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"cancer detection": models, code, and papers

Cross-view Relation Networks for Mammogram Mass Detection

Jul 01, 2019
Jiechao Ma, Sen Liang, Xiang Li, Hongwei Li, Bjoern H Menze, Rongguo Zhang, Wei-Shi Zheng

Mammogram is the most effective imaging modality for the mass lesion detection of breast cancer at the early stage. The information from the two paired views (i.e., medio-lateral oblique and cranio-caudal) are highly relational and complementary, and this is crucial for doctors' decisions in clinical practice. However, existing mass detection methods do not consider jointly learning effective features from the two relational views. To address this issue, this paper proposes a novel mammogram mass detection framework, termed Cross-View Relation Region-based Convolutional Neural Networks (CVR-RCNN). The proposed CVR-RCNN is expected to capture the latent relation information between the corresponding mass region of interests (ROIs) from the two paired views. Evaluations on a new large-scale private dataset and a public mammogram dataset show that the proposed CVR-RCNN outperforms existing state-of-the-art mass detection methods. Meanwhile, our experimental results suggest that incorporating the relation information across two views helps to train a superior detection model, which is a promising avenue for mammogram mass detection.


Transfer learning with class-weighted and focal loss function for automatic skin cancer classification

Sep 13, 2020
Duyen N. T. Le, Hieu X. Le, Lua T. Ngo, Hoan T. Ngo

Skin cancer is by far in top-3 of the world's most common cancer. Among different skin cancer types, melanoma is particularly dangerous because of its ability to metastasize. Early detection is the key to success in skin cancer treatment. However, skin cancer diagnosis is still a challenge, even for experienced dermatologists, due to strong resemblances between benign and malignant lesions. To aid dermatologists in skin cancer diagnosis, we developed a deep learning system that can effectively and automatically classify skin lesions into one of the seven classes: (1) Actinic Keratoses, (2) Basal Cell Carcinoma, (3) Benign Keratosis, (4) Dermatofibroma, (5) Melanocytic nevi, (6) Melanoma, (7) Vascular Skin Lesion. The HAM10000 dataset was used to train the system. An end-to-end deep learning process, transfer learning technique, utilizing multiple pre-trained models, combining with class-weighted and focal loss were applied for the classification process. The result was that our ensemble of modified ResNet50 models can classify skin lesions into one of the seven classes with top-1, top-2 and top-3 accuracy 93%, 97% and 99%, respectively. This deep learning system can potentially be integrated into computer-aided diagnosis systems that support dermatologists in skin cancer diagnosis.

* 7 pages, 8 figures 

Towards a Computed-Aided Diagnosis System in Colonoscopy: Automatic Polyp Segmentation Using Convolution Neural Networks

Jan 15, 2021
Patrick Brandao, Odysseas Zisimopoulos, Evangelos Mazomenos, Gastone Ciuti, Jorge Bernal, Marco Visentini-Scarzanella, Arianna Menciassi, Paolo Dario, Anastasios Koulaouzidis, Alberto Arezzo, David J Hawkes, Danail Stoyanov

Early diagnosis is essential for the successful treatment of bowel cancers including colorectal cancer (CRC) and capsule endoscopic imaging with robotic actuation can be a valuable diagnostic tool when combined with automated image analysis. We present a deep learning rooted detection and segmentation framework for recognizing lesions in colonoscopy and capsule endoscopy images. We restructure established convolution architectures, such as VGG and ResNets, by converting them into fully-connected convolution networks (FCNs), fine-tune them and study their capabilities for polyp segmentation and detection. We additionally use Shape from-Shading (SfS) to recover depth and provide a richer representation of the tissue's structure in colonoscopy images. Depth is incorporated into our network models as an additional input channel to the RGB information and we demonstrate that the resulting network yields improved performance. Our networks are tested on publicly available datasets and the most accurate segmentation model achieved a mean segmentation IU of 47.78% and 56.95% on the ETIS-Larib and CVC-Colon datasets, respectively. For polyp detection, the top performing models we propose surpass the current state of the art with detection recalls superior to 90% for all datasets tested. To our knowledge, we present the first work to use FCNs for polyp segmentation in addition to proposing a novel combination of SfS and RGB that boosts performance

* Journal of Medical Robotics Research, Volume 03, No. 02, 1840002 (2018) G 
* 10 pages, 6 figures 

Cancer image classification based on DenseNet model

Nov 23, 2020
Ziliang Zhong, Muhang Zheng, Huafeng Mai, Jianan Zhao, Xinyi Liu

Computer-aided diagnosis establishes methods for robust assessment of medical image-based examination. Image processing introduced a promising strategy to facilitate disease classification and detection while diminishing unnecessary expenses. In this paper, we propose a novel metastatic cancer image classification model based on DenseNet Block, which can effectively identify metastatic cancer in small image patches taken from larger digital pathology scans. We evaluate the proposed approach to the slightly modified version of the PatchCamelyon (PCam) benchmark dataset. The dataset is the slightly modified version of the PatchCamelyon (PCam) benchmark dataset provided by Kaggle competition, which packs the clinically-relevant task of metastasis detection into a straight-forward binary image classification task. The experiments indicated that our model outperformed other classical methods like Resnet34, Vgg19. Moreover, we also conducted data augmentation experiment and study the relationship between Batches processed and loss value during the training and validation process.

