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Transformers in medical image analysis

Intelligent Medicine 2023年第1期3卷 59-78页

作者： Kelei He Chen Gan Zhuoyuan Li Islem Rekik Zihao Yin Wen Ji Yang Gao Qian Wang Junfeng Zhang Dinggang Shen medical School of Nanjing University NanjingJiangsu 210093China National Institute of Healthcare Data Science at Nanjing University NanjingJiangsu 210093China BASIRA Laboratory Faculty of Computer and Informatics EngineeringIstanbul Technical UniversityIstanbulTurkey School of Science and Engineering ComputingUniversity of DundeeUK State Key Laboratory for Novel Software Technology Nanjing UniversityNanjingJiangsu 210093China School of Biomedical Engineering ShanghaiTech UniversityShanghai 201210China Department of Research and Development Shanghai United Imaging Intelligence Co.Ltd.Shanghai 200030China Shanghai Clinical Research and Trial Center Shanghai 201703China

Transformers have dominated the field of natural language processing and have recently made an impact in the area of computer vision.In the field of medical image analysis,transformers have also been successfully used in to full-stack clinical applications,including image synthesis/reconstruction,registration,segmentation,detection,and diagnosis.This paper aimed to promote awareness of the applications of transformers in medical image analysis.Specifically,we first provided an overview of the core concepts of the attention mechanism built into transformers and other basic components.Second,we reviewed various transformer architectures tailored for medical image applications and discuss their limitations.Within this review,we investigated key challenges including the use of transformers in different learning paradigms,improving model efficiency,and coupling with other techniques.We hope this review would provide a comprehensive picture of transformers to readers with an interest in medical image analysis.

关键词： Transformer medical image analysis Deep learning Diagnosis Registration Segmentation image synthesis Multi-task learning Multi-modal learning Weakly-supervised learning

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Enhanced Tunicate Swarm Optimization with Transfer Learning Enabled medical image analysis System

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Computer Systems Science & Engineering 2023年第12期47卷 3109-3126页

作者： Nojood O Aljehane Faculty of Computers and Information Technology University of TabukTabukSaudiArabia

medical image analysis is an active research topic,with thousands of studies published in the past few years.Transfer learning(TL)including convolutional neural networks(CNNs)focused to enhance efficiency on an innovative task using the knowledge of the same tasks learnt in advance.It has played a major role in medical image analysis since it solves the data scarcity issue along with that it saves hardware resources and time.This study develops an EnhancedTunicate SwarmOptimization withTransfer Learning Enabledmedical image analysis System(ETSOTL-MIAS).The goal of the ETSOTL-MIAS technique lies in the identification and classification of diseases through medical imaging.The ETSOTL-MIAS technique involves the Chan Vese segmentation technique to identify the affected regions in the medical image.For feature extraction purposes,the ETSOTL-MIAS technique designs a modified DarkNet-53 model.To avoid the manual hyperparameter adjustment process,the ETSOTLMIAS technique exploits the ETSO algorithm,showing the novelty of the work.Finally,the classification of medical images takes place by random forest(RF)classifier.The performance validation of the ETSOTL-MIAS technique is tested on a benchmark medical image database.The extensive experimental analysis showed the promising performance of the ETSOTL-MIAS technique under different measures.

关键词： medical image analysis transfer learning tunicate swarm optimization disease diagnosis healthcare

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ThyroidNet:A Deep Learning Network for Localization and Classification of Thyroid Nodules

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Computer Modeling in Engineering & Sciences 2024年第4期139卷 361-382页

作者： Lu Chen Huaqiang Chen Zhikai Pan Sheng Xu Guangsheng Lai Shuwen Chen Shuihua Wang Xiaodong Gu Yudong Zhang Ultrasonic Department Zhongda Hospital Affiliated to Southeast UniversityNanjing210009China School of Physics and Information Engineering Jiangsu Second Normal UniversityNanjing211200China School of Computing and Mathematical Sciences University of LeicesterLeicesterLE17RHUK Department of Information Systems Faculty of Computing and Information TechnologyKing Abdulaziz UniversityJeddah21589Saudi Arabia State Key Laboratory of MillimeterWaves Southeast UniversityNanjing210096China Jiangsu Province Engineering Research Center of Basic Education Big Data Application Jiangsu Second Normal UniversityNanjing211200China School of Software Engineering Quanzhou Normal UniversityQuanzhou362000China Department of Biological Sciences Xi’an Jiaotong-Liverpool UniversitySuzhou215123China

