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"cancer detection": models, code, and papers

Explainable Disease Classification via weakly-supervised segmentation

Aug 24, 2020
Aniket Joshi, Gaurav Mishra, Jayanthi Sivaswamy

Deep learning based approaches to Computer Aided Diagnosis (CAD) typically pose the problem as an image classification (Normal or Abnormal) problem. These systems achieve high to very high accuracy in specific disease detection for which they are trained but lack in terms of an explanation for the provided decision/classification result. The activation maps which correspond to decisions do not correlate well with regions of interest for specific diseases. This paper examines this problem and proposes an approach which mimics the clinical practice of looking for an evidence prior to diagnosis. A CAD model is learnt using a mixed set of information: class labels for the entire training set of images plus a rough localisation of suspect regions as an extra input for a smaller subset of training images for guiding the learning. The proposed approach is illustrated with detection of diabetic macular edema (DME) from OCT slices. Results of testing on on a large public dataset show that with just a third of images with roughly segmented fluid filled regions, the classification accuracy is on par with state of the art methods while providing a good explanation in the form of anatomically accurate heatmap /region of interest. The proposed solution is then adapted to Breast Cancer detection from mammographic images. Good evaluation results on public datasets underscores the generalisability of the proposed solution.


Segmentation and ABCD rule extraction for skin tumors classification

Jun 08, 2021
Mahammed Messadi, Hocine Cherifi, Abdelhafid Bessaid

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.

* Journal of Convergence for Information Technology, 2014 

Segmentation of Breast Microcalcifications: A Multi-Scale Approach

Feb 01, 2021
Chrysostomos Marasinou, Bo Li, Jeremy Paige, Akinyinka Omigbodun, Noor Nakhaei, Anne Hoyt, William Hsu

Accurate characterization of microcalcifications (MCs) in 2D full-field digital screening mammography is a necessary step towards reducing diagnostic uncertainty associated with the callback of women with suspicious MCs. Quantitative analysis of MCs has the potential to better identify MCs that have a higher likelihood of corresponding to invasive cancer. However, automated identification and segmentation of MCs remains a challenging task with high false positive rates. We present Hessian Difference of Gaussians Regression (HDoGReg), a two stage multi-scale approach to MC segmentation. Candidate high optical density objects are first delineated using blob detection and Hessian analysis. A regression convolutional network, trained to output a function with higher response near MCs, chooses the objects which constitute actual MCs. The method is trained and validated on 435 mammograms from two separate datasets. HDoGReg achieved a mean intersection over the union of 0.670$\pm$0.121 per image, intersection over the union per MC object of 0.607$\pm$0.250 and true positive rate of 0.744 at 0.4 false positive detections per $cm^2$. The results of HDoGReg perform better when compared to state-of-the-art MC segmentation and detection methods.

* Electronic Preprint version 1 

Deep Learning Ensembles for Melanoma Recognition in Dermoscopy Images

Oct 18, 2016
Noel Codella, Quoc-Bao Nguyen, Sharath Pankanti, David Gutman, Brian Helba, Allan Halpern, John R. Smith

Melanoma is the deadliest form of skin cancer. While curable with early detection, only highly trained specialists are capable of accurately recognizing the disease. As expertise is in limited supply, automated systems capable of identifying disease could save lives, reduce unnecessary biopsies, and reduce costs. Toward this goal, we propose a system that combines recent developments in deep learning with established machine learning approaches, creating ensembles of methods that are capable of segmenting skin lesions, as well as analyzing the detected area and surrounding tissue for melanoma detection. The system is evaluated using the largest publicly available benchmark dataset of dermoscopic images, containing 900 training and 379 testing images. New state-of-the-art performance levels are demonstrated, leading to an improvement in the area under receiver operating characteristic curve of 7.5% (0.843 vs. 0.783), in average precision of 4% (0.649 vs. 0.624), and in specificity measured at the clinically relevant 95% sensitivity operating point 2.9 times higher than the previous state-of-the-art (36.8% specificity compared to 12.5%). Compared to the average of 8 expert dermatologists on a subset of 100 test images, the proposed system produces a higher accuracy (76% vs. 70.5%), and specificity (62% vs. 59%) evaluated at an equivalent sensitivity (82%).

