan Key Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, Zhengzhou, 450052, China
| | - Xin Song
- State Key Laboratory of Esophageal Cancer Prevention and Treatment and Henan Key Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, Zhengzhou, 450052, China
| | - Xueke Zhao
- State Key Laboratory of Esophageal Cancer Prevention and Treatment and Henan Key Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, Zhengzhou, 450052, China
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Sheehy J, Rutledge H, Acharya UR, Loh HW, Gururajan R, Tao X, Zhou X, Li Y, Gurney T, Kondalsamy-Chennakesavan S. Gynecological cancer prognosis using machine learning techniques: A systematic review of last three decades (1990–2022). Artif Intell Med 2023; 139:102536. [PMID: 37100507 DOI: 10.1016/j.artmed.2023.102536] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 03/19/2023] [Accepted: 03/23/2023] [Indexed: 03/30/2023]
Abstract
OBJECTIVE Many Computer Aided Prognostic (CAP) systems based on machine learning techniques have been proposed in the field of oncology. The objective of this systematic review was to assess and critically appraise the methodologies and approaches used in predicting the prognosis of gynecological cancers using CAPs. METHODS Electronic databases were used to systematically search for studies utilizing machine learning methods in gynecological cancers. Study risk of bias (ROB) and applicability were assessed using the PROBAST tool. 139 studies met the inclusion criteria, of which 71 predicted outcomes for ovarian cancer patients, 41 predicted outcomes for cervical cancer patients, 28 predicted outcomes for uterine cancer patients, and 2 predicted outcomes for gynecological malignancies broadly. RESULTS Random forest (22.30 %) and support vector machine (21.58 %) classifiers were used most commonly. Use of clinicopathological, genomic and radiomic data as predictors was observed in 48.20 %, 51.08 % and 17.27 % of studies, respectively, with some studies using multiple modalities. 21.58 % of studies were externally validated. Twenty-three individual studies compared ML and non-ML methods. Study quality was highly variable and methodologies, statistical reporting and outcome measures were inconsistent, preventing generalized commentary or meta-analysis of performance outcomes. CONCLUSION There is significant variability in model development when prognosticating gynecological malignancies with respect to variable selection, machine learning (ML) methods and endpoint selection. This heterogeneity prevents meta-analysis and conclusions regarding the superiority of ML methods. Furthermore, PROBAST-mediated ROB and applicability analysis demonstrates concern for the translatability of existing models. This review identifies ways that this can be improved upon in future works to develop robust, clinically translatable models within this promising field.
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Xu D, Chen R, Jiang Y, Wang S, Liu Z, Chen X, Fan X, Zhu J, Li J. Application of machine learning in the prediction of deficient mismatch repair in patients with colorectal cancer based on routine preoperative characterization. Front Oncol 2022; 12:1049305. [PMID: 36620593 PMCID: PMC9814116 DOI: 10.3389/fonc.2022.1049305] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Simple summary Detecting deficient mismatch repair (dMMR) in patients with colorectal cancer is essential for clinical decision-making, including evaluation of prognosis, guidance of adjuvant chemotherapy and immunotherapy, and primary screening for Lynch syndrome. However, outside of tertiary care centers, existing detection methods are not widely disseminated and highly depend on the experienced pathologist. Therefore, it is of great clinical significance to develop a broadly accessible and low-cost tool for dMMR prediction, particularly prior to surgery. In this study, we developed a convenient and reliable model for predicting dMMR status in CRC patients on routine preoperative characterization utilizing multiple machine learning algorithms. This model will work as an automated screening tool for identifying patients suitable for mismatch repair testing and consequently for improving the detection rate of dMMR, while reducing unnecessary labor and cost in patients with proficient mismatch repair. Background Deficient mismatch repair (dMMR) indicates a sustained anti-tumor immune response and has a favorable prognosis in patients with colorectal cancer (CRC). Although all CRC patients are recommended to undergo dMMR testing after surgery, current diagnostic approaches are not available for all country hospitals and patients. Therefore, efficient and low-cost predictive models for dMMR, especially for preoperative evaluations, are warranted. Methods A large scale of 5596 CRC patients who underwent surgical resection and mismatch repair testing were enrolled and randomly divided into training and validation cohorts. The clinical features exploited for predicting dMMR comprised the demographic characteristics, preoperative laboratory data, and tumor burden information. Machine learning (ML) methods involving eight basic algorithms, ensemble learning methods, and fusion algorithms were adopted with 10-fold cross-validation, and their performance was evaluated based on the area under the receiver operating characteristic curve (AUC) and calibration curves. The clinical net benefits were assessed using a decision curve analysis (DCA), and a nomogram was developed to facilitate model clinical practicality. Results All models achieved an AUC of nearly 0.80 in the validation cohort, with the stacking model exhibiting the best performance (AUC = 0.832). Logistical DCA revealed that the stacking model yielded more clinical net benefits than the conventional regression models. In the subgroup analysis, the stacking model also predicted dMMR regardless of the clinical stage. The nomogram showed a favorable consistence with the actual outcome in the calibration curve. Conclusion With the aid of ML algorithms, we developed a novel and robust model for predicting dMMR in CRC patients with satisfactory discriminative performance and designed a user-friendly and convenient nomogram.