Aim:This study aims to establish an artificial intelligence model,ThyroidNet,to diagnose thyroid nodules using deep learning techniques accurately.Methods:A novel method,ThyroidNet,is introduced and evaluated based on deep learning for the localization and classification of thyroid nodules.First,we propose the multitask TransUnet,which combines the TransUnet encoder and decoder with multitask learning.Second,we propose the DualLoss function,tailored to the thyroid nodule localization and classification tasks.It balances the learning of the localization and classification tasks to help improve the model’s generalization ability.Third,we introduce strategies for augmenting the data.Finally,we submit a novel deep learning model,ThyroidNet,to accurately detect thyroid nodules.Results:ThyroidNet was evaluated on private datasets and was comparable to other existing methods,including U-Net and TransUnet.Experimental results show that ThyroidNet outperformed these methods in localizing and classifying thyroid nodules.It achieved improved accuracy of 3.9%and 1.5%,respectively.Conclusion:ThyroidNet significantly improves the clinical diagnosis of thyroid nodules and supports medical image analysis tasks.Future research directions include optimization of the model structure,expansion of the dataset size,reduction of computational complexity and memory requirements,and exploration of additional applications of ThyroidNet in medical image analysis.

关键词： ThyroidNet deep learning TransUnet multitask learning medical image analysis

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DeepSVDNet:A Deep Learning-Based Approach for Detecting and Classifying Vision-Threatening Diabetic Retinopathy in Retinal Fundus images

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Computer Systems Science & Engineering 2024年第2期48卷 511-528页

作者： Anas Bilal Azhar Imran Talha Imtiaz Baig Xiaowen Liu Haixia Long Abdulkareem Alzahrani Muhammad Shafiq College of Information Science and Technology Hainan Normal UniversityHaikou571158China Department of Creative Technologies Air UniversityIslamabadPakistan School of Life Science and Technology University of Electronic Science and Technology of China UESTCChengduChina School of Science and Technology University of Management and Technology UMTLahorePunjabPakistan Faculty of Computer Science&Information Technology Al Baha UniversityAl BahaSaudi Arabia School of Information Engineering Qujing Normal UniversityQujingChina

Artificial Intelligence(AI)is being increasingly used for diagnosing Vision-Threatening Diabetic Retinopathy(VTDR),which is a leading cause of visual impairment and blindness worldwide.However,previous automated VTDR detection methods have mainly relied on manual feature extraction and classification,leading to errors.This paper proposes a novel VTDR detection and classification model that combines different models through majority voting.Our proposed methodology involves preprocessing,data augmentation,feature extraction,and classification stages.We use a hybrid convolutional neural network-singular value decomposition(CNN-SVD)model for feature extraction and selection and an improved SVM-RBF with a Decision Tree(DT)and K-Nearest Neighbor(KNN)for classification.We tested our model on the IDRiD dataset and achieved an accuracy of 98.06%,a sensitivity of 83.67%,and a specificity of 100%for DR detection and evaluation tests,respectively.Our proposed approach outperforms baseline techniques and provides a more robust and accurate method for VTDR detection.

关键词： Diabetic retinopathy(DR) fundus images(FIs) support vector machine(SVM) medical image analysis convolutional neural networks(CNN) singular value decomposition(SVD) classification

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Enhancing Pneumonia Detection in Pediatric Chest X-Rays Using CGAN-Augmented Datasets and Lightweight Deep Transfer Learning Models

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Journal of Data analysis and Information Processing 2024年第1期12卷 1-23页

作者： Coulibaly Mohamed Ronald Waweru Mwangi John M. Kihoro Department of Mathematics Pan African University Institute for Basic Sciences Technology and Innovation (PAUSTI) Nairobi Kenya Department of Computing Jomo Kenyatta University of Agriculture and Technology Nairobi Kenya School of Computing and Mathematics The Cooperative University of Kenya Nairobi Kenya

