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Liang X, Tang K, Ke X, Jiang J, Li S, Xue C, Deng J, Liu X, Yan C, Gao M, Zhou J, Zhao L. Development of an MRI-Based Comprehensive Model Fusing Clinical, Radiomics and Deep Learning Models for Preoperative Histological Stratification in Intracranial Solitary Fibrous Tumor. J Magn Reson Imaging 2024; 60:523-533. [PMID: 37897302 DOI: 10.1002/jmri.29098] [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: 02/20/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/30/2023] Open
Abstract
BACKGROUND Accurate preoperative histological stratification (HS) of intracranial solitary fibrous tumors (ISFTs) can help predict patient outcomes and develop personalized treatment plans. However, the role of a comprehensive model based on clinical, radiomics and deep learning (CRDL) features in preoperative HS of ISFT remains unclear. PURPOSE To investigate the feasibility of a CRDL model based on magnetic resonance imaging (MRI) in preoperative HS in ISFT. STUDY TYPE Retrospective. POPULATION Three hundred and ninety-eight patients from Beijing Tiantan Hospital, Capital Medical University (primary training cohort) and 49 patients from Lanzhou University Second Hospital (external validation cohort) with ISFT based on histopathological findings (237 World Health Organization [WHO] tumor grade 1 or 2, and 210 WHO tumor grade 3). FIELD STRENGTH/SEQUENCE 3.0 T/T1-weighted imaging (T1) by using spin echo sequence, T2-weighted imaging (T2) by using fast spin echo sequence, and T1-weighted contrast-enhanced imaging (T1C) by using two-dimensional fast spin echo sequence. ASSESSMENT Area under the receiver operating characteristic curve (AUC) was used to assess the performance of the CRDL model and a clinical model (CM) in preoperative HS in the external validation cohort. The decision curve analysis (DCA) was used to evaluate the clinical net benefit provided by the CRDL model. STATISTICAL TESTS Cohen's kappa, intra-/inter-class correlation coefficients (ICCs), Chi-square test, Fisher's exact test, Student's t-test, AUC, DCA, calibration curves, DeLong test. A P value <0.05 was considered statistically significant. RESULTS The CRDL model had significantly better discrimination ability than the CM (AUC [95% confidence interval, CI]: 0.895 [0.807-0.912] vs. 0.810 [0.745-0.874], respectively) in the external validation cohort. The CRDL model can provide a clinical net benefit for preoperative HS at a threshold probability >20%. DATA CONCLUSION The proposed CRDL model holds promise for preoperative HS in ISFT, which is important for predicting patient outcomes and developing personalized treatment plans. LEVEL OF EVIDENCE 3 TECHNICAL EFFICACY: Stage 2.
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Affiliation(s)
- Xiaohong Liang
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Kaiqiang Tang
- Department of Orthopedics, The Third Affiliated Hospital of Beijing University of Chinese Medicine, Beijing, China
| | - Xiaoai Ke
- Department of Radiology, Lanzhou University Second Hospital, Lanzhou, China
| | - Jian Jiang
- Department of Radiology, Lanzhou University Second Hospital, Lanzhou, China
| | - Shenglin Li
- Department of Radiology, Lanzhou University Second Hospital, Lanzhou, China
| | - Caiqiang Xue
- Department of Radiology, Lanzhou University Second Hospital, Lanzhou, China
| | - Juan Deng
- Department of Radiology, Lanzhou University Second Hospital, Lanzhou, China
| | - Xianwang Liu
- Department of Radiology, Lanzhou University Second Hospital, Lanzhou, China
| | - Cheng Yan
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Mingzi Gao
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Junlin Zhou
- Department of Radiology, Lanzhou University Second Hospital, Lanzhou, China
| | - Liqin Zhao
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
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Lyu X, Dong L, Fan Z, Sun Y, Zhang X, Liu N, Wang D. Artificial intelligence-based graded training of pulmonary nodules for junior radiology residents and medical imaging students. BMC MEDICAL EDUCATION 2024; 24:740. [PMID: 38982410 PMCID: PMC11234785 DOI: 10.1186/s12909-024-05723-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 06/28/2024] [Indexed: 07/11/2024]
Abstract
BACKGROUND To evaluate the efficiency of artificial intelligence (AI)-assisted diagnosis system in the pulmonary nodule detection and diagnosis training of junior radiology residents and medical imaging students. METHODS The participants were divided into three groups. Medical imaging students of Grade 2020 in the Jinzhou Medical University were randomly divided into Groups 1 and 2; Group 3 comprised junior radiology residents. Group 1 used the traditional case-based teaching mode; Groups 2 and 3 used the 'AI intelligent assisted diagnosis system' teaching mode. All participants performed localisation, grading and qualitative diagnosed of 1,057 lung nodules in 420 cases for seven rounds of testing after training. The sensitivity and number of false positive nodules in different densities (solid, pure ground glass, mixed ground glass and calcification), sizes (less than 5 mm, 5-10 mm and over 10 mm) and positions (subpleural, peripheral and central) of the pulmonary nodules in the three groups were detected. The pathological results and diagnostic opinions of radiologists formed the criteria. The detection rate, diagnostic compliance rate, false positive number/case, and kappa scores of the three groups were compared. RESULTS There was no statistical difference in baseline test scores between Groups 1 and 2, and there were statistical differences with Group 3 (P = 0.036 and 0.011). The detection rate of solid, pure ground glass and calcified nodules; small-, medium-, and large-diameter nodules; and peripheral nodules were significantly different among the three groups (P<0.05). After seven rounds of training, the diagnostic compliance rate increased in all three groups, with the largest increase in Group 2. The average kappa score increased from 0.508 to 0.704. The average kappa score for Rounds 1-4 and 5-7 were 0.595 and 0.714, respectively. The average kappa scores of Groups 1,2 and 3 increased from 0.478 to 0.658, 0.417 to 0.757, and 0.638 to 0.791, respectively. CONCLUSION The AI assisted diagnosis system is a valuable tool for training junior radiology residents and medical imaging students to perform pulmonary nodules detection and diagnosis.
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Affiliation(s)
- Xiaohong Lyu
- Department of Radiology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Liang Dong
- School of Electrical Engineering, Liaoning University of Technology, Jinzhou, China
| | - Zhongkai Fan
- Office of Educational Administration, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Yu Sun
- Department of Radiology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Xianglin Zhang
- Department of Radiology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Ning Liu
- Department of Radiology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China.
| | - Dongdong Wang
- Department of Radiology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China.
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Ayyoubzadeh SM, Ahmadi M, Yazdipour AB, Ghorbani‐Bidkorpeh F, Ahmadi M. Prediction of ovarian cancer using artificial intelligence tools. Health Sci Rep 2024; 7:e2203. [PMID: 38946777 PMCID: PMC11211920 DOI: 10.1002/hsr2.2203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 06/05/2024] [Accepted: 06/10/2024] [Indexed: 07/02/2024] Open
Abstract
Purpose Ovarian cancer is a common type of cancer and a leading cause of death in women. Therefore, accurate and fast prediction of ovarian tumors is crucial. One of the appropriate and precise methods for predicting and diagnosing this cancer is to build a model based on artificial intelligence methods. These methods provide a tool for predicting ovarian cancer according to the characteristics and conditions of each person. Method In this study, a data set included records related to 171 cases of benign ovarian tumors, and 178 records related to cases of ovarian cancer were analyzed. The data set contains the records of blood test results and tumor markers of the patients. After data preprocessing, including removing outliers and replacing missing values, the weight of the effective factors was determined using information gain indices and the Gini index. In the next step, predictive models were created using random forest (RF), support vector machine (SVM), decision trees (DT), and artificial neural network (ANN) models. The performance of these models was evaluated using the 10-fold cross-validation method using the indicators of specificity, sensitivity, accuracy, and the area under the receiver operating characteristic curve. Finally, by comparing the performance of the models, the best predictive model of ovarian cancer was selected. Results The most important predictive factors were HE4, CA125, and NEU. The RF model was identified as the best predictive model, with an accuracy of more than 86%. The predictive accuracy of DT, SVM, and ANN models was estimated as 82.91%, 85.25%, and 79.35%, respectively. Various artificial intelligence (AI) tools can be used with high accuracy and sensitivity in predicting ovarian cancer. Conclusion Therefore, the use of these tools can help specialists and patients with early, easier, and less expensive diagnosis of ovarian cancer. Future studies can leverage AI to integrate image data with serum biomarkers, thereby facilitating the creation of novel models and advancing the diagnosis and treatment of ovarian cancer.
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Affiliation(s)
- Seyed Mohammad Ayyoubzadeh
- Department of Health Information Management, School of Allied Medical SciencesTehran University of Medical SciencesTehranIran
- Health Information Management Research CenterTehran University of Medical SciencesTehranIran
| | - Marjan Ahmadi
- Department of Obstetrics and GynecologyTehran University of Medical SciencesTehranIran
| | - Alireza Banaye Yazdipour
- Department of Health Information Management, School of Allied Medical SciencesTehran University of Medical SciencesTehranIran
- Students' Scientific Research Center (SSRC)Tehran University of Medical SciencesTehranIran
- Department of Health Information Technology, School of Paramedical and Rehabilitation SciencesMashhad University of Medical SciencesMashhadIran
| | - Fatemeh Ghorbani‐Bidkorpeh
- Department of Pharmaceutics and Pharmaceutical Nanotechnology, School of PharmacyShahid Beheshti University of Medical SciencesTehranIran
| | - Mahnaz Ahmadi
- Medical Nanotechnology and Tissue Engineering Research CenterShahid Beheshti University of Medical SciencesTehranIran
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Fu X, Ma W, Zuo Q, Qi Y, Zhang S, Zhao Y. Application of machine learning for high-throughput tumor marker screening. Life Sci 2024; 348:122634. [PMID: 38685558 DOI: 10.1016/j.lfs.2024.122634] [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: 01/16/2024] [Revised: 03/26/2024] [Accepted: 04/10/2024] [Indexed: 05/02/2024]
Abstract
High-throughput sequencing and multiomics technologies have allowed increasing numbers of biomarkers to be mined and used for disease diagnosis, risk stratification, efficacy assessment, and prognosis prediction. However, the large number and complexity of tumor markers make screening them a substantial challenge. Machine learning (ML) offers new and effective ways to solve the screening problem. ML goes beyond mere data processing and is instrumental in recognizing intricate patterns within data. ML also has a crucial role in modeling dynamic changes associated with diseases. Used together, ML techniques have been included in automatic pipelines for tumor marker screening, thereby enhancing the efficiency and accuracy of the screening process. In this review, we discuss the general processes and common ML algorithms, and highlight recent applications of ML in tumor marker screening of genomic, transcriptomic, proteomic, and metabolomic data of patients with various types of cancers. Finally, the challenges and future prospects of the application of ML in tumor therapy are discussed.
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Affiliation(s)
- Xingxing Fu
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, Dalian Minzu University, Dalian 116600, China
| | - Wanting Ma
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, Dalian Minzu University, Dalian 116600, China
| | - Qi Zuo
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, Dalian Minzu University, Dalian 116600, China
| | - Yanfei Qi
- Centenary Institute, The University of Sydney, Sydney, NSW 2050, Australia
| | - Shubiao Zhang
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, Dalian Minzu University, Dalian 116600, China.
| | - Yinan Zhao
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, Dalian Minzu University, Dalian 116600, China
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Baniasadi A, Das JP, Prendergast CM, Beizavi Z, Ma HY, Jaber MY, Capaccione KM. Imaging at the nexus: how state of the art imaging techniques can enhance our understanding of cancer and fibrosis. J Transl Med 2024; 22:567. [PMID: 38872212 PMCID: PMC11177383 DOI: 10.1186/s12967-024-05379-1] [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: 02/11/2024] [Accepted: 06/06/2024] [Indexed: 06/15/2024] Open
Abstract
Both cancer and fibrosis are diseases involving dysregulation of cell signaling pathways resulting in an altered cellular microenvironment which ultimately leads to progression of the condition. The two disease entities share common molecular pathophysiology and recent research has illuminated the how each promotes the other. Multiple imaging techniques have been developed to aid in the early and accurate diagnosis of each disease, and given the commonalities between the pathophysiology of the conditions, advances in imaging one disease have opened new avenues to study the other. Here, we detail the most up-to-date advances in imaging techniques for each disease and how they have crossed over to improve detection and monitoring of the other. We explore techniques in positron emission tomography (PET), magnetic resonance imaging (MRI), second generation harmonic Imaging (SGHI), ultrasound (US), radiomics, and artificial intelligence (AI). A new diagnostic imaging tool in PET/computed tomography (CT) is the use of radiolabeled fibroblast activation protein inhibitor (FAPI). SGHI uses high-frequency sound waves to penetrate deeper into the tissue, providing a more detailed view of the tumor microenvironment. Artificial intelligence with the aid of advanced deep learning (DL) algorithms has been highly effective in training computer systems to diagnose and classify neoplastic lesions in multiple organs. Ultimately, advancing imaging techniques in cancer and fibrosis can lead to significantly more timely and accurate diagnoses of both diseases resulting in better patient outcomes.
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Affiliation(s)
- Alireza Baniasadi
- Department of Radiology, Columbia University Irving Medical Center, 622 W 168Th Street, New York, NY, 10032, USA.
| | - Jeeban P Das
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Conor M Prendergast
- Department of Radiology, Columbia University Irving Medical Center, 622 W 168Th Street, New York, NY, 10032, USA
| | - Zahra Beizavi
- Department of Radiology, Columbia University Irving Medical Center, 622 W 168Th Street, New York, NY, 10032, USA
| | - Hong Y Ma
- Department of Radiology, Columbia University Irving Medical Center, 622 W 168Th Street, New York, NY, 10032, USA
| | | | - Kathleen M Capaccione
- Department of Radiology, Columbia University Irving Medical Center, 622 W 168Th Street, New York, NY, 10032, USA
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Pathan RK, Shorna IJ, Hossain MS, Khandaker MU, Almohammed HI, Hamd ZY. The efficacy of machine learning models in lung cancer risk prediction with explainability. PLoS One 2024; 19:e0305035. [PMID: 38870229 PMCID: PMC11175504 DOI: 10.1371/journal.pone.0305035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 05/22/2024] [Indexed: 06/15/2024] Open
Abstract
Among many types of cancers, to date, lung cancer remains one of the deadliest cancers around the world. Many researchers, scientists, doctors, and people from other fields continuously contribute to this subject regarding early prediction and diagnosis. One of the significant problems in prediction is the black-box nature of machine learning models. Though the detection rate is comparatively satisfactory, people have yet to learn how a model came to that decision, causing trust issues among patients and healthcare workers. This work uses multiple machine learning models on a numerical dataset of lung cancer-relevant parameters and compares performance and accuracy. After comparison, each model has been explained using different methods. The main contribution of this research is to give logical explanations of why the model reached a particular decision to achieve trust. This research has also been compared with a previous study that worked with a similar dataset and took expert opinions regarding their proposed model. We also showed that our research achieved better results than their proposed model and specialist opinion using hyperparameter tuning, having an improved accuracy of almost 100% in all four models.
