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Maqsood S, Damaševičius R, Maskeliūnas R, Forkert ND, Haider S, Latif S. Csec-net: a novel deep features fusion and entropy-controlled firefly feature selection framework for leukemia classification. Health Inf Sci Syst 2025; 13:9. [PMID: 39736875 PMCID: PMC11682032 DOI: 10.1007/s13755-024-00327-1] [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: 06/05/2024] [Accepted: 12/10/2024] [Indexed: 01/01/2025] Open
Abstract
Leukemia, a life-threatening form of cancer, poses a significant global health challenge affecting individuals of all age groups, including both children and adults. Currently, the diagnostic process relies on manual analysis of microscopic images of blood samples. In recent years, machine learning employing deep learning approaches has emerged as cutting-edge solutions for image classification problems. Thus, the aim of this work was to develop and evaluate deep learning methods to enable a computer-aided leukemia diagnosis. The proposed method is composed of multiple stages: Firstly, the given dataset images undergo preprocessing. Secondly, five pre-trained convolutional neural network models, namely MobileNetV2, EfficientNetB0, ConvNeXt-V2, EfficientNetV2, and DarkNet-19, are modified and transfer learning is used for training. Thirdly, deep feature vectors are extracted from each of the convolutional neural network and combined using a convolutional sparse image decomposition fusion strategy. Fourthly, the proposed approach employs an entropy-controlled firefly feature selection technique, which selects the most optimal features for subsequent classification. Finally, the selected features are fed into a multi-class support vector machine for the final classification. The proposed algorithm was applied to a total of 15562 images having four datasets, namely ALLID_B1, ALLID_B2, C_NMC 2019, and ASH and demonstrated superior accuracies of 99.64%, 98.96%, 96.67%, and 98.89%, respectively, surpassing the performance of previous works in the field.
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Affiliation(s)
- Sarmad Maqsood
- Centre of Real Time Computer Systems, Faculty of Informatics, Kaunas University of Technology, LT-51386 Kaunas, Lithuania
- Department of Radiology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1 Canada
| | - Robertas Damaševičius
- Centre of Real Time Computer Systems, Faculty of Informatics, Kaunas University of Technology, LT-51386 Kaunas, Lithuania
| | - Rytis Maskeliūnas
- Centre of Real Time Computer Systems, Faculty of Informatics, Kaunas University of Technology, LT-51386 Kaunas, Lithuania
| | - Nils D. Forkert
- Department of Radiology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1 Canada
| | - Shahab Haider
- Faculty of Computer Science and Engineering, GIK Institute of Engineering Sciences and Technology, Topi, 23640 Pakistan
| | - Shahid Latif
- Department of Electrical Engineering, Iqra National University, Peshawar, 25000 Pakistan
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2
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Zhang M, Zhang Y, Liu S, Han Y, Cao H, Qiao B. Dual-attention transformer-based hybrid network for multi-modal medical image segmentation. Sci Rep 2024; 14:25704. [PMID: 39465274 PMCID: PMC11514281 DOI: 10.1038/s41598-024-76234-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 10/11/2024] [Indexed: 10/29/2024] Open
Abstract
Accurate medical image segmentation plays a vital role in clinical practice. Convolutional Neural Network and Transformer are mainstream architectures for this task. However, convolutional neural network lacks the ability of modeling global dependency while Transformer cannot extract local details. In this paper, we propose DATTNet, Dual ATTention Network, an encoder-decoder deep learning model for medical image segmentation. DATTNet is exploited in hierarchical fashion with two novel components: (1) Dual Attention module is designed to model global dependency in spatial and channel dimensions. (2) Context Fusion Bridge is presented to remix the feature maps with multiple scales and construct their correlations. The experiments on ACDC, Synapse and Kvasir-SEG datasets are conducted to evaluate the performance of DATTNet. Our proposed model shows superior performance, effectiveness and robustness compared to SOTA methods, with mean Dice Similarity Coefficient scores of 92.2%, 84.5% and 89.1% on cardiac, abdominal organs and gastrointestinal poly segmentation tasks. The quantitative and qualitative results demonstrate that our proposed DATTNet attains favorable capability across different modalities (MRI, CT, and endoscopy) and can be generalized to various tasks. Therefore, it is envisaged as being potential for practicable clinical applications. The code has been released on https://github.com/MhZhang123/DATTNet/tree/main .
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Affiliation(s)
- Menghui Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450001, China
| | - Yuchen Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450001, China
| | - Shuaibing Liu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450001, China
| | - Yahui Han
- Department of Pediatric Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450001, China
| | - Honggang Cao
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450001, China
| | - Bingbing Qiao
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450001, China.
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3
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Mostafa RR, Khedr AM, Aghbari ZA, Afyouni I, Kamel I, Ahmed N. Medical image segmentation approach based on hybrid adaptive differential evolution and crayfish optimizer. Comput Biol Med 2024; 180:109011. [PMID: 39146840 DOI: 10.1016/j.compbiomed.2024.109011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 07/18/2024] [Accepted: 08/07/2024] [Indexed: 08/17/2024]
Abstract
Image segmentation plays a pivotal role in medical image analysis, particularly for accurately isolating tumors and lesions. Effective segmentation improves diagnostic precision and facilitates quantitative analysis, which is vital for medical professionals. However, traditional segmentation methods often struggle with multilevel thresholding due to the associated computational complexity. Therefore, determining the optimal threshold set is an NP-hard problem, highlighting the pressing need for efficient optimization strategies to overcome these challenges. This paper introduces a multi-threshold image segmentation (MTIS) method that integrates a hybrid approach combining Differential Evolution (DE) and the Crayfish Optimization Algorithm (COA), known as HADECO. Utilizing two-dimensional (2D) Kapur's entropy and a 2D histogram, this method aims to enhance the efficiency and accuracy of subsequent image analysis and diagnosis. HADECO is a hybrid algorithm that combines DE and COA by exchanging information based on predefined rules, leveraging the strengths of both for superior optimization results. It employs Latin Hypercube Sampling (LHS) to generate a high-quality initial population. HADECO introduces an improved DE algorithm (IDE) with adaptive and dynamic adjustments to key DE parameters and new mutation strategies to enhance its search capability. In addition, it incorporates an adaptive COA (ACOA) with dynamic adjustments to the switching probability parameter, effectively balancing exploration and exploitation. To evaluate the effectiveness of HADECO, its performance is initially assessed using CEC'22 benchmark functions. HADECO is evaluated against several contemporary algorithms using the Wilcoxon signed rank test (WSRT) and the Friedman test (FT) to integrate the results. The findings highlight HADECO's superior optimization abilities, demonstrated by its lowest average Friedman ranking of 1.08. Furthermore, the HADECO-based MTIS method is evaluated using MRI images for knee and CT scans for brain intracranial hemorrhage (ICH). Quantitative results in brain hemorrhage image segmentation show that the proposed method achieves a superior average peak signal-to-noise ratio (PSNR) and feature similarity index (FSIM) of 1.5 and 1.7 at the 6-level threshold. In knee image segmentation, it attains an average PSNR and FSIM of 1.3 and 1.2 at the 5-level threshold, demonstrating the method's effectiveness in solving image segmentation problems.
