Objective: We develop a computer-aided diagnosis (CAD) system using deep learning approaches for lesion detection and classification on whole-slide images (WSIs) with breast cancer. The deep features being distinguishing in classification from the convolutional neural networks (CNN) are demonstrated in this study to provide comprehensive interpretability for the proposed CAD system using pathological knowledge. Methods: In the experiment, a total of 186 slides of WSIs were collected and classified into three categories: Non-Carcinoma, Ductal Carcinoma in Situ (DCIS), and Invasive Ductal Carcinoma (IDC). Instead of conducting pixel-wise classification into three classes directly, we designed a hierarchical framework with the multi-view scheme that performs lesion detection for region proposal at higher magnification first and then conducts lesion classification at lower magnification for each detected lesion. Results: The slide-level accuracy rate for three-category classification reaches 90.8% (99/109) through 5-fold cross-validation and achieves 94.8% (73/77) on the testing set. The experimental results show that the morphological characteristics and co-occurrence properties learned by the deep learning models for lesion classification are accordant with the clinical rules in diagnosis. Conclusion: The pathological interpretability of the deep features not only enhances the reliability of the proposed CAD system to gain acceptance from medical specialists, but also facilitates the development of deep learning frameworks for various tasks in pathology. Significance: This paper presents a CAD system for pathological image analysis, which fills the clinical requirements and can be accepted by medical specialists with providing its interpretability from the pathological perspective.
We present ENHANCE, an open dataset with multiple annotations to complement the existing ISIC and PH2 skin lesion classification datasets. This dataset contains annotations of visual ABC (asymmetry, border, colour) features from non-expert annotation sources: undergraduate students, crowd workers from Amazon MTurk and classic image processing algorithms. In this paper we first analyse the correlations between the annotations and the diagnostic label of the lesion, as well as study the agreement between different annotation sources. Overall we find weak correlations of non-expert annotations with the diagnostic label, and low agreement between different annotation sources. We then study multi-task learning (MTL) with the annotations as additional labels, and show that non-expert annotations can improve (ensembles of) state-of-the-art convolutional neural networks via MTL. We hope that our dataset can be used in further research into multiple annotations and/or MTL. All data and models are available on Github: https://github.com/raumannsr/ENHANCE.
Deep learning has played a major role in the interpretation of dermoscopic images for detecting skin defects and abnormalities. However, current deep learning solutions for dermatological lesion analysis are typically limited in providing probabilistic predictions which highlights the importance of concerning uncertainties. This concept of uncertainty can provide a confidence level for each feature which prevents overconfident predictions with poor generalization on unseen data. In this paper, we propose an overall framework that jointly considers dermatological classification and uncertainty estimation together. The estimated confidence of each feature to avoid uncertain feature and undesirable shift, which are caused by environmental difference of input image, in the latent space is pooled from confidence network. Our qualitative results show that modeling uncertainties not only helps to quantify model confidence for each prediction but also helps classification layers to focus on confident features, therefore, improving the accuracy for dermatological lesion classification. We demonstrate the potential of the proposed approach in two state-of-the-art dermoscopic datasets (ISIC 2018 and ISIC 2019).
During the last years, computer vision-based diagnosis systems have been widely used in several hospitals and dermatology clinics, aiming at the early detection of malignant melanoma tumor, which is among the most frequent types of skin cancer. In this work, we present an automated diagnosis system based on the ABCD rule used in clinical diagnosis in order to discriminate benign from malignant skin lesions. First, to reduce the influence of small structures, a preprocessing step based on morphological and fast marching schemes is used. In the second step, an unsupervised approach for lesion segmentation is proposed. Iterative thresholding is applied to initialize level set automatically. As the detection of an automated border is an important step for the correctness of subsequent phases in the computerized melanoma recognition systems, we compare its accuracy with growcut and mean shift algorithms, and discuss how these results may influence in the following steps: the feature extraction and the final lesion classification. Relying on visual diagnosis four features: Asymmetry (A), Border (B), Color (C) and Diversity (D) are computed and used to construct a classification module based on artificial neural network for the recognition of malignant melanoma. This framework has been tested on a dermoscopic database [16] of 320 images. The classification results show an increasing true detection rate and a decreasing false positive rate.