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Affiliation(s)
- Refat Khan Pathan
- Department of Computing and Information Systems, School of Engineering and Technology, Sunway University, Selangor, Malaysia
| | | | - Md. Sayem Hossain
- School of Computing Science, Faculty of Innovation and Technology, Taylor’s University Lakeside Campus, Selangor, Malaysia
| | - Mayeen Uddin Khandaker
- Applied Physics and Radiation Technologies Group, CCDCU, School of Engineering and Technology, Sunway University, Selangor, Malaysia
- Faculty of Graduate Studies, Daffodil International University, Daffodil Smart City, Savar, Dhaka, Bangladesh
| | - Huda I. Almohammed
- Department of Radiological Sciences, College of Health and Rehabilitation Sciences, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Zuhal Y. Hamd
- Department of Radiological Sciences, College of Health and Rehabilitation Sciences, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
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Yasar S, Yagin FH, Melekoglu R, Ardigò LP. Integrating proteomics and explainable artificial intelligence: a comprehensive analysis of protein biomarkers for endometrial cancer diagnosis and prognosis. Front Mol Biosci 2024; 11:1389325. [PMID: 38894711 PMCID: PMC11184912 DOI: 10.3389/fmolb.2024.1389325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024] Open
Abstract
Endometrial cancer, which is the most common gynaecological cancer in women after breast, colorectal and lung cancer, can be diagnosed at an early stage. The first aim of this study is to classify age, tumor grade, myometrial invasion and tumor size, which play an important role in the diagnosis and prognosis of endometrial cancer, with machine learning methods combined with explainable artificial intelligence. 20 endometrial cancer patients proteomic data obtained from tumor biopsies taken from different regions of EC tissue were used. The data obtained were then classified according to age, tumor size, tumor grade and myometrial invasion. Then, by using three different machine learning methods, explainable artificial intelligence was applied to the model that best classifies these groups and possible protein biomarkers that can be used in endometrial prognosis were evaluated. The optimal model for age classification was XGBoost with AUC (98.8%), for tumor grade classification was XGBoost with AUC (98.6%), for myometrial invasion classification was LightGBM with AUC (95.1%), and finally for tumor size classification was XGBoost with AUC (94.8%). By combining the optimal models and the SHAP approach, possible protein biomarkers and their expressions were obtained for classification. Finally, EWRS1 protein was found to be common in three groups (age, myometrial invasion, tumor size). This article's findings indicate that models have been developed that can accurately classify factors including age, tumor grade, and myometrial invasion all of which are critical for determining the prognosis of endometrial cancer as well as potential protein biomarkers associated with these factors. Furthermore, we were able to provide an analysis of how the quantities of the proteins suggested as biomarkers varied throughout the classes by combining the SHAP values with these ideal models.
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Affiliation(s)
- Seyma Yasar
- Department of Biostatistics, and Medical Informatics, Medicine Faculty, Inonu University, Malatya, Türkiye
| | - Fatma Hilal Yagin
- Department of Biostatistics, and Medical Informatics, Medicine Faculty, Inonu University, Malatya, Türkiye
| | - Rauf Melekoglu
- Department of Obstetrics and Gynecology, Faculty of Medicine, Inonu University, Malatya, Türkiye
| | - Luca Paolo Ardigò
- Department of Teacher Education, NLA University College, Oslo, Norway
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Teixeira PF, Battelino T, Carlsson A, Gudbjörnsdottir S, Hannelius U, von Herrath M, Knip M, Korsgren O, Elding Larsson H, Lindqvist A, Ludvigsson J, Lundgren M, Nowak C, Pettersson P, Pociot F, Sundberg F, Åkesson K, Lernmark Å, Forsander G. Assisting the implementation of screening for type 1 diabetes by using artificial intelligence on publicly available data. Diabetologia 2024; 67:985-994. [PMID: 38353727 PMCID: PMC11058797 DOI: 10.1007/s00125-024-06089-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 12/06/2023] [Indexed: 04/30/2024]
Abstract
The type 1 diabetes community is coalescing around the benefits and advantages of early screening for disease risk. To be accepted by healthcare providers, regulatory authorities and payers, screening programmes need to show that the testing variables allow accurate risk prediction and that individualised risk-informed monitoring plans are established, as well as operational feasibility, cost-effectiveness and acceptance at population level. Artificial intelligence (AI) has the potential to contribute to solving these issues, starting with the identification and stratification of at-risk individuals. ASSET (AI for Sustainable Prevention of Autoimmunity in the Society; www.asset.healthcare ) is a public/private consortium that was established to contribute to research around screening for type 1 diabetes and particularly to how AI can drive the implementation of a precision medicine approach to disease prevention. ASSET will additionally focus on issues pertaining to operational implementation of screening. The authors of this article, researchers and clinicians active in the field of type 1 diabetes, met in an open forum to independently debate key issues around screening for type 1 diabetes and to advise ASSET. The potential use of AI in the analysis of longitudinal data from observational cohort studies to inform the design of improved, more individualised screening programmes was also discussed. A key issue was whether AI would allow the research community and industry to capitalise on large publicly available data repositories to design screening programmes that allow the early detection of individuals at high risk and enable clinical evaluation of preventive therapies. Overall, AI has the potential to revolutionise type 1 diabetes screening, in particular to help identify individuals who are at increased risk of disease and aid in the design of appropriate follow-up plans. We hope that this initiative will stimulate further research on this very timely topic.
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Affiliation(s)
| | - Tadej Battelino
- University Medical Center Ljubljana, University of Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Anneli Carlsson
- Department of Clinical Sciences, Lund University/CRC, Skåne University Hospital, Malmö, Sweden
| | - Soffia Gudbjörnsdottir
- Swedish National Diabetes Register, Centre of Registers, Gothenburg, Sweden
- Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | | | - Matthias von Herrath
- Global Chief Medical Office, Novo Nordisk, A/S, Søborg, Denmark
- Diabetes Research Institute, University of Miami, Miami, FL, USA
| | - Mikael Knip
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Center for Child Health Research, Tampere University Hospital, Tampere, Finland
| | - Olle Korsgren
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Helena Elding Larsson
- Department of Clinical Sciences, Lund University/CRC, Skåne University Hospital, Malmö, Sweden
- Department of Pediatrics, Skåne University Hospital, Malmö, Sweden
| | | | - Johnny Ludvigsson
- Crown Princess Victoria Children's Hospital and Division of Pediatrics, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Markus Lundgren
- Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
- Department of Paediatrics, Kristianstad Hospital, Kristianstad, Sweden
| | | | - Paul Pettersson
- Division of Networked and Embedded Systems, Mälardalen University, Västerås, Sweden
- MainlyAI AB, Stockholm, Sweden
| | - Flemming Pociot
- Steno Diabetes Center Copenhagen, Herlev, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Frida Sundberg
- Department of Paediatrics, Institute for Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Queen Silvia Children's Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Karin Åkesson
- Department of Clinical and Experimental Medicine, Division of Pediatrics and Diabetes Research Center, Linköping University, Linköping, Sweden
- Department of Pediatrics, Ryhov County Hospital, Jönköping, Sweden
| | - Åke Lernmark
- Department of Clinical Sciences, Lund University/CRC, Skåne University Hospital, Malmö, Sweden.
| | - Gun Forsander
- Department of Paediatrics, Institute for Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
- Queen Silvia Children's Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden.
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Romero-Morelos P, Herrera-López E, González-Yebra B. Development, Application and Utility of a Machine Learning Approach for Melanoma and Non-Melanoma Lesion Classification Using Counting Box Fractal Dimension. Diagnostics (Basel) 2024; 14:1132. [PMID: 38893659 PMCID: PMC11171650 DOI: 10.3390/diagnostics14111132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/16/2024] [Accepted: 05/09/2024] [Indexed: 06/21/2024] Open
Abstract
The diagnosis and identification of melanoma are not always accurate, even for experienced dermatologists. Histopathology continues to be the gold standard, assessing specific parameters such as the Breslow index. However, it remains invasive and may lack effectiveness. Therefore, leveraging mathematical modeling and informatics has been a pursuit of diagnostic methods favoring early detection. Fractality, a mathematical parameter quantifying complexity and irregularity, has proven useful in melanoma diagnosis. Nonetheless, no studies have implemented this metric to feed artificial intelligence algorithms for the automatic classification of dermatological lesions, including melanoma. Hence, this study aimed to determine the combined utility of fractal dimension and unsupervised low-computational-requirements machine learning models in classifying melanoma and non-melanoma lesions. We analyzed 39,270 dermatological lesions obtained from the International Skin Imaging Collaboration. Box-counting fractal dimensions were calculated for these lesions. Fractal values were used to implement classification methods by unsupervised machine learning based on principal component analysis and iterated K-means (100 iterations). A clear separation was observed, using only fractal dimension values, between benign or malignant lesions (sensibility 72.4% and specificity 50.1%) and melanoma or non-melanoma lesions (sensibility 72.8% and specificity 50%) and subsequently, the classification quality based on the machine learning model was ≈80% for both benign and malignant or melanoma and non-melanoma lesions. However, the grouping of metastatic melanoma versus non-metastatic melanoma was less effective, probably due to the small sample size included in MM lesions. Nevertheless, we could suggest a decision algorithm based on fractal dimension for dermatological lesion discrimination. On the other hand, it was also determined that the fractal dimension is sufficient to generate unsupervised artificial intelligence models that allow for a more efficient classification of dermatological lesions.
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Affiliation(s)
- Pablo Romero-Morelos
- Department of Research, State University of the Valley of Ecatepec, Ecatepec 55210, México State, Mexico; (P.R.-M.); (E.H.-L.)
- National Laboratory of Artificial Intelligence and Data Science, CONAHCyT (LNC-IACD), Ecatepec 55210, México State, Mexico
| | - Elizabeth Herrera-López
- Department of Research, State University of the Valley of Ecatepec, Ecatepec 55210, México State, Mexico; (P.R.-M.); (E.H.-L.)
- National Laboratory of Artificial Intelligence and Data Science, CONAHCyT (LNC-IACD), Ecatepec 55210, México State, Mexico
| | - Beatriz González-Yebra
- Department of Medicine and Nutrition, Division of Health Sciences, University of Guanajuato, Campus León, León 37670, Guanajuato, Mexico
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Khorsandi D, Rezayat D, Sezen S, Ferrao R, Khosravi A, Zarepour A, Khorsandi M, Hashemian M, Iravani S, Zarrabi A. Application of 3D, 4D, 5D, and 6D bioprinting in cancer research: what does the future look like? J Mater Chem B 2024; 12:4584-4612. [PMID: 38686396 DOI: 10.1039/d4tb00310a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
The application of three- and four-dimensional (3D/4D) printing in cancer research represents a significant advancement in understanding and addressing the complexities of cancer biology. 3D/4D materials provide more physiologically relevant environments compared to traditional two-dimensional models, allowing for a more accurate representation of the tumor microenvironment that enables researchers to study tumor progression, drug responses, and interactions with surrounding tissues under conditions similar to in vivo conditions. The dynamic nature of 4D materials introduces the element of time, allowing for the observation of temporal changes in cancer behavior and response to therapeutic interventions. The use of 3D/4D printing in cancer research holds great promise for advancing our understanding of the disease and improving the translation of preclinical findings to clinical applications. Accordingly, this review aims to briefly discuss 3D and 4D printing and their advantages and limitations in the field of cancer. Moreover, new techniques such as 5D/6D printing and artificial intelligence (AI) are also introduced as methods that could be used to overcome the limitations of 3D/4D printing and opened promising ways for the fast and precise diagnosis and treatment of cancer.
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Affiliation(s)
- Danial Khorsandi
- Terasaki Institute for Biomedical Innovation, Los Angeles, CA, 90024, USA
| | - Dorsa Rezayat
- Center for Global Design and Manufacturing, College of Engineering and Applied Science, University of Cincinnati, 2901 Woodside Drive, Cincinnati, OH 45221, USA
| | - Serap Sezen
- Faculty of Engineering and Natural Sciences, Sabanci University, Tuzla 34956 Istanbul, Türkiye
- Nanotechnology Research and Application Center, Sabanci University, Tuzla 34956 Istanbul, Türkiye
| | - Rafaela Ferrao
- Terasaki Institute for Biomedical Innovation, Los Angeles, CA, 90024, USA
- University of Coimbra, Institute for Interdisciplinary Research, Doctoral Programme in Experimental Biology and Biomedicine (PDBEB), Portugal
| | - Arezoo Khosravi
- Department of Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, Istanbul Okan University, Istanbul 34959, Türkiye
| | - Atefeh Zarepour
- Department of Research Analytics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai - 600 077, India
| | - Melika Khorsandi
- Department of Cellular and Molecular Biology, Najafabad Branch, Islamic Azad University, Isfahan, Iran
| | - Mohammad Hashemian
- Department of Cellular and Molecular Biology, Najafabad Branch, Islamic Azad University, Isfahan, Iran
| | - Siavash Iravani
- Independent Researcher, W Nazar ST, Boostan Ave, Isfahan, Iran.
| | - Ali Zarrabi
- Department of Biomedical Engineering, Faculty of Engineering and Natural Sciences, Istinye University, Istanbul 34396, Türkiye.
- Graduate School of Biotechnology and Bioengineering, Yuan Ze University, Taoyuan 320315, Taiwan
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11
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Wahid KA, Kaffey ZY, Farris DP, Humbert-Vidan L, Moreno AC, Rasmussen M, Ren J, Naser MA, Netherton TJ, Korreman S, Balakrishnan G, Fuller CD, Fuentes D, Dohopolski MJ. Artificial Intelligence Uncertainty Quantification in Radiotherapy Applications - A Scoping Review. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.13.24307226. [PMID: 38798581 PMCID: PMC11118597 DOI: 10.1101/2024.05.13.24307226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Background/purpose The use of artificial intelligence (AI) in radiotherapy (RT) is expanding rapidly. However, there exists a notable lack of clinician trust in AI models, underscoring the need for effective uncertainty quantification (UQ) methods. The purpose of this study was to scope existing literature related to UQ in RT, identify areas of improvement, and determine future directions. Methods We followed the PRISMA-ScR scoping review reporting guidelines. We utilized the population (human cancer patients), concept (utilization of AI UQ), context (radiotherapy applications) framework to structure our search and screening process. We conducted a systematic search spanning seven databases, supplemented by manual curation, up to January 2024. Our search yielded a total of 8980 articles for initial review. Manuscript screening and data extraction was performed in Covidence. Data extraction categories included general study characteristics, RT characteristics, AI characteristics, and UQ characteristics. Results We identified 56 articles published from 2015-2024. 10 domains of RT applications were represented; most studies evaluated auto-contouring (50%), followed by image-synthesis (13%), and multiple applications simultaneously (11%). 12 disease sites were represented, with head and neck cancer being the most common disease site independent of application space (32%). Imaging data was used in 91% of studies, while only 13% incorporated RT dose information. Most studies focused on failure detection as the main application of UQ (60%), with Monte Carlo dropout being the most commonly implemented UQ method (32%) followed by ensembling (16%). 55% of studies did not share code or datasets. Conclusion Our review revealed a lack of diversity in UQ for RT applications beyond auto-contouring. Moreover, there was a clear need to study additional UQ methods, such as conformal prediction. Our results may incentivize the development of guidelines for reporting and implementation of UQ in RT.
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Affiliation(s)
- Kareem A. Wahid
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Zaphanlene Y. Kaffey
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - David P. Farris
- Research Medical Library, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Laia Humbert-Vidan
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Amy C. Moreno
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Jintao Ren
- Department of Oncology, Aarhus University Hospital, Denmark
| | - Mohamed A. Naser
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Tucker J. Netherton
- Department of Radiation Physics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stine Korreman
- Department of Oncology, Aarhus University Hospital, Denmark
| | | | - Clifton D. Fuller
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - David Fuentes
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Michael J. Dohopolski
- Department of Radiation Oncology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
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12
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Bui DC, Song B, Kim K, Kwak JT. DAX-Net: A dual-branch dual-task adaptive cross-weight feature fusion network for robust multi-class cancer classification in pathology images. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2024; 248:108112. [PMID: 38479146 DOI: 10.1016/j.cmpb.2024.108112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/15/2024] [Accepted: 03/01/2024] [Indexed: 04/02/2024]
Abstract
BACKGROUND AND OBJECTIVE Multi-class cancer classification has been extensively studied in digital and computational pathology due to its importance in clinical decision-making. Numerous computational tools have been proposed for various types of cancer classification. Many of them are built based on convolutional neural networks. Recently, Transformer-style networks have shown to be effective for cancer classification. Herein, we present a hybrid design that leverages both convolutional neural networks and transformer architecture to obtain superior performance in cancer classification. METHODS We propose a dual-branch dual-task adaptive cross-weight feature fusion network, called DAX-Net, which exploits heterogeneous feature representations from the convolutional neural network and Transformer network, adaptively combines them to boost their representation power, and conducts cancer classification as categorical classification and ordinal classification. For an efficient and effective optimization of the proposed model, we introduce two loss functions that are tailored to the two classification tasks. RESULTS To evaluate the proposed method, we employed colorectal and prostate cancer datasets, of which each contains both in-domain and out-of-domain test sets. For colorectal cancer, the proposed method obtained an accuracy of 88.4%, a quadratic kappa score of 0.945, and an F1 score of 0.831 for the in-domain test set, and 84.4%, 0.910, and 0.768 for the out-of-domain test set. For prostate cancer, it achieved an accuracy of 71.6%, a kappa score of 0.635, and an F1 score of 0.655 for the in-domain test set, 79.2% accuracy, 0.721 kappa score, and 0.686 F1 score for the first out-of-domain test set, and 58.1% accuracy, 0.564 kappa score, and 0.493 F1 score for the second out-of-domain test set. It is worth noting that the performance of the proposed method outperformed other competitors by significant margins, in particular, with respect to the out-of-domain test sets. CONCLUSIONS The experimental results demonstrate that the proposed method is not only accurate but also robust to varying conditions of the test sets in comparison to several, related methods. These results suggest that the proposed method can facilitate automated cancer classification in various clinical settings.