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Affiliation(s)
- Reham R Mostafa
- Big Data Mining and Multimedia Research Group, Centre for Data Analytics and Cybersecurity (CDAC), Research Institute of Sciences and Engineering (RISE), University of Sharjah, Sharjah 27272, United Arab Emirates; Information Systems Department, Faculty of Computers and Information Sciences, Mansoura University, Mansoura 35516, Egypt.
| | - Ahmed M Khedr
- Computer Science Department, University of Sharjah, Sharjah 27272, United Arab Emirates.
| | - Zaher Al Aghbari
- Computer Science Department, University of Sharjah, Sharjah 27272, United Arab Emirates.
| | - Imad Afyouni
- Computer Science Department, University of Sharjah, Sharjah 27272, United Arab Emirates.
| | - Ibrahim Kamel
- Electrical & Computer Engineering Department, University of Sharjah, Sharjah 27272, United Arab Emirates.
| | - Naveed Ahmed
- Computer Science Department, University of Sharjah, Sharjah 27272, United Arab Emirates.
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4
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Liu H, Zhuang Y, Song E, Liao Y, Ye G, Yang F, Xu X, Xiao X, Hung CC. A 3D boundary-guided hybrid network with convolutions and Transformers for lung tumor segmentation in CT images. Comput Biol Med 2024; 180:109009. [PMID: 39137673 DOI: 10.1016/j.compbiomed.2024.109009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 07/19/2024] [Accepted: 08/06/2024] [Indexed: 08/15/2024]
Abstract
-Accurate lung tumor segmentation from Computed Tomography (CT) scans is crucial for lung cancer diagnosis. Since the 2D methods lack the volumetric information of lung CT images, 3D convolution-based and Transformer-based methods have recently been applied in lung tumor segmentation tasks using CT imaging. However, most existing 3D methods cannot effectively collaborate the local patterns learned by convolutions with the global dependencies captured by Transformers, and widely ignore the important boundary information of lung tumors. To tackle these problems, we propose a 3D boundary-guided hybrid network using convolutions and Transformers for lung tumor segmentation, named BGHNet. In BGHNet, we first propose the Hybrid Local-Global Context Aggregation (HLGCA) module with parallel convolution and Transformer branches in the encoding phase. To aggregate local and global contexts in each branch of the HLGCA module, we not only design the Volumetric Cross-Stripe Window Transformer (VCSwin-Transformer) to build the Transformer branch with local inductive biases and large receptive fields, but also design the Volumetric Pyramid Convolution with transformer-based extensions (VPConvNeXt) to build the convolution branch with multi-scale global information. Then, we present a Boundary-Guided Feature Refinement (BGFR) module in the decoding phase, which explicitly leverages the boundary information to refine multi-stage decoding features for better performance. Extensive experiments were conducted on two lung tumor segmentation datasets, including a private dataset (HUST-Lung) and a public benchmark dataset (MSD-Lung). Results show that BGHNet outperforms other state-of-the-art 2D or 3D methods in our experiments, and it exhibits superior generalization performance in both non-contrast and contrast-enhanced CT scans.
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Affiliation(s)
- Hong Liu
- Center for Biomedical Imaging and Bioinformatics, School of Computer Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | - Yuzhou Zhuang
- Center for Biomedical Imaging and Bioinformatics, School of Computer Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | - Enmin Song
- Center for Biomedical Imaging and Bioinformatics, School of Computer Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | - Yongde Liao
- Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | - Guanchao Ye
- Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | - Fan Yang
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | - Xiangyang Xu
- Center for Biomedical Imaging and Bioinformatics, School of Computer Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | - Xvhao Xiao
- Research Institute of High-Tech, Xi'an, 710025, Shaanxi, China.
| | - Chih-Cheng Hung
- Center for Machine Vision and Security Research, Kennesaw State University, Marietta, MA, 30060, USA.
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5
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Emam MM, Houssein EH, Samee NA, Alkhalifa AK, Hosney ME. Optimizing cancer diagnosis: A hybrid approach of genetic operators and Sinh Cosh Optimizer for tumor identification and feature gene selection. Comput Biol Med 2024; 180:108984. [PMID: 39128177 DOI: 10.1016/j.compbiomed.2024.108984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 06/30/2024] [Accepted: 08/02/2024] [Indexed: 08/13/2024]
Abstract
The identification of tumors through gene analysis in microarray data is a pivotal area of research in artificial intelligence and bioinformatics. This task is challenging due to the large number of genes relative to the limited number of observations, making feature selection a critical step. This paper introduces a novel wrapper feature selection method that leverages a hybrid optimization algorithm combining a genetic operator with a Sinh Cosh Optimizer (SCHO), termed SCHO-GO. The SCHO-GO algorithm is designed to avoid local optima, streamline the search process, and select the most relevant features without compromising classifier performance. Traditional methods often falter with extensive search spaces, necessitating hybrid approaches. Our method aims to reduce the dimensionality and improve the classification accuracy, which is essential in pattern recognition and data analysis. The SCHO-GO algorithm, integrated with a support vector machine (SVM) classifier, significantly enhances cancer classification accuracy. We evaluated the performance of SCHO-GO using the CEC'2022 benchmark function and compared it with seven well-known metaheuristic algorithms. Statistical analyses indicate that SCHO-GO consistently outperforms these algorithms. Experimental tests on eight microarray gene expression datasets, particularly the Gene Expression Cancer RNA-Seq dataset, demonstrate an impressive accuracy of 99.01% with the SCHO-GO-SVM model, highlighting its robustness and precision in handling complex datasets. Furthermore, the SCHO-GO algorithm excels in feature selection and solving mathematical benchmark problems, presenting a promising approach for tumor identification and classification in microarray data analysis.
