Computer-aided grading of prostate cancer from MRI images using Convolutional Neural Networks

Computer-Aided detection of tuberculosis from X-ray images using CNN and PatternNet classifier

BACKGROUND

Tuberculosis (TB) is a highly infectious disease that mainly affects the human lungs. The gold standard for TB diagnosis is Xpert Mycobacterium tuberculosis/ resistance to rifampicin (MTB/RIF) testing. X-ray, a relatively inexpensive and widely used imaging modality, can be employed as an alternative for early diagnosis of the disease. Computer-aided techniques can be used to assist radiologists in interpreting X-ray images, which can improve the ease and accuracy of diagnosis.

OBJECTIVE

To develop a computer-aided technique for the diagnosis of TB from X-ray images using deep learning techniques.

METHODS

This research paper presents a novel approach for TB diagnosis from X-ray using deep learning methods. The proposed method uses an ensemble of two pre-trained neural networks, namely EfficientnetB0 and Densenet201, for feature extraction. The features extracted using two CNNs are expected to generate more accurate and representative features than a single CNN. A custom-built artificial neural network (ANN) called PatternNet with two hidden layers is utilized to classify the extracted features.

RESULTS

The effectiveness of the proposed method was assessed on two publicly accessible datasets, namely the Montgomery and Shenzhen datasets. The Montgomery dataset comprises 138 X-ray images, while the Shenzhen dataset has 662 X-ray images. The method was further evaluated after combining both datasets. The method performed exceptionally well on all three datasets, achieving high Area Under the Curve (AUC) scores of 0.9978, 0.9836, and 0.9914, respectively, using a 10-fold cross-validation technique.

CONCLUSION

The experiments performed in this study prove the effectiveness of features extracted using EfficientnetB0 and Densenet201 in combination with PatternNet classifier in the diagnosis of tuberculosis from X-ray images.

Dual attention guided multiscale neural network trained with curriculum learning for noninvasive prediction of Gleason Grade Group from MRI

BACKGROUND

The Gleason Grade Group (GG) is essential in assessing the malignancy of prostate cancer (PCa) and is typically obtained by invasive biopsy procedures in which sampling errors could lead to inaccurately scored GGs. With the gradually recognized value of bi-parametric magnetic resonance imaging (bpMRI) in PCa, it is beneficial to noninvasively predict GGs from bpMRI for early diagnosis and treatment planning of PCa. However, it is challenging to establish the connection between bpMRI features and GGs.

PURPOSE

In this study, we propose a dual attention-guided multiscale neural network (DAMS-Net) to predict the 5-scored GG from bpMRI and design a training curriculum to further improve the prediction performance.

METHODS

The proposed DAMS-Net incorporates a feature pyramid network (FPN) to fully extract the multiscale features for lesions of varying sizes and a dual attention module to focus on lesion and surrounding regions while avoiding the influence of irrelevant ones. Furthermore, to enhance the differential ability for lesions with the inter-grade similarity and intra-grade variation in bpMRI, the training process employs a specially designed curriculum based on the differences between the radiological evaluations and the ground truth GGs.

RESULTS

Extensive experiments were conducted on a private dataset of 382 patients and the public PROSTATEx-2 dataset. For the private dataset, the experimental results showed that the proposed network performed better than the plain baseline model for GG prediction, achieving a mean quadratic weighted Kappa (K_w ) of 0.4902 and a mean positive predictive value of 0.9098 for predicting clinically significant cancer (PPV_GG>1 ). With the application of curriculum learning, the mean K_w and PPV_GG>1 further increased to 0.5144 and 0.9118, respectively. For the public dataset, the proposed method achieved state-of-the-art results of 0.5413 K_w and 0.9747 PPV_GG>1 .

CONCLUSION

The proposed DAMS-Net trained with curriculum learning can effectively predict GGs from bpMRI, which may assist clinicians in early diagnosis and treatment planning for PCa patients.

Diabetic retinopathy screening using deep learning for multi-class imbalanced datasets

Screening and diagnosis of diabetic retinopathy disease is a well known problem in the biomedical domain. The use of medical imagery from a patient's eye for detecting the damage caused to blood vessels is a part of the computer-aided diagnosis that has immensely progressed over the past few years due to the advent and success of deep learning. The challenges related to imbalanced datasets, inconsistent annotations, less number of sample images and inappropriate performance evaluation metrics has caused an adverse impact on the performance of the deep learning models. In order to tackle the effect caused by class imbalance, we have done extensive comparative analysis between various state-of-the-art methods on three benchmark datasets of diabetic retinopathy: - Kaggle DR detection, IDRiD and DDR, for classification, object detection and segmentation tasks. This research could serve as a concrete baseline for future research in this field to find appropriate approaches and deep learning architectures for imbalanced datasets.