* 2004-present Journal of Physics: Conference Series 

Data Augmentation for Detection of Architectural Distortion in Digital Mammography using Deep Learning Approach

Jul 06, 2018
Arthur C. Costa, Helder C. R. Oliveira, Juliana H. Catani, Nestor de Barros, Carlos F. E. Melo, Marcelo A. C. Vieira

Early detection of breast cancer can increase treatment efficiency. Architectural Distortion (AD) is a very subtle contraction of the breast tissue and may represent the earliest sign of cancer. Since it is very likely to be unnoticed by radiologists, several approaches have been proposed over the years but none using deep learning techniques. To train a Convolutional Neural Network (CNN), which is a deep neural architecture, is necessary a huge amount of data. To overcome this problem, this paper proposes a data augmentation approach applied to clinical image dataset to properly train a CNN. Results using receiver operating characteristic analysis showed that with a very limited dataset we could train a CNN to detect AD in digital mammography with area under the curve (AUC = 0.74).


Joint 2D-3D Breast Cancer Classification

Feb 27, 2020
Gongbo Liang, Xiaoqin Wang, Yu Zhang, Xin Xing, Hunter Blanton, Tawfiq Salem, Nathan Jacobs

Breast cancer is the malignant tumor that causes the highest number of cancer deaths in females. Digital mammograms (DM or 2D mammogram) and digital breast tomosynthesis (DBT or 3D mammogram) are the two types of mammography imagery that are used in clinical practice for breast cancer detection and diagnosis. Radiologists usually read both imaging modalities in combination; however, existing computer-aided diagnosis tools are designed using only one imaging modality. Inspired by clinical practice, we propose an innovative convolutional neural network (CNN) architecture for breast cancer classification, which uses both 2D and 3D mammograms, simultaneously. Our experiment shows that the proposed method significantly improves the performance of breast cancer classification. By assembling three CNN classifiers, the proposed model achieves 0.97 AUC, which is 34.72% higher than the methods using only one imaging modality.

* Accepted by IEEE International Conference of Bioinformatics and Biomedicine (BIBM), 2019 

Scalable privacy-preserving cancer type prediction with homomorphic encryption

Apr 12, 2022
Esha Sarkar, Eduardo Chielle, Gamze Gursoy, Leo Chen, Mark Gerstein, Michail Maniatakos

Machine Learning (ML) alleviates the challenges of high-dimensional data analysis and improves decision making in critical applications like healthcare. Effective cancer type from high-dimensional genetic mutation data can be useful for cancer diagnosis and treatment, if the distinguishable patterns between cancer types are identified. At the same time, analysis of high-dimensional data is computationally expensive and is often outsourced to cloud services. Privacy concerns in outsourced ML, especially in the field of genetics, motivate the use of encrypted computation, like Homomorphic Encryption (HE). But restrictive overheads of encrypted computation deter its usage. In this work, we explore the challenges of privacy preserving cancer detection using a real-world dataset consisting of more than 2 million genetic information for several cancer types. Since the data is inherently high-dimensional, we explore smaller ML models for cancer prediction to enable fast inference in the privacy preserving domain. We develop a solution for privacy preserving cancer inference which first leverages the domain knowledge on somatic mutations to efficiently encode genetic mutations and then uses statistical tests for feature selection. Our logistic regression model, built using our novel encoding scheme, achieves 0.98 micro-average area under curve with 13% higher test accuracy than similar studies. We exhaustively test our model's predictive capabilities by analyzing the genes used by the model. Furthermore, we propose a fast matrix multiplication algorithm that can efficiently handle high-dimensional data. Experimental results show that, even with 40,000 features, our proposed matrix multiplication algorithm can speed up concurrent inference of multiple individuals by approximately 10x and inference of a single individual by approximately 550x, in comparison to standard matrix multiplication.