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Affiliation(s)
- Doanh C Bui
- School of Electrical Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Boram Song
- Department of Pathology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, 03181, Republic of Korea
| | - Kyungeun Kim
- Department of Pathology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, 03181, Republic of Korea
| | - Jin Tae Kwak
- School of Electrical Engineering, Korea University, Seoul, 02841, Republic of Korea.
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13
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Chen CC, Ting WC, Lee HC, Chang CC, Lin TC, Yang SF. A Cost-Effective Model for Predicting Recurrent Gastric Cancer Using Clinical Features. Diagnostics (Basel) 2024; 14:842. [PMID: 38667487 PMCID: PMC11049390 DOI: 10.3390/diagnostics14080842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/14/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
This study used artificial intelligence techniques to identify clinical cancer biomarkers for recurrent gastric cancer survivors. From a hospital-based cancer registry database in Taiwan, the datasets of the incidence of recurrence and clinical risk features were included in 2476 gastric cancer survivors. We benchmarked Random Forest using MLP, C4.5, AdaBoost, and Bagging algorithms on metrics and leveraged the synthetic minority oversampling technique (SMOTE) for imbalanced dataset issues, cost-sensitive learning for risk assessment, and SHapley Additive exPlanations (SHAPs) for feature importance analysis in this study. Our proposed Random Forest outperformed the other models with an accuracy of 87.9%, a recall rate of 90.5%, an accuracy rate of 86%, and an F1 of 88.2% on the recurrent category by a 10-fold cross-validation in a balanced dataset. We identified clinical features of recurrent gastric cancer, which are the top five features, stage, number of regional lymph node involvement, Helicobacter pylori, BMI (body mass index), and gender; these features significantly affect the prediction model's output and are worth paying attention to in the following causal effect analysis. Using an artificial intelligence model, the risk factors for recurrent gastric cancer could be identified and cost-effectively ranked according to their feature importance. In addition, they should be crucial clinical features to provide physicians with the knowledge to screen high-risk patients in gastric cancer survivors as well.
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Affiliation(s)
- Chun-Chia Chen
- Institute of Medicine, Chung Shan Medical University, Taichung 40201, Taiwan; (C.-C.C.); (S.-F.Y.)
- Division of Plastic Surgery, Department of Surgery, Chi Mei Medical Center, Tainan 704, Taiwan
- Division of Colorectal Surgery, Department of Surgery, Chung Shan Medical University Hospital, Taichung 40201, Taiwan;
| | - Wen-Chien Ting
- Division of Colorectal Surgery, Department of Surgery, Chung Shan Medical University Hospital, Taichung 40201, Taiwan;
- School of Medicine, Chung Shan Medical University, Taichung 40201, Taiwan
| | - Hsi-Chieh Lee
- Department of Computer Science and Information Engineering, National Quemoy University, Kinmen County 892, Taiwan;
| | - Chi-Chang Chang
- School of Medical Informatics, Chung Shan Medical University & IT Office, Chung Shan Medical University Hospital, Taichung 40201, Taiwan
- Department of Information Management, Ming Chuan University, Taoyuan City 33300, Taiwan
| | - Tsung-Chieh Lin
- Department of Computer Science and Information Engineering, National Quemoy University, Kinmen County 892, Taiwan;
| | - Shun-Fa Yang
- Institute of Medicine, Chung Shan Medical University, Taichung 40201, Taiwan; (C.-C.C.); (S.-F.Y.)
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Rolland J, Boutin R, Eveillard D, Delahaye B. Datascape: exploring heterogeneous dataspace. Sci Rep 2024; 14:7041. [PMID: 38580694 PMCID: PMC10997776 DOI: 10.1038/s41598-024-52493-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/19/2024] [Indexed: 04/07/2024] Open
Abstract
Data science is a powerful field for gaining insights, comparing, and predicting behaviors from datasets. However, the diversity of methods and hypotheses needed to abstract a dataset exhibits a lack of genericity. Moreover, the shape of a dataset, which structures its contained information and uncertainties, is rarely considered. Inspired by state-of-the-art manifold learning and hull estimations algorithms, we propose a novel framework, the datascape, that leverages topology and graph theory to abstract heterogeneous datasets. Built upon the combination of a nearest neighbor graph, a set of convex hulls, and a metric distance that respects the shape of the data, the datascape allows exploration of the dataset's underlying space. We show that the datascape can uncover underlying functions from simulated datasets, build predictive algorithms with performance close to state-of-the-art algorithms, and reveal insightful geodesic paths between points. It demonstrates versatility through ecological, medical, and simulated data use cases.
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Affiliation(s)
- Jakez Rolland
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, 44322, Nantes, France.
- Bio Logbook, 44200, Nantes, France.
| | | | - Damien Eveillard
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, 44322, Nantes, France
| | - Benoit Delahaye
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, 44322, Nantes, France
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Muthupandian S, Arockiaraj J, Belete MA. A commentary on 'The use of multilayer perceptron and radial basis function: an artificial intelligence model to predict progression of oral cancer': correspondence. Int J Surg 2024; 110:2438-2439. [PMID: 38668666 PMCID: PMC11020071 DOI: 10.1097/js9.0000000000001058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 12/20/2023] [Indexed: 04/29/2024]
Affiliation(s)
- Saravanan Muthupandian
- AMR and Nanomedicine Laboratory, Department of Pharmacology, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Chennai
| | - Jesu Arockiaraj
- Toxicology and Pharmacology Laboratory, Department of Biotechnology, Faculty of Science and Humanities, SRM Institute of Science and Technology, Chengalpattu District, Kattankulathur, Tamil Nadu, India
| | - Melaku A. Belete
- Department of Medical Laboratory Science, College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia
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16
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Partiot E, Gorda B, Lutz W, Lebrun S, Khalfi P, Mora S, Charlot B, Majzoub K, Desagher S, Ganesh G, Colomb S, Gaudin R. Organotypic culture of human brain explants as a preclinical model for AI-driven antiviral studies. EMBO Mol Med 2024; 16:1004-1026. [PMID: 38472366 PMCID: PMC11018746 DOI: 10.1038/s44321-024-00039-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 03/14/2024] Open
Abstract
Viral neuroinfections represent a major health burden for which the development of antivirals is needed. Antiviral compounds that target the consequences of a brain infection (symptomatic treatment) rather than the cause (direct-acting antivirals) constitute a promising mitigation strategy that requires to be investigated in relevant models. However, physiological surrogates mimicking an adult human cortex are lacking, limiting our understanding of the mechanisms associated with viro-induced neurological disorders. Here, we optimized the Organotypic culture of Post-mortem Adult human cortical Brain explants (OPAB) as a preclinical platform for Artificial Intelligence (AI)-driven antiviral studies. OPAB shows robust viability over weeks, well-preserved 3D cytoarchitecture, viral permissiveness, and spontaneous local field potential (LFP). Using LFP as a surrogate for neurohealth, we developed a machine learning framework to predict with high confidence the infection status of OPAB. As a proof-of-concept, we showed that antiviral-treated OPAB could partially restore LFP-based electrical activity of infected OPAB in a donor-dependent manner. Together, we propose OPAB as a physiologically relevant and versatile model to study neuroinfections and beyond, providing a platform for preclinical drug discovery.
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Affiliation(s)
- Emma Partiot
- CNRS, Institut de Recherche en Infectiologie de Montpellier (IRIM), 34293, Montpellier, France
- Univ Montpellier, 34090, Montpellier, France
| | - Barbara Gorda
- CNRS, Institut de Recherche en Infectiologie de Montpellier (IRIM), 34293, Montpellier, France
- Univ Montpellier, 34090, Montpellier, France
| | - Willy Lutz
- CNRS, Institut de Recherche en Infectiologie de Montpellier (IRIM), 34293, Montpellier, France
- Univ Montpellier, 34090, Montpellier, France
| | - Solène Lebrun
- CNRS, Institut de Recherche en Infectiologie de Montpellier (IRIM), 34293, Montpellier, France
- Univ Montpellier, 34090, Montpellier, France
| | - Pierre Khalfi
- Univ Montpellier, 34090, Montpellier, France
- CNRS, Institut de Génétique Moléculaire de Montpellier (IGMM), 34293, Montpellier, France
| | - Stéphan Mora
- Univ Montpellier, 34090, Montpellier, France
- CNRS, Institut de Génétique Moléculaire de Montpellier (IGMM), 34293, Montpellier, France
| | - Benoit Charlot
- Univ Montpellier, 34090, Montpellier, France
- Institut d'Electronique et des Systèmes IES, CNRS, 860 Rue de St - Priest Bâtiment 5, 34090, Montpellier, France
| | - Karim Majzoub
- Univ Montpellier, 34090, Montpellier, France
- CNRS, Institut de Génétique Moléculaire de Montpellier (IGMM), 34293, Montpellier, France
| | - Solange Desagher
- CNRS, Institut de Recherche en Infectiologie de Montpellier (IRIM), 34293, Montpellier, France
- Univ Montpellier, 34090, Montpellier, France
- CNRS, Institut de Génétique Moléculaire de Montpellier (IGMM), 34293, Montpellier, France
| | - Gowrishankar Ganesh
- Univ Montpellier, 34090, Montpellier, France
- UM-CNRS Laboratoire d'Informatique de Robotique et de Microelectronique de Montpellier (LIRMM), 161, Rue Ada, 34090, Montpellier, France
| | - Sophie Colomb
- Univ Montpellier, 34090, Montpellier, France
- Equipe de droit pénal et sciences forensiques de Montpellier (EDPFM), Univ. Montpellier, Département de médecine légale, Pôle Urgences, Centre Hospitalo-Universitaire de Montpellier, 371 Avenue du Doyen Gaston Giraud, 34285, Montpellier, France
| | - Raphael Gaudin
- CNRS, Institut de Recherche en Infectiologie de Montpellier (IRIM), 34293, Montpellier, France.
- Univ Montpellier, 34090, Montpellier, France.
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Chitluri KK, Emerson IA. The importance of protein domain mutations in cancer therapy. Heliyon 2024; 10:e27655. [PMID: 38509890 PMCID: PMC10950675 DOI: 10.1016/j.heliyon.2024.e27655] [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: 10/11/2023] [Revised: 02/28/2024] [Accepted: 03/05/2024] [Indexed: 03/22/2024] Open
Abstract
Cancer is a complex disease that is caused by multiple genetic factors. Researchers have been studying protein domain mutations to understand how they affect the progression and treatment of cancer. These mutations can significantly impact the development and spread of cancer by changing the protein structure, function, and signalling pathways. As a result, there is a growing interest in how these mutations can be used as prognostic indicators for cancer prognosis. Recent studies have shown that protein domain mutations can provide valuable information about the severity of the disease and the patient's response to treatment. They may also be used to predict the response and resistance to targeted therapy in cancer treatment. The clinical implications of protein domain mutations in cancer are significant, and they are regarded as essential biomarkers in oncology. However, additional techniques and approaches are required to characterize changes in protein domains and predict their functional effects. Machine learning and other computational tools offer promising solutions to this challenge, enabling the prediction of the impact of mutations on protein structure and function. Such predictions can aid in the clinical interpretation of genetic information. Furthermore, the development of genome editing tools like CRISPR/Cas9 has made it possible to validate the functional significance of mutants more efficiently and accurately. In conclusion, protein domain mutations hold great promise as prognostic and predictive biomarkers in cancer. Overall, considerable research is still needed to better define genetic and molecular heterogeneity and to resolve the challenges that remain, so that their full potential can be realized.
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Affiliation(s)
- Kiran Kumar Chitluri
- Bioinformatics Programming Lab, Department of Bio-Sciences, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, TN, 632014, India
| | - Isaac Arnold Emerson
- Bioinformatics Programming Lab, Department of Bio-Sciences, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, TN, 632014, India
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Alinia S, Asghari-Jafarabadi M, Mahmoudi L, Roshanaei G, Safari M. Predicting mortality and recurrence in colorectal cancer: Comparative assessment of predictive models. Heliyon 2024; 10:e27854. [PMID: 38515707 PMCID: PMC10955293 DOI: 10.1016/j.heliyon.2024.e27854] [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: 08/04/2023] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 03/23/2024] Open
Abstract
Introduction Colorectal cancer (CRC), also known as colorectal cancer, is a significant disease marked by high fatality rates, ranking as the third leading cause of global mortality. The main objective of this study was to assess the accuracy of predictive models in predicting both mortality events and the probability of disease recurrence. Method A retrospective analysis was conducted on a cohort of 284 individuals diagnosed with colorectal cancer between 2001 and 2017. Demographic and clinical data, including gender, disease stage, age at diagnosis, recurrence status, and treatment details, were meticulously recorded. We rigorously evaluated various predictive models, including Decision Trees, Random Forests, Random Survival Forests (RSF), Gradient Boosting, mboost, Deep Learning Neural Network (DLNN), and Cox regression. Performance metrics, such as sensitivity, positive predictive value (PPV), specificity, area under the receiver operating characteristic curve (ROC area), and overall accuracy, were calculated for each model to predict mortality and disease recurrence. The analysis was performed using R version 4.1.3 software and the Python programming language. Results For mortality prediction, the mboost model demonstrated the highest sensitivity at 96.9% (95% CI: 0.83-0.99) and an ROC area of 0.88. It also exhibited high specificity at 80% (95% CI: 0.59-0.93), a positive predictive value of 86.1% (95% CI: 0.70-0.95), and an overall accuracy of 89% (95% CI: 0.78-0.96). Random Forests showed perfect sensitivity of 100% (95% CI: 0.85-1) but had low specificity at 0% (95% CI: 0-0.52) and poor overall accuracy (50%). On the other hand, DLNN had the lowest performance metrics for mortality prediction, with a sensitivity of 24% (95% CI: 0.222-0.268), specificity of 75% (95% CI: 0.73-0.77), and a lower positive predictive value of 42% (95% CI: 0.38-0.45). The Gradient Boosting model showed the best performance in predicting recurrence, achieving perfect sensitivity of 100% (95% CI: 0.87-1) and high specificity at 92.9% (95% CI: 0.76-0.99). It also had a high positive predictive value of 93.3% (95% CI: 0.77-0.99). Gradient Boosting, with an ROC area of 96.4%, and mboost, with an ROC area of 75%, demonstrated remarkable performance. DLNN had the lowest performance metrics for recurrence prediction, with sensitivity at 1.75% (95% CI: 0.01-0.02), specificity at 98% (95% CI: 0.97-0.98), and a lower positive predictive value at 52.6% (95% CI: 0.39-0.65). Conclusion In summary, the mboost model demonstrated outstanding performance in predicting mortality, achieving exceptional results across various evaluation metrics. Random Forests exhibited perfect sensitivity but showed poor specificity and overall accuracy. The DLNN model displayed the lowest performance metrics for mortality prediction. In terms of recurrence prediction, the Gradient Boosting model outperformed other models with perfect sensitivity, high specificity, and positive predictive value. The DLNN model had the lowest performance metrics for recurrence prediction. Overall, the results emphasize the effectiveness of the mboost and Gradient Boosting models in predicting mortality and recurrence in colorectal cancer patients.
