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Onakpojeruo EP, Mustapha MT, Ozsahin DU, Ozsahin I. Enhanced MRI-based brain tumour classification with a novel Pix2pix generative adversarial network augmentation framework. Brain Commun 2024; 6:fcae372. [PMID: 39494363 PMCID: PMC11528519 DOI: 10.1093/braincomms/fcae372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 09/02/2024] [Accepted: 10/21/2024] [Indexed: 11/05/2024] Open
Abstract
The scarcity of medical imaging datasets and privacy concerns pose significant challenges in artificial intelligence-based disease prediction. This poses major concerns to patient confidentiality as there are now tools capable of extracting patient information by merely analysing patient's imaging data. To address this, we propose the use of synthetic data generated by generative adversarial networks as a solution. Our study pioneers the utilisation of a novel Pix2Pix generative adversarial network model, specifically the 'image-to-image translation with conditional adversarial networks,' to generate synthetic datasets for brain tumour classification. We focus on classifying four tumour types: glioma, meningioma, pituitary and healthy. We introduce a novel conditional deep convolutional neural network architecture, developed from convolutional neural network architectures, to process the pre-processed generated synthetic datasets and the original datasets obtained from the Kaggle repository. Our evaluation metrics demonstrate the conditional deep convolutional neural network model's high performance with synthetic images, achieving an accuracy of 86%. Comparative analysis with state-of-the-art models such as Residual Network50, Visual Geometry Group 16, Visual Geometry Group 19 and InceptionV3 highlights the superior performance of our conditional deep convolutional neural network model in brain tumour detection, diagnosis and classification. Our findings underscore the efficacy of our novel Pix2Pix generative adversarial network augmentation technique in creating synthetic datasets for accurate brain tumour classification, offering a promising avenue for improved disease prediction and treatment planning.
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Affiliation(s)
- Efe Precious Onakpojeruo
- Operational Research Centre in Healthcare, Near East University, Nicosia 99138, Turkey
- Department of Biomedical Engineering, Near East University, Nicosia 99138, Turkey
| | - Mubarak Taiwo Mustapha
- Operational Research Centre in Healthcare, Near East University, Nicosia 99138, Turkey
- Department of Biomedical Engineering, Near East University, Nicosia 99138, Turkey
| | - Dilber Uzun Ozsahin
- Operational Research Centre in Healthcare, Near East University, Nicosia 99138, Turkey
- Department of Medical Diagnostic Imaging, College of Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Ilker Ozsahin
- Operational Research Centre in Healthcare, Near East University, Nicosia 99138, Turkey
- Department of Biomedical Engineering, Near East University, Nicosia 99138, Turkey
- Department of Radiology, Weill Cornell Medicine, Brain Health Imaging Institute, New York, NY 10065, USA
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Onakpojeruo EP, Mustapha MT, Ozsahin DU, Ozsahin I. A Comparative Analysis of the Novel Conditional Deep Convolutional Neural Network Model, Using Conditional Deep Convolutional Generative Adversarial Network-Generated Synthetic and Augmented Brain Tumor Datasets for Image Classification. Brain Sci 2024; 14:559. [PMID: 38928561 PMCID: PMC11201720 DOI: 10.3390/brainsci14060559] [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: 05/17/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
Disease prediction is greatly challenged by the scarcity of datasets and privacy concerns associated with real medical data. An approach that stands out to circumvent this hurdle is the use of synthetic data generated using Generative Adversarial Networks (GANs). GANs can increase data volume while generating synthetic datasets that have no direct link to personal information. This study pioneers the use of GANs to create synthetic datasets and datasets augmented using traditional augmentation techniques for our binary classification task. The primary aim of this research was to evaluate the performance of our novel Conditional Deep Convolutional Neural Network (C-DCNN) model in classifying brain tumors by leveraging these augmented and synthetic datasets. We utilized advanced GAN models, including Conditional Deep Convolutional Generative Adversarial Network (DCGAN), to produce synthetic data that retained essential characteristics of the original datasets while ensuring privacy protection. Our C-DCNN model was trained on both augmented and synthetic datasets, and its performance was benchmarked against state-of-the-art models such as ResNet50, VGG16, VGG19, and InceptionV3. The evaluation metrics demonstrated that our C-DCNN model achieved accuracy, precision, recall, and F1 scores of 99% on both synthetic and augmented images, outperforming the comparative models. The findings of this study highlight the potential of using GAN-generated synthetic data in enhancing the training of machine learning models for medical image classification, particularly in scenarios with limited data available. This approach not only improves model accuracy but also addresses privacy concerns, making it a viable solution for real-world clinical applications in disease prediction and diagnosis.
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Affiliation(s)
- Efe Precious Onakpojeruo
- Department of Medical Diagnostic Imaging, College of Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates;
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Mubarak Taiwo Mustapha
- Department of Medical Diagnostic Imaging, College of Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates;
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Dilber Uzun Ozsahin
- Department of Medical Diagnostic Imaging, College of Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates;
- Operational Research Centre in Healthcare, Near East University, TRNC Mersin 10, Nicosia 99138, Turkey; (E.P.O.)