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Affiliation(s)
- Marwa M Emam
- Faculty of Computers and Information, Minia University, Minia, Egypt.
| | - Essam H Houssein
- Faculty of Computers and Information, Minia University, Minia, Egypt.
| | - Nagwan Abdel Samee
- Department of Information Technology, College of Computer and Information Sciences, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia.
| | - Amal K Alkhalifa
- Department of Computer Science and Information Technology, Applied College, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia.
| | - Mosa E Hosney
- Faculty of Computers and Information, Luxor University, Luxor, Egypt.
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6
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Yuan W, Cheng J, Gong Y, He L, Zhang J. MACG-Net: Multi-axis cross gating network for deformable medical image registration. Comput Biol Med 2024; 178:108673. [PMID: 38905891 DOI: 10.1016/j.compbiomed.2024.108673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 04/18/2024] [Accepted: 05/26/2024] [Indexed: 06/23/2024]
Abstract
Deformable Image registration is a fundamental yet vital task for preoperative planning, intraoperative information fusion, disease diagnosis and follow-ups. It solves the non-rigid deformation field to align an image pair. Latest approaches such as VoxelMorph and TransMorph compute features from a simple concatenation of moving and fixed images. However, this often leads to weak alignment. Moreover, the convolutional neural network (CNN) or the hybrid CNN-Transformer based backbones are constrained to have limited sizes of receptive field and cannot capture long range relations while full Transformer based approaches are computational expensive. In this paper, we propose a novel multi-axis cross grating network (MACG-Net) for deformable medical image registration, which combats these limitations. MACG-Net uses a dual stream multi-axis feature fusion module to capture both long-range and local context relationships from the moving and fixed images. Cross gate blocks are integrated with the dual stream backbone to consider both independent feature extractions in the moving-fixed image pair and the relationship between features from the image pair. We benchmark our method on several different datasets including 3D atlas-based brain MRI, inter-patient brain MRI and 2D cardiac MRI. The results demonstrate that the proposed method has achieved state-of-the-art performance. The source code has been released at https://github.com/Valeyards/MACG.
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Affiliation(s)
- Wei Yuan
- College of Biomedical Engineering, Sichuan University, Chengdu 610065, China
| | - Jun Cheng
- Institute for Infocomm Research, Agency for Science, Technology and Research, 138632, Singapore
| | - Yuhang Gong
- College of Biomedical Engineering, Sichuan University, Chengdu 610065, China
| | - Ling He
- College of Biomedical Engineering, Sichuan University, Chengdu 610065, China.
| | - Jing Zhang
- College of Biomedical Engineering, Sichuan University, Chengdu 610065, China
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7
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Fan Y, Hong Y, Bao H, Huang Y, Zhang P, Zhu D, Jiang Q, Zuo Y, Swain M, Elsheikh A, Chen S, Zheng X. Biomechanical and histological changes associated with riboflavin ultraviolet-A-induced CXL with different irradiances in young human corneal stroma. Comput Biol Med 2024; 178:108607. [PMID: 38897147 DOI: 10.1016/j.compbiomed.2024.108607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 05/08/2024] [Accepted: 05/11/2024] [Indexed: 06/21/2024]
Abstract
Keratoconus (KC) is a degenerative condition affecting the cornea, characterized by progressive thinning and bulging, which can ultimately result in serious visual impairment. The onset and progression of KC are closely tied to the gradual weakening of the cornea's biomechanical properties. KC progression can be prevented with corneal cross-linking (CXL), but this treatment has shortcomings, and evaluating its tissue stiffening effect is important for determining its efficacy. In this field, the shortage of human corneas has made it necessary for most previous studies to rely on animal corneas, which have different microstructure and may be affected differently from human corneas. In this research, we have used the lenticules obtained through small incision lenticule extraction (SMILE) surgeries as a source of human tissue to assess CXL. And to further improve the results' reliability, we used inflation testing, personalized finite element modeling, numerical optimization and histology microstructure analysis. These methods enabled determining the biomechanical and histological effects of CXL protocols involving different irradiation intensities of 3, 9, 18, and 30 mW/cm2, all delivering the same total energy dose of 5.4 J/cm2. The results showed that the CXL effect did not vary significantly with protocols using 3-18 mW/cm2 irradiance, but there was a significant efficacy drop with 30 mW/cm2 irradiance. This study validated the updated algorithm and provided guidance for corneal lenticule reuse and the effects of different CXL protocols on the biomechanical properties of the human corneal stroma.
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Affiliation(s)
- YiWen Fan
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - YuXin Hong
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Han Bao
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - YunYun Huang
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Pei Zhang
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; Key Laboratory of Coastal Environment and Resources Research of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, 310000, China
| | - DeXi Zhu
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - QiuRuo Jiang
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Yi Zuo
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Michael Swain
- AMME, Biomechanics Engineering, The University of Sydney, Sydney, Australia
| | - Ahmed Elsheikh
- School of Engineering, University of Liverpool, Liverpool, L69 3GH, UK
| | - ShiHao Chen
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China.
| | - XiaoBo Zheng
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China.