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Affiliation(s)
- Dong Xu
- Division of Digestive Surgery, Xijing Hospital of Digestive Diseases, Air force Medical University, Xi’an, China,School of Clinical Medicine, Xi’an Medical University, Xi’an, China
| | - Rujie Chen
- Division of Digestive Surgery, Xijing Hospital of Digestive Diseases, Air force Medical University, Xi’an, China,Department of Neurosurgery, Xijing Hospital, Air Force Medical University, Xi’an, China,State Key Laboratory of Cancer Biology, Institute of Digestive Diseases, Xijing Hospital, The Fourth Military Medical University, Xi’an, China
| | - Yu Jiang
- Division of Digestive Surgery, Xijing Hospital of Digestive Diseases, Air force Medical University, Xi’an, China,School of Clinical Medicine, Xi’an Medical University, Xi’an, China
| | - Shuai Wang
- Xi’an Institute of Flight of the Air Force, Ming Gang Station Hospital, Minggang, China
| | - Zhiyu Liu
- Division of Digestive Surgery, Xijing Hospital of Digestive Diseases, Air force Medical University, Xi’an, China,School of Clinical Medicine, Xi’an Medical University, Xi’an, China
| | - Xihao Chen
- Division of Digestive Surgery, Xijing Hospital of Digestive Diseases, Air force Medical University, Xi’an, China,School of Clinical Medicine, Xi’an Medical University, Xi’an, China
| | - Xiaoyan Fan
- Department of Experiment Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Jun Zhu
- Department of General Surgery, The Southern Theater Air Force Hospital, Guangzhou, China,*Correspondence: Jipeng Li, ; Jun Zhu,
| | - Jipeng Li
- Division of Digestive Surgery, Xijing Hospital of Digestive Diseases, Air force Medical University, Xi’an, China,State Key Laboratory of Cancer Biology, Institute of Digestive Diseases, Xijing Hospital, The Fourth Military Medical University, Xi’an, China,Department of Experiment Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, China,*Correspondence: Jipeng Li, ; Jun Zhu,
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Das R, Saleh S, Nielsen I, Kaviraj A, Sharma P, Dey K, Saha S. Performance analysis of machine learning algorithms and screening formulae for β-thalassemia trait screening of Indian antenatal women. Int J Med Inform 2022; 167:104866. [PMID: 36174416 DOI: 10.1016/j.ijmedinf.2022.104866] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/19/2022] [Accepted: 09/07/2022] [Indexed: 10/31/2022]
Abstract
BACKGROUND Currently, more than forty discrimination formulae based on red blood cell (RBC) parameters and some supervised machine learning algorithms (MLAs) have been recommended for β-thalassemia trait (BTT) screening. The present study was aimed to evaluate and compare the performance of 26 such formulae and 13 MLAs on antenatal woman data with a recently developed formula SCSBTT, which is available for evaluation in over seventy countries as an Android app, called SUSOKA[16]. METHODS A diagnostic database of 2942 antenatal females were collected from PGIMER, Chandigarh, India and was used for this analysis. The data set consists of hypochromic microcytic anemia, BTT, Hemoglobin E trait, double heterozygote for Hemoglobin S and BTT, heterozygote for Hemoglobin D Punjab and normal subjects. Performance of the formulae and the MLAs were assessed by Sensitivity, Specificity, Youden's Index, and AUC-ROC measures. A final recommendation was made from the ranking obtained through two Multiple Criteria Decision-Making (MCDM) techniques, namely, Simultaneous Evaluation of Criteria and Alternatives (SECA) and TOPSIS. RESULTS It was observed that Extreme Learning Machine (ELM) and Gradient Boosting Classifier (GBC) showed maximum Youden's index and AUC-ROC