Lesion detection in contrast enhanced spectral mammography

Jul 20, 2022
Clément Jailin, Pablo Milioni, Zhijin Li, Răzvan Iordache, Serge Muller

Background \& purpose: The recent emergence of neural networks models for the analysis of breast images has been a breakthrough in computer aided diagnostic. This approach was not yet developed in Contrast Enhanced Spectral Mammography (CESM) where access to large databases is complex. This work proposes a deep-learning-based Computer Aided Diagnostic development for CESM recombined images able to detect lesions and classify cases. Material \& methods: A large CESM diagnostic dataset with biopsy-proven lesions was collected from various hospitals and different acquisition systems. The annotated data were split on a patient level for the training (55%), validation (15%) and test (30%) of a deep neural network with a state-of-the-art detection architecture. Free Receiver Operating Characteristic (FROC) was used to evaluate the model for the detection of 1) all lesions, 2) biopsied lesions and 3) malignant lesions. ROC curve was used to evaluate breast cancer classification. The metrics were finally compared to clinical results. Results: For the evaluation of the malignant lesion detection, at high sensitivity (Se>0.95), the false positive rate was at 0.61 per image. For the classification of malignant cases, the model reached an Area Under the Curve (AUC) in the range of clinical CESM diagnostic results. Conclusion: This CAD is the first development of a lesion detection and classification model for CESM images. Trained on a large dataset, it has the potential to be used for helping the management of biopsy decision and for helping the radiologist detecting complex lesions that could modify the clinical treatment.

* Sixteenth International Workshop on Breast Imaging, May 2022, Leuven, Belgium. pp.24 

Machine Intelligence-Driven Classification of Cancer Patients-Derived Extracellular Vesicles using Fluorescence Correlation Spectroscopy: Results from a Pilot Study

Feb 01, 2022
Abicumaran Uthamacumaran, Mohamed Abdouh, Kinshuk Sengupta, Zu-hua Gao, Stefano Forte, Thupten Tsering, Julia V Burnier, Goffredo Arena

Patient-derived extracellular vesicles (EVs) that contains a complex biological cargo is a valuable source of liquid biopsy diagnostics to aid in early detection, cancer screening, and precision nanotherapeutics. In this study, we predicted that coupling cancer patient blood-derived EVs to time-resolved spectroscopy and artificial intelligence (AI) could provide a robust cancer screening and follow-up tools. Methods: Fluorescence correlation spectroscopy (FCS) measurements were performed on 24 blood samples-derived EVs. Blood samples were obtained from 15 cancer patients (presenting 5 different types of cancers), and 9 healthy controls (including patients with benign lesions). The obtained FCS autocorrelation spectra were processed into power spectra using the Fast-Fourier Transform algorithm and subjected to various machine learning algorithms to distinguish cancer spectra from healthy control spectra. Results and Applications: The performance of AdaBoost Random Forest (RF) classifier, support vector machine, and multilayer perceptron, were tested on selected frequencies in the N=118 power spectra. The RF classifier exhibited a 90% classification accuracy and high sensitivity and specificity in distinguishing the FCS power spectra of cancer patients from those of healthy controls. Further, an image convolutional neural network (CNN), ResNet network, and a quantum CNN were assessed on the power spectral images as additional validation tools. All image-based CNNs exhibited a nearly equal classification performance with an accuracy of roughly 82% and reasonably high sensitivity and specificity scores. Our pilot study demonstrates that AI-algorithms coupled to time-resolved FCS power spectra can accurately and differentially classify the complex patient-derived EVs from different cancer samples of distinct tissue subtypes.

* 23 pages, 6 figures 

Scalable Reinforcement-Learning-Based Neural Architecture Search for Cancer Deep Learning Research

Sep 01, 2019
Prasanna Balaprakash, Romain Egele, Misha Salim, Stefan Wild, Venkatram Vishwanath, Fangfang Xia, Tom Brettin, Rick Stevens

Cancer is a complex disease, the understanding and treatment of which are being aided through increases in the volume of collected data and in the scale of deployed computing power. Consequently, there is a growing need for the development of data-driven and, in particular, deep learning methods for various tasks such as cancer diagnosis, detection, prognosis, and prediction. Despite recent successes, however, designing high-performing deep learning models for nonimage and nontext cancer data is a time-consuming, trial-and-error, manual task that requires both cancer domain and deep learning expertise. To that end, we develop a reinforcement-learning-based neural architecture search to automate deep-learning-based predictive model development for a class of representative cancer data. We develop custom building blocks that allow domain experts to incorporate the cancer-data-specific characteristics. We show that our approach discovers deep neural network architectures that have significantly fewer trainable parameters, shorter training time, and accuracy similar to or higher than those of manually designed architectures. We study and demonstrate the scalability of our approach on up to 1,024 Intel Knights Landing nodes of the Theta supercomputer at the Argonne Leadership Computing Facility.

* SC '19: IEEE/ACM International Conference on High Performance Computing, Networking, Storage and Analysis, November 17--22, 2019, Denver, CO