COVID‐19 pneumonia started in December 2019 and caused large casualties and huge economic losses. In this study, we intended to develop a computer‐aided diagnosis system based on artificial ...intelligence to automatically identify the COVID‐19 in chest computed tomography images. We utilized transfer learning to obtain the image‐level representation (ILR) based on the backbone deep convolutional neural network. Then, a novel neighboring aware representation (NAR) was proposed to exploit the neighboring relationships between the ILR vectors. To obtain the neighboring information in the feature space of the ILRs, an ILR graph was generated based on the k‐nearest neighbors algorithm, in which the ILRs were linked with their k‐nearest neighboring ILRs. Afterward, the NARs were computed by the fusion of the ILRs and the graph. On the basis of this representation, a novel end‐to‐end COVID‐19 classification architecture called neighboring aware graph neural network (NAGNN) was proposed. The private and public data sets were used for evaluation in the experiments. Results revealed that our NAGNN outperformed all the 10 state‐of‐the‐art methods in terms of generalization ability. Therefore, the proposed NAGNN is effective in detecting COVID‐19, which can be used in clinical diagnosis.
Computer-aided diagnosis system is becoming a more and more important tool in clinical treatment, which can provide a verification of the doctors’ decisions. In this paper, we proposed a novel ...abnormal brain detection method for magnetic resonance image. Firstly, a pre-trained AlexNet was modified with batch normalization layers and trained on our brain images. Then, the last several layers were replaced with an extreme learning machine. A searching method was proposed to find the best number of layers to be replaced. Finally, the extreme learning machine was optimized by chaotic bat algorithm to obtain better classification performance. Experiment results based on 5 × hold-out validation revealed that our method achieved state-of-the-art performance.
Identifying essential genes in a given organism is important for research on their fundamental roles in organism survival. Furthermore, if possible, uncovering the links between core functions or ...pathways with these essential genes will further help us obtain deep insight into the key roles of these genes. In this study, we investigated the essential and non-essential genes reported in a previous study and extracted gene ontology (GO) terms and biological pathways that are important for the determination of essential genes. Through the enrichment theory of GO and KEGG pathways, we encoded each essential/non-essential gene into a vector in which each component represented the relationship between the gene and one GO term or KEGG pathway. To analyze these relationships, the maximum relevance minimum redundancy (mRMR) was adopted. Then, the incremental feature selection (IFS) and support vector machine (SVM) were employed to extract important GO terms and KEGG pathways. A prediction model was built simultaneously using the extracted GO terms and KEGG pathways, which yielded nearly perfect performance, with a Matthews correlation coefficient of 0.951, for distinguishing essential and non-essential genes. To fully investigate the key factors influencing the fundamental roles of essential genes, the 21 most important GO terms and three KEGG pathways were analyzed in detail. In addition, several genes was provided in this study, which were predicted to be essential genes by our prediction model. We suggest that this study provides more functional and pathway information on the essential genes and provides a new way to investigate related problems.
In radiomics studies, researchers usually need to develop a supervised machine learning model to map image features onto the clinical conclusion. A classical machine learning pipeline consists of ...several steps, including normalization, feature selection, and classification. It is often tedious to find an optimal pipeline with appropriate combinations. We designed an open-source software package named FeAture Explorer (FAE). It was programmed with Python and used NumPy, pandas, and scikit-learning modules. FAE can be used to extract image features, preprocess the feature matrix, develop different models automatically, and evaluate them with common clinical statistics. FAE features a user-friendly graphical user interface that can be used by radiologists and researchers to build many different pipelines, and to compare their results visually. To prove the effectiveness of FAE, we developed a candidate model to classify the clinical-significant prostate cancer (CS PCa) and non-CS PCa using the PROSTATEx dataset. We used FAE to try out different combinations of feature selectors and classifiers, compare the area under the receiver operating characteristic curve of different models on the validation dataset, and evaluate the model using independent test data. The final model with the analysis of variance as the feature selector and linear discriminate analysis as the classifier was selected and evaluated conveniently by FAE. The area under the receiver operating characteristic curve on the training, validation, and test dataset achieved results of 0.838, 0.814, and 0.824, respectively. FAE allows researchers to build radiomics models and evaluate them using an independent testing dataset. It also provides easy model comparison and result visualization. We believe FAE can be a convenient tool for radiomics studies and other medical studies involving supervised machine learning.
A systematic survey of deep learning in breast cancer Yu, Xiang; Zhou, Qinghua; Wang, Shuihua ...