Pneumonia ranks as a leading cause of mortality, particularly in children aged five and under. Detecting this disease typically requires radiologists to examine chest X-rays and report their findings to physicians, a task susceptible to human error. The application of Deep Transfer Learning (DTL) for the identification of pneumonia through chest X-rays is hindered by a shortage of available images, which has led to less than optimal DTL performance and issues with overfitting. Overfitting is characterized by a model’s learning that is too closely fitted to the training data, reducing its effectiveness on unseen data. The problem of overfitting is especially prevalent in medical image processing due to the high costs and extensive time required for image annotation, as well as the challenge of collecting substantial datasets that also respect patient privacy concerning infectious diseases such as pneumonia. To mitigate these challenges, this paper introduces the use of conditional generative adversarial networks (CGAN) to enrich the pneumonia dataset with 2690 synthesized X-ray images of the minority class, aiming to even out the dataset distribution for improved diagnostic performance. Subsequently, we applied four modified lightweight deep transfer learning models such as Xception, MobileNetV2, MobileNet, and EfficientNetB0. These models have been fine-tuned and evaluated, demonstrating remarkable detection accuracies of 99.26%, 98.23%, 97.06%, and 94.55%, respectively, across fifty epochs. The experimental results validate that the models we have proposed achieve high detection accuracy rates, with the best model reaching up to 99.26% effectiveness, outperforming other models in the diagnosis of pneumonia from X-ray images.

关键词： Pneumonia Detection Pediatric Radiology CGAN (Conditional Generative Adversarial Networks) Deep Transfer Learning medical image analysis

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A Review of Predictive and Contrastive Self-supervised Learning for medical images

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Machine Intelligence Research 2023年第4期20卷 483-513页

作者： Wei-Chien Wang Euijoon Ahn Dagan Feng Jinman Kim Biomedical and Multimedia Information Technology(BMIT)Research Group School of Computer ScienceThe University of SydneySydneyNSW2006Australia College of Science and Engineering James Cook UniversityCairnsQLD4811Australia

Over the last decade, supervised deep learning on manually annotated big data has been progressing significantly on computer vision tasks. But, the application of deep learning in medical image analysis is limited by the scarcity of high-quality annotated medical imaging data. An emerging solution is self-supervised learning (SSL), among which contrastive SSL is the most successful approach to rivalling or outperforming supervised learning. This review investigates several state-of-the-art contrastive SSL algorithms originally on natural images as well as their adaptations for medical images, and concludes by discussing recent advances, current limitations, and future directions in applying contrastive SSL in the medical domain.

关键词： Self-supervised learning(SSL) contrastive learning deep learning medical image analysis computer vision

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image Color Rendering Based on Hinge-Cross-Entropy GAN in Internet of medical Things

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Computer Modeling in Engineering & Sciences 2023年第4期135卷 779-794页

作者： Hong’an Li Min Zhang Dufeng Chen Jing Zhang Meng Yang Zhanli Li College of Computer Science and Technology Xi’an University of Science and TechnologyXi’an710054China Beijing Geotechnical and Investigation Engineering Insititute Beijing100080China Xi’an Institute of Applied Optics Xi’an710065China

Computer-aided diagnosis based on image color rendering promotes medical image analysis and doctor-patient communication by highlighting important information of medical diagnosis.To overcome the limitations of the color rendering method based on deep learning,such as poor model stability,poor rendering quality,fuzzy boundaries and crossed color boundaries,we propose a novel hinge-cross-entropy generative adversarial network(HCEGAN).The self-attention mechanism was added and improved to focus on the important information of the image.And the hinge-cross-entropy loss function was used to stabilize the training process of GAN models.In this study,we implement the HCEGAN model for image color rendering based on DIV2K and COCO datasets,and evaluate the results using SSIM and PSNR.The experimental results show that the proposed HCEGAN automatically re-renders images,significantly improves the quality of color rendering and greatly improves the stability of prior GAN models.

关键词： Internet of medical Things medical image analysis image color rendering loss function self-attention generative adversarial networks

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Recent advances in computerized imaging and its vital roles in liverdisease diagnosis, preoperative planning, and interventional liversurgery: A review

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World Journal of Gastrointestinal Surgery 2023年第11期15卷 2382-2397页

作者： Paramate Horkaew Jirapa Chansangrat Nattawut Keeratibharat Doan Cong Le School of Computer Engineering Suranaree University of TechnologyNakhon Ratchasima 30000Thailand School of Radiology Institute of MedicineSuranaree University of TechnologyNakhon Ratchasima 30000Thailand School of Surgery Institute of MedicineSuranaree University of TechnologyNakhon Ratchasima 30000Thailand Faculty of Information Technology An Giang UniversityVietnam National University(Ho Chi Minh City)An Giang 90000Vietnam

