1
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Obite CP, Chukwudi EO, Uchechukwu M, Nwosu UI. Factor enhanced DeepSurv: A deep learning approach for predicting survival probabilities in cirrhosis data. Comput Biol Med 2025; 189:109963. [PMID: 40037171 DOI: 10.1016/j.compbiomed.2025.109963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 02/27/2025] [Accepted: 02/28/2025] [Indexed: 03/06/2025]
Abstract
BACKGROUND Over the years, various models, including both traditional and machine learning models, have been employed to predict survival probabilities for diverse survival datasets. The objective is to obtain models that provide more accurate estimates of survival probabilities. Certain datasets exhibit complex nonlinear effects and interactions between variables that may necessitate the application of deep learning algorithms to comprehend the underlying data generation process. METHOD In this paper, we introduced Factor Enhanced DeepSurv (FE-DeepSurv), a novel deep neural network designed to study complex structures and excels at filtering noise within predictors, thereby enhancing precision of survival probability estimates. FE-DeepSurv incorporates factor analysis to reduce predictor dimensionality, applies a transformation technique to account for data censoring, and employs a deep neural network to predict conditional failure probabilities for each time interval. These predictions are subsequently utilized to estimate survival probabilities for each subject. We applied our proposed model to study cirrhosis survival data, a secondary data from Mayo Clinic trial focused on primary biliary cirrhosis (PBC) of the liver and compared its performance with the Cox proportional hazard model (Cox model), random survival forest (RSF), DeepHit, and DeepSurv, using the concordance index (C-index), brier score (BS), and integrated brier score (IBS). RESULTS The results show that FE-DeepSurv outperforms many existing survival models. FE-DeepSurv's accurate predictions of survival probabilities and hazard rates can drive improvements in clinical practice, healthcare management, insurance risk assessment, and various other domains. CONCLUSIONS By adopting FE-DeepSurv, institutions can harness the power of advanced analytics to make more informed decisions, ultimately leading to better outcomes across multiple sectors.
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Affiliation(s)
- Chukwudi Paul Obite
- School of Mathematical and Statistical Sciences, Arizona State University, USA.
| | | | - Merit Uchechukwu
- Department of Statistics, Federal University of Technology, Owerri, Nigeria
| | - Ugochinyere Ihuoma Nwosu
- Department of Statistics, Federal University of Technology, Owerri, Nigeria; Department of Computing and Mathematics, Manchester Metropolitan University, UK
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Dafni MF, Shih M, Manoel AZ, Yousif MYE, Spathi S, Harshal C, Bhatt G, Chodnekar SY, Chune NS, Rasool W, Umar TP, Moustakas DC, Achkar R, Kumar H, Naz S, Acuña-Chavez LM, Evgenikos K, Gulraiz S, Ali ESM, Elaagib A, Uggh IHP. Empowering cancer prevention with AI: unlocking new frontiers in prediction, diagnosis, and intervention. Cancer Causes Control 2024:10.1007/s10552-024-01942-9. [PMID: 39672997 DOI: 10.1007/s10552-024-01942-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2024] [Accepted: 11/18/2024] [Indexed: 12/15/2024]
Abstract
Artificial intelligence is rapidly changing our world at an exponential rate and its transformative power has extensively reached important sectors like healthcare. In the fight against cancer, AI proved to be a novel and powerful tool, offering new hope for prevention and early detection. In this review, we will comprehensively explore the medical applications of AI, including early cancer detection through pathological and imaging analysis, risk stratification, patient triage, and the development of personalized prevention approaches. However, despite the successful impact AI has contributed to, we will also discuss the myriad of challenges that we have faced so far toward optimal AI implementation. There are problems when it comes to the best way in which we can use AI systemically. Having the correct data that can be understood easily must remain one of the most significant concerns in all its uses including sharing information. Another challenge that exists is how to interpret AI models because they are too complicated for people to follow through examples used in their developments which may affect trust, especially among medical professionals. Other considerations like data privacy, algorithm bias, and equitable access to AI tools have also arisen. Finally, we will evaluate possible future directions for this promising field that highlight AI's capacity to transform preventative cancer care.
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Affiliation(s)
- Marianna-Foteini Dafni
- School of Medicine, Laboratory of Forensic Medicine and Toxicology, Aristotle Univerisity of Thessaloniki, Thessaloniki, Greece
- Cancer Prevention Research Group in Greece, Kifisias Avenue 44, Marousi, Greece
| | - Mohamed Shih
- School of Medicine, Newgiza University, Giza, Egypt.
- Cancer Prevention Research Group in Greece, Kifisias Avenue 44, Marousi, Greece.
| | - Agnes Zanotto Manoel
- Faculty of Medicine, Federal University of Rio Grande, Rio Grande do Sul, Brazil
- Cancer Prevention Research Group in Greece, Kifisias Avenue 44, Marousi, Greece
| | - Mohamed Yousif Elamin Yousif
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
- Cancer Prevention Research Group in Greece, Kifisias Avenue 44, Marousi, Greece
| | - Stavroula Spathi
- Faculty of Medicine, National and Kapodistrian University of Athens, Athens, Greece
- Cancer Prevention Research Group in Greece, Kifisias Avenue 44, Marousi, Greece
| | - Chorya Harshal
- Faculty of Medicine, Medical College Baroda, Vadodara, India
- Cancer Prevention Research Group in Greece, Kifisias Avenue 44, Marousi, Greece
| | - Gaurang Bhatt
- All India Institute of Medical Sciences, Rishikesh, India
- Cancer Prevention Research Group in Greece, Kifisias Avenue 44, Marousi, Greece
| | - Swarali Yatin Chodnekar
- Faculty of Medicine, Teaching University Geomedi LLC, Tbilisi, Georgia
- Cancer Prevention Research Group in Greece, Kifisias Avenue 44, Marousi, Greece
| | - Nicholas Stam Chune
- Faculty of Medicine, University of Nairobi, Nairobi, Kenya
- Cancer Prevention Research Group in Greece, Kifisias Avenue 44, Marousi, Greece
| | - Warda Rasool
- Faculty of Medicine, King Edward Medical University, Lahore, Pakistan
- Cancer Prevention Research Group in Greece, Kifisias Avenue 44, Marousi, Greece
| | - Tungki Pratama Umar
- Division of Surgery and Interventional Science, Faculty of Medical Sciences, University College London, London, UK
- Cancer Prevention Research Group in Greece, Kifisias Avenue 44, Marousi, Greece
| | - Dimitrios C Moustakas
- Faculty of Medicine, National and Kapodistrian University of Athens, Athens, Greece
- Cancer Prevention Research Group in Greece, Kifisias Avenue 44, Marousi, Greece
| | - Robert Achkar
- Faculty of Medicine, Poznan University of Medical Sciences, Poznan, Poland
- Cancer Prevention Research Group in Greece, Kifisias Avenue 44, Marousi, Greece
| | - Harendra Kumar
- Dow University of Health Sciences, Karachi, Pakistan
- Cancer Prevention Research Group in Greece, Kifisias Avenue 44, Marousi, Greece
| | - Suhaila Naz
- Tbilisi State Medical University, Tbilisi, Georgia
- Cancer Prevention Research Group in Greece, Kifisias Avenue 44, Marousi, Greece
| | - Luis M Acuña-Chavez
- Facultad de Medicina de la Universidad Nacional de Trujillo, Trujillo, Peru
- Cancer Prevention Research Group in Greece, Kifisias Avenue 44, Marousi, Greece
| | - Konstantinos Evgenikos
- Faculty of Medicine, National and Kapodistrian University of Athens, Athens, Greece
- Cancer Prevention Research Group in Greece, Kifisias Avenue 44, Marousi, Greece
| | - Shaina Gulraiz
- Royal Bournemouth Hospital (University Hospitals Dorset), Bournemouth, UK
- Cancer Prevention Research Group in Greece, Kifisias Avenue 44, Marousi, Greece
| | - Eslam Salih Musa Ali
- University of Dongola Faculty of Medicine and Health Science, Dongola, Sudan
- Cancer Prevention Research Group in Greece, Kifisias Avenue 44, Marousi, Greece
| | - Amna Elaagib
- Faculty of Medicine AlMughtaribeen University, Khartoum, Sudan
- Cancer Prevention Research Group in Greece, Kifisias Avenue 44, Marousi, Greece
| | - Innocent H Peter Uggh
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
- Cancer Prevention Research Group in Greece, Kifisias Avenue 44, Marousi, Greece
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Mehrbakhsh Z, Hassanzadeh R, Behnampour N, Tapak L, Zarrin Z, Khazaei S, Dinu I. Machine learning-based evaluation of prognostic factors for mortality and relapse in patients with acute lymphoblastic leukemia: a comparative simulation study. BMC Med Inform Decis Mak 2024; 24:261. [PMID: 39285373 PMCID: PMC11404043 DOI: 10.1186/s12911-024-02645-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 08/21/2024] [Indexed: 09/22/2024] Open
Abstract
BACKGROUND Predicting mortality and relapse in children with acute lymphoblastic leukemia (ALL) is crucial for effective treatment and follow-up management. ALL is a common and deadly childhood cancer that often relapses after remission. In this study, we aimed to apply and evaluate machine learning-based models for predicting mortality and relapse in pediatric ALL patients. METHODS This retrospective cohort study was conducted on 161 children aged less than 16 years with ALL. Survival status (dead/alive) and patient experience of relapse (yes/no) were considered as the outcome variables. Ten machine learning (ML) algorithms were used to predict mortality and relapse. The performance of the algorithms was evaluated by cross-validation and reported as mean sensitivity, specificity, accuracy and area under the curve (AUC). Finally, prognostic factors were identified based on the best algorithms. RESULTS The mean accuracy of the ML algorithms for prediction of patient mortality ranged from 64 to 74% and for prediction of relapse, it varied from 64 to 84% on test data sets. The mean AUC of the ML algorithms for mortality and relapse was above 64%. The most important prognostic factors for predicting both mortality and relapse were identified as age at diagnosis, hemoglobin and platelets. In addition, significant prognostic factors for predicting mortality included clinical side effects such as splenomegaly, hepatomegaly and lymphadenopathy. CONCLUSIONS Our results showed that artificial neural networks and bagging algorithms outperformed other algorithms in predicting mortality, while boosting and random forest algorithms excelled in predicting relapse in ALL patients across all criteria. These results offer significant clinical insights into the prognostic factors for children with ALL, which can inform treatment decisions and improve patient outcomes.