- Department of Biomedical Engineering, Near East University, TRNC Mersin 10, Nicosia 99138, Turkey
| | - Ilker Ozsahin
- Department of Medical Diagnostic Imaging, College of Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates;
- Brain Health Imaging Institute, Department of Radiology, Weill Cornell Medicine, New York, NY 10065, USA
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Uzun Ozsahin D, Duwa BB, Ozsahin I, Uzun B. Quantitative Forecasting of Malaria Parasite Using Machine Learning Models: MLR, ANN, ANFIS and Random Forest. Diagnostics (Basel) 2024; 14:385. [PMID: 38396424 PMCID: PMC10888406 DOI: 10.3390/diagnostics14040385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 01/23/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Malaria continues to be a major barrier to socioeconomic development in Africa, where its death rate is over 90%. The predictive power of many machine learning models-such as multi-linear regression (MLR), artificial neural networks (ANN), adaptive neuro-fuzzy inference systems (ANFISs) and Random Forest classifier-is investigated in this study using data from 2207 patients. The dataset was reduced from the initial dataset of thirty-two criteria samples to fifteen. Assessment measures such as the root mean square error (RMSE), mean square error (MSE), coefficient of determination (R2), and adjusted correlation coefficient R were used. ANFIS, Random Forest, MLR, and ANN are among the models. After training, ANN outperforms ANFIS (97%), MLR (92%), and Random Forest (68%) with the greatest R (99%) and R2 (99%), respectively. The testing stage confirms the superiority of ANN. The paper also presents a statistical forecasting sheet with few errors and excellent accuracy for MLR models. When the models are assessed with Random Forest, the latter shows the least results, thus broadening the modeling techniques and offering significant insights into the prediction of malaria and healthcare decision making. The outcomes of using machine learning models for precise and efficient illness prediction add to an expanding body of knowledge, assisting healthcare systems in making better decisions and allocating resources more effectively.
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Affiliation(s)
- Dilber Uzun Ozsahin
- Department of Medical Diagnostic Imaging, College of Health Science, University of Sharjah, Sharjah 27272, United Arab Emirates
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- Operational Research Centre in Healthcare, Near East University, TRNC Mersin 10, Nicosia 99138, Turkey; (B.B.D.); (I.O.)
| | - Basil Barth Duwa
- Operational Research Centre in Healthcare, Near East University, TRNC Mersin 10, Nicosia 99138, Turkey; (B.B.D.); (I.O.)
| | - Ilker Ozsahin
- Operational Research Centre in Healthcare, Near East University, TRNC Mersin 10, Nicosia 99138, Turkey; (B.B.D.); (I.O.)
- Brain Health Imaging Institute, Department of Radiology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Berna Uzun
- Operational Research Centre in Healthcare, Near East University, TRNC Mersin 10, Nicosia 99138, Turkey; (B.B.D.); (I.O.)
- Department of Mathematics, Near East University, TRNC Mersin 10, Nicosia 99138, Turkey
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Ozsahin I, Onakpojeruo EP, Uzun B, Uzun Ozsahin D, Butler TA. A Multi-Criteria Decision Aid Tool for Radiopharmaceutical Selection in Tau PET Imaging. Pharmaceutics 2023; 15:1304. [PMID: 37111789 PMCID: PMC10147085 DOI: 10.3390/pharmaceutics15041304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/09/2023] [Accepted: 04/19/2023] [Indexed: 04/29/2023] Open
Abstract
The accumulation of pathologically misfolded tau is a feature shared by a group of neurodegenerative disorders collectively referred to as tauopathies. Alzheimer's disease (AD) is the most prevalent of these tauopathies. Immunohistochemical evaluation allows neuropathologists to visualize paired-helical filaments (PHFs)-tau pathological lesions, but this is possible only after death and only shows tau in the portion of brain sampled. Positron emission tomography (PET) imaging allows both the quantitative and qualitative analysis of pathology over the whole brain of a living subject. The ability to detect and quantify tau pathology in vivo using PET can aid in the early diagnosis of AD, provide a way to monitor disease progression, and determine the effectiveness of therapeutic interventions aimed at reducing tau pathology. Several tau-specific PET radiotracers are now available for research purposes, and one is approved for clinical use. This study aims to analyze, compare, and rank currently available tau PET radiotracers using the fuzzy preference ranking organization method for enrichment of evaluations (PROMETHEE), which is a multi-criteria decision-making (MCDM) tool. The evaluation is based on relatively weighted criteria, such as specificity, target binding affinity, brain uptake, brain penetration, and rates of adverse reactions. Based on the selected criteria and assigned weights, this study shows that a second-generation tau tracer, [18F]RO-948, may be the most favorable. This flexible method can be extended and updated to include new tracers, additional criteria, and modified weights to help researchers and clinicians select the optimal tau PET tracer for specific purposes. Additional work is needed to confirm these results, including a systematic approach to defining and weighting criteria and clinical validation of tracers in different diseases and patient populations.