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8
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Wu Z, Su R, Dai Y, Wu X, Wu H, Wang X, Wang Z, Bao J, Chen J, Xia E. Deep pan-cancer analysis and multi-omics evidence reveal that ALG3 inhibits CD8 + T cell infiltration by suppressing chemokine secretion and is associated with 5-fluorouracil sensitivity. Comput Biol Med 2024; 177:108666. [PMID: 38820773 DOI: 10.1016/j.compbiomed.2024.108666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/23/2024] [Accepted: 05/26/2024] [Indexed: 06/02/2024]
Abstract
BACKGROUND α-1,3-mannosyltransferase (ALG3) holds significance as a key member within the mannosyltransferase family. Nevertheless, the exact function of ALG3 in cancer remains ambiguous. Consequently, the current research aimed to examine the function and potential mechanisms of ALG3 in various types of cancer. METHODS Deep pan-cancer analyses were conducted to investigate the expression patterns, prognostic value, genetic variations, single-cell omics, immunology, and drug responses associated with ALG3. Subsequently, in vitro experiments were executed to ascertain the biological role of ALG3 in breast cancer. Moreover, the link between ALG3 and CD8+ T cells was verified using immunofluorescence. Lastly, the association between ALG3 and chemokines was assessed using qRT-PCR and ELISA. RESULTS Deep pan-cancer analysis demonstrated a heightened expression of ALG3 in the majority of tumors based on multi-omics evidence. ALG3 emerges as a diagnostic and prognostic biomarker across diverse cancer types. In addition, ALG3 participates in regulating the tumor immune microenvironment. Elevated levels of ALG3 were closely linked to the infiltration of bone marrow-derived suppressor cells (MDSC) and CD8+ T cells. According to in vitro experiments, ALG3 promotes proliferation and migration of breast cancer cells. Moreover, ALG3 inhibited CD8+ T cell infiltration by suppressing chemokine secretion. Finally, the inhibition of ALG3 enhanced the responsiveness of breast cancer cells to 5-fluorouracil treatment. CONCLUSION ALG3 shows potential as both a prognostic indicator and immune infiltration biomarker across various types of cancer. Inhibition of ALG3 may represent a promising therapeutic strategy for tumor treatment.
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Affiliation(s)
- Zhixuan Wu
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China; Department of Thyroid and Breast Surgery, The Third Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325200, China
| | - Rusi Su
- Department of Thyroid and Breast Surgery, The Third Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325200, China
| | - Yinwei Dai
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Xue Wu
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Haodong Wu
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Xiaowu Wang
- Department of Burns and Skin Repair Surgery, The Third Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325200, China
| | - Ziqiong Wang
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Jingxia Bao
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Jiong Chen
- Department of Burns and Skin Repair Surgery, The Third Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325200, China
| | - Erjie Xia
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China.
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9
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Heman-Ackah SM, Blue R, Quimby AE, Abdallah H, Sweeney EM, Chauhan D, Hwa T, Brant J, Ruckenstein MJ, Bigelow DC, Jackson C, Zenonos G, Gardner P, Briggs SE, Cohen Y, Lee JYK. A multi-institutional machine learning algorithm for prognosticating facial nerve injury following microsurgical resection of vestibular schwannoma. Sci Rep 2024; 14:12963. [PMID: 38839778 PMCID: PMC11153496 DOI: 10.1038/s41598-024-63161-1] [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: 11/18/2023] [Accepted: 05/26/2024] [Indexed: 06/07/2024] Open
Abstract
Vestibular schwannomas (VS) are the most common tumor of the skull base with available treatment options that carry a risk of iatrogenic injury to the facial nerve, which can significantly impact patients' quality of life. As facial nerve outcomes remain challenging to prognosticate, we endeavored to utilize machine learning to decipher predictive factors relevant to facial nerve outcomes following microsurgical resection of VS. A database of patient-, tumor- and surgery-specific features was constructed via retrospective chart review of 242 consecutive patients who underwent microsurgical resection of VS over a 7-year study period. This database was then used to train non-linear supervised machine learning classifiers to predict facial nerve preservation, defined as House-Brackmann (HB) I vs. facial nerve injury, defined as HB II-VI, as determined at 6-month outpatient follow-up. A random forest algorithm demonstrated 90.5% accuracy, 90% sensitivity and 90% specificity in facial nerve injury prognostication. A random variable (rv) was generated by randomly sampling a Gaussian distribution and used as a benchmark to compare the predictiveness of other features. This analysis revealed age, body mass index (BMI), case length and the tumor dimension representing tumor growth towards the brainstem as prognosticators of facial nerve injury. When validated via prospective assessment of facial nerve injury risk, this model demonstrated 84% accuracy. Here, we describe the development of a machine learning algorithm to predict the likelihood of facial nerve injury following microsurgical resection of VS. In addition to serving as a clinically applicable tool, this highlights the potential of machine learning to reveal non-linear relationships between variables which may have clinical value in prognostication of outcomes for high-risk surgical procedures.
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Affiliation(s)
- Sabrina M Heman-Ackah
- Department of Neurosurgery, Perelman Center for Advanced Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, 15th Floor, Philadelphia, PA, 19104, USA.
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA.
| | - Rachel Blue
- Department of Neurosurgery, Perelman Center for Advanced Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, 15th Floor, Philadelphia, PA, 19104, USA
| | - Alexandra E Quimby
- Department of Otorhinolaryngology, University of Pennsylvania, Philadelphia, PA, USA
- Department of Otolaryngology and Communication Sciences, SUNY Upstate Medical University Hospital, Syracuse, NY, USA
| | - Hussein Abdallah
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Elizabeth M Sweeney
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Daksh Chauhan
- University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Tiffany Hwa
- Department of Otorhinolaryngology, University of Pennsylvania, Philadelphia, PA, USA
| | - Jason Brant
- Department of Otorhinolaryngology, University of Pennsylvania, Philadelphia, PA, USA
- Corporal Michael J. Crescenz VAMC, Philadelphia, PA, USA
| | - Michael J Ruckenstein
- Department of Otorhinolaryngology, University of Pennsylvania, Philadelphia, PA, USA
| | - Douglas C Bigelow
- Department of Otorhinolaryngology, University of Pennsylvania, Philadelphia, PA, USA
| | - Christina Jackson
- Department of Neurosurgery, Perelman Center for Advanced Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, 15th Floor, Philadelphia, PA, 19104, USA
| | - Georgios Zenonos
- Center for Cranial Base Surgery, University of Pittsburgh, Pittsburgh, PA, USA
| | - Paul Gardner
- Center for Cranial Base Surgery, University of Pittsburgh, Pittsburgh, PA, USA
| | - Selena E Briggs
- Department of Otolaryngology, MedStar Washington Hospital Center, Washington, DC, USA
- Department of Otolaryngology, Georgetown University, Washington, DC, USA
| | - Yale Cohen
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
- Department of Otorhinolaryngology, University of Pennsylvania, Philadelphia, PA, USA
- University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - John Y K Lee
- Department of Neurosurgery, Perelman Center for Advanced Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, 15th Floor, Philadelphia, PA, 19104, USA
- Department of Otorhinolaryngology, University of Pennsylvania, Philadelphia, PA, USA
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10
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Chen YR, Chen CC, Kuo CF, Lin CH. An efficient deep neural network for automatic classification of acute intracranial hemorrhages in brain CT scans. Comput Biol Med 2024; 176:108587. [PMID: 38735238 DOI: 10.1016/j.compbiomed.2024.108587] [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: 11/20/2023] [Revised: 05/08/2024] [Accepted: 05/08/2024] [Indexed: 05/14/2024]
Abstract
BACKGROUND Recent advancements in deep learning models have demonstrated their potential in the field of medical imaging, achieving remarkable performance surpassing human capabilities in tasks such as classification and segmentation. However, these modern state-of-the-art network architectures often demand substantial computational resources, which limits their practical application in resource-constrained settings. This study aims to propose an efficient diagnostic deep learning model specifically designed for the classification of intracranial hemorrhage in brain CT scans. METHOD Our proposed model utilizes a combination of depthwise separable convolutions and a multi-receptive field mechanism to achieve a trade-off between performance and computational efficiency. The model was trained on RSNA datasets and validated on CQ500 dataset and PhysioNet dataset. RESULT Through a comprehensive comparison with state-of-the-art models, our model achieves an average AUROC score of 0.952 on RSNA datasets and exhibits robust generalization capabilities, comparable to SE-ResNeXt, across other open datasets. Furthermore, the parameter count of our model is just 3 % of that of MobileNet V3. CONCLUSION This study presents a diagnostic deep-learning model that is optimized for classifying intracranial hemorrhages in brain CT scans. The efficient characteristics make our proposed model highly promising for broader applications in medical settings.