measures compared to all discriminating formulae. Sensitivity remains maximum for SCSBTT. K-means clustering and the ranking from MCDM methods show that SCSBTT, Shine & Lal and Ravanbakhsh-F4 formula ensures higher performance among all formulae. The discriminant power of some MLAs and formulae was found considerably lower than that reported in original studies. CONCLUSION Comparative information on MLAs can aid researchers in developing new discriminating formulae that simultaneously ensure higher sensitivity and specificity. More multi-centric verification of the formulae on heterogeneous data is indispensable. SCSBTT and Shine & Lal formula, and ELM and GBC are recommended for screening BTT based on MCDM. SCSBTT can be used with certainty as a tangible cost-saving screening tool for mass screening for antenatal women in India and other countries.
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Affiliation(s)
- Reena Das
- Department of Hematology, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Sarkaft Saleh
- Department of Materials and Production, Aalborg University, DK 9220 Aalborg, Denmark
| | - Izabela Nielsen
- Department of Materials and Production, Aalborg University, DK 9220 Aalborg, Denmark
| | - Anilava Kaviraj
- Department of Zoology, University of Kalyani, Kalyani 741235, India
| | - Prashant Sharma
- Department of Hematology, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Kartick Dey
- Department of Mathematics, University of Engineering & Management, Kolkata 700160, India
| | - Subrata Saha
- Department of Materials and Production, Aalborg University, DK 9220 Aalborg, Denmark
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Li G, Yang M, Ran L, Jin F. Classification prediction of early pulmonary nodes based on weighted gene correlation network analysis and machine learning. J Cancer Res Clin Oncol 2022:10.1007/s00432-022-04312-7. [PMID: 36018512 DOI: 10.1007/s00432-022-04312-7] [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: 07/10/2022] [Accepted: 08/15/2022] [Indexed: 10/15/2022]
Abstract
OBJECTIVE To use weighted gene correlation network analysis (WGCNA) and machine learning algorithm to predict classification of early pulmonary nodes with public databases. METHODS The expression data and clinical data of lung cancer patients were firstly extracted from public database (GTEx and TCGA) to study the differentially expressed genes (DEGs) of lung adenocarcinoma (LUAD). The intersection of three R packages (Dseq2, Limma, EdgeR) methods were selected as candidate DEGs for further study. WGCNA was used to obtain relevant modules and key genes of lung cancer classification, GO and KEGG enrichment analysis was performed. The model was built using two machine learning methods, Least Absolute Shrinkage and Selection Operator (LASSO) regression and tumor classification was also predicted with extreme Gradient Boosting (XGBoost) algorithm. RESULTS DEGs analysis revealed that there were 1306 LUAD genes. WGCNA module analysis showed that a total of 116 genes were significantly related to classification, and module genes were mainly related to 14 KEGG pathways. The machine learning algorithm identified 10 target genes by LASSO regression analysis of differential genes, and 18 genes were identified by XGBoost model. A total of 6 genes were found from the intersection of the above methods as classification signatures of early pulmonary nodules, including "HMGB3" "ARHGAP6" "TCF21" "FCN3" "COL6A6" "GOLM1". CONCLUSION Using DEGs analysis, WGCNA method and machine learning algorithm, six gene signatures related to early stage of LUAD, which can assist clinicians in disease classification prediction.