The diagnosis of prostate cancer faces a problem with overdiagnosis that leads to damaging side effects due to unnecessary treatment. Research has shown that the use of multi-parametric magnetic resonance images to conduct biopsies can drastically help to mitigate the overdiagnosis, thus reducing the side effects on healthy patients. This study aims to investigate the use of deep learning techniques to explore computer-aid diagnosis based on MRI as input. Several diagnosis problems ranging from classification of lesions as being clinically significant or not to the detection and segmentation of lesions are addressed with deep learning based approaches. This thesis tackled two main problems regarding the diagnosis of prostate cancer. Firstly, XmasNet was used to conduct two large experiments on the classification of lesions. Secondly, detection and segmentation experiments were conducted, first on the prostate and afterward on the prostate cancer lesions. The former experiments explored the lesions through a two-dimensional space, while the latter explored models to work with three-dimensional inputs. For this task, the 3D models explored were the 3D U-Net and a pretrained 3D ResNet-18. A rigorous analysis of all these problems was conducted with a total of two networks, two cropping techniques, two resampling techniques, two crop sizes, five input sizes and data augmentations experimented for lesion classification. While for segmentation two models, two input sizes and data augmentations were experimented. However, while the binary classification of the clinical significance of lesions and the detection and segmentation of the prostate already achieve the desired results (0.870 AUC and 0.915 dice score respectively), the classification of the PIRADS score and the segmentation of lesions still have a large margin to improve (0.664 accuracy and 0.690 dice score respectively).
Deep learning has received extensive research interest in developing new medical image processing algorithms, and deep learning based models have been remarkably successful in a variety of medical imaging tasks to support disease detection and diagnosis. Despite the success, the further improvement of deep learning models in medical image analysis is majorly bottlenecked by the lack of large-sized and well-annotated datasets. In the past five years, many studies have focused on addressing this challenge. In this paper, we reviewed and summarized these recent studies to provide a comprehensive overview of applying deep learning methods in various medical image analysis tasks. Especially, we emphasize the latest progress and contributions of state-of-the-art unsupervised and semi-supervised deep learning in medical image analysis, which are summarized based on different application scenarios, including classification, segmentation, detection, and image registration. We also discuss the major technical challenges and suggest the possible solutions in future research efforts.
Skin cancer, the most commonly found human malignancy, is primarily diagnosed visually via dermoscopic analysis, biopsy, and histopathological examination. However, unlike other types of cancer, automated image classification of skin lesions is deemed more challenging due to the irregularity and variability in the lesions' appearances. In this work, we propose an adaptation of the Neural Style Transfer (NST) as a novel image pre-processing step for skin lesion classification problems. We represent each dermoscopic image as the style image and transfer the style of the lesion onto a homogeneous content image. This transfers the main variability of each lesion onto the same localized region, which allows us to integrate the generated images together and extract latent, low-rank style features via tensor decomposition. We train and cross-validate our model on a dermoscopic data set collected and preprocessed from the International Skin Imaging Collaboration (ISIC) database. We show that the classification performance based on the extracted tensor features using the style-transferred images significantly outperforms that of the raw images by more than 10%, and is also competitive with well-studied, pre-trained CNN models through transfer learning. Additionally, the tensor decomposition further identifies latent style clusters, which may provide clinical interpretation and insights.
In clinical applications, neural networks must focus on and highlight the most important parts of an input image. Soft-Attention mechanism enables a neural network toachieve this goal. This paper investigates the effectiveness of Soft-Attention in deep neural architectures. The central aim of Soft-Attention is to boost the value of important features and suppress the noise-inducing features. We compare the performance of VGG, ResNet, InceptionResNetv2 and DenseNet architectures with and without the Soft-Attention mechanism, while classifying skin lesions. The original network when coupled with Soft-Attention outperforms the baseline[16] by 4.7% while achieving a precision of 93.7% on HAM10000 dataset [25]. Additionally, Soft-Attention coupling improves the sensitivity score by 3.8% compared to baseline[31] and achieves 91.6% on ISIC-2017 dataset [2]. The code is publicly available at github.