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Affiliation(s)
- Zahra Mehrbakhsh
- Department of Biostatistics, School of Public Health, Hamadan University of Medical Sciences, Hamadan, Iran
- Student Research Committee, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Roghayyeh Hassanzadeh
- Department of Biostatistics, School of Public Health, Hamadan University of Medical Sciences, Hamadan, Iran
- Student Research Committee, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Nasser Behnampour
- Department of Biostatistics and Epidemiology, School of Health, Golestan University of Medical Sciences, Gorgan, Iran
| | - Leili Tapak
- Department of Biostatistics, School of Public Health, Hamadan University of Medical Sciences, Hamadan, Iran.
- Modeling of Noncommunicable Diseases Research Center, Hamadan University of Medical Sciences, Hamadan, Iran.
| | - Ziba Zarrin
- Department of Photogrammetry and Remote Sensing, K.N. Toosi University of Technology, Tehran, Iran
| | - Salman Khazaei
- Health Sciences Research Center, Health Sciences & Technology Research Institute, Hamadan University of Medical Science, Hamadan, Iran
| | - Irina Dinu
- School of Public Health, University of Alberta, Edmonton, Canada
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Cox DJ, Jennings AM. The Promises and Possibilities of Artificial Intelligence in the Delivery of Behavior Analytic Services. Behav Anal Pract 2024; 17:123-136. [PMID: 38405282 PMCID: PMC10890993 DOI: 10.1007/s40617-023-00864-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/22/2023] [Indexed: 02/27/2024] Open
Abstract
Artificial intelligence (AI) has begun to affect nearly every aspect of our daily lives and nearly every industry and profession. Many readers of this journal likely work in one or more areas of behavioral health. For readers who work in behavioral health and who are interested in AI, the purpose of this article is to highlight the pervasiveness of AI research being conducted around many facets of behavioral health service delivery. To do this, we first provide a brief overview of some of the areas within AI and the types of problems each area of AI attempts to solve. We then outline the prototypical client journey in behavioral healthcare beginning with diagnosis/assessment and ending with intervention withdrawal or ongoing monitoring. Next, for each stage in the client journey, we highlight several areas that parallel existing behavior analytic practice where researchers have begun to use AI, often to improve the efficiency of service delivery or to learn new things that improve the effectiveness of behavioral health services. Finally, for those whose appetite has been whet for getting involved with AI, we close by describing three roles they might consider trying out and that parallel the three main domains of behavior analysis. These three roles are an AI tool designer (akin to EAB), AI tool implementer (akin to ABA), or AI tool supporter (akin to practice).
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Affiliation(s)
- David J. Cox
- Department of Applied Behavior Analysis, Endicott College, Beverly, MA USA
| | - Adrienne M. Jennings
- Department of Behavioral Science, Daemen University, 4380 Main Street, Amherst, NY USA
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Kierner S, Kucharski J, Kierner Z. Taxonomy of hybrid architectures involving rule-based reasoning and machine learning in clinical decision systems: A scoping review. J Biomed Inform 2023; 144:104428. [PMID: 37355025 DOI: 10.1016/j.jbi.2023.104428] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 03/28/2023] [Accepted: 06/15/2023] [Indexed: 06/26/2023]
Abstract
BACKGROUND As the application of Artificial Intelligence (AI) technologies increases in the healthcare sector, the industry faces a need to combine medical knowledge, often expressed as clinical rules, with advances in machine learning (ML), which offer high prediction accuracy at the expense of transparency of decision making. PURPOSE This paper seeks to review the present literature, identify hybrid architecture patterns that incorporate rules and machine learning, and evaluate the rationale behind their selection to inform future development and research on the design of transparent and precise clinical decision systems. METHODS PubMed, IEEE Explore, and Google Scholar were queried in search for papers from 1992 to 2022, with the keywords: "clinical decision system", "hybrid clinical architecture", "machine learning and clinical rules". Excluded articles did not use both ML and rules or did not provide any explanation of employed architecture. A proposed taxonomy was used to organize the results, analyze them, and depict them in graphical and tabular form. Two researchers, one with expertise in rule-based systems and another in ML, reviewed identified papers and discussed the work to minimize bias, and the third one re-reviewed the work to ensure consistency of reporting. RESULTS The authors screened 957 papers and reviewed 71 that met their criteria. Five distinct architecture archetypes were determined: Rules are Embedded in ML architecture (REML) (most used), ML pre-processes input data for Rule-Based inference (MLRB), Rule-Based method pre-processes input data for ML prediction (RBML), Rules influence ML training (RMLT), Parallel Ensemble of Rules and ML (PERML), which was rarely observed in clinical contexts. CONCLUSIONS Most architectures in the reviewed literature prioritize prediction accuracy over explainability and trustworthiness, which has led to more complex embedded approaches. Alternatively, parallel (PERML) architectures may be employed, allowing for a more transparent system that is easier to explain to patients and clinicians. The potential of this approach warrants further research. OTHER A limitation of the study may be that it reviews scientific literature, while algorithms implemented in clinical practice may present different distributions of motivations and implementations of hybrid architectures.
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Affiliation(s)
- Slawomir Kierner
- Lodz University of Technology, Faculty of Electrical, Electronic, Computer and Control Engineering, 27 Isabella Street, 02116 Boston, MA, USA.
| | - Jacek Kucharski
- Lodz University of Technology, Faculty of Electrical, Electronic, Computer and Control Engineering, 18/22 Stefanowskiego St., 90-924 Łodź, Poland.
| | - Zofia Kierner
- University of California, Berkeley College of Letters & Science, Berkeley, CA 94720-1786, USA.
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Su F, Chao J, Liu P, Zhang B, Zhang N, Luo Z, Han J. Prognostic models for breast cancer: based on logistics regression and Hybrid Bayesian Network. BMC Med Inform Decis Mak 2023; 23:120. [PMID: 37443001 PMCID: PMC10347801 DOI: 10.1186/s12911-023-02224-1] [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: 01/04/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND To construct two prognostic models to predict survival in breast cancer patients; to compare the efficacy of the two models in the whole group and the advanced human epidermal growth factor receptor-2-positive (HER2+) subgroup of patients; to conclude whether the Hybrid Bayesian Network (HBN) model outperformed the logistics regression (LR) model. METHODS In this paper, breast cancer patient data were collected from the SEER database. Data processing and analysis were performed using Rstudio 4.2.0, including data preprocessing, model construction and validation. The L_DVBN algorithm in Julia0.4.7 and bnlearn package in R was used to build and evaluate the HBN model. Data with a diagnosis time of 2018(n = 23,384) were distributed randomly as training and testing sets in the ratio of 7:3 using the leave-out method for model construction and internal validation. External validation of the model was done using the dataset of 2019(n = 8128). Finally, the late HER2 + patients(n = 395) was selected for subgroup analysis. Accuracy, calibration and net benefit of clinical decision making were evaluated for both models. RESULTS The HBN model showed that seventeen variables were associated with survival outcome, including age, tumor size, site, histologic type, radiotherapy, surgery, chemotherapy, distant metastasis, subtype, clinical stage, ER receptor, PR receptor, clinical grade, race, marital status, tumor laterality, and lymph node. The AUCs for the internal validation of the LR and HBN models were 0.831 and 0.900; The AUCs for the external validation of the LR and HBN models on the whole population were 0.786 and 0.871; the AUCs for the external validation of the two models on the subgroup population were 0.601 and 0.813. CONCLUSION The accuracy, net clinical benefit, and calibration of the HBN model were better than LR model. The predictive efficacy of both models decreased and the difference was greater in advanced HER2 + patients, which means the HBN model had higher robustness and more stable predictive performance in the subgroup.
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Affiliation(s)
- Fan Su
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, No. 87 Ding Jia Qiao, Central Gate Street, Gulou District, Nanjing, Jiangsu China
| | - Jianqian Chao
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, No. 87 Ding Jia Qiao, Central Gate Street, Gulou District, Nanjing, Jiangsu China
- Department of Medical Insurance, School of Public Health, Southeast University, No. 87 Ding Jia Qiao, Central Gate Street, Gulou District, Nanjing, Jiangsu China
| | - Pei Liu
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, No. 87 Ding Jia Qiao, Central Gate Street, Gulou District, Nanjing, Jiangsu China
| | - Bowen Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, No. 87 Ding Jia Qiao, Central Gate Street, Gulou District, Nanjing, Jiangsu China
| | - Na Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, No. 87 Ding Jia Qiao, Central Gate Street, Gulou District, Nanjing, Jiangsu China
| | - Zongyu Luo
- Department of Medical Insurance, School of Public Health, Southeast University, No. 87 Ding Jia Qiao, Central Gate Street, Gulou District, Nanjing, Jiangsu China
| | - Jiaying Han
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, No. 87 Ding Jia Qiao, Central Gate Street, Gulou District, Nanjing, Jiangsu China
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Ranjbarzadeh R, Dorosti S, Jafarzadeh Ghoushchi S, Caputo A, Tirkolaee EB, Ali SS, Arshadi Z, Bendechache M. Breast tumor localization and segmentation using machine learning techniques: Overview of datasets, findings, and methods. Comput Biol Med 2023; 152:106443. [PMID: 36563539 DOI: 10.1016/j.compbiomed.2022.106443] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/24/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022]
Abstract
The Global Cancer Statistics 2020 reported breast cancer (BC) as the most common diagnosis of cancer type. Therefore, early detection of such type of cancer would reduce the risk of death from it. Breast imaging techniques are one of the most frequently used techniques to detect the position of cancerous cells or suspicious lesions. Computer-aided diagnosis (CAD) is a particular generation of computer systems that assist experts in detecting medical image abnormalities. In the last decades, CAD has applied deep learning (DL) and machine learning approaches to perform complex medical tasks in the computer vision area and improve the ability to make decisions for doctors and radiologists. The most popular and widely used technique of image processing in CAD systems is segmentation which consists of extracting the region of interest (ROI) through various techniques. This research provides a detailed description of the main categories of segmentation procedures which are classified into three classes: supervised, unsupervised, and DL. The main aim of this work is to provide an overview of each of these techniques and discuss their pros and cons. This will help researchers better understand these techniques and assist them in choosing the appropriate method for a given use case.