* IBM Journal of Research and Development, vol. 61, no. 4/5, 2017 
* URL for the IBM Journal of Research and Development: 

A Feature Transfer Enabled Multi-Task Deep Learning Model on Medical Imaging

Jun 05, 2019
Fei Gao, Hyunsoo Yoon, Teresa Wu, Xianghua Chu

Object detection, segmentation and classification are three common tasks in medical image analysis. Multi-task deep learning (MTL) tackles these three tasks jointly, which provides several advantages saving computing time and resources and improving robustness against overfitting. However, existing multitask deep models start with each task as an individual task and integrate parallelly conducted tasks at the end of the architecture with one cost function. Such architecture fails to take advantage of the combined power of the features from each individual task at an early stage of the training. In this research, we propose a new architecture, FTMTLNet, an MTL enabled by feature transferring. Traditional transfer learning deals with the same or similar task from different data sources (a.k.a. domain). The underlying assumption is that the knowledge gained from source domains may help the learning task on the target domain. Our proposed FTMTLNet utilizes the different tasks from the same domain. Considering features from the tasks are different views of the domain, the combined feature maps can be well exploited using knowledge from multiple views to enhance the generalizability. To evaluate the validity of the proposed approach, FTMTLNet is compared with models from literature including 8 classification models, 4 detection models and 3 segmentation models using a public full field digital mammogram dataset for breast cancer diagnosis. Experimental results show that the proposed FTMTLNet outperforms the competing models in classification and detection and has comparable results in segmentation.


Multimodal Spatial Attention Module for Targeting Multimodal PET-CT Lung Tumor Segmentation

Aug 06, 2020
Xiaohang Fu, Lei Bi, Ashnil Kumar, Michael Fulham, Jinman Kim

Multimodal positron emission tomography-computed tomography (PET-CT) is used routinely in the assessment of cancer. PET-CT combines the high sensitivity for tumor detection with PET and anatomical information from CT. Tumor segmentation is a critical element of PET-CT but at present, there is not an accurate automated segmentation method. Segmentation tends to be done manually by different imaging experts and it is labor-intensive and prone to errors and inconsistency. Previous automated segmentation methods largely focused on fusing information that is extracted separately from the PET and CT modalities, with the underlying assumption that each modality contains complementary information. However, these methods do not fully exploit the high PET tumor sensitivity that can guide the segmentation. We introduce a multimodal spatial attention module (MSAM) that automatically learns to emphasize regions (spatial areas) related to tumors and suppress normal regions with physiologic high-uptake. The resulting spatial attention maps are subsequently employed to target a convolutional neural network (CNN) for segmentation of areas with higher tumor likelihood. Our MSAM can be applied to common backbone architectures and trained end-to-end. Our experimental results on two clinical PET-CT datasets of non-small cell lung cancer (NSCLC) and soft tissue sarcoma (STS) validate the effectiveness of the MSAM in these different cancer types. We show that our MSAM, with a conventional U-Net backbone, surpasses the state-of-the-art lung tumor segmentation approach by a margin of 7.6% in Dice similarity coefficient (DSC).