Globally, Skin carcinoma is among the most lethal diseases. Millions of people are diagnosed with this cancer every year. Sill, early detection can decrease the medication cost and mortality rate substantially. The recent improvement in automated cancer classification using deep learning methods has reached a human-level performance requiring a large amount of annotated data assembled in one location, yet, finding such conditions usually is not feasible. Recently, federated learning (FL) has been proposed to train decentralized models in a privacy-preserved fashion depending on labeled data at the client-side, which is usually not available and costly. To address this, we propose \verb!FedPerl!, a semi-supervised federated learning method. Our method is inspired by peer learning from educational psychology and ensemble averaging from committee machines. FedPerl builds communities based on clients' similarities. Then it encourages communities members to learn from each other to generate more accurate pseudo labels for the unlabeled data. We also proposed the peer anonymization (PA) technique to anonymize clients. As a core component of our method, PA is orthogonal to other methods without additional complexity and reduces the communication cost while enhancing performance. Finally, we propose a dynamic peer-learning policy that controls the learning stream to avoid any degradation in the performance, especially for individual clients. Our experimental setup consists of 71,000 skin lesion images collected from 5 publicly available datasets. We test our method in four different scenarios in SSFL. With few annotated data, FedPerl is on par with a state-of-the-art method in skin lesion classification in the standard setup while outperforming SSFLs and the baselines by 1.8% and 15.8%, respectively. Also, it generalizes better to unseen clients while being less sensitive to noisy ones.
Deep convolutional neural network (DCNN) models have been widely explored for skin disease diagnosis and some of them have achieved the diagnostic outcomes comparable or even superior to those of dermatologists. However, broad implementation of DCNN in skin disease detection is hindered by small size and data imbalance of the publically accessible skin lesion datasets. This paper proposes a novel single-model based strategy for classification of skin lesions on small and imbalanced datasets. First, various DCNNs are trained on different small and imbalanced datasets to verify that the models with moderate complexity outperform the larger models. Second, regularization DropOut and DropBlock are added to reduce overfitting and a Modified RandAugment augmentation strategy is proposed to deal with the defects of sample underrepresentation in the small dataset. Finally, a novel Multi-Weighted New Loss (MWNL) function and an end-to-end cumulative learning strategy (CLS) are introduced to overcome the challenge of uneven sample size and classification difficulty and to reduce the impact of abnormal samples on training. By combining Modified RandAugment, MWNL and CLS, our single DCNN model method achieved the classification accuracy comparable or superior to those of multiple ensembling models on different dermoscopic image datasets. Our study shows that this method is able to achieve a high classification performance at a low cost of computational resources and inference time, potentially suitable to implement in mobile devices for automated screening of skin lesions and many other malignancies in low resource settings.
We introduce FELICIA (FEderated LearnIng with a CentralIzed Adversary) a generative mechanism enabling collaborative learning. In particular, we show how a data owner with limited and biased data could benefit from other data owners while keeping data from all the sources private. This is a common scenario in medical image analysis where privacy legislation prevents data from being shared outside local premises. FELICIA works for a large family of Generative Adversarial Networks (GAN) architectures including vanilla and conditional GANs as demonstrated in this work. We show that by using the FELICIA mechanism, a data owner with limited image samples can generate high-quality synthetic images with high utility while neither data owners has to provide access to its data. The sharing happens solely through a central discriminator that has access limited to synthetic data. Here, utility is defined as classification performance on a real test set. We demonstrate these benefits on several realistic healthcare scenarions using benchmark image datasets (MNIST, CIFAR-10) as well as on medical images for the task of skin lesion classification. With multiple experiments, we show that even in the worst cases, combining FELICIA with real data gracefully achieves performance on par with real data while most results significantly improves the utility.
Although deep convolutional neural networks (DCNNs) have achieved significant accuracy in skin lesion classification comparable or even superior to those of dermatologists, practical implementation of these models for skin cancer screening in low resource settings is hindered by their limitations in computational cost and training dataset. To overcome these limitations, we propose a low-cost and high-performance data augmentation strategy that includes two consecutive stages of augmentation search and network search. At the augmentation search stage, the augmentation strategy is optimized in the search space of Low-Cost-Augment (LCA) under the criteria of balanced accuracy (BACC) with 5-fold cross validation. At the network search stage, the DCNNs are fine-tuned with the full training set in order to select the model with the highest BACC. The efficiency of the proposed data augmentation strategy is verified on the HAM10000 dataset using EfficientNets as a baseline. With the proposed strategy, we are able to reduce the search space to 60 and achieve a high BACC of 0.853 by using a single DCNN model without external database, suitable to be implemented in mobile devices for DCNN-based skin lesion detection in low resource settings.
