Brain Tumour Segmentation Using Convolutional Neural Network with Tensor Flow

Neuro-XAI: Explainable deep learning framework based on deeplabV3+ and bayesian optimization for segmentation and classification of brain tumor in MRI scans

The prevalence of brain tumor disorders is currently a global issue. In general, radiography, which includes a large number of images, is an efficient method for diagnosing these life-threatening disorders. The biggest issue in this area is that it takes a radiologist a long time and is physically strenuous to look at all the images. As a result, research into developing systems based on machine learning to assist radiologists in diagnosis continues to rise daily. Convolutional neural networks (CNNs), one type of deep learning approach, have been pivotal in achieving state-of-the-art results in several medical imaging applications, including the identification of brain tumors. CNN hyperparameters are typically set manually for segmentation and classification, which might take a while and increase the chance of using suboptimal hyperparameters for both tasks. Bayesian optimization is a useful method for updating the deep CNN's optimal hyperparameters. The CNN network, however, can be considered a "black box" model because of how difficult it is to comprehend the information it stores because of its complexity. Therefore, this problem can be solved by using Explainable Artificial Intelligence (XAI) tools, which provide doctors with a realistic explanation of CNN's assessments. Implementation of deep learning-based systems in real-time diagnosis is still rare. One of the causes could be that these methods don't quantify the Uncertainty in the predictions, which could undermine trust in the AI-based diagnosis of diseases. To be used in real-time medical diagnosis, CNN-based models must be realistic and appealing, and uncertainty needs to be evaluated. So, a novel three-phase strategy is proposed for segmenting and classifying brain tumors. Segmentation of brain tumors using the DeeplabV3+ model is first performed with tuning of hyperparameters using Bayesian optimization. For classification, features from state-of-the-art deep learning models Darknet53 and mobilenetv2 are extracted and fed to SVM for classification, and hyperparameters of SVM are also optimized using a Bayesian approach. The second step is to understand whatever portion of the images CNN uses for feature extraction using XAI algorithms. Using confusion entropy, the Uncertainty of the Bayesian optimized classifier is finally quantified. Based on a Bayesian-optimized deep learning framework, the experimental findings demonstrate that the proposed method outperforms earlier techniques, achieving a 97 % classification accuracy and a 0.98 global accuracy.

Pediatric Brain Tissue Segmentation Using a Snapshot Hyperspectral Imaging (sHSI) Camera and Machine Learning Classifier

Pediatric brain tumors are the second most common type of cancer, accounting for one in four childhood cancer types. Brain tumor resection surgery remains the most common treatment option for brain cancer. While assessing tumor margins intraoperatively, surgeons must send tissue samples for biopsy, which can be time-consuming and not always accurate or helpful. Snapshot hyperspectral imaging (sHSI) cameras can capture scenes beyond the human visual spectrum and provide real-time guidance where we aim to segment healthy brain tissues from lesions on pediatric patients undergoing brain tumor resection. With the institutional research board approval, Pro00011028, 139 red-green-blue (RGB), 279 visible, and 85 infrared sHSI data were collected from four subjects with the system integrated into an operating microscope. A random forest classifier was used for data analysis. The RGB, infrared sHSI, and visible sHSI models achieved average intersection of unions (IoUs) of 0.76, 0.59, and 0.57, respectively, while the tumor segmentation achieved a specificity of 0.996, followed by the infrared HSI and visible HSI models at 0.93 and 0.91, respectively. Despite the small dataset considering pediatric cases, our research leveraged sHSI technology and successfully segmented healthy brain tissues from lesions with a high specificity during pediatric brain tumor resection procedures.