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Affiliation(s)
- Yu-Ruei Chen
- School of Medicine, Chang Gung University, Taoyuan, Taiwan; Medical Education Department, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Chih-Chieh Chen
- Center for Artificial Intelligence in Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Chang-Fu Kuo
- Medical Education Department, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Center for Artificial Intelligence in Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Division of Rheumatology, Allergy and Immunology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Ching-Heng Lin
- Center for Artificial Intelligence in Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Bachelor Program in Artificial Intelligence, Chang Gung University, Taoyuan, Taiwan.
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11
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Chen C, Chen Y, Li X, Ning H, Xiao R. Linear semantic transformation for semi-supervised medical image segmentation. Comput Biol Med 2024; 173:108331. [PMID: 38522252 DOI: 10.1016/j.compbiomed.2024.108331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/29/2024] [Accepted: 03/17/2024] [Indexed: 03/26/2024]
Abstract
Medical image segmentation is a focus research and foundation in developing intelligent medical systems. Recently, deep learning for medical image segmentation has become a standard process and succeeded significantly, promoting the development of reconstruction, and surgical planning of disease diagnosis. However, semantic learning is often inefficient owing to the lack of supervision of feature maps, resulting in that high-quality segmentation models always rely on numerous and accurate data annotations. Learning robust semantic representation in latent spaces remains a challenge. In this paper, we propose a novel semi-supervised learning framework to learn vital attributes in medical images, which constructs generalized representation from diverse semantics to realize medical image segmentation. We first build a self-supervised learning part that achieves context recovery by reconstructing space and intensity of medical images, which conduct semantic representation for feature maps. Subsequently, we combine semantic-rich feature maps and utilize simple linear semantic transformation to convert them into image segmentation. The proposed framework was tested using five medical segmentation datasets. Quantitative assessments indicate the highest scores of our method on IXI (73.78%), ScaF (47.50%), COVID-19-Seg (50.72%), PC-Seg (65.06%), and Brain-MR (72.63%) datasets. Finally, we compared our method with the latest semi-supervised learning methods and obtained 77.15% and 75.22% DSC values, respectively, ranking first on two representative datasets. The experimental results not only proved that the proposed linear semantic transformation was effectively applied to medical image segmentation, but also presented its simplicity and ease-of-use to pursue robust segmentation in semi-supervised learning. Our code is now open at: https://github.com/QingYunA/Linear-Semantic-Transformation-for-Semi-Supervised-Medical-Image-Segmentation.
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Affiliation(s)
- Cheng Chen
- School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Yunqing Chen
- School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Xiaoheng Li
- School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Huansheng Ning
- School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Ruoxiu Xiao
- School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing, 100083, China; Shunde Innovation School, University of Science and Technology Beijing, Foshan, 100024, China.
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12
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Xing X, Li X, Wei C, Zhang Z, Liu O, Xie S, Chen H, Quan S, Wang C, Yang X, Jiang X, Shuai J. DP-GAN+B: A lightweight generative adversarial network based on depthwise separable convolutions for generating CT volumes. Comput Biol Med 2024; 174:108393. [PMID: 38582001 DOI: 10.1016/j.compbiomed.2024.108393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/17/2024] [Accepted: 04/01/2024] [Indexed: 04/08/2024]
Abstract
X-rays, commonly used in clinical settings, offer advantages such as low radiation and cost-efficiency. However, their limitation lies in the inability to distinctly visualize overlapping organs. In contrast, Computed Tomography (CT) scans provide a three-dimensional view, overcoming this drawback but at the expense of higher radiation doses and increased costs. Hence, from both the patient's and hospital's standpoints, there is substantial medical and practical value in attempting the reconstruction from two-dimensional X-ray images to three-dimensional CT images. In this paper, we introduce DP-GAN+B as a pioneering approach for transforming two-dimensional frontal and lateral lung X-rays into three-dimensional lung CT volumes. Our method innovatively employs depthwise separable convolutions instead of traditional convolutions and introduces vector and fusion loss for superior performance. Compared to prior models, DP-GAN+B significantly reduces the generator network parameters by 21.104 M and the discriminator network parameters by 10.82 M, resulting in a total reduction of 31.924 M (44.17%). Experimental results demonstrate that our network can effectively generate clinically relevant, high-quality CT images from X-ray data, presenting a promising solution for enhancing diagnostic imaging while mitigating cost and radiation concerns.
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Affiliation(s)
- Xinlong Xing
- Postgraduate Training Base Alliance of Wenzhou Medical University, Wenzhou, Zhejiang, 325000, China; Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Xiaosen Li
- School of Artificial Intelligence, Guangxi Minzu University, Nanning, 530006, China
| | - Chaoyi Wei
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Zhantian Zhang
- Postgraduate Training Base Alliance of Wenzhou Medical University, Wenzhou, Zhejiang, 325000, China; Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Ou Liu
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China.
| | - Senmiao Xie
- Department of Radiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Haoman Chen
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Shichao Quan
- Department of Big Data in Health Science, The First Affiliated Hospital of Wenzhou Medical University, China
| | - Cong Wang
- Department of Mathematics and Statistics, Carleton College, 300 N College St, Northfield, MN, 55057, USA
| | - Xin Yang
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan, 114051, China
| | - Xiaoming Jiang
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Jianwei Shuai
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China.