A new approach for data augmentation in a deep neural network to implement a monitoring system for detecting prostate cancer in MRI images

Prostate cancer is one of the most common cancers in men, which takes many victims every year due to its latent symptoms. Thus, early diagnosis of the extent of the lesion can help the physician and the patient in the treatment process. Nowadays, detection and labeling of objects in medical images has become especially important. In this article, the prostate gland is first detected in T2 W MRI images by the Faster R-CNN network based on the AlexNet architecture and separated from the rest of the image. Using the Faster R-CNN network in the separation phase, the accuracy will increase as this network is a model of CNN-based target detection networks and is functionally coordinated with the subsequent CNN network. Meanwhile, the problem of insufficient data with the data augmentation method was corrected in the preprocessing stage, for which different filters were used. Use of different filters to increase the data instead of the usual augmentation methods would eliminate the preprocessing stage. Also, with the presence of raw images in the next steps, it was proven that there was no need for a preprocessing step and the main images could also be the input data. By eliminating the preprocessing step, the response speed increased. Then, in order to classify benign and malignant cancer images, two deep learning architectures were used under the supervision of ResNet18 and GoogleNet. Then, by calculating the Confusion Matrix parameters and drawing the ROC diagram, the capability of this process was measured. By obtaining Accuracy = 95.7%, DSC = 96.77% and AUC = 99.17%, The results revealed that this method could outperform other well-known methods in this field (DSC = 95%) and (AUC = 91%).

Machine and Deep Learning Prediction Of Prostate Cancer Aggressiveness Using Multiparametric MRI

Prostate cancer (PCa) is the most frequent male malignancy and the assessment of PCa aggressiveness, for which a biopsy is required, is fundamental for patient management. Currently, multiparametric (mp) MRI is strongly recommended before biopsy. Quantitative assessment of mpMRI might provide the radiologist with an objective and noninvasive tool for supporting the decision-making in clinical practice and decreasing intra- and inter-reader variability. In this view, high dimensional radiomics features and Machine Learning (ML) techniques, along with Deep Learning (DL) methods working on raw images directly, could assist the radiologist in the clinical workflow. The aim of this study was to develop and validate ML/DL frameworks on mpMRI data to characterize PCas according to their aggressiveness. We optimized several ML/DL frameworks on T2w, ADC and T2w+ADC data, using a patient-based nested validation scheme. The dataset was composed of 112 patients (132 peripheral lesions with Prostate Imaging Reporting and Data System (PI-RADS) score ≥ 3) acquired following both PI-RADS 2.0 and 2.1 guidelines. Firstly, ML/DL frameworks trained and validated on PI-RADS 2.0 data were tested on both PI-RADS 2.0 and 2.1 data. Then, we trained, validated and tested ML/DL frameworks on a multi PI-RADS dataset. We reported the performances in terms of Area Under the Receiver Operating curve (AUROC), specificity and sensitivity. The ML/DL frameworks trained on T2w data achieved the overall best performance. Notably, ML and DL frameworks trained and validated on PI-RADS 2.0 data obtained median AUROC values equal to 0.750 and 0.875, respectively, on unseen PI-RADS 2.0 test set. Similarly, ML/DL frameworks trained and validated on multi PI-RADS T2w data showed median AUROC values equal to 0.795 and 0.750, respectively, on unseen multi PI-RADS test set. Conversely, all the ML/DL frameworks trained and validated on PI-RADS 2.0 data, achieved AUROC values no better than the chance level when tested on PI-RADS 2.1 data. Both ML/DL techniques applied on mpMRI seem to be a valid aid in predicting PCa aggressiveness. In particular, ML/DL frameworks fed with T2w images data (objective, fast and non-invasive) show good performances and might support decision-making in patient diagnostic and therapeutic management, reducing intra- and inter-reader variability.

Computer-aided detection of COVID-19 from CT scans using an ensemble of CNNs and KSVM classifier

Corona Virus Disease-2019 (COVID-19) is a global pandemic which is spreading briskly across the globe. The gold standard for the diagnosis of COVID-19 is viral nucleic acid detection with real-time polymerase chain reaction (RT-PCR). However, the sensitivity of RT-PCR in the diagnosis of early-stage COVID-19 is less. Recent research works have shown that computed tomography (CT) scans of the chest are effective for the early diagnosis of COVID-19. Convolutional neural networks (CNNs) are proven successful for diagnosing various lung diseases from CT scans. CNNs are composed of multiple layers which represent a hierarchy of features at each level. CNNs require a big number of labeled instances for training from scratch. In medical imaging tasks like the detection of COVID-19 where there is a difficulty in acquiring a large number of labeled CT scans, pre-trained CNNs trained on a huge number of natural images can be employed for extracting features. Feature representation of each CNN varies and an ensemble of features generated from various pre-trained CNNs can increase the diagnosis capability significantly. In this paper, features extracted from an ensemble of 5 different CNNs (MobilenetV2, Shufflenet, Xception, Darknet53 and EfficientnetB0) in combination with kernel support vector machine is used for the diagnosis of COVID-19 from CT scans. The method was tested using a public dataset and it attained an area under the receiver operating characteristic curve of 0.963, accuracy of 0.916, kappa score of 0.8305, F-score of 0.91, sensitivity of 0.917 and positive predictive value of 0.904 in the prediction of COVID-19.