Automatic brain tumor detection using CNN transfer learning approach

Automatic brain tumor detection is a challenging task as tumors vary in their position, mass, nature, and similarities found between brain lesions and normal tissues. The tumor detection is vital and urgent as it is related to the lifespan of the affected person. Medical experts commonly utilize advanced imaging practices such as magnetic resonance imaging (MRI), computed tomography (CT), and ultrasound images to decide the presence of abnormal tissues. It is a very time-consuming task to extract the tumor information from the enormous quantity of information produced by MRI volumetric data examination using a manual approach. In manual tumor detection, precise identification of tumor along with its details is a complex task. Henceforth, reliable and automatic detection systems are vital. In this paper, convolutional neural network based automated brain tumor recognition approach is proposed to analyze the MRI images and classify them into tumorous and non-tumorous classes. Various convolutional neutral network architectures like Alexnet, VGG-16, GooGLeNet, and RNN are explored and compared together. The paper focuses on the tuning of the hyperparameters for the two architectures namely Alexnet and VGG-16. Exploratory results on BRATS 2013, BRATS 2015, and OPEN I dataset with 621 images confirmed that the accuracy of 98.67% is achieved using CNN Alexnet for automatic detection of brain tumors while testing on 125 images.

MRI-based brain tumor detection using convolutional deep learning methods and chosen machine learning techniques

BACKGROUND

Detecting brain tumors in their early stages is crucial. Brain tumors are classified by biopsy, which can only be performed through definitive brain surgery. Computational intelligence-oriented techniques can help physicians identify and classify brain tumors. Herein, we proposed two deep learning methods and several machine learning approaches for diagnosing three types of tumor, i.e., glioma, meningioma, and pituitary gland tumors, as well as healthy brains without tumors, using magnetic resonance brain images to enable physicians to detect with high accuracy tumors in early stages.

MATERIALS AND METHODS

A dataset containing 3264 Magnetic Resonance Imaging (MRI) brain images comprising images of glioma, meningioma, pituitary gland tumors, and healthy brains were used in this study. First, preprocessing and augmentation algorithms were applied to MRI brain images. Next, we developed a new 2D Convolutional Neural Network (CNN) and a convolutional auto-encoder network, both of which were already trained by our assigned hyperparameters. Then 2D CNN includes several convolution layers; all layers in this hierarchical network have a 2*2 kernel function. This network consists of eight convolutional and four pooling layers, and after all convolution layers, batch-normalization layers were applied. The modified auto-encoder network includes a convolutional auto-encoder network and a convolutional network for classification that uses the last output encoder layer of the first part. Furthermore, six machine-learning techniques that were applied to classify brain tumors were also compared in this study.

RESULTS

The training accuracy of the proposed 2D CNN and that of the proposed auto-encoder network were found to be 96.47% and 95.63%, respectively. The average recall values for the 2D CNN and auto-encoder networks were 95% and 94%, respectively. The areas under the ROC curve for both networks were 0.99 or 1. Among applied machine learning methods, Multilayer Perceptron (MLP) (28%) and K-Nearest Neighbors (KNN) (86%) achieved the lowest and highest accuracy rates, respectively. Statistical tests showed a significant difference between the means of the two methods developed in this study and several machine learning methods (p-value < 0.05).

CONCLUSION

The present study shows that the proposed 2D CNN has optimal accuracy in classifying brain tumors. Comparing the performance of various CNNs and machine learning methods in diagnosing three types of brain tumors revealed that the 2D CNN achieved exemplary performance and optimal execution time without latency. This proposed network is less complex than the auto-encoder network and can be employed by radiologists and physicians in clinical systems for brain tumor detection.

Deep learning characterization of brain tumours with diffusion weighted imaging

Glioblastoma multiforme (GBM) is one of the most deadly forms of cancer. Methods of characterizing these tumours are valuable for improving predictions of their progression and response to treatment. A mathematical model called the proliferation-invasion (PI) model has been used extensively in the literature to model the growth of these tumours, though it relies on known values of two key parameters: the tumour cell diffusivity and proliferation rate. Unfortunately, these parameters are difficult to estimate in a patient-specific manner, making personalized tumour forecasting challenging. In this paper, we develop and apply a deep learning model capable of making accurate estimates of these key GBM-characterizing parameters while simultaneously producing a full prediction of the tumour progression curve. Our method uses two sets of multi sequence MRI in order to produce estimations and relies on a preprocessing pipeline which includes brain tumour segmentation and conversion to tumour cellularity. We first apply our deep learning model to synthetic tumours to showcase the model's capabilities and identify situations where prediction errors are likely to occur. We then apply our model to a clinical dataset consisting of five patients diagnosed with GBM. For all patients, we derive evidence-based estimates for each of the PI model parameters and predictions for the future progression of the tumour, along with estimates of the parameter uncertainties. Our work provides a new, easily generalizable method for the estimation of patient-specific tumour parameters, which can be built upon to aid physicians in designing personalized treatments.