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13
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Wang D, Yan Y. Improving inceptionV4 model based on fractional-order snow leopard optimization algorithm for diagnosing of ACL tears. Sci Rep 2024; 14:9843. [PMID: 38684782 PMCID: PMC11059154 DOI: 10.1038/s41598-024-60419-6] [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: 12/07/2023] [Accepted: 04/23/2024] [Indexed: 05/02/2024] Open
Abstract
In the current research study, a new method is presented to diagnose Anterior Cruciate Ligament (ACL) tears by introducing an optimized version of the InceptionV4 model. Our proposed methodology utilizes a custom-made variant of the Snow Leopard Optimization Algorithm, known as the Fractional-order Snow Leopard Optimization Algorithm (FO-LOA), to extract essential features from knee magnetic resonance imaging (MRI) images. This results in a substantial improvement in the accuracy of ACL tear detection. By effectively extracting critical features from knee MRI images, our proposed methodology significantly enhances diagnostic accuracy, potentially reducing false negatives and false positives. The enhanced model based on FO-LOA underwent thorough testing using the MRNet dataset, demonstrating exceptional performance metrics including an accuracy rate of 98.00%, sensitivity of 98.00%, precision of 97.00%, specificity of 98.00%, F1-score of 98.00%, and Matthews Correlation Coefficient (MCC) of 88.00%. These findings surpass current methodologies like Convolutional Neural Network (CNN), Inception-v3, Deep Belief Networks and Improved Honey Badger Algorithm (DBN/IHBA), integration of the CNN with an Amended Cooking Training-based Optimizer version (CNN/ACTO), Self-Supervised Representation Learning (SSRL), signifying a significant breakthrough in ACL injury diagnosis. Using FO-SLO to optimize the InceptionV4 framework shows promise in improving the accuracy of ACL tear identification, enabling prompt and efficient treatment interventions.
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Affiliation(s)
- Delei Wang
- Zhejiang Pharmaceutical University, Ningbo, 315500, Zhejiang, China
| | - Yanqing Yan
- Guangdong University of Science and Technology, Dongguan, 523000, Guangdong, China.
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14
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Sun Y, Wang C. Brain tumor detection based on a novel and high-quality prediction of the tumor pixel distributions. Comput Biol Med 2024; 172:108196. [PMID: 38493601 DOI: 10.1016/j.compbiomed.2024.108196] [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: 08/27/2023] [Revised: 01/31/2024] [Accepted: 02/18/2024] [Indexed: 03/19/2024]
Abstract
The work presented in this paper is in the area of brain tumor detection. We propose a fast detection system with 3D MRI scans of Flair modality. It performs 2 functions, predicting the gray level distribution and location distribution of the pixels in the tumor regions and generating tumor masks with pixel-wise precision. To facilitate 3D data analysis and processing, we introduce a 2D histogram presentation encompassing the gray-level distribution and pixel-location distribution of a 3D object. In the proposed system, specific 2D histograms highlighting tumor-related features are established by exploiting the left-right asymmetry of a brain structure. A modulation function, generated from the input data of each patient case, is applied to the 2D histograms to transform them into coarsely or finely predicted distributions of tumor pixels. The prediction result helps to identify/remove tumor-free slices. The prediction and removal operations are performed to the axial, coronal and sagittal slice series of a brain image, transforming it into a 3D minimum bounding box of its tumor region. The bounding box is utilized to finalize the prediction and generate a 3D tumor mask. The proposed system has been tested extensively with the data of more than 1200 patient cases in BraTS2018∼2021 datasets. The test results demonstrate that the predicted 2D histograms resemble closely the true ones. The system delivers also very good tumor detection results, comparable to those of state-of-the-art CNN systems with mono-modality inputs. They are reproducible and obtained at an extremely low computation cost and without need for training.
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Affiliation(s)
- Yanming Sun
- Department of Electrical and Computer Engineering, Concordia University, 1455 De Maisonneuve Blvd. W, Montreal, Quebec, Canada, H3G 1M8
| | - Chunyan Wang
- Department of Electrical and Computer Engineering, Concordia University, 1455 De Maisonneuve Blvd. W, Montreal, Quebec, Canada, H3G 1M8.
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15
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Yin Y, Tang Z, Weng H. Application of visual transformer in renal image analysis. Biomed Eng Online 2024; 23:27. [PMID: 38439100 PMCID: PMC10913284 DOI: 10.1186/s12938-024-01209-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 01/22/2024] [Indexed: 03/06/2024] Open
Abstract
Deep Self-Attention Network (Transformer) is an encoder-decoder architectural model that excels in establishing long-distance dependencies and is first applied in natural language processing. Due to its complementary nature with the inductive bias of convolutional neural network (CNN), Transformer has been gradually applied to medical image processing, including kidney image processing. It has become a hot research topic in recent years. To further explore new ideas and directions in the field of renal image processing, this paper outlines the characteristics of the Transformer network model and summarizes the application of the Transformer-based model in renal image segmentation, classification, detection, electronic medical records, and decision-making systems, and compared with CNN-based renal image processing algorithm, analyzing the advantages and disadvantages of this technique in renal image processing. In addition, this paper gives an outlook on the development trend of Transformer in renal image processing, which provides a valuable reference for a lot of renal image analysis.
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Affiliation(s)
- Yuwei Yin
- The College of Health Sciences and Engineering, University of Shanghai for Science and Technology, 516 Jungong Highway, Yangpu Area, Shanghai, 200093, China
- The College of Medical Technology, Shanghai University of Medicine & Health Sciences, 279 Zhouzhu Highway, Pudong New Area, Shanghai, 201318, China
| | - Zhixian Tang
- The College of Medical Technology, Shanghai University of Medicine & Health Sciences, 279 Zhouzhu Highway, Pudong New Area, Shanghai, 201318, China.
| | - Huachun Weng
- The College of Health Sciences and Engineering, University of Shanghai for Science and Technology, 516 Jungong Highway, Yangpu Area, Shanghai, 200093, China.