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Affiliation(s)
- Ramin Ranjbarzadeh
- School of Computing, Faculty of Engineering and Computing, Dublin City University, Ireland.
| | - Shadi Dorosti
- Department of Industrial Engineering, Urmia University of Technology, Urmia, Iran.
| | | | - Annalina Caputo
- School of Computing, Faculty of Engineering and Computing, Dublin City University, Ireland.
| | | | - Sadia Samar Ali
- Department of Industrial Engineering, Faculty of Engineering, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Zahra Arshadi
- Faculty of Electronics, Telecommunications and Physics Engineering, Polytechnic University, Turin, Italy.
| | - Malika Bendechache
- Lero & ADAPT Research Centres, School of Computer Science, University of Galway, Ireland.
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8
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Syed AH, Khan T. Evolution of research trends in artificial intelligence for breast cancer diagnosis and prognosis over the past two decades: A bibliometric analysis. Front Oncol 2022; 12:854927. [PMID: 36267967 PMCID: PMC9578338 DOI: 10.3389/fonc.2022.854927] [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: 01/14/2022] [Accepted: 08/30/2022] [Indexed: 01/27/2023] Open
Abstract
Objective In recent years, among the available tools, the concurrent application of Artificial Intelligence (AI) has improved the diagnostic performance of breast cancer screening. In this context, the present study intends to provide a comprehensive overview of the evolution of AI for breast cancer diagnosis and prognosis research using bibliometric analysis. Methodology Therefore, in the present study, relevant peer-reviewed research articles published from 2000 to 2021 were downloaded from the Scopus and Web of Science (WOS) databases and later quantitatively analyzed and visualized using Bibliometrix (R package). Finally, open challenges areas were identified for future research work. Results The present study revealed that the number of literature studies published in AI for breast cancer detection and survival prediction has increased from 12 to 546 between the years 2000 to 2021. The United States of America (USA), the Republic of China, and India are the most productive publication-wise in this field. Furthermore, the USA leads in terms of the total citations; however, hungry and Holland take the lead positions in average citations per year. Wang J is the most productive author, and Zhan J is the most relevant author in this field. Stanford University in the USA is the most relevant affiliation by the number of published articles. The top 10 most relevant sources are Q1 journals with PLOS ONE and computer in Biology and Medicine are the leading journals in this field. The most trending topics related to our study, transfer learning and deep learning, were identified. Conclusion The present findings provide insight and research directions for policymakers and academic researchers for future collaboration and research in AI for breast cancer patients.
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Affiliation(s)
- Asif Hassan Syed
- Department of Computer Science, Faculty of Computing and Information Technology Rabigh (FCITR), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Tabrej Khan
- Department of Information Systems, Faculty of Computing and Information Technology Rabigh (FCITR), King Abdulaziz University, Jeddah, Saudi Arabia
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Mikhailova V, Anbarjafari G. Comparative analysis of classification algorithms on the breast cancer recurrence using machine learning. Med Biol Eng Comput 2022; 60:2589-2600. [DOI: 10.1007/s11517-022-02623-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 06/15/2022] [Indexed: 10/17/2022]
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10
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Gasparini A, Humphreys K. Estimating latent, dynamic processes of breast cancer tumour growth and distant metastatic spread from mammography screening data. Stat Methods Med Res 2022; 31:862-881. [PMID: 35103530 PMCID: PMC9099158 DOI: 10.1177/09622802211072496] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We propose a framework for jointly modelling tumour size at diagnosis and time to
distant metastatic spread, from diagnosis, based on latent dynamic sub-models of
growth of the primary tumour and of distant metastatic detection. The framework
also includes a sub-model for screening sensitivity as a function of latent
tumour size. Our approach connects post-diagnosis events to the natural history
of cancer and, once refined, may prove useful for evaluating new interventions,
such as personalised screening regimes. We evaluate our model-fitting procedure
using Monte Carlo simulation, showing that the estimation algorithm can retrieve
the correct model parameters, that key patterns in the data can be captured by
the model even with misspecification of some structural assumptions, and that,
still, with enough data it should be possible to detect strong
misspecifications. Furthermore, we fit our model to observational data from an
extension of a case-control study of post-menopausal breast cancer in Sweden,
providing model-based estimates of the probability of being free from detected
distant metastasis as a function of tumour size, mode of detection (of the
primary tumour), and screening history. For women with screen-detected cancer
and two previous negative screens, the probabilities of being free from detected
distant metastases 5 years after detection and removal of the primary tumour are
0.97, 0.89 and 0.59 for tumours of diameter 5, 15 and 35 mm, respectively. We
also study the probability of having latent/dormant metastases at detection of
the primary tumour, estimating that 33% of patients in our study had such
metastases.
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Affiliation(s)
- Alessandro Gasparini
- Alessandro Gasparini, Department of Medical
Epidemiology and Biostatistics, Karolinska Institutet, PO Box 281, SE-17177,
Stockholm, Sweden.
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Musa IH, Afolabi LO, Zamit I, Musa TH, Musa HH, Tassang A, Akintunde TY, Li W. Artificial Intelligence and Machine Learning in Cancer Research: A Systematic and Thematic Analysis of the Top 100 Cited Articles Indexed in Scopus Database. Cancer Control 2022; 29:10732748221095946. [PMID: 35688650 PMCID: PMC9189515 DOI: 10.1177/10732748221095946] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
INTRODUCTION Cancer is a major public health problem and a global leading cause of death where the screening, diagnosis, prediction, survival estimation, and treatment of cancer and control measures are still a major challenge. The rise of Artificial Intelligence (AI) and Machine Learning (ML) techniques and their applications in various fields have brought immense value in providing insights into advancement in support of cancer control. METHODS A systematic and thematic analysis was performed on the Scopus database to identify the top 100 cited articles in cancer research. Data were analyzed using RStudio and VOSviewer.Var1.6.6. RESULTS The top 100 articles in AI and ML in cancer received a 33 920 citation score with a range of 108 to 5758 times. Doi Kunio from the USA was the most cited author with total number of citations (TNC = 663). Out of 43 contributed countries, 30% of the top 100 cited articles originated from the USA, and 10% originated from China. Among the 57 peer-reviewed journals, the "Expert Systems with Application" published 8% of the total articles. The results were presented in highlight technological advancement through AI and ML via the widespread use of Artificial Neural Network (ANNs), Deep Learning or machine learning techniques, Mammography-based Model, Convolutional Neural Networks (SC-CNN), and text mining techniques in the prediction, diagnosis, and prevention of various types of cancers towards cancer control. CONCLUSIONS This bibliometric study provides detailed overview of the most cited empirical evidence in AI and ML adoption in cancer research that could efficiently help in designing future research. The innovations guarantee greater speed by using AI and ML in the detection and control of cancer to improve patient experience.
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Affiliation(s)
- Ibrahim H. Musa
- Department of Software Engineering, School of Computer Science and Engineering, Southeast University, Nanjing, China
- Key Laboratory of Computer Network and Information Integration, Ministry of Education, Southeast University, Nanjing, China
| | - Lukman O. Afolabi
- Guangdong Immune Cell Therapy Engineering and Technology Research Center, Center for Protein and Cell-Based Drugs, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ibrahim Zamit
- University of Chinese Academy of Sciences, Beijing, China
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China
| | - Taha H. Musa
- Biomedical Research Institute, Darfur University College, Nyala, South Darfur, Sudan
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, Jiangsu Province, China
| | - Hassan H. Musa
- Faculty of Medical Laboratory Sciences, University of Khartoum, Khartoum, Sudan
| | - Andrew Tassang
- Faculty of Health Sciences, University of Buea, Cameroon
- Buea Regional Hospital, Annex, Cameroon
| | - Tosin Y. Akintunde
- Department of Sociology, School of Public Administration, Hohai University, Nanjing, China
| | - Wei Li
- Department of quality management, Children’s hospital of Nanjing Medical University, Nanjing, China
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12
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A survey on artificial intelligence techniques for chronic diseases: open issues and challenges. Artif Intell Rev 2021. [DOI: 10.1007/s10462-021-10084-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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13
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Coates JTT, Pirovano G, El Naqa I. Radiomic and radiogenomic modeling for radiotherapy: strategies, pitfalls, and challenges. J Med Imaging (Bellingham) 2021; 8:031902. [PMID: 33768134 PMCID: PMC7985651 DOI: 10.1117/1.jmi.8.3.031902] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/12/2021] [Indexed: 12/14/2022] Open
Abstract
The power of predictive modeling for radiotherapy outcomes has historically been limited by an inability to adequately capture patient-specific variabilities; however, next-generation platforms together with imaging technologies and powerful bioinformatic tools have facilitated strategies and provided optimism. Integrating clinical, biological, imaging, and treatment-specific data for more accurate prediction of tumor control probabilities or risk of radiation-induced side effects are high-dimensional problems whose solutions could have widespread benefits to a diverse patient population-we discuss technical approaches toward this objective. Increasing interest in the above is specifically reflected by the emergence of two nascent fields, which are distinct but complementary: radiogenomics, which broadly seeks to integrate biological risk factors together with treatment and diagnostic information to generate individualized patient risk profiles, and radiomics, which further leverages large-scale imaging correlates and extracted features for the same purpose. We review classical analytical and data-driven approaches for outcomes prediction that serve as antecedents to both radiomic and radiogenomic strategies. Discussion then focuses on uses of conventional and deep machine learning in radiomics. We further consider promising strategies for the harmonization of high-dimensional, heterogeneous multiomics datasets (panomics) and techniques for nonparametric validation of best-fit models. Strategies to overcome common pitfalls that are unique to data-intensive radiomics are also discussed.