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Affiliation(s)
- Shayeste Alinia
- Department of Statistics and Epidemiology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | | | - Leila Mahmoudi
- Department of Statistics and Epidemiology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Ghodratollah Roshanaei
- Modeling of Non-communicable Diseases Research Canter, Department of Biostatistics, School of Public Health, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Maliheh Safari
- Department of Biostatistics, School of Medicine, Arak University of Medical Sciences, Arak, Iran
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Maleki Varnosfaderani S, Forouzanfar M. The Role of AI in Hospitals and Clinics: Transforming Healthcare in the 21st Century. Bioengineering (Basel) 2024; 11:337. [PMID: 38671759 PMCID: PMC11047988 DOI: 10.3390/bioengineering11040337] [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: 02/28/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
As healthcare systems around the world face challenges such as escalating costs, limited access, and growing demand for personalized care, artificial intelligence (AI) is emerging as a key force for transformation. This review is motivated by the urgent need to harness AI's potential to mitigate these issues and aims to critically assess AI's integration in different healthcare domains. We explore how AI empowers clinical decision-making, optimizes hospital operation and management, refines medical image analysis, and revolutionizes patient care and monitoring through AI-powered wearables. Through several case studies, we review how AI has transformed specific healthcare domains and discuss the remaining challenges and possible solutions. Additionally, we will discuss methodologies for assessing AI healthcare solutions, ethical challenges of AI deployment, and the importance of data privacy and bias mitigation for responsible technology use. By presenting a critical assessment of AI's transformative potential, this review equips researchers with a deeper understanding of AI's current and future impact on healthcare. It encourages an interdisciplinary dialogue between researchers, clinicians, and technologists to navigate the complexities of AI implementation, fostering the development of AI-driven solutions that prioritize ethical standards, equity, and a patient-centered approach.
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Affiliation(s)
| | - Mohamad Forouzanfar
- Département de Génie des Systèmes, École de Technologie Supérieure (ÉTS), Université du Québec, Montréal, QC H3C 1K3, Canada
- Centre de Recherche de L’institut Universitaire de Gériatrie de Montréal (CRIUGM), Montréal, QC H3W 1W5, Canada
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Hussain S, Ali M, Naseem U, Nezhadmoghadam F, Jatoi MA, Gulliver TA, Tamez-Peña JG. Breast cancer risk prediction using machine learning: a systematic review. Front Oncol 2024; 14:1343627. [PMID: 38571502 PMCID: PMC10987819 DOI: 10.3389/fonc.2024.1343627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/26/2024] [Indexed: 04/05/2024] Open
Abstract
Background Breast cancer is the leading cause of cancer-related fatalities among women worldwide. Conventional screening and risk prediction models primarily rely on demographic and patient clinical history to devise policies and estimate likelihood. However, recent advancements in artificial intelligence (AI) techniques, particularly deep learning (DL), have shown promise in the development of personalized risk models. These models leverage individual patient information obtained from medical imaging and associated reports. In this systematic review, we thoroughly investigated the existing literature on the application of DL to digital mammography, radiomics, genomics, and clinical information for breast cancer risk assessment. We critically analyzed these studies and discussed their findings, highlighting the promising prospects of DL techniques for breast cancer risk prediction. Additionally, we explored ongoing research initiatives and potential future applications of AI-driven approaches to further improve breast cancer risk prediction, thereby facilitating more effective screening and personalized risk management strategies. Objective and methods This study presents a comprehensive overview of imaging and non-imaging features used in breast cancer risk prediction using traditional and AI models. The features reviewed in this study included imaging, radiomics, genomics, and clinical features. Furthermore, this survey systematically presented DL methods developed for breast cancer risk prediction, aiming to be useful for both beginners and advanced-level researchers. Results A total of 600 articles were identified, 20 of which met the set criteria and were selected. Parallel benchmarking of DL models, along with natural language processing (NLP) applied to imaging and non-imaging features, could allow clinicians and researchers to gain greater awareness as they consider the clinical deployment or development of new models. This review provides a comprehensive guide for understanding the current status of breast cancer risk assessment using AI. Conclusion This study offers investigators a different perspective on the use of AI for breast cancer risk prediction, incorporating numerous imaging and non-imaging features.
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Affiliation(s)
- Sadam Hussain
- School of Engineering and Sciences, Tecnologico de Monterrey, Monterrey, Mexico
- Department of Electrical and Computer Engineering, University of Victoria, Victoria, BC, Canada
| | - Mansoor Ali
- School of Engineering and Sciences, Tecnologico de Monterrey, Monterrey, Mexico
| | - Usman Naseem
- College of Science and Engineering, James Cook University, Cairns, QLD, Australia
| | | | - Munsif Ali Jatoi
- Department of Biomedical Engineering, Salim Habib University, Karachi, Pakistan
| | - T. Aaron Gulliver
- Department of Electrical and Computer Engineering, University of Victoria, Victoria, BC, Canada
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Chugh V, Basu A, Kaushik A, Manshu, Bhansali S, Basu AK. Employing nano-enabled artificial intelligence (AI)-based smart technologies for prediction, screening, and detection of cancer. NANOSCALE 2024; 16:5458-5486. [PMID: 38391246 DOI: 10.1039/d3nr05648a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Cancer has been classified as a diverse illness with a wide range of subgroups. Its early identification and prognosis, which have become a requirement of cancer research, are essential for clinical treatment. Patients have already benefited greatly from the use of artificial intelligence (AI), machine learning (ML), and deep learning (DL) algorithms in the field of healthcare. AI simulates and combines data, pre-programmed rules, and knowledge to produce predictions. Data are used to improve efficiency across several pursuits and tasks through the art of ML. DL is a larger family of ML methods based on representational learning and simulated neural networks. Support vector machines, convulsion neural networks, and artificial neural networks, among others, have been widely used in cancer research to construct prediction models that enable precise and effective decision-making. Although using these innovative methods can enhance our comprehension of how cancer progresses, further validation is required before these techniques can be used in routine clinical practice. We cover contemporary methods used in the modelling of cancer development in this article. The presented prediction models are built using a variety of guided ML approaches, as well as numerous input attributes and data collections. Early identification and cost-effective detection of cancer's progression are equally necessary for successful treatment of the disease. Smart material-based detection techniques can give end consumers a portable, affordable instrument to easily detect and monitor their health issues without the need for specialized knowledge. Owing to their cost-effectiveness, excellent sensitivity, multimodal detection capacity, and miniaturization aptitude, two-dimensional (2D) materials have a lot of prospects for clinical examination of various compounds as well as cancer biomarkers. The effectiveness of traditional devices is moving faster towards more useful techniques thanks to developments in 2D material-based biosensors/sensors. The most current developments in the design of 2D material-based biosensors/sensors-the next wave of cancer screening instruments-are also outlined in this article.
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Affiliation(s)
- Vibhas Chugh
- Quantum Materials and Devices Unit, Institute of Nano Science and Technology, Mohali, Punjab 140306, India.
| | - Adreeja Basu
- Biological Science, St. John's University, New York, NY 10301, United States
| | - Ajeet Kaushik
- NanoBioTech Laboratory, Department of Environmental Engineering, Florida Polytechnic University, Lakeland, Florida 33805, USA
| | - Manshu
- Quantum Materials and Devices Unit, Institute of Nano Science and Technology, Mohali, Punjab 140306, India.
| | - Shekhar Bhansali
- Electrical and Computer Engineering, Florida International University, Miami, FL 33199, USA
| | - Aviru Kumar Basu
- Quantum Materials and Devices Unit, Institute of Nano Science and Technology, Mohali, Punjab 140306, India.
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He X, Xu Y, Zhou C, Song R, Liu Y, Zhang H, Wang Y, Fan Q, Wang D, Chen W, Wang J, Guo D. Prediction of microvascular invasion and pathological differentiation of hepatocellular carcinoma based on a deep learning model. Eur J Radiol 2024; 172:111348. [PMID: 38325190 DOI: 10.1016/j.ejrad.2024.111348] [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: 10/18/2023] [Revised: 01/12/2024] [Accepted: 01/25/2024] [Indexed: 02/09/2024]
Abstract
PURPOSE To develop a deep learning (DL) model based on preoperative contrast-enhanced computed tomography (CECT) images to predict microvascular invasion (MVI) and pathological differentiation of hepatocellular carcinoma (HCC). METHODS This retrospective study included 640 consecutive patients who underwent surgical resection and were pathologically diagnosed with HCC at two medical institutions from April 2017 to May 2022. CECT images and relevant clinical parameters were collected. All the data were divided into 368 training sets, 138 test sets and 134 validation sets. Through DL, a segmentation model was used to obtain a region of interest (ROI) of the liver, and a classification model was established to predict the pathological status of HCC. RESULTS The liver segmentation model based on the 3D U-Network had a mean intersection over union (mIoU) score of 0.9120 and a Dice score of 0.9473. Among all the classification prediction models based on the Swin transformer, the fusion models combining image information and clinical parameters exhibited the best performance. The area under the curve (AUC) of the fusion model for predicting the MVI status was 0.941, its accuracy was 0.917, and its specificity was 0.908. The AUC values of the fusion model for predicting poorly differentiated, moderately differentiated and highly differentiated HCC based on the test set were 0.962, 0.957 and 0.996, respectively. CONCLUSION The established DL models established can be used to noninvasively and effectively predict the MVI status and the degree of pathological differentiation of HCC, and aid in clinical diagnosis and treatment.
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Affiliation(s)
- Xiaojuan He
- Department of Radiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, PR China.
| | - Yang Xu
- Department of Radiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, PR China.
| | - Chaoyang Zhou
- Department of Radiology, The First Affiliated Hospital of Army Military Medical University, Chongqing 400038, PR China.
| | - Rao Song
- Department of Radiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, PR China.
| | - Yangyang Liu
- Department of Radiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, PR China.
| | - Haiping Zhang
- Department of Radiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, PR China.
| | - Yudong Wang
- Institute of Research, InferVision, Ocean International Center, Chaoyang District, Beijing 100025, PR China.
| | - Qianrui Fan
- Institute of Research, InferVision, Ocean International Center, Chaoyang District, Beijing 100025, PR China.
| | - Dawei Wang
- Institute of Research, InferVision, Ocean International Center, Chaoyang District, Beijing 100025, PR China.
| | - Weidao Chen
- Institute of Research, InferVision, Ocean International Center, Chaoyang District, Beijing 100025, PR China.
| | - Jian Wang
- Department of Radiology, The First Affiliated Hospital of Army Military Medical University, Chongqing 400038, PR China.
| | - Dajing Guo
- Department of Radiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, PR China.
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Lokaj B, Pugliese MT, Kinkel K, Lovis C, Schmid J. Barriers and facilitators of artificial intelligence conception and implementation for breast imaging diagnosis in clinical practice: a scoping review. Eur Radiol 2024; 34:2096-2109. [PMID: 37658895 PMCID: PMC10873444 DOI: 10.1007/s00330-023-10181-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/07/2023] [Accepted: 07/10/2023] [Indexed: 09/05/2023]
Abstract
OBJECTIVE Although artificial intelligence (AI) has demonstrated promise in enhancing breast cancer diagnosis, the implementation of AI algorithms in clinical practice encounters various barriers. This scoping review aims to identify these barriers and facilitators to highlight key considerations for developing and implementing AI solutions in breast cancer imaging. METHOD A literature search was conducted from 2012 to 2022 in six databases (PubMed, Web of Science, CINHAL, Embase, IEEE, and ArXiv). The articles were included if some barriers and/or facilitators in the conception or implementation of AI in breast clinical imaging were described. We excluded research only focusing on performance, or with data not acquired in a clinical radiology setup and not involving real patients. RESULTS A total of 107 articles were included. We identified six major barriers related to data (B1), black box and trust (B2), algorithms and conception (B3), evaluation and validation (B4), legal, ethical, and economic issues (B5), and education (B6), and five major facilitators covering data (F1), clinical impact (F2), algorithms and conception (F3), evaluation and validation (F4), and education (F5). CONCLUSION This scoping review highlighted the need to carefully design, deploy, and evaluate AI solutions in clinical practice, involving all stakeholders to yield improvement in healthcare. CLINICAL RELEVANCE STATEMENT The identification of barriers and facilitators with suggested solutions can guide and inform future research, and stakeholders to improve the design and implementation of AI for breast cancer detection in clinical practice. KEY POINTS • Six major identified barriers were related to data; black-box and trust; algorithms and conception; evaluation and validation; legal, ethical, and economic issues; and education. • Five major identified facilitators were related to data, clinical impact, algorithms and conception, evaluation and validation, and education. • Coordinated implication of all stakeholders is required to improve breast cancer diagnosis with AI.
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Affiliation(s)
- Belinda Lokaj
- Geneva School of Health Sciences, HES-SO University of Applied Sciences and Arts Western Switzerland, Delémont, Switzerland.
- Faculty of Medicine, University of Geneva, Geneva, Switzerland.
- Division of Medical Information Sciences, Geneva University Hospitals, Geneva, Switzerland.
| | - Marie-Thérèse Pugliese
- Geneva School of Health Sciences, HES-SO University of Applied Sciences and Arts Western Switzerland, Delémont, Switzerland
| | - Karen Kinkel
- Réseau Hospitalier Neuchâtelois, Neuchâtel, Switzerland
| | - Christian Lovis
- Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Division of Medical Information Sciences, Geneva University Hospitals, Geneva, Switzerland
| | - Jérôme Schmid
- Geneva School of Health Sciences, HES-SO University of Applied Sciences and Arts Western Switzerland, Delémont, Switzerland
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Cheng D, Liu D, Li X, Mi Z, Zhang Z, Tao W, Dang J, Zhu D, Fu J, Fan H. A deep learning model for accurately predicting cancer-specific survival in patients with primary bone sarcoma of the extremity: a population-based study. Clin Transl Oncol 2024; 26:709-719. [PMID: 37552409 DOI: 10.1007/s12094-023-03291-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/21/2023] [Indexed: 08/09/2023]
Abstract
PURPOSE Primary bone and joint sarcomas of the long bone are relatively rare neoplasms with poor prognosis. An efficient clinical tool that can accurately predict patient prognosis is not available. The current study aimed to use deep learning algorithms to develop a prediction model for the prognosis of patients with long bone sarcoma. METHODS Data of patients with long bone sarcoma in the extremities was collected from the Surveillance, Epidemiology, and End Results Program database from 2004 to 2014. Univariate and multivariate analyses were performed to select possible prediction features. DeepSurv, a deep learning model, was constructed for predicting cancer-specific survival rates. In addition, the classical cox proportional hazards model was established for comparison. The predictive accuracy of our models was assessed using the C-index, Integrated Brier Score, receiver operating characteristic curve, and calibration curve. RESULTS Age, tumor extension, histological grade, tumor size, surgery, and distant metastasis were associated with cancer-specific survival in patients with long bone sarcoma. According to loss function values, our models converged successfully and effectively learned the survival data of the training cohort. Based on the C-index, area under the curve, calibration curve, and Integrated Brier Score, the deep learning model was more accurate and flexible in predicting survival rates than the cox proportional hazards model. CONCLUSION A deep learning model for predicting the survival probability of patients with long bone sarcoma was constructed and validated. It is more accurate and flexible in predicting prognosis than the classical CoxPH model.
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Affiliation(s)
- Debin Cheng
- Department of Orthopaedics, Xijing Hospital, The Fourth Military Medical University, Xi'an, 710032, China
| | - Dong Liu
- Department of Orthopaedics, Xijing Hospital, The Fourth Military Medical University, Xi'an, 710032, China
| | - Xian Li
- Department of Orthopaedics, Shenzhen University General Hospital, Shenzhen, 518052, China
| | - Zhenzhou Mi
- Department of Orthopaedics, Xijing Hospital, The Fourth Military Medical University, Xi'an, 710032, China
| | - Zhao Zhang
- Department of Orthopaedics, Xijing Hospital, The Fourth Military Medical University, Xi'an, 710032, China
| | - Weidong Tao
- Department of Orthopaedics, Xijing Hospital, The Fourth Military Medical University, Xi'an, 710032, China
| | - Jingyi Dang
- Department of Orthopaedics, Xijing Hospital, The Fourth Military Medical University, Xi'an, 710032, China
| | - Dongze Zhu
- Department of Orthopaedics, Xijing Hospital, The Fourth Military Medical University, Xi'an, 710032, China
| | - Jun Fu
- Department of Orthopaedics, Xijing Hospital, The Fourth Military Medical University, Xi'an, 710032, China
| | - Hongbin Fan
- Department of Orthopaedics, Xijing Hospital, The Fourth Military Medical University, Xi'an, 710032, China.