- The College of Medical Technology, Shanghai University of Medicine & Health Sciences, 279 Zhouzhu Highway, Pudong New Area, Shanghai, 201318, China.
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16
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Liu X, Tian J, Duan P, Yu Q, Wang G, Wang Y. GrMoNAS: A granularity-based multi-objective NAS framework for efficient medical diagnosis. Comput Biol Med 2024; 171:108118. [PMID: 38394799 DOI: 10.1016/j.compbiomed.2024.108118] [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: 09/18/2023] [Revised: 01/31/2024] [Accepted: 02/04/2024] [Indexed: 02/25/2024]
Abstract
Neural Architecture Search (NAS) has been widely applied to automate medical image diagnostics. However, traditional NAS methods require significant computational resources and time for performance evaluation. To address this, we introduce the GrMoNAS framework, designed to balance diagnostic accuracy and efficiency using proxy datasets for granularity transformation and multi-objective optimization algorithms. The approach initiates with a coarse granularity phase, wherein diverse candidate neural architectures undergo evaluation utilizing a reduced proxy dataset. This initial phase facilitates the swift and effective identification of architectures exhibiting promise. Subsequently, in the fine granularity phase, a comprehensive validation and optimization process is undertaken for these identified architectures. Concurrently, employing multi-objective optimization and Pareto frontier sorting aims to enhance both accuracy and computational efficiency simultaneously. Importantly, the GrMoNAS framework is particularly suitable for hospitals with limited computational resources. We evaluated GrMoNAS in a range of medical scenarios, such as COVID-19, Skin cancer, Lung, Colon, and Acute Lymphoblastic Leukemia diseases, comparing it against traditional models like VGG16, VGG19, and recent NAS approaches including GA-CNN, EBNAS, NEXception, and CovNAS. The results show that GrMoNAS achieves comparable or superior diagnostic precision, significantly enhancing diagnostic efficiency. Moreover, GrMoNAS effectively avoids local optima, indicating its significant potential for precision medical diagnosis.
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Affiliation(s)
- Xin Liu
- College of Information Science and Engineering, Shandong Normal University, Street, Jinan, 250358, Shandong, China.
| | - Jie Tian
- College of Data Science and Computer Science, Shandong Women's University, Street, Jinan, 250300, Shandong, China.
| | - Peiyong Duan
- College of Information Science and Engineering, Shandong Normal University, Street, Jinan, 250358, Shandong, China.
| | - Qian Yu
- College of Data Science and Computer Science, Shandong Women's University, Street, Jinan, 250300, Shandong, China.
| | - Gaige Wang
- School of Computer Science and Technology, Ocean University of China, Street, Qingdao, 266100, Shandong, China.
| | - Yingjie Wang
- College of Computer and Control Engineering, Yantai University, Street, Yantai, 264005, Shandong, China.
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17
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Zhang J, Gong W, Ye L, Wang F, Shangguan Z, Cheng Y. A Review of deep learning methods for denoising of medical low-dose CT images. Comput Biol Med 2024; 171:108112. [PMID: 38387380 DOI: 10.1016/j.compbiomed.2024.108112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/18/2024] [Accepted: 02/04/2024] [Indexed: 02/24/2024]
Abstract
To prevent patients from being exposed to excess of radiation in CT imaging, the most common solution is to decrease the radiation dose by reducing the X-ray, and thus the quality of the resulting low-dose CT images (LDCT) is degraded, as evidenced by more noise and streaking artifacts. Therefore, it is important to maintain high quality CT image while effectively reducing radiation dose. In recent years, with the rapid development of deep learning technology, deep learning-based LDCT denoising methods have become quite popular because of their data-driven and high-performance features to achieve excellent denoising results. However, to our knowledge, no relevant article has so far comprehensively introduced and reviewed advanced deep learning denoising methods such as Transformer structures in LDCT denoising tasks. Therefore, based on the literatures related to LDCT image denoising published from year 2016-2023, and in particular from 2020 to 2023, this study presents a systematic survey of current situation, and challenges and future research directions in LDCT image denoising field. Four types of denoising networks are classified according to the network structure: CNN-based, Encoder-Decoder-based, GAN-based, and Transformer-based denoising networks, and each type of denoising network is described and summarized from the perspectives of structural features and denoising performances. Representative deep-learning denoising methods for LDCT are experimentally compared and analyzed. The study results show that CNN-based denoising methods capture image details efficiently through multi-level convolution operation, demonstrating superior denoising effects and adaptivity. Encoder-decoder networks with MSE loss, achieve outstanding results in objective metrics. GANs based methods, employing innovative generators and discriminators, obtain denoised images that exhibit perceptually a closeness to NDCT. Transformer-based methods have potential for improving denoising performances due to their powerful capability in capturing global information. Challenges and opportunities for deep learning based LDCT denoising are analyzed, and future directions are also presented.
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Affiliation(s)
- Ju Zhang
- College of Information Science and Technology, Hangzhou Normal University, Hangzhou, China.
| | - Weiwei Gong
- College of Computer Science and Technology, Zhejiang University of Technology, Hangzhou, China.
| | - Lieli Ye
- College of Information Science and Technology, Hangzhou Normal University, Hangzhou, China.
| | - Fanghong Wang
- Zhijiang College, Zhejiang University of Technology, Shaoxing, China.
| | - Zhibo Shangguan
- College of Computer Science and Technology, Zhejiang University of Technology, Hangzhou, China.
| | - Yun Cheng
- Department of Medical Imaging, Zhejiang Hospital, Hangzhou, China.