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Affiliation(s)
- James T. T. Coates
- Massachusetts General Hospital & Harvard Medical School, Center for Cancer Research, Boston, Massachusetts, United States
| | - Giacomo Pirovano
- Memorial Sloan Kettering Cancer Center, Department of Radiology, New York, New York, United States
| | - Issam El Naqa
- Moffitt Cancer Center and Research Institute, Department of Machine Learning, Tampa, Florida, United States
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14
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15
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Gated Graph Attention Network for Cancer Prediction. SENSORS 2021; 21:s21061938. [PMID: 33801894 PMCID: PMC7998488 DOI: 10.3390/s21061938] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 03/02/2021] [Accepted: 03/05/2021] [Indexed: 01/17/2023]
Abstract
With its increasing incidence, cancer has become one of the main causes of worldwide mortality. In this work, we mainly propose a novel attention-based neural network model named Gated Graph ATtention network (GGAT) for cancer prediction, where a gating mechanism (GM) is introduced to work with the attention mechanism (AM), to break through the previous work's limitation of 1-hop neighbourhood reasoning. In this way, our GGAT is capable of fully mining the potential correlation between related samples, helping for improving the cancer prediction accuracy. Additionally, to simplify the datasets, we propose a hybrid feature selection algorithm to strictly select gene features, which significantly reduces training time without affecting prediction accuracy. To the best of our knowledge, our proposed GGAT achieves the state-of-the-art results in cancer prediction task on LIHC, LUAD, KIRC compared to other traditional machine learning methods and neural network models, and improves the accuracy by 1% to 2% on Cora dataset, compared to the state-of-the-art graph neural network methods.
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16
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Pham Q, Gamble A, Hearn J, Cafazzo JA. The Need for Ethnoracial Equity in Artificial Intelligence for Diabetes Management: Review and Recommendations. J Med Internet Res 2021; 23:e22320. [PMID: 33565982 PMCID: PMC7904401 DOI: 10.2196/22320] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 11/02/2020] [Accepted: 01/16/2021] [Indexed: 12/13/2022] Open
Abstract
There is clear evidence to suggest that diabetes does not affect all populations equally. Among adults living with diabetes, those from ethnoracial minority communities—foreign-born, immigrant, refugee, and culturally marginalized—are at increased risk of poor health outcomes. Artificial intelligence (AI) is actively being researched as a means of improving diabetes management and care; however, several factors may predispose AI to ethnoracial bias. To better understand whether diabetes AI interventions are being designed in an ethnoracially equitable manner, we conducted a secondary analysis of 141 articles included in a 2018 review by Contreras and Vehi entitled “Artificial Intelligence for Diabetes Management and Decision Support: Literature Review.” Two members of our research team independently reviewed each article and selected those reporting ethnoracial data for further analysis. Only 10 articles (7.1%) were ultimately selected for secondary analysis in our case study. Of the 131 excluded articles, 118 (90.1%) failed to mention participants’ ethnic or racial backgrounds. The included articles reported ethnoracial data under various categories, including race (n=6), ethnicity (n=2), race/ethnicity (n=3), and percentage of Caucasian participants (n=1). Among articles specifically reporting race, the average distribution was 69.5% White, 17.1% Black, and 3.7% Asian. Only 2 articles reported inclusion of Native American participants. Given the clear ethnic and racial differences in diabetes biomarkers, prevalence, and outcomes, the inclusion of ethnoracial training data is likely to improve the accuracy of predictive models. Such considerations are imperative in AI-based tools, which are predisposed to negative biases due to their black-box nature and proneness to distributional shift. Based on our findings, we propose a short questionnaire to assess ethnoracial equity in research describing AI-based diabetes interventions. At this unprecedented time in history, AI can either mitigate or exacerbate disparities in health care. Future accounts of the infancy of diabetes AI must reflect our early and decisive action to confront ethnoracial inequities before they are coded into our systems and perpetuate the very biases we aim to eliminate. If we take deliberate and meaningful steps now toward training our algorithms to be ethnoracially inclusive, we can architect innovations in diabetes care that are bound by the diverse fabric of our society.
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Affiliation(s)
- Quynh Pham
- Centre for Global eHealth Innovation, Techna Institute, University Health Network, Toronto, ON, Canada.,Institute of Health Policy, Management and Evaluation, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Anissa Gamble
- Centre for Global eHealth Innovation, Techna Institute, University Health Network, Toronto, ON, Canada
| | - Jason Hearn
- Centre for Global eHealth Innovation, Techna Institute, University Health Network, Toronto, ON, Canada.,Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Joseph A Cafazzo
- Centre for Global eHealth Innovation, Techna Institute, University Health Network, Toronto, ON, Canada.,Institute of Health Policy, Management and Evaluation, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.,Institute of Biomedical Engineering, University of Toronto, Toronto, ON, Canada
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17
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Quantitative sleep EEG synchronization analysis for automatic arousals detection. Biomed Signal Process Control 2020. [DOI: 10.1016/j.bspc.2020.101895] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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18
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Su C, Xu Z, Pathak J, Wang F. Deep learning in mental health outcome research: a scoping review. Transl Psychiatry 2020; 10:116. [PMID: 32532967 PMCID: PMC7293215 DOI: 10.1038/s41398-020-0780-3] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 02/17/2020] [Accepted: 02/26/2020] [Indexed: 12/17/2022] Open
Abstract
Mental illnesses, such as depression, are highly prevalent and have been shown to impact an individual's physical health. Recently, artificial intelligence (AI) methods have been introduced to assist mental health providers, including psychiatrists and psychologists, for decision-making based on patients' historical data (e.g., medical records, behavioral data, social media usage, etc.). Deep learning (DL), as one of the most recent generation of AI technologies, has demonstrated superior performance in many real-world applications ranging from computer vision to healthcare. The goal of this study is to review existing research on applications of DL algorithms in mental health outcome research. Specifically, we first briefly overview the state-of-the-art DL techniques. Then we review the literature relevant to DL applications in mental health outcomes. According to the application scenarios, we categorize these relevant articles into four groups: diagnosis and prognosis based on clinical data, analysis of genetics and genomics data for understanding mental health conditions, vocal and visual expression data analysis for disease detection, and estimation of risk of mental illness using social media data. Finally, we discuss challenges in using DL algorithms to improve our understanding of mental health conditions and suggest several promising directions for their applications in improving mental health diagnosis and treatment.
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Affiliation(s)
- Chang Su
- Department of Healthcare Policy and Research, Weill Cornell Medicine, New York, NY, USA
| | - Zhenxing Xu
- Department of Healthcare Policy and Research, Weill Cornell Medicine, New York, NY, USA
| | - Jyotishman Pathak
- Department of Healthcare Policy and Research, Weill Cornell Medicine, New York, NY, USA
| | - Fei Wang
- Department of Healthcare Policy and Research, Weill Cornell Medicine, New York, NY, USA.
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19
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Abouzari M, Goshtasbi K, Sarna B, Khosravi P, Reutershan T, Mostaghni N, Lin HW, Djalilian HR. Prediction of vestibular schwannoma recurrence using artificial neural network. Laryngoscope Investig Otolaryngol 2020; 5:278-285. [PMID: 32337359 PMCID: PMC7178452 DOI: 10.1002/lio2.362] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/28/2020] [Accepted: 02/08/2020] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES To compare two statistical models, namely logistic regression and artificial neural network (ANN), in prediction of vestibular schwannoma (VS) recurrence. METHODS Seven hundred eighty-nine patients with VS diagnosis completed an online survey. Potential predictors for recurrence were derived from univariate analysis by reaching the cut off P value of .05. Those nine potential predictors were years since treatment, surgeon's specialty, resection amount, and having incomplete eye closure, dry eye, double vision, facial pain, seizure, and voice/swallowing problem as a complication following treatment. Multivariate binary logistic regression model was compared with a four-layer 9-5-10-1 feedforward backpropagation ANN for prediction of recurrence. RESULTS The overall recurrence rate was 14.5%. Significant predictors of recurrence in the regression model were years since treatment and resection amount (both P < .001). The regression model did not show an acceptable performance (area under the curve [AUC] = 0.64; P = .27). The regression model's sensitivity and specificity were 44% and 69%, respectively and correctly classified 56% of cases. The ANN showed a superior performance compared to the regression model (AUC = 0.79; P = .001) with higher sensitivity (61%) and specificity (81%), and correctly classified 70% of cases. CONCLUSION The constructed ANN model was superior to logistic regression in predicting patient-answered VS recurrence in an anonymous survey with higher sensitivity and specificity. Since artificial intelligence tools such as neural networks can have higher predictive abilities compared to logistic regression models, continuous investigation into their utility as complementary clinical tools in predicting certain surgical outcomes is warranted.
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Affiliation(s)
- Mehdi Abouzari
- Division of Neurotology and Skull Base Surgery, Department of Otolaryngology‐Head and Neck SurgeryUniversity of CaliforniaIrvineCalifornia
- Division of Pediatric OtolaryngologyChildren's Hospital of Orange CountyOrangeCalifornia
| | - Khodayar Goshtasbi
- Division of Neurotology and Skull Base Surgery, Department of Otolaryngology‐Head and Neck SurgeryUniversity of CaliforniaIrvineCalifornia
| | - Brooke Sarna
- Division of Neurotology and Skull Base Surgery, Department of Otolaryngology‐Head and Neck SurgeryUniversity of CaliforniaIrvineCalifornia
| | - Pooya Khosravi
- Division of Neurotology and Skull Base Surgery, Department of Otolaryngology‐Head and Neck SurgeryUniversity of CaliforniaIrvineCalifornia
- Department of Biomedical EngineeringUniversity of CaliforniaIrvineCalifornia
| | - Trevor Reutershan
- Division of Neurotology and Skull Base Surgery, Department of Otolaryngology‐Head and Neck SurgeryUniversity of CaliforniaIrvineCalifornia
- Department of Biomedical EngineeringUniversity of CaliforniaIrvineCalifornia
| | - Navid Mostaghni
- Division of Neurotology and Skull Base Surgery, Department of Otolaryngology‐Head and Neck SurgeryUniversity of CaliforniaIrvineCalifornia
- Department of Biomedical EngineeringUniversity of CaliforniaIrvineCalifornia
| | - Harrison W. Lin
- Division of Neurotology and Skull Base Surgery, Department of Otolaryngology‐Head and Neck SurgeryUniversity of CaliforniaIrvineCalifornia
| | - Hamid R. Djalilian
- Division of Neurotology and Skull Base Surgery, Department of Otolaryngology‐Head and Neck SurgeryUniversity of CaliforniaIrvineCalifornia
- Department of Biomedical EngineeringUniversity of CaliforniaIrvineCalifornia
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20
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Santiago-Montero R, Sossa H, Gutiérrez-Hernández DA, Zamudio V, Hernández-Bautista I, Valadez-Godínez S. Novel Mathematical Model of Breast Cancer Diagnostics Using an Associative Pattern Classification. Diagnostics (Basel) 2020; 10:diagnostics10030136. [PMID: 32121569 PMCID: PMC7151177 DOI: 10.3390/diagnostics10030136] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/18/2020] [Accepted: 02/18/2020] [Indexed: 12/14/2022] Open
Abstract
Breast cancer is a disease that has emerged as the second leading cause of cancer deaths in women worldwide. The annual mortality rate is estimated to continue growing. Cancer detection at an early stage could significantly reduce breast cancer death rates long-term. Many investigators have studied different breast diagnostic approaches, such as mammography, magnetic resonance imaging, ultrasound, computerized tomography, positron emission tomography and biopsy. However, these techniques have limitations, such as being expensive, time consuming and not suitable for women of all ages. Proposing techniques that support the effective medical diagnosis of this disease has undoubtedly become a priority for the government, for health institutions and for civil society in general. In this paper, an associative pattern classifier (APC) was used for the diagnosis of breast cancer. The rate of efficiency obtained on the Wisconsin breast cancer database was 97.31%. The APC’s performance was compared with the performance of a support vector machine (SVM) model, back-propagation neural networks, C4.5, naive Bayes, k-nearest neighbor (k-NN) and minimum distance classifiers. According to our results, the APC performed best. The algorithm of the APC was written and executed in a JAVA platform, as well as the experimental and comparativeness between algorithms.