The earliest and most accurate detection of the pathological manifestations of hepatic diseases ensures effective treatments and thus positive prognostic outcomes.In clinical settings,screening and determining the extent of a pathology are prominent factors in preparing remedial agents and administering approp-riate therapeutic procedures.Moreover,in a patient undergoing liver resection,a realistic preoperative simulation of the subject-specific anatomy and physiology also plays a vital part in conducting initial assessments,making surgical decisions during the procedure,and anticipating postoperative results.Conventionally,various medical imaging modalities,e.g.,computed tomography,magnetic resonance imaging,and positron emission tomography,have been employed to assist in these tasks.In fact,several standardized procedures,such as lesion detection and liver segmentation,are also incorporated into prominent commercial software packages.Thus far,most integrated software as a medical device typically involves tedious interactions from the physician,such as manual delineation and empirical adjustments,as per a given patient.With the rapid progress in digital health approaches,especially medical image analysis,a wide range of computer algorithms have been proposed to facilitate those procedures.They include pattern recognition of a liver,its periphery,and lesion,as well as pre-and postoperative simulations.Prior to clinical adoption,however,software must conform to regulatory requirements set by the governing agency,for instance,valid clinical association and analytical and clinical validation.Therefore,this paper provides a detailed account and discussion of the state-of-the-art methods for liver image analyses,visualization,and simulation in the literature.Emphasis is placed upon their concepts,algorithmic classifications,merits,limitations,clinical considerations,and future research trends.

关键词： Computer aided diagnosis medical image analysis Pattern recognition Artificial intelligence Surgical simulation Liver surgery

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A Post-Processing Algorithm for Boosting Contrast of MRI images

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Computers, Materials & Continua 2022年第8期72卷 2749-2763页

作者： B.Priestly Shan O.Jeba Shiney Sharzeel Saleem V.Rajinikanth Atef Zaguia Dilbag Singh Department of Electronics&Communication Engineering Chandigarh UniversityMohali140413India Department of Electrical Electronics&Communication EngineeringGalgotias UniversityGreater Noida201310India Department of Electronics and Instrumentation Engineering St.Joseph’s College of EngineeringChennai600119Tamil NaduIndia Department of Computer Science College of Computers and Information TechnologyTaif UniversityTaif21944Saudi Arabia School of Electrical Engineering and Computer Science Gwangju Institute of Science and TechnologyGwangju61005Korea

Low contrast of Magnetic Resonance(MR)images limits the visibility of subtle structures and adversely affects the outcome of both subjective and automated diagnosis.State-of-the-art contrast boosting techniques intolerably alter inherent features of MR images.Drastic changes in brightness features,induced by post-processing are not appreciated in medical imaging as the grey level values have certain diagnostic meanings.To overcome these issues this paper proposes an algorithm that enhance the contrast of MR images while preserving the underlying features as well.This method termed as Power-law and Logarithmic Modification-based Histogram Equalization(PLMHE)partitions the histogram of the image into two sub histograms after a power-law transformation and a log compression.After a modification intended for improving the dispersion of the sub-histograms and subsequent normalization,cumulative histograms are computed.Enhanced grey level values are computed from the resultant cumulative histograms.The performance of the PLMHE algorithm is comparedwith traditional histogram equalization based algorithms and it has been observed from the results that PLMHE can boost the image contrast without causing dynamic range compression,a significant change in mean brightness,and contrast-overshoot.

关键词： Contrast enhancement histogram equalisation image quality magnetic resonance imaging medical image analysis post-processing

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Hybrid Active Contour Mammographic Mass Segmentation and Classification

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Computer Systems Science & Engineering 2022年第3期40卷 823-834页

作者： K.Yuvaraj U.S.Ragupathy Department of Electronics and Instrumentation Engineering Kongu Engineering College PerunduraiErode638060India

This research implements a novel segmentation of mammographic mass.Three methods are proposed,namely,segmentation of mass based on iterative active contour,automatic region growing,and fully automatic mask selectionbased active contour techniques.In the first method,iterative threshold is performed for manual cropped preprocessed image,and active contour is applied thereafter.To overcome manual cropping in the second method,an automatic seed selection followed by region growing is performed.Given that the result is only a few images owing to over segmentation,the third method uses a fully automatic active contour.Results of the segmentation techniques are compared with the manual markup by experts,specifically by taking the difference in their mean values.Accordingly,the difference in the mean value of the third method is 1.0853,which indicates the closeness of the segmentation.Moreover,the proposed method is compared with the existing fuzzy C means and level set methods.The automatic mass segmentation based on active contour technique results in segmentation with high accuracy.By using adaptive neuro fuzzy inference system,classification is done and results in a sensitivity of 94.73%,accuracy of 93.93%,and Mathew’s correlation coefficient(MCC)of 0.876.

关键词： Feature optimization hybrid active contour segmentation mass classification mass feature extraction medical image analysis

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