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Affiliation(s)
- Ilker Ozsahin
- Brain Health Imaging Institute, Department of Radiology, Weill Cornell Medicine, New York, NY 10065, USA
- Operational Research Center in Healthcare, Near East University, Nicosia 99138, TRNC, Turkey
| | | | - Berna Uzun
- Operational Research Center in Healthcare, Near East University, Nicosia 99138, TRNC, Turkey
- Department of Statistics, Carlos III University of Madrid, Getafe, 28903 Madrid, Spain
| | - Dilber Uzun Ozsahin
- Operational Research Center in Healthcare, Near East University, Nicosia 99138, TRNC, Turkey
- Medical Diagnostic Imaging Department, College of Health Sciences & Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 26666, United Arab Emirates
| | - Tracy A. Butler
- Brain Health Imaging Institute, Department of Radiology, Weill Cornell Medicine, New York, NY 10065, USA
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Akshay A, Abedi M, Shekarchizadeh N, Burkhard FC, Katoch M, Bigger-Allen A, Adam RM, Monastyrskaya K, Gheinani AH. MLcps: machine learning cumulative performance score for classification problems. Gigascience 2022; 12:giad108. [PMID: 38091508 PMCID: PMC10716825 DOI: 10.1093/gigascience/giad108] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/02/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Assessing the performance of machine learning (ML) models requires careful consideration of the evaluation metrics used. It is often necessary to utilize multiple metrics to gain a comprehensive understanding of a trained model's performance, as each metric focuses on a specific aspect. However, comparing the scores of these individual metrics for each model to determine the best-performing model can be time-consuming and susceptible to subjective user preferences, potentially introducing bias. RESULTS We propose the Machine Learning Cumulative Performance Score (MLcps), a novel evaluation metric for classification problems. MLcps integrates several precomputed evaluation metrics into a unified score, enabling a comprehensive assessment of the trained model's strengths and weaknesses. We tested MLcps on 4 publicly available datasets, and the results demonstrate that MLcps provides a holistic evaluation of the model's robustness, ensuring a thorough understanding of its overall performance. CONCLUSIONS By utilizing MLcps, researchers and practitioners no longer need to individually examine and compare multiple metrics to identify the best-performing models. Instead, they can rely on a single MLcps value to assess the overall performance of their ML models. This streamlined evaluation process saves valuable time and effort, enhancing the efficiency of model evaluation. MLcps is available as a Python package at https://pypi.org/project/MLcps/.
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Affiliation(s)
- Akshay Akshay
- Functional Urology Research Group, Department for BioMedical Research DBMR, University of Bern, 3008 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Masoud Abedi
- Department of Medical Data Science, Leipzig University Medical Centre, 04107 Leipzig, Germany
| | - Navid Shekarchizadeh
- Department of Medical Data Science, Leipzig University Medical Centre, 04107 Leipzig, Germany
- Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI) Dresden/Leipzig, 04105 Leipzig, Germany
| | - Fiona C Burkhard
- Functional Urology Research Group, Department for BioMedical Research DBMR, University of Bern, 3008 Bern, Switzerland
- Department of Urology, Inselspital University Hospital, 3010 Bern, Switzerland
| | - Mitali Katoch
- Institute of Neuropathology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Alex Bigger-Allen
- Biological & Biomedical Sciences Program, Division of Medical Sciences, Harvard Medical School, 02115 Boston, MA, USA
- Urological Diseases Research Center, Boston Children's Hospital, 02115 Boston, MA, USA
- Department of Surgery, Harvard Medical School, 02115 Boston, MA, USA
- Broad Institute of MIT and Harvard, 02142 Cambridge, MA, USA
| | - Rosalyn M Adam
- Urological Diseases Research Center, Boston Children's Hospital, 02115 Boston, MA, USA
- Department of Surgery, Harvard Medical School, 02115 Boston, MA, USA
- Broad Institute of MIT and Harvard, 02142 Cambridge, MA, USA
| | - Katia Monastyrskaya
- Functional Urology Research Group, Department for BioMedical Research DBMR, University of Bern, 3008 Bern, Switzerland
- Department of Urology, Inselspital University Hospital, 3010 Bern, Switzerland
| | - Ali Hashemi Gheinani
- Functional Urology Research Group, Department for BioMedical Research DBMR, University of Bern, 3008 Bern, Switzerland
- Department of Urology, Inselspital University Hospital, 3010 Bern, Switzerland
- Urological Diseases Research Center, Boston Children's Hospital, 02115 Boston, MA, USA
- Department of Surgery, Harvard Medical School, 02115 Boston, MA, USA
- Broad Institute of MIT and Harvard, 02142 Cambridge, MA, USA
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