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Affiliation(s)
- Raúl Santiago-Montero
- Tecnológico Nacional de México/Instituto Tecnológico de León, León 37290, Guanajuato, Mexico; (R.S.-M.); (V.Z.)
| | - Humberto Sossa
- Instituto Politécnico Nacional (CIC), CD de México 07738, Mexico;
- Tecnológico de Monterrey, Campus Guadalajara, Zapopan 45138, Jalisco, Mexico
| | - David A. Gutiérrez-Hernández
- Tecnológico Nacional de México/Instituto Tecnológico de León, León 37290, Guanajuato, Mexico; (R.S.-M.); (V.Z.)
- Correspondence:
| | - Víctor Zamudio
- Tecnológico Nacional de México/Instituto Tecnológico de León, León 37290, Guanajuato, Mexico; (R.S.-M.); (V.Z.)
| | | | - Sergio Valadez-Godínez
- Universidad Humani Mundial, Campus San Francisco del Rincón, San Francisco del Rincón 37378, Guanajuato, Mexico;
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Dalwinder S, Birmohan S, Manpreet K. Simultaneous feature weighting and parameter determination of Neural Networks using Ant Lion Optimization for the classification of breast cancer. Biocybern Biomed Eng 2020. [DOI: 10.1016/j.bbe.2019.12.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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22
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Zarin Mousavi SS, Mohammadi Zanjireh M, Oghbaie M. Applying computational classification methods to diagnose Congenital Hypothyroidism: A comparative study. INFORMATICS IN MEDICINE UNLOCKED 2020. [DOI: 10.1016/j.imu.2019.100281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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23
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Vazifehdan M, Moattar MH, Jalali M. A hybrid Bayesian network and tensor factorization approach for missing value imputation to improve breast cancer recurrence prediction. JOURNAL OF KING SAUD UNIVERSITY-COMPUTER AND INFORMATION SCIENCES 2019. [DOI: 10.1016/j.jksuci.2018.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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24
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Iraji MS. Prediction of fetal state from the cardiotocogram recordings using neural network models. Artif Intell Med 2019; 96:33-44. [PMID: 31164209 DOI: 10.1016/j.artmed.2019.03.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 02/02/2019] [Accepted: 03/17/2019] [Indexed: 02/05/2023]
Abstract
The combination of machine vision and soft computing approaches in the clinical decisions, using training data, can improve medical decisions and treatments. The cardiotocography (CTG) monitoring and uterine activity (UA) provides useful information about the condition of the fetus and the cesarean or natural delivery. The visual assessment by the pathologists takes a lot of time and may be incompatible. Therefore, creating a computer intelligent method to assess fetal wellbeing before the mother labour is very important. In this study, many diverse approaches are suggested for predicting fetal state classes based on artificial intelligence. The various topologies of multi-layer architecture of a sub-adaptive neuro fuzzy inference system (MLA-ANFIS) using multiple input features, neural networks (NN), deep stacked sparse auto-encoders (DSSAEs), and deep-ANFIS models are implemented on a CTG data set. Experimental results contributing to DSSAE are more accurate than other suggested techniques to predict fetal state. The proposed method achieved a sensitivity of 99.716, specificity of 97.500 and geometric mean of 98.602 with accuracy of 99.503.
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Affiliation(s)
- Mohammad Saber Iraji
- Faculty Member of Department of Computer Engineering and Information Technology, Payame Noor University (PNU), Iran.
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25
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Lin PH, Yang HJ, Hsieh WC, Lin C, Chan YC, Wang YF, Yang YT, Lin KJ, Lin LS, Chen DR. Albumin and hemoglobin adducts of estrogen quinone as biomarkers for early detection of breast cancer. PLoS One 2018; 13:e0201241. [PMID: 30222738 PMCID: PMC6141067 DOI: 10.1371/journal.pone.0201241] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 07/11/2018] [Indexed: 12/21/2022] Open
Abstract
Cumulative estrogen concentration is an important determinant of the risk of developing breast cancer. Estrogen carcinogenesis is attributed to the combination of receptor-driven mitogenesis and DNA damage induced by quinonoid metabolites of estrogen. The present study was focused on developing an improved breast cancer prediction model using estrogen quinone-protein adduct concentrations. Blood samples from 152 breast cancer patients and 71 healthy women were collected, and albumin (Alb) and hemoglobin (Hb) adducts of estrogen-3,4-quinone and estrogen-2,3-quinone were extracted and evaluated as potential biomarkers of breast cancer. A multilayer perceptron (MLP) was used as the predictor model and the resultant prediction of breast cancer was more accurate than other existing detection methods. A MLP using the logarithm of the concentrations of the estrogen quinone-derived adducts (four input nodes, 10 hidden nodes, and one output node) was used to predict breast cancer risk with accuracy close to 100% and area under curve (AUC) close to one. The AUC value of one showed that both data sets were separable. We conclude that Alb and Hb adducts of estrogen quinones are promising biomarkers for the early detection of breast cancer.
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Affiliation(s)
- Po-Hsiung Lin
- Department of Environmental Engineering, National Chung Hsing University, South Dist., Taichung, Taiwan, R.O.C
| | - Hui-Ju Yang
- Department of Dermatology, Changhua Christian Hospital, Changhua, Taiwan, R.O.C
| | - Wei-Chung Hsieh
- Department of Internal Medicine, Da-Chien General Hospital, Miaoli, Taiwan, R.O.C
| | - Che Lin
- Comprehensive Breast Cancer Center, Changhua Christian Hospital, Changhua, Taiwan, R.O.C
| | - Ya-Chi Chan
- Cancer Research Center, Department of Research, Changhua Christian Hospital, Changhua, Taiwan, R.O.C
| | - Yu-Fen Wang
- Cancer Research Center, Department of Research, Changhua Christian Hospital, Changhua, Taiwan, R.O.C
| | - Yuan-Ting Yang
- Department of Pharmacy, Changhua Christian Hospital, Changhua, Taiwan, R.O.C
| | - Kuo-Juei Lin
- Department of Surgery, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan, R.O.C
| | - Li-Sheng Lin
- Department of Breast Surgery, the Affiliated Hospital (Group) of Putian University, Putian, Fujian, China
| | - Dar-Ren Chen
- Comprehensive Breast Cancer Center, Changhua Christian Hospital, Changhua, Taiwan, R.O.C
- Cancer Research Center, Department of Research, Changhua Christian Hospital, Changhua, Taiwan, R.O.C
- School of Medicine, Chung Shan Medical University, South Dist., Taichung, Taiwan, R.O.C
- * E-mail:
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26
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Katuwal R, Suganthan P, Zhang L. An ensemble of decision trees with random vector functional link networks for multi-class classification. Appl Soft Comput 2018. [DOI: 10.1016/j.asoc.2017.09.020] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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27
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A review of statistical and machine learning methods for modeling cancer risk using structured clinical data. Artif Intell Med 2018; 90:1-14. [DOI: 10.1016/j.artmed.2018.06.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 09/08/2017] [Accepted: 06/13/2018] [Indexed: 02/06/2023]
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28
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Hafizi-Rastani I, Khalili H, Paydar S, Pourahmad S. Identifying Important Attributes for Prognostic Prediction in Traumatic Brain Injury Patients. Methods Inf Med 2018; 55:440-449. [DOI: 10.3414/me15-01-0080] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 05/23/2016] [Indexed: 12/19/2022]
Abstract
SummaryBackground: Generally, traumatic brain injury (TBI) patients do not have a stable condition, particularly after the first week of TBI. Hence, indicating the attributes in prognosis through a prediction model is of utmost importance since it helps caregivers with treatment-decision options, or prepares the relatives for the most-likely outcome. Objectives: This study attempted to determine and order the attributes in prognostic prediction in TBI patients, based on early clinical findings. A hybrid method was employed, which combines a decision tree (DT) and an artificial neural network (ANN) in order to improve the modeling process. Methods: The DT approach was applied as the initial analysis of the network architecture to increase accuracy in prediction. Afterwards, the ANN structure was mapped from the initial DT based on a part of the data. Subsequently, the designed network was trained and validated by the remaining data. 5-fold cross-validation method was applied to train the network. The area under the receiver operating characteristic (ROC) curve, sensitivity, specificity, and accuracy rate were utilized as performance measures. The important attributes were then determined from the trained network using two methods: change of mean squared error (MSE), and sensitivity analysis (SA). Results: The hybrid method offered better results compared to the DT method. The accuracy rate of 86.3 % vs. 82.2 %, sensitivity value of 55.1 % vs. 47.6 %, specificity value of 93.6 % vs. 91.1 %, and the area under the ROC curve of 0.705 vs. 0.695 were achieved for the hybrid method and DT, respectively. However, the attributes’ order by DT method was more consistent with the clinical literature. Conclusions: The combination of different modeling methods can enhance their performance. However, it may create some complexities in computations and interpretations. The outcome of the present study could deliver some useful hints in prognostic prediction on the basis of early clinical findings for TBI patients.