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Rey R, Gualtieri R, La Scala G, Posfay Barbe K. Artificial Intelligence in the Diagnosis and Management of Appendicitis in Pediatric Departments: A Systematic Review. Eur J Pediatr Surg 2024. [PMID: 38290564 DOI: 10.1055/a-2257-5122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
INTRODUCTION Artificial intelligence (AI) is a growing field in medical research that could potentially help in the challenging diagnosis of acute appendicitis (AA) in children. However, usefulness of AI in clinical settings remains unclear. Our aim was to assess the accuracy of AIs in the diagnosis of AA in the pediatric population through a systematic literature review. METHODS PubMed, Embase, and Web of Science were searched using the following keywords: "pediatric," "artificial intelligence," "standard practices," and "appendicitis," up to September 2023. The risk of bias was assessed using PROBAST. RESULTS A total of 302 articles were identified and nine articles were included in the final review. Two studies had prospective validation, seven were retrospective, and no randomized control trials were found. All studies developed their own algorithms and had an accuracy greater than 90% or area under the curve >0.9. All studies were rated as a "high risk" concerning their overall risk of bias. CONCLUSION We analyzed the current status of AI in the diagnosis of appendicitis in children. The application of AI shows promising potential, but the need for more rigor in study design, reporting, and transparency is urgent to facilitate its clinical implementation.
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Affiliation(s)
- Robin Rey
- Department of Human Medicine, Faculty of Medicine, University of Geneva, Genève, Switzerland
| | - Renato Gualtieri
- Department of Pediatrics, Gynecology and Obstetrics, University of Geneva, Genève, Switzerland
| | - Giorgio La Scala
- Division of Pediatric Surgery, Hôpital des enfants, Geneva University Hospitals, Genève, Switzerland
| | - Klara Posfay Barbe
- Division of General Pediatrics, Hôpital des enfants, Geneva University Hospitals, Genève, Switzerland
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Hassan J, Saeed SM, Deka L, Uddin MJ, Das DB. Applications of Machine Learning (ML) and Mathematical Modeling (MM) in Healthcare with Special Focus on Cancer Prognosis and Anticancer Therapy: Current Status and Challenges. Pharmaceutics 2024; 16:260. [PMID: 38399314 PMCID: PMC10892549 DOI: 10.3390/pharmaceutics16020260] [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: 12/08/2023] [Revised: 01/29/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
The use of data-driven high-throughput analytical techniques, which has given rise to computational oncology, is undisputed. The widespread use of machine learning (ML) and mathematical modeling (MM)-based techniques is widely acknowledged. These two approaches have fueled the advancement in cancer research and eventually led to the uptake of telemedicine in cancer care. For diagnostic, prognostic, and treatment purposes concerning different types of cancer research, vast databases of varied information with manifold dimensions are required, and indeed, all this information can only be managed by an automated system developed utilizing ML and MM. In addition, MM is being used to probe the relationship between the pharmacokinetics and pharmacodynamics (PK/PD interactions) of anti-cancer substances to improve cancer treatment, and also to refine the quality of existing treatment models by being incorporated at all steps of research and development related to cancer and in routine patient care. This review will serve as a consolidation of the advancement and benefits of ML and MM techniques with a special focus on the area of cancer prognosis and anticancer therapy, leading to the identification of challenges (data quantity, ethical consideration, and data privacy) which are yet to be fully addressed in current studies.
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Affiliation(s)
- Jasmin Hassan
- Drug Delivery & Therapeutics Lab, Dhaka 1212, Bangladesh; (J.H.); (S.M.S.)
| | | | - Lipika Deka
- Faculty of Computing, Engineering and Media, De Montfort University, Leicester LE1 9BH, UK;
| | - Md Jasim Uddin
- Department of Pharmaceutical Technology, Faculty of Pharmacy, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Diganta B. Das
- Department of Chemical Engineering, Loughborough University, Loughborough LE11 3TU, UK
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Santeramo R, Damiani C, Wei J, Montana G, Brentnall AR. Are better AI algorithms for breast cancer detection also better at predicting risk? A paired case-control study. Breast Cancer Res 2024; 26:25. [PMID: 38326868 PMCID: PMC10848404 DOI: 10.1186/s13058-024-01775-z] [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: 10/02/2023] [Accepted: 01/20/2024] [Indexed: 02/09/2024] Open
Abstract
BACKGROUND There is increasing evidence that artificial intelligence (AI) breast cancer risk evaluation tools using digital mammograms are highly informative for 1-6 years following a negative screening examination. We hypothesized that algorithms that have previously been shown to work well for cancer detection will also work well for risk assessment and that performance of algorithms for detection and risk assessment is correlated. METHODS To evaluate our hypothesis, we designed a case-control study using paired mammograms at diagnosis and at the previous screening visit. The study included n = 3386 women from the OPTIMAM registry, that includes mammograms from women diagnosed with breast cancer in the English breast screening program 2010-2019. Cases were diagnosed with invasive breast cancer or ductal carcinoma in situ at screening and were selected if they had a mammogram available at the screening examination that led to detection, and a paired mammogram at their previous screening visit 3y prior to detection when no cancer was detected. Controls without cancer were matched 1:1 to cases based on age (year), screening site, and mammography machine type. Risk assessment was conducted using a deep-learning model designed for breast cancer risk assessment (Mirai), and three open-source deep-learning algorithms designed for breast cancer detection. Discrimination was assessed using a matched area under the curve (AUC) statistic. RESULTS Overall performance using the paired mammograms followed the same order by algorithm for risk assessment (AUC range 0.59-0.67) and detection (AUC 0.81-0.89), with Mirai performing best for both. There was also a correlation in performance for risk and detection within algorithms by cancer size, with much greater accuracy for large cancers (30 mm+, detection AUC: 0.88-0.92; risk AUC: 0.64-0.74) than smaller cancers (0 to < 10 mm, detection AUC: 0.73-0.86, risk AUC: 0.54-0.64). Mirai was relatively strong for risk assessment of smaller cancers (0 to < 10 mm, risk, Mirai AUC: 0.64 (95% CI 0.57 to 0.70); other algorithms AUC 0.54-0.56). CONCLUSIONS Improvements in risk assessment could stem from enhancing cancer detection capabilities of smaller cancers. Other state-of-the-art AI detection algorithms with high performance for smaller cancers might achieve relatively high performance for risk assessment.
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Affiliation(s)
- Ruggiero Santeramo
- Wolfson Institute of Population Health, Queen Mary University of London, Charterhouse square, London, EC1M 6BQ, England, UK.
- Warwick Manufacturing Group, University of Warwick, Coventry, CV4 7AL, England, UK.
| | - Celeste Damiani
- Wolfson Institute of Population Health, Queen Mary University of London, Charterhouse square, London, EC1M 6BQ, England, UK
- Fondazione Istituto Italiano di Tecnologia (IIT), 16163, Genoa, Italy
| | - Jiefei Wei
- Department of Statistics, University of Warwick, Coventry, CV4 7AL, England, UK
| | - Giovanni Montana
- Warwick Manufacturing Group, University of Warwick, Coventry, CV4 7AL, England, UK.
- Department of Statistics, University of Warwick, Coventry, CV4 7AL, England, UK.
| | - Adam R Brentnall
- Wolfson Institute of Population Health, Queen Mary University of London, Charterhouse square, London, EC1M 6BQ, England, UK.
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Jenul A, Stokmo HL, Schrunner S, Hjortland GO, Revheim ME, Tomic O. Novel ensemble feature selection techniques applied to high-grade gastroenteropancreatic neuroendocrine neoplasms for the prediction of survival. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2024; 244:107934. [PMID: 38016391 DOI: 10.1016/j.cmpb.2023.107934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/05/2023] [Accepted: 11/17/2023] [Indexed: 11/30/2023]
Abstract
BACKGROUND AND OBJECTIVE Determining the most informative features for predicting the overall survival of patients diagnosed with high-grade gastroenteropancreatic neuroendocrine neoplasms is crucial to improve individual treatment plans for patients, as well as the biological understanding of the disease. The main objective of this study is to evaluate the use of modern ensemble feature selection techniques for this purpose with respect to (a) quantitative performance measures such as predictive performance, (b) clinical interpretability, and (c) the effect of integrating prior expert knowledge. METHODS The Repeated Elastic Net Technique for Feature Selection (RENT) and the User-Guided Bayesian Framework for Feature Selection (UBayFS) are recently developed ensemble feature selectors investigated in this work. Both allow the user to identify informative features in datasets with low sample sizes and focus on model interpretability. While RENT is purely data-driven, UBayFS can integrate expert knowledge a priori in the feature selection process. In this work, we compare both feature selectors on a dataset comprising 63 patients and 110 features from multiple sources, including baseline patient characteristics, baseline blood values, tumor histology, imaging, and treatment information. RESULTS Our experiments involve data-driven and expert-driven setups, as well as combinations of both. In a five-fold cross-validated experiment without expert knowledge, our results demonstrate that both feature selectors allow accurate predictions: A reduction from 110 to approximately 20 features (around 82%) delivers near-optimal predictive performances with minor variations according to the choice of the feature selector, the predictive model, and the fold. Thereafter, we use findings from clinical literature as a source of expert knowledge. In addition, expert knowledge has a stabilizing effect on the feature set (an increase in stability of approximately 40%), while the impact on predictive performance is limited. CONCLUSIONS The features WHO Performance Status, Albumin, Platelets, Ki-67, Tumor Morphology, Total MTV, Total TLG, and SUVmax are the most stable and predictive features in our study. Overall, this study demonstrated the practical value of feature selection in medical applications not only to improve quantitative performance but also to deliver potentially new insights to experts.
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Affiliation(s)
- Anna Jenul
- Department of Data Science, Norwegian University of Life Sciences, Universitetstunet 3, 1433 Ås, Norway.
| | - Henning Langen Stokmo
- Department of Nuclear Medicine, Division of Radiology and Nuclear Medicine, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
| | - Stefan Schrunner
- Department of Data Science, Norwegian University of Life Sciences, Universitetstunet 3, 1433 Ås, Norway.
| | | | - Mona-Elisabeth Revheim
- Department of Nuclear Medicine, Division of Radiology and Nuclear Medicine, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway; The Intervention Centre, Division of Technology and Innovation, Oslo University Hospital, Oslo, Norway.
| | - Oliver Tomic
- Department of Data Science, Norwegian University of Life Sciences, Universitetstunet 3, 1433 Ås, Norway.
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Li F, Wang B, Li H, Kong L, Zhu B. G6PD and machine learning algorithms as prognostic and diagnostic indicators of liver hepatocellular carcinoma. BMC Cancer 2024; 24:157. [PMID: 38297250 PMCID: PMC10829225 DOI: 10.1186/s12885-024-11887-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/16/2024] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND Liver Hepatocellular carcinoma (LIHC) exhibits a high incidence of liver cancer with escalating mortality rates over time. Despite this, the underlying pathogenic mechanism of LIHC remains poorly understood. MATERIALS & METHODS To address this gap, we conducted a comprehensive investigation into the role of G6PD in LIHC using a combination of bioinformatics analysis with database data and rigorous cell experiments. LIHC samples were obtained from TCGA, ICGC and GEO databases, and the differences in G6PD expression in different tissues were investigated by differential expression analysis, followed by the establishment of Nomogram to determine the percentage of G6PD in causing LIHC by examining the relationship between G6PD and clinical features, and the subsequent validation of the effect of G6PD on the activity, migration, and invasive ability of hepatocellular carcinoma cells by using the low expression of LI-7 and SNU-449. Additionally, we employed machine learning to validate and compare the predictive capacity of four algorithms for LIHC patient prognosis. RESULTS Our findings revealed significantly elevated G6PD expression levels in liver cancer tissues as compared to normal tissues. Meanwhile, Nomogram and Adaboost, Catboost, and Gbdt Regression analyses showed that G6PD accounted for 46%, 31%, and 49% of the multiple factors leading to LIHC. Furthermore, we observed that G6PD knockdown in hepatocellular carcinoma cells led to reduced proliferation, migration, and invasion abilities. Remarkably, the Decision Tree C5.0 decision tree algorithm demonstrated superior discriminatory performance among the machine learning methods assessed. CONCLUSION The potential diagnostic utility of G6PD and Decision Tree C5.0 for LIHC opens up a novel avenue for early detection and improved treatment strategies for hepatocellular carcinoma.
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Affiliation(s)
- Fei Li
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, 87 Dingjiaqiao, Nanjing, 210009, Jiangsu, China
| | - Boshen Wang
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, 87 Dingjiaqiao, Nanjing, 210009, Jiangsu, China
- Institute of Occupational Disease Prevention, Jiangsu Provincial Center for Disease Prevention and Control, Nanjing, Jiangsu, 210009, China
| | - Hao Li
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, 87 Dingjiaqiao, Nanjing, 210009, Jiangsu, China
| | - Lu Kong
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, 87 Dingjiaqiao, Nanjing, 210009, Jiangsu, China.
| | - Baoli Zhu
- Institute of Occupational Disease Prevention, Jiangsu Provincial Center for Disease Prevention and Control, Nanjing, Jiangsu, 210009, China.
- Jiangsu Preventive Medical Association, Nanjing, 210000, Jiangsu, China.
- Center for Global Health, Nanjing Medical University, Nanjing, 211112, China.
- Jiangsu Province Engineering Research Center of Public Health Emergency, Nanjing, 210000, Jiangsu, China.
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Ma W, Wu H, Chen Y, Xu H, Jiang J, Du B, Wan M, Ma X, Chen X, Lin L, Su X, Bao X, Shen Y, Xu N, Ruan J, Jiang H, Ding Y. New techniques to identify the tissue of origin for cancer of unknown primary in the era of precision medicine: progress and challenges. Brief Bioinform 2024; 25:bbae028. [PMID: 38343328 PMCID: PMC10859692 DOI: 10.1093/bib/bbae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 12/10/2023] [Accepted: 01/11/2024] [Indexed: 02/15/2024] Open
Abstract
Despite a standardized diagnostic examination, cancer of unknown primary (CUP) is a rare metastatic malignancy with an unidentified tissue of origin (TOO). Patients diagnosed with CUP are typically treated with empiric chemotherapy, although their prognosis is worse than those with metastatic cancer of a known origin. TOO identification of CUP has been employed in precision medicine, and subsequent site-specific therapy is clinically helpful. For example, molecular profiling, including genomic profiling, gene expression profiling, epigenetics and proteins, has facilitated TOO identification. Moreover, machine learning has improved identification accuracy, and non-invasive methods, such as liquid biopsy and image omics, are gaining momentum. However, the heterogeneity in prediction accuracy, sample requirements and technical fundamentals among the various techniques is noteworthy. Accordingly, we systematically reviewed the development and limitations of novel TOO identification methods, compared their pros and cons and assessed their potential clinical usefulness. Our study may help patients shift from empirical to customized care and improve their prognoses.
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Affiliation(s)
- Wenyuan Ma
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hui Wu
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yiran Chen
- Department of Surgical Oncology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hongxia Xu
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Haining, China
| | - Junjie Jiang
- Department of Gastroenterology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Bang Du
- Real Doctor AI Research Centre, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Mingyu Wan
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaolu Ma
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoyu Chen
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lili Lin
- Department of Nuclear Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xinhui Su
- Department of Nuclear Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xuanwen Bao
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yifei Shen
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Nong Xu
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jian Ruan
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Haiping Jiang
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yongfeng Ding
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Lin WC, Chen A, Song X, Weiskopf NG, Chiang MF, Hribar MR. Prediction of multiclass surgical outcomes in glaucoma using multimodal deep learning based on free-text operative notes and structured EHR data. J Am Med Inform Assoc 2024; 31:456-464. [PMID: 37964658 PMCID: PMC10797280 DOI: 10.1093/jamia/ocad213] [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: 06/13/2023] [Revised: 10/16/2023] [Accepted: 10/25/2023] [Indexed: 11/16/2023] Open
Abstract
OBJECTIVE Surgical outcome prediction is challenging but necessary for postoperative management. Current machine learning models utilize pre- and post-op data, excluding intraoperative information in surgical notes. Current models also usually predict binary outcomes even when surgeries have multiple outcomes that require different postoperative management. This study addresses these gaps by incorporating intraoperative information into multimodal models for multiclass glaucoma surgery outcome prediction. MATERIALS AND METHODS We developed and evaluated multimodal deep learning models for multiclass glaucoma trabeculectomy surgery outcomes using both structured EHR data and free-text operative notes. We compare those to baseline models that use structured EHR data exclusively, or neural network models that leverage only operative notes. RESULTS The multimodal neural network had the highest performance with a macro AUROC of 0.750 and F1 score of 0.583. It outperformed the baseline machine learning model with structured EHR data alone (macro AUROC of 0.712 and F1 score of 0.486). Additionally, the multimodal model achieved the highest recall (0.692) for hypotony surgical failure, while the surgical success group had the highest precision (0.884) and F1 score (0.775). DISCUSSION This study shows that operative notes are an important source of predictive information. The multimodal predictive model combining perioperative notes and structured pre- and post-op EHR data outperformed other models. Multiclass surgical outcome prediction can provide valuable insights for clinical decision-making. CONCLUSIONS Our results show the potential of deep learning models to enhance clinical decision-making for postoperative management. They can be applied to other specialties to improve surgical outcome predictions.