Skin cancer is considered to be the most common human malignancy. Around 5 million new cases of skin cancer are recorded in the United States annually. Early identification and evaluation of skin lesions is of great clinical significance, but the disproportionate dermatologist-patient ratio poses significant problem in most developing nations. Therefore a deep learning based architecture, known as SkiNet, is proposed with an objective to provide faster screening solution and assistance to newly trained physicians in the clinical diagnosis process. The main motive behind Skinet's design and development is to provide a white box solution, addressing a critical problem of trust and interpretability which is crucial for the wider adoption of Computer-aided diagnosis systems by the medical practitioners. SkiNet is a two-stage pipeline wherein the lesion segmentation is followed by the lesion classification. In our SkiNet methodology, Monte Carlo dropout and test time augmentation techniques have been employed to estimate epistemic and aleatoric uncertainty, while saliency-based methods are explored to provide post-hoc explanations of the deep learning models. The publicly available dataset, ISIC-2018, is used to perform experimentation and ablation studies. The results establish the robustness of the model on the traditional benchmarks while addressing the black-box nature of such models to alleviate the skepticism of medical practitioners by incorporating transparency and confidence to the model's prediction.
We present an automatic method for joint liver lesion segmentation and classification using a hierarchical fine-tuning framework. Our dataset is small, containing 332 2-D CT examinations with lesion annotated into 3 lesion types: cysts, hemangiomas, and metastases. Using a cascaded U-net that performs segmentation and classification simultaneously, we trained a strong lesion segmentation model on the dataset of MICCAI 2017 Liver Tumor Segmentation (LiTS) Challenge. We used the trained weights to fine-tune a slightly modified model to obtain improved lesion segmentation and classification, on the smaller dataset. Since pre-training was done with similar data on a related task, we were able to learn more representative features (especially higher-level features in the U-Net's encoder), and improve pixel-wise classification results. We show an improvement of over 10\% in Dice score and classification accuracy, compared to a baseline model. We further improve the classification performance by hierarchically freezing the encoder part of the network and achieve an improvement of over 15\% in Dice score and classification accuracy. We compare our results with an existing method and show an improvement of 14\% in the success rate and 12\% in the classification accuracy.
Mammography and ultrasound are extensively used by radiologists as complementary modalities to achieve better performance in breast cancer diagnosis. However, existing computer-aided diagnosis (CAD) systems for the breast are generally based on a single modality. In this work, we propose a deep-learning based method for classifying breast cancer lesions from their respective mammography and ultrasound images. We present various approaches and show a consistent improvement in performance when utilizing both modalities. The proposed approach is based on a GoogleNet architecture, fine-tuned for our data in two training steps. First, a distinct neural network is trained separately for each modality, generating high-level features. Then, the aggregated features originating from each modality are used to train a multimodal network to provide the final classification. In quantitative experiments, the proposed approach achieves an AUC of 0.94, outperforming state-of-the-art models trained over a single modality. Moreover, it performs similarly to an average radiologist, surpassing two out of four radiologists participating in a reader study. The promising results suggest that the proposed method may become a valuable decision support tool for breast radiologists.
Distinguishing visually similar objects like forged/authentic bills and healthy/unhealthy plants is beyond the capabilities of even the most sophisticated classifiers. We propose the use of multiplexed illumination to extend the range of objects that can be successfully classified. We construct a compact RGB-IR light stage that images samples under different combinations of illuminant position and colour. We then develop a methodology for selecting illumination patterns and training a classifier using the resulting imagery. We use the light stage to model and synthetically relight training samples, and propose a greedy pattern selection scheme that exploits this ability to train in simulation. We then apply the trained patterns to carry out fast classification of new objects. We demonstrate the approach on visually similar artificial and real fruit samples, showing a marked improvement compared with fixed-illuminant approaches as well as a more conventional code selection scheme. This work allows fast classification of previously indistinguishable objects, with potential applications in forgery detection, quality control in agriculture and manufacturing, and skin lesion classification.