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Abstract
Machine learning is a branch of artificial intelligence that employs a variety of statistical, probabilistic and optimization techniques that allows computers to “learn” from past examples and to detect hard-to-discern patterns from large, noisy or complex data sets. This capability is particularly well-suited to medical applications, especially those that depend on complex proteomic and genomic measurements. As a result, machine learning is frequently used in cancer diagnosis and detection. More recently machine learning has been applied to cancer prognosis and prediction. This latter approach is particularly interesting as it is part of a growing trend towards personalized, predictive medicine. In assembling this review we conducted a broad survey of the different types of machine learning methods being used, the types of data being integrated and the performance of these methods in cancer prediction and prognosis. A number of trends are noted, including a growing dependence on protein biomarkers and microarray data, a strong bias towards applications in prostate and breast cancer, and a heavy reliance on “older” technologies such artificial neural networks (ANNs) instead of more recently developed or more easily interpretable machine learning methods. A number of published studies also appear to lack an appropriate level of validation or testing. Among the better designed and validated studies it is clear that machine learning methods can be used to substantially (15–25%) improve the accuracy of predicting cancer susceptibility, recurrence and mortality. At a more fundamental level, it is also evident that machine learning is also helping to improve our basic understanding of cancer development and progression.
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Affiliation(s)
- Joseph A. Cruz
- Departments of Biological Science and Computing Science, University of Alberta Edmonton, AB, Canada T6G 2E8
| | - David S. Wishart
- Departments of Biological Science and Computing Science, University of Alberta Edmonton, AB, Canada T6G 2E8
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30
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Pan L, Liu G, Lin F, Zhong S, Xia H, Sun X, Liang H. Machine learning applications for prediction of relapse in childhood acute lymphoblastic leukemia. Sci Rep 2017; 7:7402. [PMID: 28784991 PMCID: PMC5547099 DOI: 10.1038/s41598-017-07408-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 06/23/2017] [Indexed: 01/17/2023] Open
Abstract
The prediction of relapse in childhood acute lymphoblastic leukemia (ALL) is a critical factor for successful treatment and follow-up planning. Our goal was to construct an ALL relapse prediction model based on machine learning algorithms. Monte Carlo cross-validation nested by 10-fold cross-validation was used to rank clinical variables on the randomly split training sets of 336 newly diagnosed ALL children, and a forward feature selection algorithm was employed to find the shortest list of most discriminatory variables. To enable an unbiased estimation of the prediction model to new patients, besides the split test sets of 150 patients, we introduced another independent data set of 84 patients to evaluate the model. The Random Forest model with 14 features achieved a cross-validation accuracy of 0.827 ± 0.031 on one set and an accuracy of 0.798 on the other, with the area under the curve of 0.902 ± 0.027 and 0.904, respectively. The model performed well across different risk-level groups, with the best accuracy of 0.829 in the standard-risk group. To our knowledge, this is the first study to use machine learning models to predict childhood ALL relapse based on medical data from Electronic Medical Record, which will further facilitate stratification treatments.
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Affiliation(s)
- Liyan Pan
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Guangjian Liu
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Fangqin Lin
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Shuling Zhong
- Department of Hematology and Oncology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Huimin Xia
- Department of Pediatric Surgery, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Xin Sun
- Department of Hematology and Oncology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.
| | - Huiying Liang
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.
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Soto-Ferrari M, Prieto D, Munene G. A Bayesian network and heuristic approach for systematic characterization of radiotherapy receipt after breast-conservation surgery. BMC Med Inform Decis Mak 2017; 17:93. [PMID: 28659177 PMCID: PMC5490206 DOI: 10.1186/s12911-017-0479-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 05/30/2017] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Breast-conservation surgery with radiotherapy is a treatment highly recommended by the guidelines from the National Comprehensive Cancer Network. However, several variables influence the final receipt of radiotherapy and it might not be administered to breast cancer patients. Our objective is to propose a systematic framework to identify the clinical and non-clinical variables that influence the receipt of unexpected radiotherapy treatment by means of Bayesian networks and a proposed heuristic approach. METHODS We used cancer registry data of Detroit, San Francisco-Oakland, and Atlanta from years 2007-2012 downloaded from the Surveillance, Epidemiology, and End Results Program. The samples had patients diagnosed with in situ and early invasive cancer with 14 clinical and non-clinical variables. Bayesian networks were fitted to the data of each region and systematically analyzed through the proposed Zoom-in heuristic. A comparative analysis with logistic regressions is also presented. RESULTS For Detroit, patients under stage 0, grade undetermined, histology lobular carcinoma in situ, and age between 26-50 were found more likely to receive breast-conservation surgery without radiotherapy. For stages I, IIA, and IIB patients with age between 51-75, and grade II were found to be more likely to receive breast-conservation surgery with radiotherapy. For San Francisco-Oakland, patients under stage 0, grade undetermined, and age >75 are more likely to receive BCS. For stages I, IIA, and IIB patients with age >75 are more likely to receive breast-conservation surgery without radiotherapy. For Atlanta, patients under stage 0, grade undetermined, year 2011, and primary site C509 are more likely to receive breast-conservation surgery without radiotherapy. For stages I, IIA, and IIB patients in year 2011, and grade III are more likely to receive breast-conservation surgery without radiotherapy. CONCLUSION For in situ breast cancer and early invasive breast cancer, the results are in accordance with the guidelines and very well demonstrates the usefulness of the Zoom-in heuristic in systematically characterizing a group receiving a treatment. We found a subset of the population from Detroit with ductal carcinoma in situ for which breast-conservation surgery without radiotherapy was received, but potential reasons for this treatment are still unknown.
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Affiliation(s)
- Milton Soto-Ferrari
- Health Systems Decision Support Laboratory (HSDS), Industrial and Entrepreneurial Engineering & Engineering Management Department, Western Michigan University, 4601 Campus Drive, Kalamazoo, 49008, MI, USA
| | - Diana Prieto
- Health Systems Decision Support Laboratory (HSDS), Industrial and Entrepreneurial Engineering & Engineering Management Department, Western Michigan University, 4601 Campus Drive, Kalamazoo, 49008, MI, USA.
| | - Gitonga Munene
- Western Michigan University School of Medicine, 1000 Oakland Drive, Kalamazoo, 49008, MI, USA
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Stage-specific predictive models for breast cancer survivability. Int J Med Inform 2017; 97:304-311. [DOI: 10.1016/j.ijmedinf.2016.11.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/12/2016] [Accepted: 11/03/2016] [Indexed: 11/20/2022]
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Mohebian MR, Marateb HR, Mansourian M, Mañanas MA, Mokarian F. A Hybrid Computer-aided-diagnosis System for Prediction of Breast Cancer Recurrence (HPBCR) Using Optimized Ensemble Learning. Comput Struct Biotechnol J 2016; 15:75-85. [PMID: 28018557 PMCID: PMC5173316 DOI: 10.1016/j.csbj.2016.11.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 11/24/2016] [Accepted: 11/26/2016] [Indexed: 02/07/2023] Open
Abstract
Cancer is a collection of diseases that involves growing abnormal cells with the potential to invade or spread to the body. Breast cancer is the second leading cause of cancer death among women. A method for 5-year breast cancer recurrence prediction is presented in this manuscript. Clinicopathologic characteristics of 579 breast cancer patients (recurrence prevalence of 19.3%) were analyzed and discriminative features were selected using statistical feature selection methods. They were further refined by Particle Swarm Optimization (PSO) as the inputs of the classification system with ensemble learning (Bagged Decision Tree: BDT). The proper combination of selected categorical features and also the weight (importance) of the selected interval-measurement-scale features were identified by the PSO algorithm. The performance of HPBCR (hybrid predictor of breast cancer recurrence) was assessed using the holdout and 4-fold cross-validation. Three other classifiers namely as supported vector machines, DT, and multilayer perceptron neural network were used for comparison. The selected features were diagnosis age, tumor size, lymph node involvement ratio, number of involved axillary lymph nodes, progesterone receptor expression, having hormone therapy and type of surgery. The minimum sensitivity, specificity, precision and accuracy of HPBCR were 77%, 93%, 95% and 85%, respectively in the entire cross-validation folds and the hold-out test fold. HPBCR outperformed the other tested classifiers. It showed excellent agreement with the gold standard (i.e. the oncologist opinion after blood tumor marker and imaging tests, and tissue biopsy). This algorithm is thus a promising online tool for the prediction of breast cancer recurrence.
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Key Words
- Breast cancer
- CAD, computer-aided diagnosis
- Cancer recurrence
- Computer-assisted diagnosis
- DT, decision tree
- FH, family history of cancer
- HPBCR, the proposed hybrid predictor of breast cancer recurrence
- HRT, hormone therapy
- I. Node, number of involved axillary lymph nodes
- Machine learning
- NR, lymph node involvement ratio
- Prognosis
- T. Node, number of dissected axillary lymph nodes
- TS, tumor size
- XRT, radiotherapy
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Affiliation(s)
- Mohammad R. Mohebian
- Biomedical Engineering Department, Engineering Faculty, University of Isfahan, Hezar Jerib St., 81746-73441, Isfahan, Iran
| | - Hamid R. Marateb
- Biomedical Engineering Department, Engineering Faculty, University of Isfahan, Hezar Jerib St., 81746-73441, Isfahan, Iran
- Department of Automatic Control, Biomedical Engineering Research Center, Universitat Politècnica de Catalunya, BarcelonaTech (UPC), C. Pau Gargallo, 5, 08028 Barcelona, Spain
| | - Marjan Mansourian
- Department of Biostatistics and Epidemiology, School of Public Health, Isfahan University of Medical Sciences, Hezar Jerib St., 81745 Isfahan, Iran
- Corresponding author.
| | - Miguel Angel Mañanas
- Department of Automatic Control, Biomedical Engineering Research Center, Universitat Politècnica de Catalunya, BarcelonaTech (UPC), C. Pau Gargallo, 5, 08028 Barcelona, Spain
| | - Fariborz Mokarian
- Cancer Prevention Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
- Department of Internal Medicine, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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Mohammed EA, Naugler CT, Far BH. Breast tumor classification using a new OWA operator. EXPERT SYSTEMS WITH APPLICATIONS 2016; 61:302-313. [DOI: 10.1016/j.eswa.2016.05.037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2025]
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Complementarity of Clinician Judgment and Evidence Based Models in Medical Decision Making: Antecedents, Prospects, and Challenges. BIOMED RESEARCH INTERNATIONAL 2016; 2016:1425693. [PMID: 27642588 PMCID: PMC5013221 DOI: 10.1155/2016/1425693] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 07/25/2016] [Indexed: 01/02/2023]
Abstract
Early accounts of the development of modern medicine suggest that the clinical skills, scientific competence, and doctors' judgment were the main impetus for treatment decision, diagnosis, prognosis, therapy assessment, and medical progress. Yet, clinician judgment has its own critics and is sometimes harshly described as notoriously fallacious and an irrational and unfathomable black box with little transparency. With the rise of contemporary medical research, the reputation of clinician judgment has undergone significant reformation in the last century as its fallacious aspects are increasingly emphasized relative to the evidence based options. Within the last decade, however, medical forecasting literature has seen tremendous change and new understanding is emerging on best ways of sharing medical information to complement the evidence based medicine practices. This review revisits and highlights the core debate on clinical judgments and its interrelations with evidence based medicine. It outlines the key empirical results of clinician judgments relative to evidence based models and identifies its key strengths and prospects, the key limitations and conditions for the effective use of clinician judgment, and the extent to which it can be optimized and professionalized for medical use.