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Affiliation(s)
- Wei-Chun Lin
- Department of Medical Informatics & Clinical Epidemiology, Oregon Health & Science University, 3181 S.W. Sam Jackson Park Rd, Portland, OR, 97239, United States
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, 545 SW Campus Dr, Portland, OR, 97239, United States
| | - Aiyin Chen
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, 545 SW Campus Dr, Portland, OR, 97239, United States
| | - Xubo Song
- Department of Medical Informatics & Clinical Epidemiology, Oregon Health & Science University, 3181 S.W. Sam Jackson Park Rd, Portland, OR, 97239, United States
| | - Nicole G Weiskopf
- Department of Medical Informatics & Clinical Epidemiology, Oregon Health & Science University, 3181 S.W. Sam Jackson Park Rd, Portland, OR, 97239, United States
| | - Michael F Chiang
- National Eye Institute, National Institutes of Health, 31 Center Dr MSC 2510, Bethesda, MD, 20892, United States
- National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894, United States
| | - Michelle R Hribar
- Department of Medical Informatics & Clinical Epidemiology, Oregon Health & Science University, 3181 S.W. Sam Jackson Park Rd, Portland, OR, 97239, United States
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, 545 SW Campus Dr, Portland, OR, 97239, United States
- National Eye Institute, National Institutes of Health, 31 Center Dr MSC 2510, Bethesda, MD, 20892, United States
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Bekbolatova M, Mayer J, Ong CW, Toma M. Transformative Potential of AI in Healthcare: Definitions, Applications, and Navigating the Ethical Landscape and Public Perspectives. Healthcare (Basel) 2024; 12:125. [PMID: 38255014 PMCID: PMC10815906 DOI: 10.3390/healthcare12020125] [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: 10/11/2023] [Revised: 12/27/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024] Open
Abstract
Artificial intelligence (AI) has emerged as a crucial tool in healthcare with the primary aim of improving patient outcomes and optimizing healthcare delivery. By harnessing machine learning algorithms, natural language processing, and computer vision, AI enables the analysis of complex medical data. The integration of AI into healthcare systems aims to support clinicians, personalize patient care, and enhance population health, all while addressing the challenges posed by rising costs and limited resources. As a subdivision of computer science, AI focuses on the development of advanced algorithms capable of performing complex tasks that were once reliant on human intelligence. The ultimate goal is to achieve human-level performance with improved efficiency and accuracy in problem-solving and task execution, thereby reducing the need for human intervention. Various industries, including engineering, media/entertainment, finance, and education, have already reaped significant benefits by incorporating AI systems into their operations. Notably, the healthcare sector has witnessed rapid growth in the utilization of AI technology. Nevertheless, there remains untapped potential for AI to truly revolutionize the industry. It is important to note that despite concerns about job displacement, AI in healthcare should not be viewed as a threat to human workers. Instead, AI systems are designed to augment and support healthcare professionals, freeing up their time to focus on more complex and critical tasks. By automating routine and repetitive tasks, AI can alleviate the burden on healthcare professionals, allowing them to dedicate more attention to patient care and meaningful interactions. However, legal and ethical challenges must be addressed when embracing AI technology in medicine, alongside comprehensive public education to ensure widespread acceptance.
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Affiliation(s)
- Molly Bekbolatova
- Department of Osteopathic Manipulative Medicine, College of Osteopathic Medicine, New York Institute of Technology, Old Westbury, NY 11568, USA; (M.B.); (J.M.)
| | - Jonathan Mayer
- Department of Osteopathic Manipulative Medicine, College of Osteopathic Medicine, New York Institute of Technology, Old Westbury, NY 11568, USA; (M.B.); (J.M.)
| | - Chi Wei Ong
- School of Chemistry, Chemical Engineering, and Biotechnology, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459, Singapore
| | - Milan Toma
- Department of Osteopathic Manipulative Medicine, College of Osteopathic Medicine, New York Institute of Technology, Old Westbury, NY 11568, USA; (M.B.); (J.M.)
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Gu J, Gao C, Wang L. The Evolution of Artificial Intelligence in Biomedicine: Bibliometric Analysis. JMIR AI 2023; 2:e45770. [PMID: 38875563 PMCID: PMC11041403 DOI: 10.2196/45770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 06/11/2023] [Accepted: 10/29/2023] [Indexed: 06/16/2024]
Abstract
BACKGROUND The utilization of artificial intelligence (AI) technologies in the biomedical field has attracted increasing attention in recent decades. Studying how past AI technologies have found their way into medicine over time can help to predict which current (and future) AI technologies have the potential to be utilized in medicine in the coming years, thereby providing a helpful reference for future research directions. OBJECTIVE The aim of this study was to predict the future trend of AI technologies used in different biomedical domains based on past trends of related technologies and biomedical domains. METHODS We collected a large corpus of articles from the PubMed database pertaining to the intersection of AI and biomedicine. Initially, we attempted to use regression on the extracted keywords alone; however, we found that this approach did not provide sufficient information. Therefore, we propose a method called "background-enhanced prediction" to expand the knowledge utilized by the regression algorithm by incorporating both the keywords and their surrounding context. This method of data construction resulted in improved performance across the six regression models evaluated. Our findings were confirmed through experiments on recurrent prediction and forecasting. RESULTS In our analysis using background information for prediction, we found that a window size of 3 yielded the best results, outperforming the use of keywords alone. Furthermore, utilizing data only prior to 2017, our regression projections for the period of 2017-2021 exhibited a high coefficient of determination (R2), which reached up to 0.78, demonstrating the effectiveness of our method in predicting long-term trends. Based on the prediction, studies related to proteins and tumors will be pushed out of the top 20 and become replaced by early diagnostics, tomography, and other detection technologies. These are certain areas that are well-suited to incorporate AI technology. Deep learning, machine learning, and neural networks continue to be the dominant AI technologies in biomedical applications. Generative adversarial networks represent an emerging technology with a strong growth trend. CONCLUSIONS In this study, we explored AI trends in the biomedical field and developed a predictive model to forecast future trends. Our findings were confirmed through experiments on current trends.
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Affiliation(s)
- Jiasheng Gu
- Department of Computer Science, University of Southern California, Los Angeles, CA, United States
| | - Chongyang Gao
- Department of Computer Science, Northwestern University, Evanston, IL, United States
| | - Lili Wang
- Department of Computer Science, Dartmouth College, Hanover, NH, United States
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Shi J, Bendig D, Vollmar HC, Rasche P. Mapping the Bibliometrics Landscape of AI in Medicine: Methodological Study. J Med Internet Res 2023; 25:e45815. [PMID: 38064255 PMCID: PMC10746970 DOI: 10.2196/45815] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 08/16/2023] [Accepted: 09/30/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Artificial intelligence (AI), conceived in the 1950s, has permeated numerous industries, intensifying in tandem with advancements in computing power. Despite the widespread adoption of AI, its integration into medicine trails other sectors. However, medical AI research has experienced substantial growth, attracting considerable attention from researchers and practitioners. OBJECTIVE In the absence of an existing framework, this study aims to outline the current landscape of medical AI research and provide insights into its future developments by examining all AI-related studies within PubMed over the past 2 decades. We also propose potential data acquisition and analysis methods, developed using Python (version 3.11) and to be executed in Spyder IDE (version 5.4.3), for future analogous research. METHODS Our dual-pronged approach involved (1) retrieving publication metadata related to AI from PubMed (spanning 2000-2022) via Python, including titles, abstracts, authors, journals, country, and publishing years, followed by keyword frequency analysis and (2) classifying relevant topics using latent Dirichlet allocation, an unsupervised machine learning approach, and defining the research scope of AI in medicine. In the absence of a universal medical AI taxonomy, we used an AI dictionary based on the European Commission Joint Research Centre AI Watch report, which emphasizes 8 domains: reasoning, planning, learning, perception, communication, integration and interaction, service, and AI ethics and philosophy. RESULTS From 2000 to 2022, a comprehensive analysis of 307,701 AI-related publications from PubMed highlighted a 36-fold increase. The United States emerged as a clear frontrunner, producing 68,502 of these articles. Despite its substantial contribution in terms of volume, China lagged in terms of citation impact. Diving into specific AI domains, as the Joint Research Centre AI Watch report categorized, the learning domain emerged dominant. Our classification analysis meticulously traced the nuanced research trajectories across each domain, revealing the multifaceted and evolving nature of AI's application in the realm of medicine. CONCLUSIONS The research topics have evolved as the volume of AI studies increases annually. Machine learning remains central to medical AI research, with deep learning expected to maintain its fundamental role. Empowered by predictive algorithms, pattern recognition, and imaging analysis capabilities, the future of AI research in medicine is anticipated to concentrate on medical diagnosis, robotic intervention, and disease management. Our topic modeling outcomes provide a clear insight into the focus of AI research in medicine over the past decades and lay the groundwork for predicting future directions. The domains that have attracted considerable research attention, primarily the learning domain, will continue to shape the trajectory of AI in medicine. Given the observed growing interest, the domain of AI ethics and philosophy also stands out as a prospective area of increased focus.
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Affiliation(s)
- Jin Shi
- Institute for Entrepreneurship, University of Münster, Münster, Germany
| | - David Bendig
- Institute for Entrepreneurship, University of Münster, Münster, Germany
| | | | - Peter Rasche
- Department of Healthcare, University of Applied Science - Hochschule Niederrhein, Krefeld, Germany
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Haq I, Mazhar T, Naz Asif R, Yasin Ghadi Y, Saleem R, Mallek F, Hamam H. A deep learning approach for the detection and counting of colon cancer cells (HT-29 cells) bunches and impurities. PeerJ Comput Sci 2023; 9:e1651. [PMID: 38192457 PMCID: PMC10773923 DOI: 10.7717/peerj-cs.1651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/22/2023] [Indexed: 01/10/2024]
Abstract
HT-29 has an epithelial appearance as a human colorectal cancer cell line. Early detection of colorectal cancer can enhance survival rates. This study aims to detect and count HT-29 cells using a deep-learning approach (ResNet-50). The cell lines were procured from Procell Life Science & Technology Co., Ltd. (Wuhan, China). Further, the dataset is self-prepared in lab experiments, cell culture, and collected 566 images. These images contain two classes; the HT-29 human colorectal adenocarcinoma cells (blue shapes in bunches) and impurities (tinny circular grey shapes). These images are annotated with the help of an image labeller as impurity and cancer cells. Then afterwards, the images are trained, validated, and tested against the deep learning approach ResNet50. Finally, in each image, the number of impurity and cancer cells are counted to find the accuracy of the proposed model. Accuracy and computational expense are used to gauge the network's performance. Each model is tested ten times with a non-overlapping train and random test splits. The effect of data pre-processing is also examined and shown in several tasks. The results show an accuracy of 95.5% during training and 95.3% in validation for detecting and counting HT-29 cells. HT-29 cell detection and counting using deep learning is novel due to the scarcity of research in this area, the application of deep learning, and potential performance improvements over traditional methods. By addressing a gap in the literature, employing a unique dataset, and using custom model architecture, this approach contributes to advancing colon cancer understanding and diagnosis techniques.
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Affiliation(s)
- Inayatul Haq
- School of Electrical and Information Engineering, Zhengzhou University, Zhengzhou, Henan, China
| | - Tehseen Mazhar
- Department of Computer Science, Virtual University of Pakistan, Lahore, Pakistan
| | - Rizwana Naz Asif
- School of Computer Science, National College of Business Administration and Economics, Lahore, Pakistan
| | - Yazeed Yasin Ghadi
- Department of computer science and software engineering, Al Ain university, Abu Dhabi, United Arab Emirates
| | - Rabea Saleem
- Department of computer science and software engineering, Air University, Multan, Pakistan
| | - Fatma Mallek
- Faculty of Engineering, University of Moncton, Moncton, Canada
| | - Habib Hamam
- Faculty of Engineering, University of Moncton, Moncton, Canada
- Spectrum of Knowledge Production, Skills Development, Sfax, Tunisia
- College of Computer Science and Engineering, University of Ha’il, Ha’il, Saudi Arabia
- International Institute of Technology and Management, Libreville, Commune d’Akanda, Gabon
- Department of Electrical and Electronic Engineering Science, School of Electrical Engineering, University of Johannesburg, Johannesburg, South Africa
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Stevens AF, Stetson P. Theory of trust and acceptance of artificial intelligence technology (TrAAIT): An instrument to assess clinician trust and acceptance of artificial intelligence. J Biomed Inform 2023; 148:104550. [PMID: 37981107 PMCID: PMC10815802 DOI: 10.1016/j.jbi.2023.104550] [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: 08/08/2023] [Revised: 11/07/2023] [Accepted: 11/16/2023] [Indexed: 11/21/2023]
Abstract
BACKGROUND Artificial intelligence and machine learning (AI/ML) technologies like generative and ambient AI solutions are proliferating in real-world healthcare settings. Clinician trust affects adoption and impact of these systems. Organizations need a validated method to assess factors underlying trust and acceptance of AI for clinical workflows in order to improve adoption and the impact of AI. OBJECTIVE Our study set out to develop and assess a novel clinician-centered model to measure and explain trust and adoption of AI technology. We hypothesized that clinicians' system-specific Trust in AI is the primary predictor of both Acceptance (i.e., willingness to adopt), and post-adoption Trusting Stance (i.e., general stance towards any AI system). We validated the new model at an urban comprehensive cancer center. We produced an easily implemented survey tool for measuring clinician trust and adoption of AI. METHODS This survey-based, cross-sectional, psychometric study included a model development phase and validation phase. Measurement was done with five-point ascending unidirectional Likert scales. The development sample included N = 93 clinicians (physicians, advanced practice providers, nurses) that used an AI-based communication application. The validation sample included N = 73 clinicians that used a commercially available AI-powered speech-to-text application for note-writing in an electronic health record (EHR). Analytical procedures included exploratory factor analysis (EFA), confirmatory factor analysis (CFA), and partial least squares structural equation modeling (PLS-SEM). The Johnson-Neyman (JN) methodology was used to determine moderator effects. RESULTS In the fully moderated causal model, clinician trust explained a large amount of variance in their acceptance of a specific AI application (56%) and their post-adoption general trusting stance towards AI in general (36%). Moderators included organizational assurances, length of time using the application, and clinician age. The final validated instrument has 20 items and takes 5 min to complete on average. CONCLUSIONS We found that clinician acceptance of AI is determined by their degree of trust formed via information credibility, perceived application value, and reliability. The novel model, TrAAIT, explains factors underlying AI trustworthiness and acceptance for clinicians. With its easy-to-use instrument and Summative Score Dashboard, TrAAIT can help organizations implementing AI to identify and intercept barriers to clinician adoption in real-world settings.
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Affiliation(s)
- Alexander F Stevens
- Digital Products and Informatics Division, DigITs, Memorial Sloan Kettering Cancer Center, New York, NY.
| | - Pete Stetson
- Digital Products and Informatics Division, DigITs, Memorial Sloan Kettering Cancer Center, New York, NY; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
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Nopour R. Prediction of five-year survival among esophageal cancer patients using machine learning. Heliyon 2023; 9:e22654. [PMID: 38125437 PMCID: PMC10730993 DOI: 10.1016/j.heliyon.2023.e22654] [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: 10/12/2023] [Revised: 11/16/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023] Open
Abstract
Background and aim Considering the silent progression of esophageal cancer, the survival prediction of this disease is crucial in enhancing the quality of life of these patients globally. So far, no prediction solution has been introduced for the survival of EC in Iran based on the machine learning approach. So, this study aims to develop a prediction model for the five-year survival of EC based on the ML approach to promote clinical outcomes and various treatment and preventive plans. Material and methods In this retrospective study, we investigated the 1656 cases of survived and non-survived EC patients belonging to Imam Khomeini Hospital in Sari City from 2013 to 2020. The multivariable regression analysis was used to select the best predictors of five-year survival. We leveraged random forest, eXtreme Gradient Boosting, support vector machine, artificial neural networks, Bayesian networks, J-48 decision tree, and K-nearest neighborhood to develop the prediction models. To get the best model for predicting the five-year survival of EC, we compared them using the area under the receiver operator characteristics. Results The age at diagnosis, body mass index, smoking, obstruction, dysphagia, weight loss, lymphadenopathy, chemotherapy, radiotherapy, family history of EC, tumor stage, type of appearance, histological type, grade of differentiation, tumor location, tumor size, lymphatic invasion, vascular invasion, and platelet albumin ratio were considered as the best predictors associated with the five-year survival of EC based on the regression analysis. In this respect, the random forest with the area under the receiver operator characteristics of 0.95 was identified as a superior model. Conclusion The experimental results of the current study showed that the random forest could have a significant role in enhancing the quality of care in EC patients by increasing the effectiveness of follow-up and treatment measures introduced by care providers.