International journal of intelligent systems,
January 2022, 2022-01-00, 20220101, Letnik:
37, Številka:
1
Journal Article
Recenzirano
Odprti dostop
In recent years, we witnessed a speeding development of deep learning in computer vision fields like categorization, detection, and semantic segmentation. Within several years after the emergence of ...AlexNet, the performance of deep neural networks has already surpassed human being experts in certain areas and showed great potential in applications such as medical image analysis. The development of automated breast cancer detection systems that integrate deep learning has received wide attention from the community. Breast cancer, a major killer of females that results in millions of deaths, can be controlled even be cured given that it is detected at an early stage with sophisticated systems. In this paper, we reviewed breast cancer diagnosis, detection, and segmentation computer‐aided (CAD) systems based on state‐of‐the‐art deep convolutional neural networks. The available data sets also indirectly determine CAD systems' performance, so we introduced and discussed the details of public data sets. The challenges remaining in CAD systems for breast cancer are discussed at the end of this paper. The highlights of this survey mainly come from three following aspects. First, we covered a wide range of the basics of breast cancer from imaging modalities to popular databases in the community; Second, we presented the key elements in deep learning to form the compactness for methods mentioned in reviewed papers; Third and lastly, the summative details in each reviewed paper are provided so that interested readers can have a refined version of these works without referring to original papers. Therefore, this systematic survey suits readers with varied backgrounds and will be beneficial to them.
Colorectal cancer is the third most common cancer in males and second in females. This disease can be caused by genetic and acquired/environmental factors. Microsatellite instability (MSI) is one of ...the major mechanisms in colorectal cancer. This mechanism is a specific condition of genetic hyper mutability that results from incompetent DNA mismatch repair. MSI has been applied to classify different colorectal cancer subtypes. However, the effects of MSI status on gene expression are largely unknown. In our study, we integrated the gene expression profile and MSI status of all CRC samples from the TCGA database, and then categorized the CRC samples into three subgroups, namely, MSI‐stable, MSI‐low, and MSI‐high, according to the MSI status. We applied a novel computational method based on machine learning and screened the genes specifically expressed for the different colorectal cancer subtypes. The results showed the distinct mechanisms of the different colorectal cancer subtypes with MSI status and provided the genes that may be the optimal standards to further classify the various molecular subtypes of colorectal cancer with distinct MSI status.
What's new?
Microsatellite instability (MSI), a key genetic mechanism implicated in colorectal cancer (CRC), is linked to drug reactivity and sensitivity in CRC patients and is useful for CRC subtype classification. Yet, little is known about the identity of MSI‐associated genes or their role in CRC. Here, combined analysis of datasets on gene‐expression profile and MSI status enabled the investigation of a number of differentially expressed genes from CRC samples. Genes optimal for the classification of CRC subtypes with different MSI statuses were identified. The gene panel could facilitate the discovery of biomarkers specific for CRCs with known MSI status.
Background
Deep learning is the most promising methodology for automatic computer‐aided diagnosis of prostate cancer (PCa) with multiparametric MRI (mp‐MRI).
Purpose
To develop an automatic approach ...based on deep convolutional neural network (DCNN) to classify PCa and noncancerous tissues (NC) with mp‐MRI.
Study Type
Retrospective.
Subjects
In all, 195 patients with localized PCa were collected from a PROSTATEx database. In total, 159/17/19 patients with 444/48/55 observations (215/23/23 PCas and 229/25/32 NCs) were randomly selected for training/validation/testing, respectively.
Sequence
T2‐weighted, diffusion‐weighted, and apparent diffusion coefficient images.
Assessment
A radiologist manually labeled the regions of interest of PCas and NCs and estimated the Prostate Imaging Reporting and Data System (PI‐RADS) scores for each region. Inspired by VGG‐Net, we designed a patch‐based DCNN model to distinguish between PCa and NCs based on a combination of mp‐MRI data. Additionally, an enhanced prediction method was used to improve the prediction accuracy. The performance of DCNN prediction was tested using a receiver operating characteristic (ROC) curve, and the area under the ROC curve (AUC), sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were calculated. Moreover, the predicted result was compared with the PI‐RADS score to evaluate its clinical value using decision curve analysis.
Statistical Test
Two‐sided Wilcoxon signed‐rank test with statistical significance set at 0.05.
Results
The DCNN produced excellent diagnostic performance in distinguishing between PCa and NC for testing datasets with an AUC of 0.944 (95% confidence interval: 0.876–0.994), sensitivity of 87.0%, specificity of 90.6%, PPV of 87.0%, and NPV of 90.6%. The decision curve analysis revealed that the joint model of PI‐RADS and DCNN provided additional net benefits compared with the DCNN model and the PI‐RADS scheme.