Temporally guided articulated hand pose tracking in surgical videos

PURPOSE

Articulated hand pose tracking is an under-explored problem that carries the potential for use in an extensive number of applications, especially in the medical domain. With a robust and accurate tracking system on surgical videos, the motion dynamics and movement patterns of the hands can be captured and analyzed for many rich tasks.

METHODS

In this work, we propose a novel hand pose estimation model, CondPose, which improves detection and tracking accuracy by incorporating a pose prior into its prediction. We show improvements over state-of-the-art methods which provide frame-wise independent predictions, by following a temporally guided approach that effectively leverages past predictions.

RESULTS

We collect Surgical Hands, the first dataset that provides multi-instance articulated hand pose annotations for videos. Our dataset provides over 8.1k annotated hand poses from publicly available surgical videos and bounding boxes, pose annotations, and tracking IDs to enable multi-instance tracking. When evaluated on Surgical Hands, we show our method outperforms the state-of-the-art approach using mean Average Precision, to measure pose estimation accuracy, and Multiple Object Tracking Accuracy, to assess pose tracking performance.

CONCLUSION

In comparison to a frame-wise independent strategy, we show greater performance in detecting and tracking hand poses and more substantial impact on localization accuracy. This has positive implications in generating more accurate representations of hands in the scene to be used for targeted downstream tasks.

Region Convolutional Neural Network for Brain Tumor Segmentation

Gliomas are often difficult to find and distinguish using typical manual segmentation approaches because of their vast range of changes in size, shape, and appearance. Furthermore, the manual annotation of cancer tissue segmentation under the close supervision of a human professional is both time-consuming and exhausting to perform. It will be easier and faster in the future to get accurate and quick diagnoses and treatments thanks to automated segmentation and survival rate prediction models that can be used now. In this article, a segmentation model is designed using RCNN that enables automatic prognosis on brain tumors using MRI. The study adopts a U-Net encoder for capturing the features during the training of the model. The feature extraction extracts geometric features for the estimation of tumor size. It is seen that the shape, location, and size of a tumor are significant factors in the estimation of prognosis. The experimental methods are conducted to test the efficacy of the model, and the results of the simulation show that the proposed method achieves a reduced error rate with increased accuracy than other methods.

Review on Hybrid Segmentation Methods for Identification of Brain Tumor in MRI

Modalities like MRI give information about organs and highlight diseases. Organ information is visualized in intensities. The segmentation method plays an important role in the identification of the region of interest (ROI). The ROI can be segmented from the image using clustering, features, and region extraction. Segmentation can be performed in steps; firstly, the region is extracted from the image. Secondly, feature extraction performed, and better features are selected. They can be shape, texture, or intensity. Thirdly, clustering segments the shape of tumor, tumor has specified shape, and shape is detected by feature. Clustering consists of FCM, K-means, FKM, and their hybrid. To support the segmentation, we conducted three studies (region extraction, feature, and clustering) which are discussed in the first line of this review paper. All these studies are targeting MRI as a modality. MRI visualization proved to be more accurate for the identification of diseases compared with other modalities. Information of the modality is compromised due to low pass image. In MRI Images, the tumor intensities are variable in tumor areas as well as in tumor boundaries.