DCGANs for Realistic Breast Mass Augmentation in X-ray Mammography

Sep 04, 2019
Basel Alyafi, Oliver Diaz, Robert Marti

Early detection of breast cancer has a major contribution to curability, and using mammographic images, this can be achieved non-invasively. Supervised deep learning, the dominant CADe tool currently, has played a great role in object detection in computer vision, but it suffers from a limiting property: the need of a large amount of labelled data. This becomes stricter when it comes to medical datasets which require high-cost and time-consuming annotations. Furthermore, medical datasets are usually imbalanced, a condition that often hinders classifiers performance. The aim of this paper is to learn the distribution of the minority class to synthesise new samples in order to improve lesion detection in mammography. Deep Convolutional Generative Adversarial Networks (DCGANs) can efficiently generate breast masses. They are trained on increasing-size subsets of one mammographic dataset and used to generate diverse and realistic breast masses. The effect of including the generated images and/or applying horizontal and vertical flipping is tested in an environment where a 1:10 imbalanced dataset of masses and normal tissue patches is classified by a fully-convolutional network. A maximum of ~ 0:09 improvement of F1 score is reported by using DCGANs along with flipping augmentation over using the original images. We show that DCGANs can be used for synthesising photo-realistic breast mass patches with considerable diversity. It is demonstrated that appending synthetic images in this environment, along with flipping, outperforms the traditional augmentation method of flipping solely, offering faster improvements as a function of the training set size.

* 4 pages, 4 figures, SPIE Medical Imaging 2020 Conference 

Deep Cytometry

Apr 09, 2019
Yueqin Li, Ata Mahjoubfar, Claire Lifan Chen, Kayvan Reza Niazi, Li Pei, Bahram Jalali

Deep learning has achieved spectacular performance in image and speech recognition and synthesis. It outperforms other machine learning algorithms in problems where large amounts of data are available. In the area of measurement technology, instruments based on the Photonic Time Stretch have established record real-time measurement throughput in spectroscopy, optical coherence tomography, and imaging flow cytometry. These extreme-throughput instruments generate approximately 1 Tbit/s of continuous measurement data and have led to the discovery of rare phenomena in nonlinear and complex systems as well as new types of biomedical instruments. Owing to the abundance of data they generate, time stretch instruments are a natural fit to deep learning classification. Previously we had shown that high-throughput label-free cell classification with high accuracy can be achieved through a combination of time stretch microscopy, image processing and feature extraction, followed by deep learning for finding cancer cells in the blood. Such a technology holds promise for early detection of primary cancer or metastasis. Here we describe a new implementation of deep learning which entirely avoids the computationally costly image processing and feature extraction pipeline. The improvement in computational efficiency makes this new technology suitable for cell sorting via deep learning. Our neural network takes less than a millisecond to classify the cells, fast enough to provide a decision to a cell sorter. We demonstrate the applicability of our new method in the classification of OT-II white blood cells and SW-480 epithelial cancer cells with more than 95\% accuracy in a label-free fashion.


Understanding Adversarial Attacks on Deep Learning Based Medical Image Analysis Systems

Jul 24, 2019
Xingjun Ma, Yuhao Niu, Lin Gu, Yisen Wang, Yitian Zhao, James Bailey, Feng Lu

Deep neural networks (DNNs) have become popular for medical image analysis tasks like cancer diagnosis and lesion detection. However, a recent study demonstrates that medical deep learning systems can be compromised by carefully-engineered adversarial examples/attacks, i.e., small imperceptible perturbations can fool DNNs to predict incorrectly. This raises safety concerns about the deployment of deep learning systems in clinical settings. In this paper, we provide a deeper understanding of adversarial examples in the context of medical images. We find that medical DNN models can be more vulnerable to adversarial attacks compared to natural ones from three different viewpoints: 1) medical image DNNs that have only a few classes are generally easier to be attacked; 2) the complex biological textures of medical images may lead to more vulnerable regions; and most importantly, 3) state-of-the-art deep networks designed for large-scale natural image processing can be overparameterized for medical imaging tasks and result in high vulnerability to adversarial attacks. Surprisingly, we also find that medical adversarial attacks can be easily detected, i.e., simple detectors can achieve over 98% detection AUCs against state-of-the-art attacks, due to their fundamental feature difference from normal examples. We show this is because adversarial attacks tend to attack a wide spread area outside the pathological regions, which results in deep features that are fundamentally different and easily separable from normal features. We believe these findings may be a useful basis to approach the design of secure medical deep learning systems.

* 15 pages, 10 figures