Data Conclusion
The proposed DCNN‐based model with enhanced prediction yielded high performance in statistical analysis, suggesting that DCNN could be used in computer‐aided diagnosis (CAD) for PCa classification.
Level of Evidence: 3
Technical Efficacy: Stage 2
J. Magn. Reson. Imaging 2018;48:1570–1577
•Convolutional block attention module is included in the proposed model.•The proposed multiple-input end-to-end model can handle CCT and CXR images simultaneously.•Multiple-way data augmentation is ...employed to overcome overfitting problem.•The proposed model gives more accurate performances than individual modality.•The proposed model offers better performances than state-of-the-art approaches.
COVID-19 has caused 3.34m deaths till 13/May/2021. It is now still causing confirmed cases and ongoing deaths every day.
This study investigated whether fusing chest CT with chest X-ray can help improve the AI's diagnosis performance. Data harmonization is employed to make a homogeneous dataset. We create an end-to-end multiple-input deep convolutional attention network (MIDCAN) by using the convolutional block attention module (CBAM). One input of our model receives 3D chest CT image, and other input receives 2D X-ray image. Besides, multiple-way data augmentation is used to generate fake data on training set. Grad-CAM is used to give explainable heatmap.
The proposed MIDCAN achieves a sensitivity of 98.10±1.88%, a specificity of 97.95±2.26%, and an accuracy of 98.02±1.35%.
Our MIDCAN method provides better results than 8 state-of-the-art approaches. We demonstrate the using multiple modalities can achieve better results than individual modality. Also, we demonstrate that CBAM can help improve the diagnosis performance.
•Decorrelation formulation based contrast improvement.•Lesion segmentation using modified MASK RCNN.•Transfer Learning based CNN features are extracted.•A Entropy-controlled LS-SVM based best CNN ...features are selected.
Malignant melanoma is considered to be one of the deadliest types of skin cancers which is responsible for the massive number of deaths worldwide. According to the American Cancer Society (ACS), more than a million Americans are living with this melanoma. Since 2019, 192,310 new cases of melanoma are registered, where 95,380 are noninvasive, and 96,480 are invasive. The numbers of deaths due to melanoma in 2019 alone are 7,230, comprising 4,740 men and 2,490 women. Melanoma may be curable if diagnosed at the earlier stages; however, the manual diagnosis is time-consuming and also dependent on the expert dermatologist. In this work, a fully automated computerized aided diagnosis (CAD) system is proposed based on the deep learning framework. In the proposed scheme, the original dermoscopic images are initially pre-processed using the decorrelation formulation technique, which later passes the resultant images to the MASK-RCNN for the lesion segmentation. In this step, the MASK RCNN model is trained using the segmented RGB images generated from the ground truth images of ISBI2016 and ISIC2017 datasets. The resultant segmented images are later passed to the DenseNet deep model for feature extraction. Two different layers, average pool and fully connected, are used for feature extraction, which are later combined, and the resultant vector is forwarded to the feature selection block for down - sampling using proposed entropy-controlled least square SVM (LS-SVM). Three datasets are utilized for validation - ISBI2016, ISBI2017, and HAM10000 to achieve an accuracy of 96.3%, 94.8%, and 88.5% respectively. Further, the performance of MASK-RCNN is also validated on ISBI2016 and ISBI2017 to attain an accuracy of 93.6% and 92.7%. To further increase our confidence in the proposed framework, a fair comparison with other state-of-the-art is also provided.
A review on extreme learning machine Wang, Jian; Lu, Siyuan; Wang, Shui-Hua ...
Multimedia tools and applications,
12/2022, Letnik:
81, Številka:
29
Journal Article
Recenzirano
Odprti dostop
Extreme learning machine (ELM) is a training algorithm for single hidden layer feedforward neural network (SLFN), which converges much faster than traditional methods and yields promising ...performance. In this paper, we hope to present a comprehensive review on ELM. Firstly, we will focus on the theoretical analysis including universal approximation theory and generalization. Then, the various improvements are listed, which help ELM works better in terms of stability, efficiency, and accuracy. Because of its outstanding performance, ELM has been successfully applied in many real-time learning tasks for classification, clustering, and regression. Besides, we report the applications of ELM in medical imaging: MRI, CT, and mammogram. The controversies of ELM were also discussed in this paper. We aim to report these advances and find some future perspectives.
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