A New Model for Brain Tumor Detection Using Ensemble Transfer Learning and Quantum Variational Classifier

A brain tumor is an abnormal enlargement of cells if not properly diagnosed. Early detection of a brain tumor is critical for clinical practice and survival rates. Brain tumors arise in a variety of shapes, sizes, and features, with variable treatment options. Manual detection of tumors is difficult, time-consuming, and error-prone. Therefore, a significant requirement for computerized diagnostics systems for accurate brain tumor detection is present. In this research, deep features are extracted from the inceptionv3 model, in which score vector is acquired from softmax and supplied to the quantum variational classifier (QVR) for discrimination between glioma, meningioma, no tumor, and pituitary tumor. The classified tumor images have been passed to the proposed Seg-network where the actual infected region is segmented to analyze the tumor severity level. The outcomes of the reported research have been evaluated on three benchmark datasets such as Kaggle, 2020-BRATS, and local collected images. The model achieved greater than 90% detection scores to prove the proposed model's effectiveness.

Brain Tumor Segmentation of MRI Images Using Processed Image Driven U-Net Architecture

Brain tumor segmentation seeks to separate healthy tissue from tumorous regions. This is an essential step in diagnosis and treatment planning to maximize the likelihood of successful treatment. Magnetic resonance imaging (MRI) provides detailed information about brain tumor anatomy, making it an important tool for effective diagnosis which is requisite to replace the existing manual detection system where patients rely on the skills and expertise of a human. In order to solve this problem, a brain tumor segmentation & detection system is proposed where experiments are tested on the collected BraTS 2018 dataset. This dataset contains four different MRI modalities for each patient as T1, T2, T1Gd, and FLAIR, and as an outcome, a segmented image and ground truth of tumor segmentation, i.e., class label, is provided. A fully automatic methodology to handle the task of segmentation of gliomas in pre-operative MRI scans is developed using a U-Net-based deep learning model. The first step is to transform input image data, which is further processed through various techniques—subset division, narrow object region, category brain slicing, watershed algorithm, and feature scaling was done. All these steps are implied before entering data into the U-Net Deep learning model. The U-Net Deep learning model is used to perform pixel label segmentation on the segment tumor region. The algorithm reached high-performance accuracy on the BraTS 2018 training, validation, as well as testing dataset. The proposed model achieved a dice coefficient of 0.9815, 0.9844, 0.9804, and 0.9954 on the testing dataset for sets HGG-1, HGG-2, HGG-3, and LGG-1, respectively.

A Systematic Review of Artificial Intelligence Techniques in Cancer Prediction and Diagnosis

Artificial intelligence has aided in the advancement of healthcare research. The availability of open-source healthcare statistics has prompted researchers to create applications that aid cancer detection and prognosis. Deep learning and machine learning models provide a reliable, rapid, and effective solution to deal with such challenging diseases in these circumstances. PRISMA guidelines had been used to select the articles published on the web of science, EBSCO, and EMBASE between 2009 and 2021. In this study, we performed an efficient search and included the research articles that employed AI-based learning approaches for cancer prediction. A total of 185 papers are considered impactful for cancer prediction using conventional machine and deep learning-based classifications. In addition, the survey also deliberated the work done by the different researchers and highlighted the limitations of the existing literature, and performed the comparison using various parameters such as prediction rate, accuracy, sensitivity, specificity, dice score, detection rate, area undercover, precision, recall, and F1-score. Five investigations have been designed, and solutions to those were explored. Although multiple techniques recommended in the literature have achieved great prediction results, still cancer mortality has not been reduced. Thus, more extensive research to deal with the challenges in the area of cancer prediction is required.

A pilot study of a machine-learning tool to assist in the diagnosis of hand arthritis

OBJECTIVE

Arthritis is a common condition, which frequently involves the hands. Patients with inflammatory arthritis have been shown to experience significant delays in diagnosis. We sought to develop and test a screening tool combining an image of a patient's hands, a short series of questions, and a single examination technique, to determine the most likely diagnosis in a patient presenting with hand arthritis. Machine learning techniques were used to develop separate algorithms for each component, which were combined to produce a diagnosis.