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Affiliation(s)
- Guang Li
- Department of Radiotherapy, Chongqing University Cancer Hospital, Chongqing, China
| | - Meng Yang
- Department of Equipment, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Longke Ran
- Department of Bioinformatics, Chongqing Medical University, Chongqing, China.
| | - Fu Jin
- Department of Radiotherapy, Chongqing University Cancer Hospital, Chongqing, China.
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Liu L, Qiao C, Zha JR, Qin H, Wang XR, Zhang XY, Wang YO, Yang XM, Zhang SL, Qin J. Early prediction of clinical scores for left ventricular reverse remodeling using extreme gradient random forest, boosting, and logistic regression algorithm representations. Front Cardiovasc Med 2022; 9:864312. [PMID: 36061535 PMCID: PMC9428443 DOI: 10.3389/fcvm.2022.864312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 07/13/2022] [Indexed: 11/13/2022] Open
Abstract
ObjectiveAt present, there is no early prediction model of left ventricular reverse remodeling (LVRR) for people who are in cardiac arrest with an ejection fraction (EF) of ≤35% at first diagnosis; thus, the purpose of this article is to provide a supplement to existing research.Materials and methodsA total of 109 patients suffering from heart attack with an EF of ≤35% at first diagnosis were involved in this single-center research study. LVRR was defined as an absolute increase in left ventricular ejection fraction (LVEF) from ≥10% to a final value of >35%, with analysis features including demographic characteristics, diseases, biochemical data, echocardiography, and drug therapy. Extreme gradient boosting (XGBoost), random forest, and logistic regression algorithm models were used to distinguish between LVRR and non-LVRR cases and to obtain the most important features.ResultsThere were 47 cases (42%) of LVRR in patients suffering from heart failure with an EF of ≤35% at first diagnosis after optimal drug therapy. General statistical analysis and machine learning methods were combined to exclude a number of significant feature groups. The median duration of disease in the LVRR group was significantly lower than that in the non-LVRR group (7 vs. 48 months); the mean values of creatine kinase (CK) and MB isoenzyme of creatine kinase (CK-MB) in the LVRR group were lower than those in the non-LVRR group (80.11 vs. 94.23 U/L; 2.61 vs. 2.99 ng/ml; 27.19 vs. 28.54 mm). Moreover, AUC values for our feature combinations ranged from 97 to 94% and to 87% when using the XGBoost, random forest, and logistic regression techniques, respectively. The ablation test revealed that beats per minute (BPM) and disease duration had a greater impact on the model’s ability to accurately forecast outcomes.ConclusionShorter disease duration, slightly lower CK and CK-MB levels, slightly smaller right and left ventricular and left atrial dimensions, and lower mean heart rates were found to be most strongly predictive of LVRR development (BPM).
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Affiliation(s)
- Lu Liu
- Heart Centre, Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Cen Qiao
- Heart Centre, Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Jun-Ren Zha
- School of Software Engineering, Dalian University, Dalian, China
| | - Huan Qin
- Heart Centre, Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Xiao-Rui Wang
- Heart Centre, Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Xin-Yu Zhang
- Medical College, Dalian University, Dalian, China
| | - Yi-Ou Wang
- Heart Centre, Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Xiu-Mei Yang
- Heart Centre, Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Shu-Long Zhang
- Heart Centre, Affiliated Zhongshan Hospital of Dalian University, Dalian, China
- *Correspondence: Shu-Long Zhang,
| | - Jing Qin
- School of Software Engineering, Dalian University, Dalian, China
- Jing Qin,
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Wang J. Prediction of postoperative recovery in patients with acoustic neuroma using machine learning and SMOTE-ENN techniques. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:10407-10423. [PMID: 36032000 DOI: 10.3934/mbe.2022487] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Acoustic neuroma is a common benign tumor that is frequently associated with postoperative complications such as facial nerve dysfunction, which greatly affects the physical and mental health of patients. In this paper, clinical data of patients with acoustic neuroma treated with microsurgery by the same operator at Xiangya Hospital of Central South University from June 2018 to March 2020 are used as the study object. Machine learning and SMOTE-ENN techniques are used to accurately predict postoperative facial nerve function recovery, thus filling a gap in auxiliary diagnosis within the field of facial nerve treatment in acoustic neuroma. First, raw clinical data are processed and dependent variables are identified based on clinical context and data characteristics. Secondly, data balancing is corrected using the SMOTE-ENN technique. Finally, XGBoost is selected to construct a prediction model for patients' postoperative recovery, and is also compared with a total of four machine learning models, LR, SVM, CART, and RF. We find that XGBoost can most accurately predict the postoperative facial nerve function recovery, with a prediction accuracy of 90.0% and an AUC value of 0.90. CART, RF, and XGBoost can further select the more important preoperative indicators and provide therapeutic assistance to physicians, thereby improving the patient's postoperative recovery. The results show that machine learning and SMOTE-ENN techniques can handle complex clinical data and achieve accurate predictions.