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18
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Xin C, Liu Z, Ma Y, Wang D, Zhang J, Li L, Zhou Q, Xu S, Zhang Y. Transformer guided self-adaptive network for multi-scale skin lesion image segmentation. Comput Biol Med 2024; 169:107846. [PMID: 38184865 DOI: 10.1016/j.compbiomed.2023.107846] [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: 09/27/2023] [Revised: 12/03/2023] [Accepted: 12/11/2023] [Indexed: 01/09/2024]
Abstract
BACKGROUND In recent years, skin lesion has become a major public health concern, and the diagnosis and management of skin lesions depend heavily on the correct segmentation of the lesions. Traditional convolutional neural networks (CNNs) have demonstrated promising results in skin lesion segmentation, but they are limited in their ability to capture distant connections and intricate features. In addition, current medical image segmentation algorithms rarely consider the distribution of different categories in different regions of the image and do not consider the spatial relationship between pixels. OBJECTIVES This study proposes a self-adaptive position-aware skin lesion segmentation model SapFormer to capture global context and fine-grained detail, better capture spatial relationships, and adapt to different positional characteristics. The SapFormer is a multi-scale dynamic position-aware structure designed to provide a more flexible representation of the relationships between skin lesion characteristics and lesion distribution. Additionally, it increases skin lesion segmentation accuracy and decreases incorrect segmentation of non-lesion areas. INNOVATIONS SapFormer designs multiple hybrid transformers for multi-scale feature encoding of skin images and multi-scale positional feature sensing of the encoded features using a transformer decoder to obtain fine-grained features of the lesion area and optimize the regional feature distribution. The self-adaptive feature framework, built upon the transformer decoder module, dynamically and automatically generates parameterizations with learnable properties at different positions. These parameterizations are derived from the multi-scale encoding characteristics of the input image. Simultaneously, this paper utilizes the cross-attention network to optimize the features of the current region according to the features of other regions, aiming to increase skin lesion segmentation accuracy. MAIN RESULTS The ISIC-2016, ISIC-2017, and ISIC-2018 datasets for skin lesions are used as the basis for the experiment. On these datasets, the proposed model has accuracy values of 97.9 %, 94.3 %, and 95.7 %, respectively. The proposed model's IOU values are, in order, 93.2 %, 86.4 %, and 89.4 %. The proposed model's DSC values are 96.4 %, 92.6 %, and 94.3 %, respectively. All three metrics surpass the performance of the majority of state-of-the-art (SOTA) models. SapFormer's metrics on these datasets demonstrate that it can precisely segment skin lesions. Notably, our approach exhibits remarkable noise resistance in non-lesion areas, while simultaneously conducting finer-grained regional feature extraction on the skin lesion image. CONCLUSIONS In conclusion, the integration of a transformer-guided position-aware network into semantic skin lesion segmentation results in a notable performance boost. The ability of our proposed network to capture spatial relationships and fine-grained details proves beneficial for effective skin lesion segmentation. By enhancing lesion localization, feature extraction, quantitative analysis, and classification accuracy, the proposed segmentation model improves the diagnostic efficiency of skin lesion analysis on dermoscopic images. It assists dermatologists in making more accurate and efficient diagnoses, ultimately leading to better patient care and outcomes. This research paves the way for advances in diagnosing and treating skin lesions, promoting better understanding and decision-making in the clinical setting.
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Affiliation(s)
- Chao Xin
- The First Affiliated Hospital of Ningbo University, Ningbo, 315211, China.
| | - Zhifang Liu
- The First Affiliated Hospital of Ningbo University, Ningbo, 315211, China.
| | - Yizhao Ma
- The First Affiliated Hospital of Ningbo University, Ningbo, 315211, China.
| | - Dianchen Wang
- The First Affiliated Hospital of Ningbo University, Ningbo, 315211, China.
| | - Jing Zhang
- The First Affiliated Hospital of Ningbo University, Ningbo, 315211, China.
| | - Lingzhi Li
- The First Affiliated Hospital of Ningbo University, Ningbo, 315211, China.
| | - Qiongyan Zhou
- The First Affiliated Hospital of Ningbo University, Ningbo, 315211, China.
| | - Suling Xu
- The First Affiliated Hospital of Ningbo University, Ningbo, 315211, China.
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19
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Lakhan A, Hamouda H, Abdulkareem KH, Alyahya S, Mohammed MA. Digital healthcare framework for patients with disabilities based on deep federated learning schemes. Comput Biol Med 2024; 169:107845. [PMID: 38118307 DOI: 10.1016/j.compbiomed.2023.107845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/21/2023] [Accepted: 12/11/2023] [Indexed: 12/22/2023]
Abstract
Utilizing digital healthcare services for patients who use wheelchairs is a vital and effective means to enhance their healthcare. Digital healthcare integrates various healthcare facilities, including local laboratories and centralized hospitals, to provide healthcare services for individuals in wheelchairs. In digital healthcare, the Internet of Medical Things (IoMT) allows local wheelchairs to connect with remote digital healthcare services and generate sensors from wheelchairs to monitor and process healthcare. Recently, it has been observed that wheelchair patients, when older than thirty, suffer from high blood pressure, heart disease, body glucose, and others due to less activity because of their disabilities. However, existing wheelchair IoMT applications are straightforward and do not consider the healthcare of wheelchair patients with their diseases during their disabilities. This paper presents a novel digital healthcare framework for patients with disabilities based on deep-federated learning schemes. In the proposed framework, we offer the federated learning deep convolutional neural network schemes (FL-DCNNS) that consist of different sub-schemes. The offloading scheme collects the sensors from integrated wheelchair bio-sensors as smartwatches such as blood pressure, heartbeat, body glucose, and oxygen. The smartwatches worked with wearable devices for disabled patients in our framework. We present the federated learning-enabled laboratories for data training and share the updated weights with the data security to the centralized node for decision and prediction. We present the decision forest for centralized healthcare nodes to decide on aggregation with the different constraints: cost, energy, time, and accuracy. We implemented a deep CNN scheme in each laboratory to train and validate the model locally on the node with the consideration of resources. Simulation results show that FL-DCNNS obtained the optimal results on the sensor data and minimized the energy by 25%, time 19%, cost 28%, and improved the accuracy of disease prediction by 99% as compared to existing digital healthcare schemes for wheelchair patients.
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Affiliation(s)
- Abdullah Lakhan
- Department of Cybersecurity and Computer Science, Dawood University of Engineering and Technology, Karachi City 74800, Sindh, Pakistan.
| | - Hassen Hamouda
- Department of Business Administration, College of Science and Humanities at Alghat, Majmaah University, Al-Majmaah 11952, Saudi Arabia.
| | - Karrar Hameed Abdulkareem
- College of Agriculture, Al-Muthanna University, Samawah 66001, Iraq; College of Engineering, University of Warith Al-Anbiyaa, Karbala 56001, Iraq.
| | - Saleh Alyahya
- Department of Electrical Engineering, College of Engineering and Information Technology, Onaizah Colleges, Onaizah 2053, Saudi Arabia.
| | - Mazin Abed Mohammed
- Department of Artificial Intelligence, College of Computer Science and Information Technology, University of Anbar, Anbar 31001, Iraq.
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