METHODS

280 consecutive new patients presenting to a Rheumatology practice with hand arthritis were enrolled. Each patient completed a 9-part questionnaire, had photographs taken of each hand, and had a single examination result recorded. The Rheumatologist diagnosis was recorded following a 45-minute consultation. The photograph algorithm was developed from 1000 previous hand images, and machine learning techniques were applied to the questionnaire results, training several models against the diagnosis from the Rheumatologist.

RESULTS

The combined algorithms in this study were able to predict inflammatory arthritis with an accuracy, precision, recall and specificity of 96·8%, 97·2%, 98·6% and 90·5% respectively. Similar results were found when inflammatory arthritis was subclassified into rheumatoid arthritis and psoriatic arthritis. The corresponding figures for osteoarthritis were 79·6%, 85·9%, 61·9% and 92·6%.

CONCLUSION

This study demonstrates a novel application combining image-processing and a patient questionnaire with applied machine-learning methods, to facilitate the diagnosis of patients presenting with hand arthritis. Preliminary results are encouraging for the application of such techniques in clinical practice. This article is protected by copyright. All rights reserved.

Introduction to radiomics and radiogenomics in neuro-oncology: implications and challenges

Neuro-oncology largely consists of malignancies of the brain and central nervous system including both primary as well as metastatic tumors. Currently, a significant clinical challenge in neuro-oncology is to tailor therapies for patients based on a priori knowledge of their survival outcome or treatment response to conventional or experimental therapies. Radiomics or the quantitative extraction of subvisual data from conventional radiographic imaging has recently emerged as a powerful data-driven approach to offer insights into clinically relevant questions related to diagnosis, prediction, prognosis, as well as assessing treatment response. Furthermore, radiogenomic approaches provide a mechanism to establish statistical correlations of radiomic features with point mutations and next-generation sequencing data to further leverage the potential of routine MRI scans to serve as "virtual biopsy" maps. In this review, we provide an introduction to radiomic and radiogenomic approaches in neuro-oncology, including a brief description of the workflow involving preprocessing, tumor segmentation, and extraction of "hand-crafted" features from the segmented region of interest, as well as identifying radiogenomic associations that could ultimately lead to the development of reliable prognostic and predictive models in neuro-oncology applications. Lastly, we discuss the promise of radiomics and radiogenomic approaches in personalizing treatment decisions in neuro-oncology, as well as the challenges with clinical adoption, which will rely heavily on their demonstrated resilience to nonstandardization in imaging protocols across sites and scanners, as well as in their ability to demonstrate reproducibility across large multi-institutional cohorts.

Molecular imaging and deep learning analysis of uMUC1 expression in response to chemotherapy in an orthotopic model of ovarian cancer

Artificial Intelligence (AI) algorithms including deep learning have recently demonstrated remarkable progress in image-recognition tasks. Here, we utilized AI for monitoring the expression of underglycosylated mucin 1 (uMUC1) tumor antigen, a biomarker for ovarian cancer progression and response to therapy, using contrast-enhanced in vivo imaging. This was done using a dual-modal (magnetic resonance and near infrared optical imaging) uMUC1-specific probe (termed MN-EPPT) consisted of iron-oxide magnetic nanoparticles (MN) conjugated to a uMUC1-specific peptide (EPPT) and labeled with a near-infrared fluorescent dye, Cy5.5. In vitro studies performed in uMUC1-expressing human ovarian cancer cell line SKOV3/Luc and control uMUC1low ES-2 cells showed preferential uptake on the probe by the high expressor (n = 3, p < .05). A decrease in MN-EPPT uptake by SKOV3/Luc cells in vitro due to uMUC1 downregulation after docetaxel therapy was paralleled by in vivo imaging studies that showed a reduction in probe accumulation in the docetaxel treated group (n = 5, p < .05). The imaging data were analyzed using deep learning-enabled segmentation and quantification of the tumor region of interest (ROI) from raw input MRI sequences by applying AI algorithms including a blend of Convolutional Neural Networks (CNN) and Fully Connected Neural Networks. We believe that the algorithms used in this study have the potential to improve studying and monitoring cancer progression, amongst other diseases.