Machine learning is widely used in developing computer-aided diagnosis (CAD) schemes of medical images. However, CAD usually computes large number of image features from the targeted regions, which creates a challenge of how to identify a small and optimal feature vector to build robust machine learning models. In this study, we investigate feasibility of applying a random projection algorithm to build an optimal feature vector from the initially CAD-generated large feature pool and improve performance of machine learning model. We assemble a retrospective dataset involving 1,487 cases of mammograms in which 644 cases have confirmed malignant mass lesions and 843 have benign lesions. A CAD scheme is first applied to segment mass regions and initially compute 181 features. Then, support vector machine (SVM) models embedded with several feature dimensionality reduction methods are built to predict likelihood of lesions being malignant. All SVM models are trained and tested using a leave-one-case-out cross-validation method. SVM generates a likelihood score of each segmented mass region depicting on one-view mammogram. By fusion of two scores of the same mass depicting on two-view mammograms, a case-based likelihood score is also evaluated. Comparing with the principle component analyses, nonnegative matrix factorization, and Chi-squared methods, SVM embedded with the random projection algorithm yielded a significantly higher case-based lesion classification performance with the area under ROC curve of 0.84+0.01 (p<0.02). The study demonstrates that the random project algorithm is a promising method to generate optimal feature vectors to help improve performance of machine learning models of medical images.
While data-driven approaches excel at many image analysis tasks, the performance of these approaches is often limited by a shortage of annotated data available for training. Recent work in semi-supervised learning has shown that meaningful representations of images can be obtained from training with large quantities of unlabeled data, and that these representations can improve the performance of supervised tasks. Here, we demonstrate that an unsupervised jigsaw learning task, in combination with supervised training, results in up to a 9.8% improvement in correctly classifying lesions in colonoscopy images when compared to a fully-supervised baseline. We additionally benchmark improvements in domain adaptation and out-of-distribution detection, and demonstrate that semi-supervised learning outperforms supervised learning in both cases. In colonoscopy applications, these metrics are important given the skill required for endoscopic assessment of lesions, the wide variety of endoscopy systems in use, and the homogeneity that is typical of labeled datasets.
Skin cancer affects a large population every year -- automated skin cancer detection algorithms can thus greatly help clinicians. Prior efforts involving deep learning models have high detection accuracy. However, most of the models have a large number of parameters, with some works even using an ensemble of models to achieve good accuracy. In this paper, we investigate a recently proposed pruning technique called Lottery Ticket Hypothesis. We find that iterative pruning of the network resulted in improved accuracy, compared to that of the unpruned network, implying that -- the lottery ticket hypothesis can be applied to the problem of skin cancer detection and this hypothesis can result in a smaller network for inference. We also examine the accuracy across sub-groups -- created by gender and age -- and it was found that some sub-groups show a larger increase in accuracy than others.
Skin cancer is the most common cancer in the existing world constituting one-third of the cancer cases. Benign skin cancers are not fatal, can be cured with proper medication. But it is not the same as the malignant skin cancers. In the case of malignant melanoma, in its peak stage, the maximum life expectancy is less than or equal to 5 years. But, it can be cured if detected in early stages. Though there are numerous clinical procedures, the accuracy of diagnosis falls between 49% to 81% and is time-consuming. So, dermoscopy has been brought into the picture. It helped in increasing the accuracy of diagnosis but could not demolish the error-prone behaviour. A quick and less error-prone solution is needed to diagnose this majorly growing skin cancer. This project deals with the usage of deep learning in skin lesion classification. In this project, an automated model for skin lesion classification using dermoscopic images has been developed with CNN(Convolution Neural Networks) as a training model. Convolution neural networks are known for capturing features of an image. So, they are preferred in analyzing medical images to find the characteristics that drive the model towards success. Techniques like data augmentation for tackling class imbalance, segmentation for focusing on the region of interest and 10-fold cross-validation to make the model robust have been brought into the picture. This project also includes usage of certain preprocessing techniques like brightening the images using piece-wise linear transformation function, grayscale conversion of the image, resize the image. This project throws a set of valuable insights on how the accuracy of the model hikes with the bringing of new input strategies, preprocessing techniques. The best accuracy this model could achieve is 0.886.