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Affiliation(s)
- Raoof Nopour
- Department of Health Information Management, Student Research Committee, School of Health Management and Information Sciences Branch, Iran University of Medical Sciences, Tehran, Iran
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Zuo D, Yang L, Jin Y, Qi H, Liu Y, Ren L. Machine learning-based models for the prediction of breast cancer recurrence risk. BMC Med Inform Decis Mak 2023; 23:276. [PMID: 38031071 PMCID: PMC10688055 DOI: 10.1186/s12911-023-02377-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 11/17/2023] [Indexed: 12/01/2023] Open
Abstract
Breast cancer is the most common malignancy diagnosed in women worldwide. The prevalence and incidence of breast cancer is increasing every year; therefore, early diagnosis along with suitable relapse detection is an important strategy for prognosis improvement. This study aimed to compare different machine algorithms to select the best model for predicting breast cancer recurrence. The prediction model was developed by using eleven different machine learning (ML) algorithms, including logistic regression (LR), random forest (RF), support vector classification (SVC), extreme gradient boosting (XGBoost), gradient boosting decision tree (GBDT), decision tree, multilayer perceptron (MLP), linear discriminant analysis (LDA), adaptive boosting (AdaBoost), Gaussian naive Bayes (GaussianNB), and light gradient boosting machine (LightGBM), to predict breast cancer recurrence. The area under the curve (AUC), accuracy, sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and F1 score were used to evaluate the performance of the prognostic model. Based on performance, the optimal ML was selected, and feature importance was ranked by Shapley Additive Explanation (SHAP) values. Compared to the other 10 algorithms, the results showed that the AdaBoost algorithm had the best prediction performance for successfully predicting breast cancer recurrence and was adopted in the establishment of the prediction model. Moreover, CA125, CEA, Fbg, and tumor diameter were found to be the most important features in our dataset to predict breast cancer recurrence. More importantly, our study is the first to use the SHAP method to improve the interpretability of clinicians to predict the recurrence model of breast cancer based on the AdaBoost algorithm. The AdaBoost algorithm offers a clinical decision support model and successfully identifies the recurrence of breast cancer.
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Affiliation(s)
- Duo Zuo
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute & Hospital, Tianjin, 300060, China
- National Clinical Research Center for Cancer, Tianjin, 300060, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, 300060, China
| | - Lexin Yang
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute & Hospital, Tianjin, 300060, China
- National Clinical Research Center for Cancer, Tianjin, 300060, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, 300060, China
| | - Yu Jin
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute & Hospital, Tianjin, 300060, China
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
| | - Huan Qi
- China Mobile Group Tianjin Company Limited, Tianjin, 300308, China
| | - Yahui Liu
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute & Hospital, Tianjin, 300060, China
- National Clinical Research Center for Cancer, Tianjin, 300060, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, 300060, China
| | - Li Ren
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute & Hospital, Tianjin, 300060, China.
- National Clinical Research Center for Cancer, Tianjin, 300060, China.
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China.
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China.
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, 300060, China.
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Zaidan AM. The leading global health challenges in the artificial intelligence era. Front Public Health 2023; 11:1328918. [PMID: 38089037 PMCID: PMC10711066 DOI: 10.3389/fpubh.2023.1328918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023] Open
Abstract
Millions of people's health is at risk because of several factors and multiple overlapping crises, all of which hit the vulnerable the most. These challenges are dynamic and evolve in response to emerging health challenges and concerns, which need effective collaboration among countries working toward achieving Sustainable Development Goals (SDGs) and securing global health. Mental Health, the Impact of climate change, cardiovascular diseases (CVDs), diabetes, Infectious diseases, health system, and population aging are examples of challenges known to pose a vast burden worldwide. We are at a point known as the "digital revolution," characterized by the expansion of artificial intelligence (AI) and a fusion of technology types. AI has emerged as a powerful tool for addressing various health challenges, and the last ten years have been influential due to the rapid expansion in the production and accessibility of health-related data. The computational models and algorithms can understand complicated health and medical data to perform various functions and deep-learning strategies. This narrative mini-review summarizes the most current AI applications to address the leading global health challenges. Harnessing its capabilities can ultimately mitigate the Impact of these challenges and revolutionize the field. It has the ability to strengthen global health through personalized health care and improved preparedness and response to future challenges. However, ethical and legal concerns about individual or community privacy and autonomy must be addressed for effective implementation.
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Affiliation(s)
- Amal Mousa Zaidan
- King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- King Abdullah International Medical Research Center (KAIMRC), Riyadh, Saudi Arabia
- Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
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Shirini D, Schwartz LH, Dercle L. Artificial intelligence for aging research in cancer drug development. Aging (Albany NY) 2023; 15:12699-12701. [PMID: 37980599 DOI: 10.18632/aging.204914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Indexed: 11/21/2023]
Affiliation(s)
- Dorsa Shirini
- Department of Radiology, Columbia University Medical Center, New York, NY 10032, USA
- Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Lawrence H Schwartz
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY10032, USA
| | - Laurent Dercle
- Department of Radiology, Columbia University Medical Center, New York, NY 10032, USA
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Park J, Lim F, Prest M, Ferris JS, Aziz Z, Agyekum A, Wagner S, Gulati R, Hur C. Quantifying the potential benefits of early detection for pancreatic cancer through a counterfactual simulation modeling analysis. Sci Rep 2023; 13:20028. [PMID: 37973858 PMCID: PMC10654404 DOI: 10.1038/s41598-023-46751-3] [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: 08/28/2023] [Accepted: 11/04/2023] [Indexed: 11/19/2023] Open
Abstract
The benefits of cancer early detection depend on various factors, including cancer type, screening method performance, stage at diagnosis, and subsequent treatment. Although numerous studies have evaluated the effectiveness of screening interventions for identifying cancer at earlier stages, there is no quantitative analysis that studies the optimal early detection time interval that results in the greatest mortality benefit; such data could serve as a target and benchmark for cancer early detection strategies. In this study, we focus on pancreatic ductal adenocarcinoma (PDAC), a cancer known for its lack of early symptoms. Consequently, it is most often detected at late stages when the 5-year survival rate is only 3%. We developed a PDAC population model that simulates an individual patient's age and stage at diagnosis, while replicating overall US cancer incidence and mortality rates. The model includes "cancer sojourn time," serving as a proxy for the speed of cancer progression, with shorter times indicating rapid progression and longer times indicating slower progression. In our PDAC model, our hypothesis was that earlier cancer detection, potentially through a hypothetical screening intervention in the counterfactual analysis, would yield reduced mortality as compared to a no-screening group. We found that the benefits of early detection, such as increased life-years gained, are greater when the sojourn time is shorter, reaching their maximum when identification is made 4-6 years prior to clinical diagnosis (e.g., when a symptomatic diagnosis is made). However, when early detection occurs even earlier, for example 6-10 years prior to clinical diagnosis, the benefits significantly diminish for shorter sojourn time cancers, and level off for longer sojourn time cancers. Our study clarifies the potential benefits of PDAC early detection that explicitly incorporates individual patient heterogeneity in cancer progression and identifies quantitative benchmarks for future interventions.
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Affiliation(s)
- Jiheum Park
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA.
| | - Francesca Lim
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Matthew Prest
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Jennifer S Ferris
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Zainab Aziz
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Alice Agyekum
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Sophie Wagner
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Roman Gulati
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Chin Hur
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA.
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Siddalingappa R, Kanagaraj S. K-nearest-neighbor algorithm to predict the survival time and classification of various stages of oral cancer: a machine learning approach. F1000Res 2023; 11:70. [PMID: 38046542 PMCID: PMC10690040 DOI: 10.12688/f1000research.75469.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/16/2023] [Indexed: 12/05/2023] Open
Abstract
Background:For years now, cancer treatments have entailed tried-and-true methods. Yet, oncologists and clinicians recommend a series of surgeries, chemotherapy, and radiation therapy. Yet, even amidst these treatments, the number of deaths due to cancer increases at an alarming rate. The prognosis of cancer patients is influenced by mutations, age, and various cancer stages. However, the association between these variables is unclear. Methods: The present work adopts a machine learning technique-k-nearest neighbor; for both regression and classification tasks, regression for predicting the survival time of oral cancer patients, and classification for classifying the patients into one of the predefined oral cancer stages. Two cross-validation approaches-hold-out and k-fold methods-have been used to examine the prediction results. Results: The experimental results show that the k-fold method performs better than the hold-out method, providing the least mean absolute error score of 0.015. Additionally, the model classifies patients into a valid group. Of the 429 records, 97 (out of 106), 99 (out of 119), 95 (out of 113), and 77 (out of 91) were classified to its correct label as stages - 1, 2, 3, and 4. The accuracy, recall, precision, and F-measure for each classification group obtained are 0.84, 0.85, 0.85, and 0.84. Conclusions: The study showed that aged patients with a higher number of mutations than young patients have a higher risk of short survival. Senior patients with a more significant number of mutations have an increased risk of getting into the last cancer stage.
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Affiliation(s)
- Rashmi Siddalingappa
- Computational and Data Sciences, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Sekar Kanagaraj
- Computational and Data Sciences, Indian Institute of Science, Bangalore, Karnataka, 560012, India
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Lee TF, Lee SH, Tseng CD, Lin CH, Chiu CM, Lin GZ, Yang J, Chang L, Chiu YH, Su CT, Yeh SA. Using machine learning algorithm to analyse the hypothyroidism complications caused by radiotherapy in patients with head and neck cancer. Sci Rep 2023; 13:19185. [PMID: 37932394 PMCID: PMC10628223 DOI: 10.1038/s41598-023-46509-x] [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: 04/06/2023] [Accepted: 11/01/2023] [Indexed: 11/08/2023] Open
Abstract
Machine learning algorithms were used to analyze the odds and predictors of complications of thyroid damage after radiation therapy in patients with head and neck cancer. This study used decision tree (DT), random forest (RF), and support vector machine (SVM) algorithms to evaluate predictors for the data of 137 head and neck cancer patients. Candidate factors included gender, age, thyroid volume, minimum dose, average dose, maximum dose, number of treatments, and relative volume of the organ receiving X dose (X: 10, 20, 30, 40, 50, 60 Gy). The algorithm was optimized according to these factors and tenfold cross-validation to analyze the state of thyroid damage and select the predictors of thyroid dysfunction. The importance of the predictors identified by the three machine learning algorithms was ranked: the top five predictors were age, thyroid volume, average dose, V50 and V60. Of these, age and volume were negatively correlated with thyroid damage, indicating that the greater the age and thyroid volume, the lower the risk of thyroid damage; the average dose, V50 and V60 were positively correlated with thyroid damage, indicating that the larger the average dose, V50 and V60, the higher the risk of thyroid damage. The RF algorithm was most accurate in predicting the probability of thyroid damage among the three algorithms optimized using the above factors. The Area under the receiver operating characteristic curve (AUC) was 0.827 and the accuracy (ACC) was 0.824. This study found that five predictors (age, thyroid volume, mean dose, V50 and V60) are important factors affecting the chance that patients with head and neck cancer who received radiation therapy will develop hypothyroidism. Using these factors as the prediction basis of the algorithm and using RF to predict the occurrence of hypothyroidism had the highest ACC, which was 82.4%. This algorithm is quite helpful in predicting the probability of radiotherapy complications. It also provides references for assisting medical decision-making in the future.
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Affiliation(s)
- Tsair-Fwu Lee
- Medical Physics and Informatics Laboratory of Electronic Engineering, National Kaohsiung University of Science and Technology, Kaohsiung, 80778, Taiwan
- Department of Electronic Engineering, National Kaohsiung University of Science and Technology, Kaohsiung, 80778, Taiwan
- Department of Medical Imaging and Radiological Sciences, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan
- PhD Program in Biomedical Engineering, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan
- School of Dentistry, College of Dental Medicine, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan
| | - Shen-Hao Lee
- Medical Physics and Informatics Laboratory of Electronic Engineering, National Kaohsiung University of Science and Technology, Kaohsiung, 80778, Taiwan
- Department of Electronic Engineering, National Kaohsiung University of Science and Technology, Kaohsiung, 80778, Taiwan
| | - Chin-Dar Tseng
- Medical Physics and Informatics Laboratory of Electronic Engineering, National Kaohsiung University of Science and Technology, Kaohsiung, 80778, Taiwan.
- Department of Electronic Engineering, National Kaohsiung University of Science and Technology, Kaohsiung, 80778, Taiwan.
| | - Chih-Hsueh Lin
- Department of Electronic Engineering, National Kaohsiung University of Science and Technology, Kaohsiung, 80778, Taiwan
- PhD Program in Biomedical Engineering, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan
| | - Chi-Min Chiu
- Medical Physics and Informatics Laboratory of Electronic Engineering, National Kaohsiung University of Science and Technology, Kaohsiung, 80778, Taiwan
- Department of Electronic Engineering, National Kaohsiung University of Science and Technology, Kaohsiung, 80778, Taiwan
| | - Guang-Zhi Lin
- Medical Physics and Informatics Laboratory of Electronic Engineering, National Kaohsiung University of Science and Technology, Kaohsiung, 80778, Taiwan
- Department of Electronic Engineering, National Kaohsiung University of Science and Technology, Kaohsiung, 80778, Taiwan
- Department of Tactical Control Air Traffic Control & Meteorology, Air Force Institute of Technology, Kaohsiung, 82047, Taiwan
| | - Jack Yang
- Department of Radiation Oncology, RWJ Medical School, Long Branch, NJ, USA
- Department of Radiation Oncology, Monmouth Medical Center, RWJBH Medical School, Long Branch, NJ, USA
| | - Liyun Chang
- Department of Medical Imaging and Radiological Sciences, I-Shou University, Kaohsiung, 82445, Taiwan
| | - Yu-Hao Chiu
- Medical Physics and Informatics Laboratory of Electronic Engineering, National Kaohsiung University of Science and Technology, Kaohsiung, 80778, Taiwan
- Department of Electronic Engineering, National Kaohsiung University of Science and Technology, Kaohsiung, 80778, Taiwan
| | - Chun-Ting Su
- Department of Medical Imaging and Radiological Sciences, I-Shou University, Kaohsiung, 82445, Taiwan
- Department of Radiation Oncology, E-DA Hospital, Kaohsiung, 82445, Taiwan
| | - Shyh-An Yeh
- Medical Physics and Informatics Laboratory of Electronic Engineering, National Kaohsiung University of Science and Technology, Kaohsiung, 80778, Taiwan.
- Department of Electronic Engineering, National Kaohsiung University of Science and Technology, Kaohsiung, 80778, Taiwan.
- Department of Medical Imaging and Radiological Sciences, I-Shou University, Kaohsiung, 82445, Taiwan.
- Department of Radiation Oncology, E-DA Hospital, Kaohsiung, 82445, Taiwan.