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Affiliation(s)
- Jianing Wang
- School of Mathematics and Statistics, Central South University, Changsha 410083, China
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11
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Yokomizo R, Lopes TJS, Takashima N, Hirose S, Kawabata A, Takenaka M, Iida Y, Yanaihara N, Yura K, Sago H, Okamoto A, Umezawa A. O3C Glass-Class: A Machine-Learning Framework for Prognostic Prediction of Ovarian Clear-Cell Carcinoma. Bioinform Biol Insights 2022. [DOI: 10.1177/11779322221134312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Ovarian clear cell carcinoma (OCCC), one of the histopathological types of ovarian cancer, has a poor prognosis when it recurs; however, it is difficult to precisely predict the risk of recurrence. Here, we analyzed pathological images of OCCC to elucidate the relationship between pathological findings and recurrence, and using machine learning, we established a classifier to predict the recurrence and several other prognosis indicators of this disease. In total, 110 patients with OCCC treated with primary surgery at a single institution were enrolled in this study. We used the deep-learning neural networks to process the whole slide images of OCCC obtained by digitally scanning the original hematoxylin and eosin-stained glass slides. The images were preprocessed and used as input to the machine learning pipeline. We fine-tuned its parameters to predict the recurrence, progression-free survival, and the overall survival days of all patients. We predicted the recurrence of OCCC with an overall accuracy of 93%, area under the receiver operating characteristic curve of 0.98, and sensitivity/specificity above 0.92 using Resnet 34. Furthermore, we predicted progression-free survival/overall survival of the patients with ~90% accuracy. In conclusion, our study demonstrates the feasibility of using a machine learning system to predict different features of OCCC samples using histopathological images as input. This novel application provides accurate prognosis information and aids in the development of personalized treatment strategies.
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Affiliation(s)
- Ryo Yokomizo
- Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, Setagaya-ku, Japan
- Center for Maternal-Fetal, Neonatal and Reproductive Medicine, National Center for Child Health and Development, Setagaya-ku, Japan
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, Minato-ku, Japan
| | - Tiago JS Lopes
- Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, Setagaya-ku, Japan
| | - Nagisa Takashima
- Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, Setagaya-ku, Japan
- Divison of Life Sciences, Graduate School of Humanities and Sciences, Ochanomizu University, Bunkyo-ku, Japan
| | - Sou Hirose
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, Minato-ku, Japan
| | - Ayako Kawabata
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, Minato-ku, Japan
| | - Masataka Takenaka
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, Minato-ku, Japan
| | - Yasushi Iida
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, Minato-ku, Japan
| | - Nozomu Yanaihara
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, Minato-ku, Japan
| | - Kei Yura
- Divison of Life Sciences, Graduate School of Humanities and Sciences, Ochanomizu University, Bunkyo-ku, Japan
- Department of Life Science & Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Japan
| | - Haruhiko Sago
- Center for Maternal-Fetal, Neonatal and Reproductive Medicine, National Center for Child Health and Development, Setagaya-ku, Japan
| | - Aikou Okamoto
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, Minato-ku, Japan
| | - Akihiro Umezawa
- Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, Setagaya-ku, Japan
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