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Coates J, Souhami L, El Naqa I. Big Data Analytics for Prostate Radiotherapy. Front Oncol 2016; 6:149. [PMID: 27379211 PMCID: PMC4905980 DOI: 10.3389/fonc.2016.00149] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 05/31/2016] [Indexed: 12/14/2022] Open
Abstract
Radiation therapy is a first-line treatment option for localized prostate cancer and radiation-induced normal tissue damage are often the main limiting factor for modern radiotherapy regimens. Conversely, under-dosing of target volumes in an attempt to spare adjacent healthy tissues limits the likelihood of achieving local, long-term control. Thus, the ability to generate personalized data-driven risk profiles for radiotherapy outcomes would provide valuable prognostic information to help guide both clinicians and patients alike. Big data applied to radiation oncology promises to deliver better understanding of outcomes by harvesting and integrating heterogeneous data types, including patient-specific clinical parameters, treatment-related dose-volume metrics, and biological risk factors. When taken together, such variables make up the basis for a multi-dimensional space (the "RadoncSpace") in which the presented modeling techniques search in order to identify significant predictors. Herein, we review outcome modeling and big data-mining techniques for both tumor control and radiotherapy-induced normal tissue effects. We apply many of the presented modeling approaches onto a cohort of hypofractionated prostate cancer patients taking into account different data types and a large heterogeneous mix of physical and biological parameters. Cross-validation techniques are also reviewed for the refinement of the proposed framework architecture and checking individual model performance. We conclude by considering advanced modeling techniques that borrow concepts from big data analytics, such as machine learning and artificial intelligence, before discussing the potential future impact of systems radiobiology approaches.
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Affiliation(s)
- James Coates
- Department of Oncology, University of Oxford, Oxford, UK
| | - Luis Souhami
- Division of Radiation Oncology, McGill University Health Centre, Montreal, QC, Canada
| | - Issam El Naqa
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
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Kim W, Kim KS, Park RW. Nomogram of Naive Bayesian Model for Recurrence Prediction of Breast Cancer. Healthc Inform Res 2016; 22:89-94. [PMID: 27200218 PMCID: PMC4871850 DOI: 10.4258/hir.2016.22.2.89] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 03/16/2016] [Accepted: 04/04/2016] [Indexed: 01/17/2023] Open
Abstract
OBJECTIVES Breast cancer has a high rate of recurrence, resulting in the need for aggressive treatment and close follow-up. However, previously established classification guidelines, based on expert panels or regression models, are controversial. Prediction models based on machine learning show excellent performance, but they are not widely used because they cannot explain their decisions and cannot be presented on paper in the way that knowledge is customarily represented in the clinical world. The principal objective of this study was to develop a nomogram based on a naïve Bayesian model for the prediction of breast cancer recurrence within 5 years after breast cancer surgery. METHODS The nomogram can provide a visual explanation of the predicted probabilities on a sheet of paper. We used a data set from a Korean tertiary teaching hospital of 679 patients who had undergone breast cancer surgery between 1994 and 2002. Seven prognostic factors were selected as independent variables for the model. RESULTS The accuracy was 80%, and the area under the receiver operating characteristics curve (AUC) of the model was 0.81. CONCLUSIONS The nomogram can be easily used in daily practice to aid physicians and patients in making appropriate treatment decisions after breast cancer surgery.
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Affiliation(s)
- Woojae Kim
- Department of Public Health and Medical Administration, Dongyang University, Yeongju, Korea
| | - Ku Sang Kim
- Department of Biomedical Informatics, Ajou University School of Medicine, Suwon, Korea.; Breast Cancer Center, Ulsan City Hospital, Ulsan, Korea
| | - Rae Woong Park
- Department of Biomedical Informatics, Ajou University School of Medicine, Suwon, Korea
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Aličković E, Subasi A. Breast cancer diagnosis using GA feature selection and Rotation Forest. Neural Comput Appl 2015. [DOI: 10.1007/s00521-015-2103-9] [Citation(s) in RCA: 165] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Zeid MAE, Abdelhalim MB, Salama GI. Accuracy Improvement of WPBC Dataset-Based Breast Cancer Diagnosis. 2015 25TH INTERNATIONAL CONFERENCE ON COMPUTER THEORY AND APPLICATIONS (ICCTA) 2015. [DOI: 10.1109/iccta37466.2015.9513449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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Mi H, Petitjean C, Dubray B, Vera P, Ruan S. Robust feature selection to predict tumor treatment outcome. Artif Intell Med 2015; 64:195-204. [PMID: 26303106 DOI: 10.1016/j.artmed.2015.07.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 07/01/2015] [Accepted: 07/01/2015] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Recurrence of cancer after treatment increases the risk of death. The ability to predict the treatment outcome can help to design the treatment planning and can thus be beneficial to the patient. We aim to select predictive features from clinical and PET (positron emission tomography) based features, in order to provide doctors with informative factors so as to anticipate the outcome of the patient treatment. METHODS In order to overcome the small sample size problem of datasets usually met in the medical domain, we propose a novel wrapper feature selection algorithm, named HFS (hierarchical forward selection), which searches forward in a hierarchical feature subset space. Feature subsets are iteratively evaluated with the prediction performance using SVM (support vector machine). All feature subsets performing better than those at the preceding iteration are retained. Moreover, as SUV (standardized uptake value) based features have been recognized as significant predictive factors for a patient outcome, we propose to incorporate this prior knowledge into the selection procedure to improve its robustness and reduce its computational cost. RESULTS Two real-world datasets from cancer patients are included in the evaluation. We extract dozens of clinical and PET-based features to characterize the patient's state, including SUV parameters and texture features. We use leave-one-out cross-validation to evaluate the prediction performance, in terms of prediction accuracy and robustness. Using SVM as the classifier, our HFS method produces accuracy values of 100% and 94% on the two datasets, respectively, and robustness values of 89% and 96%. Without accuracy loss, the prior-based version (pHFS) improves the robustness up to 100% and 98% on the two datasets, respectively. CONCLUSIONS Compared with other feature selection methods, the proposed HFS and pHFS provide the most promising results. For our HFS method, we have empirically shown that the addition of prior knowledge improves the robustness and accelerates the convergence.
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Affiliation(s)
- Hongmei Mi
- QUANTification en Imagerie Fonctionnelle - Laboratoire d'Informatique, du Traitement de l'Information et des Systèmes (EA4108 - FR CNRS 3638), University of Rouen, 22, Boulevard GAMBETTA, 76183 Rouen, France.
| | - Caroline Petitjean
- QUANTification en Imagerie Fonctionnelle - Laboratoire d'Informatique, du Traitement de l'Information et des Systèmes (EA4108 - FR CNRS 3638), University of Rouen, 22, Boulevard GAMBETTA, 76183 Rouen, France
| | - Bernard Dubray
- QUANTification en Imagerie Fonctionnelle - Laboratoire d'Informatique, du Traitement de l'Information et des Systèmes (EA4108 - FR CNRS 3638), University of Rouen, 22, Boulevard GAMBETTA, 76183 Rouen, France; Centre Henri Becquerel, Rue d'Amiens, 76038 Rouen, France
| | - Pierre Vera
- QUANTification en Imagerie Fonctionnelle - Laboratoire d'Informatique, du Traitement de l'Information et des Systèmes (EA4108 - FR CNRS 3638), University of Rouen, 22, Boulevard GAMBETTA, 76183 Rouen, France; Centre Henri Becquerel, Rue d'Amiens, 76038 Rouen, France
| | - Su Ruan
- QUANTification en Imagerie Fonctionnelle - Laboratoire d'Informatique, du Traitement de l'Information et des Systèmes (EA4108 - FR CNRS 3638), University of Rouen, 22, Boulevard GAMBETTA, 76183 Rouen, France
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Abstract
Data mining, also known as Knowledge-Discovery in Databases (KDD), is the process of automatically searching large volumes of data for patterns. For instance, a clinical pattern might indicate a female who have diabetes or hypertension are easier suffered from stroke for 5 years in a future. Then, a physician can learn valuable knowledge from the data mining processes. Here, we present a study focused on the investigation of the application of artificial intelligence and data mining techniques to the prediction models of breast cancer. The artificial neural network, decision tree, logistic regression, and genetic algorithm were used for the comparative studies and the accuracy and positive predictive value of each algorithm were used as the evaluation indicators. 699 records acquired from the breast cancer patients at the University of Wisconsin, nine predictor variables, and one outcome variable were incorporated for the data analysis followed by the tenfold cross-validation. The results revealed that the accuracies of logistic regression model were 0.9434 (sensitivity 0.9716 and specificity 0.9482), the decision tree model 0.9434 (sensitivity 0.9615, specificity 0.9105), the neural network model 0.9502 (sensitivity 0.9628, specificity 0.9273), and the genetic algorithm model 0.9878 (sensitivity 1, specificity 0.9802). The accuracy of the genetic algorithm was significantly higher than the average predicted accuracy of 0.9612. The predicted outcome of the logistic regression model was higher than that of the neural network model but no significant difference was observed. The average predicted accuracy of the decision tree model was 0.9435 which was the lowest of all four predictive models. The standard deviation of the tenfold cross-validation was rather unreliable. This study indicated that the genetic algorithm model yielded better results than other data mining models for the analysis of the data of breast cancer patients in terms of the overall accuracy of the patient classification, the expression and complexity of the classification rule. The results showed that the genetic algorithm described in the present study was able to produce accurate results in the classification of breast cancer data and the classification rule identified was more acceptable and comprehensible.