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Rai HM, Yoo J. A comprehensive analysis of recent advancements in cancer detection using machine learning and deep learning models for improved diagnostics. J Cancer Res Clin Oncol 2023; 149:14365-14408. [PMID: 37540254 DOI: 10.1007/s00432-023-05216-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 07/26/2023] [Indexed: 08/05/2023]
Abstract
PURPOSE There are millions of people who lose their life due to several types of fatal diseases. Cancer is one of the most fatal diseases which may be due to obesity, alcohol consumption, infections, ultraviolet radiation, smoking, and unhealthy lifestyles. Cancer is abnormal and uncontrolled tissue growth inside the body which may be spread to other body parts other than where it has originated. Hence it is very much required to diagnose the cancer at an early stage to provide correct and timely treatment. Also, manual diagnosis and diagnostic error may cause of the death of many patients hence much research are going on for the automatic and accurate detection of cancer at early stage. METHODS In this paper, we have done the comparative analysis of the diagnosis and recent advancement for the detection of various cancer types using traditional machine learning (ML) and deep learning (DL) models. In this study, we have included four types of cancers, brain, lung, skin, and breast and their detection using ML and DL techniques. In extensive review we have included a total of 130 pieces of literature among which 56 are of ML-based and 74 are from DL-based cancer detection techniques. Only the peer reviewed research papers published in the recent 5-year span (2018-2023) have been included for the analysis based on the parameters, year of publication, feature utilized, best model, dataset/images utilized, and best accuracy. We have reviewed ML and DL-based techniques for cancer detection separately and included accuracy as the performance evaluation metrics to maintain the homogeneity while verifying the classifier efficiency. RESULTS Among all the reviewed literatures, DL techniques achieved the highest accuracy of 100%, while ML techniques achieved 99.89%. The lowest accuracy achieved using DL and ML approaches were 70% and 75.48%, respectively. The difference in accuracy between the highest and lowest performing models is about 28.8% for skin cancer detection. In addition, the key findings, and challenges for each type of cancer detection using ML and DL techniques have been presented. The comparative analysis between the best performing and worst performing models, along with overall key findings and challenges, has been provided for future research purposes. Although the analysis is based on accuracy as the performance metric and various parameters, the results demonstrate a significant scope for improvement in classification efficiency. CONCLUSION The paper concludes that both ML and DL techniques hold promise in the early detection of various cancer types. However, the study identifies specific challenges that need to be addressed for the widespread implementation of these techniques in clinical settings. The presented results offer valuable guidance for future research in cancer detection, emphasizing the need for continued advancements in ML and DL-based approaches to improve diagnostic accuracy and ultimately save more lives.
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Affiliation(s)
- Hari Mohan Rai
- School of Computing, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, 13120, Gyeonggi-do, Republic of Korea.
| | - Joon Yoo
- School of Computing, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, 13120, Gyeonggi-do, Republic of Korea
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Carmichael J, Abdi S, Balaskas K, Costanza E, Blandford A. The effectiveness of interventions for optometric referrals into the hospital eye service: A review. Ophthalmic Physiol Opt 2023; 43:1510-1523. [PMID: 37632154 PMCID: PMC10947293 DOI: 10.1111/opo.13219] [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: 03/16/2023] [Revised: 08/05/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023]
Abstract
PURPOSE Ophthalmic services are currently under considerable stress; in the UK, ophthalmology departments have the highest number of outpatient appointments of any department within the National Health Service. Recognising the need for intervention, several approaches have been trialled to tackle the high numbers of false-positive referrals initiated in primary care and seen face to face within the hospital eye service (HES). In this mixed-methods narrative synthesis, we explored interventions based on their clinical impact, cost and acceptability to determine whether they are clinically effective, safe and sustainable. A systematic literature search of PubMed, MEDLINE and CINAHL, guided by the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA), was used to identify appropriate studies published between December 2001 and December 2022. RECENT FINDINGS A total of 55 studies were reviewed. Four main interventions were assessed, where two studies covered more than one type: training and guidelines (n = 8), referral filtering schemes (n = 32), asynchronous teleophthalmology (n = 13) and synchronous teleophthalmology (n = 5). All four approaches demonstrated effectiveness for reducing false-positive referrals to the HES. There was sufficient evidence for stakeholder acceptance and cost-effectiveness of referral filtering schemes; however, cost comparisons involved assumptions. Referral filtering and asynchronous teleophthalmology reported moderate levels of false-negative cases (2%-20%), defined as discharged patients requiring HES monitoring. SUMMARY The effectiveness of interventions varied depending on which outcome and stakeholder was considered. More studies are required to explore stakeholder opinions around all interventions. In order to maximise clinical safety, it may be appropriate to combine more than one approach, such as referral filtering schemes with virtual review of discharged patients to assess the rate of false-negative cases. The implementation of a successful intervention is more complex than a 'one-size-fits-all' approach and there is potential space for newer types of interventions, such as artificial intelligence clinical support systems within the referral pathway.
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Affiliation(s)
- Josie Carmichael
- University College London Interaction Centre (UCLIC), UCLLondonUK
- NIHR Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust and UCLInstitute of OphthalmologyLondonUK
| | - Sarah Abdi
- University College London Interaction Centre (UCLIC), UCLLondonUK
| | - Konstantinos Balaskas
- NIHR Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust and UCLInstitute of OphthalmologyLondonUK
| | - Enrico Costanza
- University College London Interaction Centre (UCLIC), UCLLondonUK
| | - Ann Blandford
- University College London Interaction Centre (UCLIC), UCLLondonUK
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Fonseca AU, Felix JP, Pinheiro H, Vieira GS, Mourão ÝC, Monteiro JCG, Soares F. An Intelligent System to Improve Diagnostic Support for Oral Squamous Cell Carcinoma. Healthcare (Basel) 2023; 11:2675. [PMID: 37830712 PMCID: PMC10572543 DOI: 10.3390/healthcare11192675] [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: 08/18/2023] [Revised: 09/12/2023] [Accepted: 09/25/2023] [Indexed: 10/14/2023] Open
Abstract
Oral squamous cell carcinoma (OSCC) is one of the most-prevalent cancer types worldwide, and it poses a serious threat to public health due to its high mortality and morbidity rates. OSCC typically has a poor prognosis, significantly reducing the chances of patient survival. Therefore, early detection is crucial to achieving a favorable prognosis by providing prompt treatment and increasing the chances of remission. Salivary biomarkers have been established in numerous studies to be a trustworthy and non-invasive alternative for early cancer detection. In this sense, we propose an intelligent system that utilizes feed-forward artificial neural networks to classify carcinoma with salivary biomarkers extracted from control and OSCC patient samples. We conducted experiments using various salivary biomarkers, ranging from 1 to 51, to train the model, and we achieved excellent results with precision, sensitivity, and specificity values of 98.53%, 96.30%, and 97.56%, respectively. Our system effectively classified the initial cases of OSCC with different amounts of biomarkers, aiding medical professionals in decision-making and providing a more-accurate diagnosis. This could contribute to a higher chance of treatment success and patient survival. Furthermore, the minimalist configuration of our model presents the potential for incorporation into resource-limited devices or environments.
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Affiliation(s)
- Afonso U. Fonseca
- Institute of Informatics, Federal University of Goiás, Goiânia 74690-900, GO, Brazil; (J.P.F.); (H.P.); (G.S.V.); (F.S.)
| | - Juliana P. Felix
- Institute of Informatics, Federal University of Goiás, Goiânia 74690-900, GO, Brazil; (J.P.F.); (H.P.); (G.S.V.); (F.S.)
| | - Hedenir Pinheiro
- Institute of Informatics, Federal University of Goiás, Goiânia 74690-900, GO, Brazil; (J.P.F.); (H.P.); (G.S.V.); (F.S.)
| | - Gabriel S. Vieira
- Institute of Informatics, Federal University of Goiás, Goiânia 74690-900, GO, Brazil; (J.P.F.); (H.P.); (G.S.V.); (F.S.)
- Federal Institute Goiano, Computer Vision Lab, Urutaí 75790-000, GO, Brazil
| | | | | | - Fabrizzio Soares
- Institute of Informatics, Federal University of Goiás, Goiânia 74690-900, GO, Brazil; (J.P.F.); (H.P.); (G.S.V.); (F.S.)
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Bai G, Sun C, Guo Z, Wang Y, Zeng X, Su Y, Zhao Q, Ma B. Accelerating antibody discovery and design with artificial intelligence: Recent advances and prospects. Semin Cancer Biol 2023; 95:13-24. [PMID: 37355214 DOI: 10.1016/j.semcancer.2023.06.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/09/2023] [Accepted: 06/18/2023] [Indexed: 06/26/2023]
Abstract
Therapeutic antibodies are the largest class of biotherapeutics and have been successful in treating human diseases. However, the design and discovery of antibody drugs remains challenging and time-consuming. Recently, artificial intelligence technology has had an incredible impact on antibody design and discovery, resulting in significant advances in antibody discovery, optimization, and developability. This review summarizes major machine learning (ML) methods and their applications for computational predictors of antibody structure and antigen interface/interaction, as well as the evaluation of antibody developability. Additionally, this review addresses the current status of ML-based therapeutic antibodies under preclinical and clinical phases. While many challenges remain, ML may offer a new therapeutic option for the future direction of fully computational antibody design.
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Affiliation(s)
- Ganggang Bai
- Engineering Research Center of Cell & Therapeutic Antibody (MOE), School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chuance Sun
- Engineering Research Center of Cell & Therapeutic Antibody (MOE), School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ziang Guo
- Cancer Center, Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macao Special Administrative Region of China
| | - Yangjing Wang
- Engineering Research Center of Cell & Therapeutic Antibody (MOE), School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xincheng Zeng
- Engineering Research Center of Cell & Therapeutic Antibody (MOE), School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuhong Su
- Engineering Research Center of Cell & Therapeutic Antibody (MOE), School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qi Zhao
- Cancer Center, Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macao Special Administrative Region of China; MoE Frontiers Science Center for Precision Oncology, University of Macau, Taipa, Macao Special Administrative Region of China.
| | - Buyong Ma
- Engineering Research Center of Cell & Therapeutic Antibody (MOE), School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China; Shanghai Digiwiser BioTechnolgy, Limited, Shanghai 201203, China.
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Bhonde SB, Wagh SK, Prasad JR. Identification of cancer types from gene expressions using learning techniques. Comput Methods Biomech Biomed Engin 2023; 26:1951-1965. [PMID: 36562388 DOI: 10.1080/10255842.2022.2160243] [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: 04/11/2022] [Revised: 10/15/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022]
Abstract
Tumor is the major cause of death all around the world in recent days. Early detection and prediction of a cancer type are important for a patient's well-being. Functional genomic data has recently been used in the effective and early detection of cancer. According to previous research, the use of microarray data in cancer prediction has evidenced two main problems as high dimensionality and limited sample size. Several researchers have used numerous statistical and machine learning-based methods to classify cancer types but still, limitations are there which makes cancer classification a difficult job. Deep Learning (DL) and Convolutional Neural Networks (CNN) have been proven with effective analyses of unstructured data including gene expression data. In the proposed method gene expression data for five types of cancer is collected from The Cancer Genome Atlas (TCGA). Prominent features are selected using a hybrid Particle Swarm Optimization (PSO) and Random Forest (RF) algorithm followed by the use of Principal Component Analysis (PCA) for dimensionality reduction. Finally, for classification blend of Convolutional Neural Network (CNN) and Bi-directional Long Short Term Memory (Bi-LSTM) is used to predict the target type of cancer. Experimental results demonstrate that accuracy of the proposed method is 96.89%. As compared to existing work, our method outperformed with better results.
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Affiliation(s)
- Swati B Bhonde
- Smt. Kashibai Navale College of Engineering, Pune, India
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Matsui K, Kawakubo H, Matsuda S, Hirata Y, Irino T, Fukuda K, Nakamura R, Okita H, Kitagawa Y. Clinical predictors of early postoperative recurrence after radical esophagectomy for thoracic esophageal cancer. Esophagus 2023; 20:679-690. [PMID: 37222963 DOI: 10.1007/s10388-023-01014-y] [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: 01/20/2022] [Accepted: 05/10/2023] [Indexed: 05/25/2023]
Abstract
PURPOSE Esophagectomy for esophageal cancer has a high incidence rate of early postoperative recurrence and death. This study aimed to identify the clinical and pathological features in early recurrence cases and to confirm the usefulness of prediction using these factors for effective adjuvant therapy and postoperative surveillance. METHODS One hundred and twenty five patients who developed postoperative recurrence after undergoing radical esophagectomy for thoracic esophageal cancer were classified into two groups as follows: those with early recurrence at ≤ 6 months and those with nonearly recurrence at > 6 months after surgery. After identifying related factors of early recurrence, usefulness of these factors for prediction were examined in all patients with and without recurrence. RESULTS The analysis cohort consisted of 43 and 82 patients in the early and nonearly recurrence groups, respectively. In multivariate analysis, factors associated with early recurrence were higher initial levels of tumor markers (squamous cell carcinoma [SCC] ≥ 1.5 ng/ml in tumors, except for adenocarcinoma, and carcinoembryonic antigen [CEA] ≥ 5.0 ng/ml in adenocarcinoma) and higher venous invasion (v), i.e., ≥ 2 (p = 0.040 and p = 0.004, respectively). The usefulness of these two factors for recurrence prediction was confirmed in 378 patients, including 253 patients without recurrence. Patients with at least one of the two factors had significantly higher early recurrence rates than those without any factors in pStages II and III (odds ratio [OR], 6.333; p = 0016 and OR, 4.346; p = 0.008, respectively). CONCLUSIONS Early recurrence of thoracic esophageal cancer (i.e., during ≤ 6 months after esophagectomy) was associated with higher initial tumor marker levels and pathological findings of v ≥ 2. The combination of these two factors is useful as a simple and critical predictor of early postoperative recurrence.
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Affiliation(s)
- Kazuaki Matsui
- Department of Surgery, Keio University School of Medicine, 35-Banchi, Shinano-Machi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Hirofumi Kawakubo
- Department of Surgery, Keio University School of Medicine, 35-Banchi, Shinano-Machi, Shinjuku-Ku, Tokyo, 160-8582, Japan.
| | - Satoru Matsuda
- Department of Surgery, Keio University School of Medicine, 35-Banchi, Shinano-Machi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Yuki Hirata
- Department of Surgery, Keio University School of Medicine, 35-Banchi, Shinano-Machi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Tomoyuki Irino
- Department of Surgery, Keio University School of Medicine, 35-Banchi, Shinano-Machi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Kazumasa Fukuda
- Department of Surgery, Keio University School of Medicine, 35-Banchi, Shinano-Machi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Rieko Nakamura
- Department of Surgery, Keio University School of Medicine, 35-Banchi, Shinano-Machi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Hajime Okita
- Division of Diagnostic Pathology, Keio University School of Medicine, 35-banchi, Shinano-machi, Shinjuku-ku, Tokyo, Japan
| | - Yuko Kitagawa
- Department of Surgery, Keio University School of Medicine, 35-Banchi, Shinano-Machi, Shinjuku-Ku, Tokyo, 160-8582, Japan
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Wang Q, He M, Guo L, Chai H. AFEI: adaptive optimized vertical federated learning for heterogeneous multi-omics data integration. Brief Bioinform 2023; 24:bbad269. [PMID: 37497720 DOI: 10.1093/bib/bbad269] [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: 05/19/2023] [Revised: 06/26/2023] [Accepted: 07/04/2023] [Indexed: 07/28/2023] Open
Abstract
Vertical federated learning has gained popularity as a means of enabling collaboration and information sharing between different entities while maintaining data privacy and security. This approach has potential applications in disease healthcare, cancer prognosis prediction, and other industries where data privacy is a major concern. Although using multi-omics data for cancer prognosis prediction provides more information for treatment selection, collecting different types of omics data can be challenging due to their production in various medical institutions. Data owners must comply with strict data protection regulations such as European Union (EU) General Data Protection Regulation. To share patient data across multiple institutions, privacy and security issues must be addressed. Therefore, we propose an adaptive optimized vertical federated-learning-based framework adaptive optimized vertical federated learning for heterogeneous multi-omics data integration (AFEI) to integrate multi-omics data collected from multiple institutions for cancer prognosis prediction. AFEI enables participating parties to build an accurate joint evaluation model for learning more information related to cancer patients from different perspectives, based on the distributed and encrypted multi-omics features shared by multiple institutions. The experimental results demonstrate that AFEI achieves higher prediction accuracy (6.5% on average) than using single omics data by utilizing the encrypted multi-omics data from different institutions, and it performs almost as well as prognosis prediction by directly integrating multi-omics data. Overall, AFEI can be seen as an efficient solution for breaking down barriers to multi-institutional collaboration and promoting the development of cancer prognosis prediction.
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Affiliation(s)
- Qingyong Wang
- School of Information and Computer, Anhui Agricultural University, Hefei 230000, China
| | - Minfan He
- School of Mathematics and Big Data, Foshan University, Foshan 528000, China
| | - Longyi Guo
- Guangdong Provincial Hospital of Traditional Chinese Medical, Guangzhou 510000, China
| | - Hua Chai
- School of Mathematics and Big Data, Foshan University, Foshan 528000, China
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