A Combined Radiomics and Machine Learning Approach to Distinguish Clinically Significant Prostate Lesions on a Publicly Available MRI Dataset

Although prostate cancer is one of the most common causes of mortality and morbidity in advancing-age males, early diagnosis improves prognosis and modifies the therapy of choice. The aim of this study was the evaluation of a combined radiomics and machine learning approach on a publicly available dataset in order to distinguish a clinically significant from a clinically non-significant prostate lesion. A total of 299 prostate lesions were included in the analysis. A univariate statistical analysis was performed to prove the goodness of the 60 extracted radiomic features in distinguishing prostate lesions. Then, a 10-fold cross-validation was used to train and test some models and the evaluation metrics were calculated; finally, a hold-out was performed and a wrapper feature selection was applied. The employed algorithms were Naïve bayes, K nearest neighbour and some tree-based ones. The tree-based algorithms achieved the highest evaluation metrics, with accuracies over 80%, and area-under-the-curve receiver-operating characteristics below 0.80. Combined machine learning algorithms and radiomics based on clinical, routine, multiparametric, magnetic-resonance imaging were demonstrated to be a useful tool in prostate cancer stratification.

Computer-aided detection of COVID-19 from X-ray images using multi-CNN and Bayesnet classifier

Corona virus disease-2019 (COVID-19) is a pandemic caused by novel coronavirus. COVID-19 is spreading rapidly throughout the world. The gold standard for diagnosing COVID-19 is reverse transcription-polymerase chain reaction (RT-PCR) test. However, the facility for RT-PCR test is limited, which causes early diagnosis of the disease difficult. Easily available modalities like X-ray can be used to detect specific symptoms associated with COVID-19. Pre-trained convolutional neural networks are widely used for computer-aided detection of diseases from smaller datasets. This paper investigates the effectiveness of multi-CNN, a combination of several pre-trained CNNs, for the automated detection of COVID-19 from X-ray images. The method uses a combination of features extracted from multi-CNN with correlation based feature selection (CFS) technique and Bayesnet classifier for the prediction of COVID-19. The method was tested using two public datasets and achieved promising results on both the datasets. In the first dataset consisting of 453 COVID-19 images and 497 non-COVID images, the method achieved an AUC of 0.963 and an accuracy of 91.16%. In the second dataset consisting of 71 COVID-19 images and 7 non-COVID images, the method achieved an AUC of 0.911 and an accuracy of 97.44%. The experiments performed in this study proved the effectiveness of pre-trained multi-CNN over single CNN in the detection of COVID-19.

Machine learning for the identification of clinically significant prostate cancer on MRI: a meta-analysis

OBJECTIVES

The aim of this study was to systematically review the literature and perform a meta-analysis of machine learning (ML) diagnostic accuracy studies focused on clinically significant prostate cancer (csPCa) identification on MRI.

METHODS

Multiple medical databases were systematically searched for studies on ML applications in csPCa identification up to July 31, 2019. Two reviewers screened all papers independently for eligibility. The area under the receiver operating characteristic curves (AUC) was pooled to quantify predictive accuracy. A random-effects model estimated overall effect size while statistical heterogeneity was assessed with the I² value. A funnel plot was used to investigate publication bias. Subgroup analyses were performed based on reference standard (biopsy or radical prostatectomy) and ML type (deep and non-deep).

RESULTS

After the final revision, 12 studies were included in the analysis. Statistical heterogeneity was high both in overall and in subgroup analyses. The overall pooled AUC for ML in csPCa identification was 0.86, with 0.81-0.91 95% confidence intervals (95%CI). The biopsy subgroup (n = 9) had a pooled AUC of 0.85 (95%CI = 0.79-0.91) while the radical prostatectomy one (n = 3) of 0.88 (95%CI = 0.76-0.99). Deep learning ML (n = 4) had a 0.78 AUC (95%CI = 0.69-0.86) while the remaining 8 had AUC = 0.90 (95%CI = 0.85-0.94).

CONCLUSIONS

ML pipelines using prostate MRI to identify csPCa showed good accuracy and should be further investigated, possibly with better standardisation in design and reporting of results.

KEY POINTS

• Overall pooled AUC was 0.86 with 0.81-0.91 95% confidence intervals. • In the reference standard subgroup analysis, algorithm accuracy was similar with pooled AUCs of 0.85 (0.79-0.91 95% confidence intervals) and 0.88 (0.76-0.99 95% confidence intervals) for studies employing biopsies and radical prostatectomy, respectively. • Deep learning pipelines performed worse (AUC = 0.78, 0.69-0.86 95% confidence intervals) than other approaches (AUC = 0.90, 0.85-0.94 95% confidence intervals).