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Affiliation(s)
- Der-Ming Liou
- Yang Ming University, No 155, Sec. 2, Li-Nong St., Taipei, 112, Taiwan R.O.C.,
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Chao CM, Yu YW, Cheng BW, Kuo YL. Construction the model on the breast cancer survival analysis use support vector machine, logistic regression and decision tree. J Med Syst 2014; 38:106. [PMID: 25119239 DOI: 10.1007/s10916-014-0106-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Accepted: 07/07/2014] [Indexed: 01/17/2023]
Abstract
The aim of the paper is to use data mining technology to establish a classification of breast cancer survival patterns, and offers a treatment decision-making reference for the survival ability of women diagnosed with breast cancer in Taiwan. We studied patients with breast cancer in a specific hospital in Central Taiwan to obtain 1,340 data sets. We employed a support vector machine, logistic regression, and a C5.0 decision tree to construct a classification model of breast cancer patients' survival rates, and used a 10-fold cross-validation approach to identify the model. The results show that the establishment of classification tools for the classification of the models yielded an average accuracy rate of more than 90% for both; the SVM provided the best method for constructing the three categories of the classification system for the survival mode. The results of the experiment show that the three methods used to create the classification system, established a high accuracy rate, predicted a more accurate survival ability of women diagnosed with breast cancer, and could be used as a reference when creating a medical decision-making frame.
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Affiliation(s)
- Cheng-Min Chao
- Department of Business Administration, National Taichung University of Science and Technology, Taichung, Taiwan
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Bountris P, Haritou M, Pouliakis A, Margari N, Kyrgiou M, Spathis A, Pappas A, Panayiotides I, Paraskevaidis EA, Karakitsos P, Koutsouris DD. An intelligent clinical decision support system for patient-specific predictions to improve cervical intraepithelial neoplasia detection. BIOMED RESEARCH INTERNATIONAL 2014; 2014:341483. [PMID: 24812614 PMCID: PMC4000928 DOI: 10.1155/2014/341483] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 02/10/2014] [Accepted: 03/16/2014] [Indexed: 12/24/2022]
Abstract
Nowadays, there are molecular biology techniques providing information related to cervical cancer and its cause: the human Papillomavirus (HPV), including DNA microarrays identifying HPV subtypes, mRNA techniques such as nucleic acid based amplification or flow cytometry identifying E6/E7 oncogenes, and immunocytochemistry techniques such as overexpression of p16. Each one of these techniques has its own performance, limitations and advantages, thus a combinatorial approach via computational intelligence methods could exploit the benefits of each method and produce more accurate results. In this article we propose a clinical decision support system (CDSS), composed by artificial neural networks, intelligently combining the results of classic and ancillary techniques for diagnostic accuracy improvement. We evaluated this method on 740 cases with complete series of cytological assessment, molecular tests, and colposcopy examination. The CDSS demonstrated high sensitivity (89.4%), high specificity (97.1%), high positive predictive value (89.4%), and high negative predictive value (97.1%), for detecting cervical intraepithelial neoplasia grade 2 or worse (CIN2+). In comparison to the tests involved in this study and their combinations, the CDSS produced the most balanced results in terms of sensitivity, specificity, PPV, and NPV. The proposed system may reduce the referral rate for colposcopy and guide personalised management and therapeutic interventions.
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Affiliation(s)
- Panagiotis Bountris
- Biomedical Engineering Laboratory, School of Electrical and Computer Engineering, National Technical University of Athens, Iroon Politechniou 9, 15773 Zografou Campus, Athens, Greece
| | - Maria Haritou
- Institute of Communication and Computer Systems, National Technical University of Athens, Iroon Politechniou 9, 15773 Zografou Campus, Athens, Greece
| | - Abraham Pouliakis
- Department of Cytopathology, School of Medicine, University General Hospital “ATTIKON”, University of Athens, Rimini 1, 12462 Athens, Greece
| | - Niki Margari
- Department of Cytopathology, School of Medicine, University General Hospital “ATTIKON”, University of Athens, Rimini 1, 12462 Athens, Greece
| | - Maria Kyrgiou
- West London Gynaecological Cancer Center, Queen Charlotte's and Chelsea, Hammersmith Hospital, Imperial Healthcare NHS Trust, London W12 0HS, UK
- Division of Surgery and Cancer, Faculty of Medicine, Imperial College, London W12 0NN, UK
| | - Aris Spathis
- Department of Cytopathology, School of Medicine, University General Hospital “ATTIKON”, University of Athens, Rimini 1, 12462 Athens, Greece
| | - Asimakis Pappas
- 3rd Department of Obstetrics and Gynecology, University General Hospital “ATTIKON”, School of Medicine, University of Athens, Rimini 1, 12462 Athens, Greece
| | - Ioannis Panayiotides
- 2nd Department of Pathology, University General Hospital “ATTIKON”, School of Medicine, University of Athens, Rimini 1, 12462 Athens, Greece
| | - Evangelos A. Paraskevaidis
- Department of Obstetrics and Gynecology, University Hospital of Ioannina, St. Niarchou Str, 45500 Ioannina, Greece
| | - Petros Karakitsos
- Department of Cytopathology, School of Medicine, University General Hospital “ATTIKON”, University of Athens, Rimini 1, 12462 Athens, Greece
| | - Dimitrios-Dionyssios Koutsouris
- Biomedical Engineering Laboratory, School of Electrical and Computer Engineering, National Technical University of Athens, Iroon Politechniou 9, 15773 Zografou Campus, Athens, Greece
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Mani S, Chen Y, Li X, Arlinghaus L, Chakravarthy AB, Abramson V, Bhave SR, Levy MA, Xu H, Yankeelov TE. Machine learning for predicting the response of breast cancer to neoadjuvant chemotherapy. J Am Med Inform Assoc 2013; 20:688-95. [PMID: 23616206 DOI: 10.1136/amiajnl-2012-001332] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
OBJECTIVE To employ machine learning methods to predict the eventual therapeutic response of breast cancer patients after a single cycle of neoadjuvant chemotherapy (NAC). MATERIALS AND METHODS Quantitative dynamic contrast-enhanced MRI and diffusion-weighted MRI data were acquired on 28 patients before and after one cycle of NAC. A total of 118 semiquantitative and quantitative parameters were derived from these data and combined with 11 clinical variables. We used Bayesian logistic regression in combination with feature selection using a machine learning framework for predictive model building. RESULTS The best predictive models using feature selection obtained an area under the curve of 0.86 and an accuracy of 0.86, with a sensitivity of 0.88 and a specificity of 0.82. DISCUSSION With the numerous options for NAC available, development of a method to predict response early in the course of therapy is needed. Unfortunately, by the time most patients are found not to be responding, their disease may no longer be surgically resectable, and this situation could be avoided by the development of techniques to assess response earlier in the treatment regimen. The method outlined here is one possible solution to this important clinical problem. CONCLUSIONS Predictive modeling approaches based on machine learning using readily available clinical and quantitative MRI data show promise in distinguishing breast cancer responders from non-responders after the first cycle of NAC.
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Affiliation(s)
- Subramani Mani
- Division of Translational Informatics, Department of Medicine, University of New Mexico, Albuquerque, New Mexico 87131-0001, USA.
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Azimi M, Kamrani A, Smadi H. Statistics-Based Prediction Analysis for Head and Neck Cancer Tumor Deformation. JOURNAL OF HEALTHCARE ENGINEERING 2012. [DOI: 10.1260/2040-2295.3.4.571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Exarchos KP, Goletsis Y, Fotiadis DI. A multiscale and multiparametric approach for modeling the progression of oral cancer. BMC Med Inform Decis Mak 2012; 12:136. [PMID: 23173873 PMCID: PMC3560119 DOI: 10.1186/1472-6947-12-136] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 11/01/2012] [Indexed: 04/12/2023] Open
Abstract
Background In this work, we propose a multilevel and multiparametric approach in order to model the growth and progression of oral squamous cell carcinoma (OSCC) after remission. OSCC constitutes the major neoplasm of the head and neck region, exhibiting a quite aggressive nature, often leading to unfavorable prognosis. Methods We formulate a Decision Support System assembling a multitude of heterogeneous data sources (clinical, imaging tissue and blood genomic), aiming to capture all manifestations of the disease. Our primary aim is to identify the factors that dictate OSCC progression and subsequently predict potential relapses of the disease. The discrimination potential of each source of data is initially explored separately, and afterwards the individual predictions are combined to yield a consensus decision achieving complete discrimination between patients with and without a disease relapse. Moreover, we collect and analyze gene expression data from circulating blood cells throughout the follow-up period in consecutive time-slices, in order to model the temporal dimension of the disease. For this purpose a Dynamic Bayesian Network (DBN) is employed which is able to capture in a transparent manner the underlying mechanism dictating the disease evolvement, and employ it for monitoring the status and prognosis of the patients after remission. Results By feeding as input to the DBN data from the baseline visit we achieve accuracy of 86%, which is further improved to complete discrimination when data from the first follow-up visit are also employed. Conclusions Knowing in advance the progression of the disease, i.e. identifying groups of patients with higher/lower risk of reoccurrence, we are able to determine the subsequent treatment protocol in a more personalized manner.
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Affiliation(s)
- Konstantinos P Exarchos
- Unit of Medical Technology and Intelligent Information Systems, Department of Materials Science and Engineering, University of Ioannina, GR45110 Ioannina, Greece.
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Evaluation of bagging ensemble method with time-domain feature extraction for diagnosing of arrhythmia beats. Neural Comput Appl 2012. [DOI: 10.1007/s00521-012-1232-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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