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"cancer detection": models, code, and papers

Assessing generalisability of deep learning-based polyp detection and segmentation methods through a computer vision challenge

Feb 24, 2022
Sharib Ali, Noha Ghatwary, Debesh Jha, Ece Isik-Polat, Gorkem Polat, Chen Yang, Wuyang Li, Adrian Galdran, Miguel-Ángel González Ballester, Vajira Thambawita, Steven Hicks, Sahadev Poudel, Sang-Woong Lee, Ziyi Jin, Tianyuan Gan, ChengHui Yu, JiangPeng Yan, Doyeob Yeo, Hyunseok Lee, Nikhil Kumar Tomar, Mahmood Haithmi, Amr Ahmed, Michael A. Riegler, Christian Daul, Pål Halvorsen, Jens Rittscher, Osama E. Salem, Dominique Lamarque, Renato Cannizzaro, Stefano Realdon, Thomas de Lange, James E. East

Polyps are well-known cancer precursors identified by colonoscopy. However, variability in their size, location, and surface largely affect identification, localisation, and characterisation. Moreover, colonoscopic surveillance and removal of polyps (referred to as polypectomy ) are highly operator-dependent procedures. There exist a high missed detection rate and incomplete removal of colonic polyps due to their variable nature, the difficulties to delineate the abnormality, the high recurrence rates, and the anatomical topography of the colon. There have been several developments in realising automated methods for both detection and segmentation of these polyps using machine learning. However, the major drawback in most of these methods is their ability to generalise to out-of-sample unseen datasets that come from different centres, modalities and acquisition systems. To test this hypothesis rigorously we curated a multi-centre and multi-population dataset acquired from multiple colonoscopy systems and challenged teams comprising machine learning experts to develop robust automated detection and segmentation methods as part of our crowd-sourcing Endoscopic computer vision challenge (EndoCV) 2021. In this paper, we analyse the detection results of the four top (among seven) teams and the segmentation results of the five top teams (among 16). Our analyses demonstrate that the top-ranking teams concentrated on accuracy (i.e., accuracy > 80% on overall Dice score on different validation sets) over real-time performance required for clinical applicability. We further dissect the methods and provide an experiment-based hypothesis that reveals the need for improved generalisability to tackle diversity present in multi-centre datasets.

* 26 pages 
  
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Act Like a Radiologist: Towards Reliable Multi-view Correspondence Reasoning for Mammogram Mass Detection

May 21, 2021
Yuhang Liu, Fandong Zhang, Chaoqi Chen, Siwen Wang, Yizhou Wang, Yizhou Yu

Mammogram mass detection is crucial for diagnosing and preventing the breast cancers in clinical practice. The complementary effect of multi-view mammogram images provides valuable information about the breast anatomical prior structure and is of great significance in digital mammography interpretation. However, unlike radiologists who can utilize the natural reasoning ability to identify masses based on multiple mammographic views, how to endow the existing object detection models with the capability of multi-view reasoning is vital for decision-making in clinical diagnosis but remains the boundary to explore. In this paper, we propose an Anatomy-aware Graph convolutional Network (AGN), which is tailored for mammogram mass detection and endows existing detection methods with multi-view reasoning ability. The proposed AGN consists of three steps. Firstly, we introduce a Bipartite Graph convolutional Network (BGN) to model the intrinsic geometric and semantic relations of ipsilateral views. Secondly, considering that the visual asymmetry of bilateral views is widely adopted in clinical practice to assist the diagnosis of breast lesions, we propose an Inception Graph convolutional Network (IGN) to model the structural similarities of bilateral views. Finally, based on the constructed graphs, the multi-view information is propagated through nodes methodically, which equips the features learned from the examined view with multi-view reasoning ability. Experiments on two standard benchmarks reveal that AGN significantly exceeds the state-of-the-art performance. Visualization results show that AGN provides interpretable visual cues for clinical diagnosis.

* Accepted by IEEE Transactions on Pattern Analysis and Machine Intelligence (TPAMI) 
  
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Deep Learning Enables Automatic Detection and Segmentation of Brain Metastases on Multi-Sequence MRI

Mar 18, 2019
Endre Grøvik, Darvin Yi, Michael Iv, Elisabeth Tong, Daniel L. Rubin, Greg Zaharchuk

Detecting and segmenting brain metastases is a tedious and time-consuming task for many radiologists, particularly with the growing use of multi-sequence 3D imaging. This study demonstrates automated detection and segmentation of brain metastases on multi-sequence MRI using a deep learning approach based on a fully convolution neural network (CNN). In this retrospective study, a total of 156 patients with brain metastases from several primary cancers were included. Pre-therapy MR images (1.5T and 3T) included pre- and post-gadolinium T1-weighted 3D fast spin echo, post-gadolinium T1-weighted 3D axial IR-prepped FSPGR, and 3D fluid attenuated inversion recovery. The ground truth was established by manual delineation by two experienced neuroradiologists. CNN training/development was performed using 100 and 5 patients, respectively, with a 2.5D network based on a GoogLeNet architecture. The results were evaluated in 51 patients, equally separated into those with few (1-3), multiple (4-10), and many (>10) lesions. Network performance was evaluated using precision, recall, Dice/F1 score, and ROC-curve statistics. For an optimal probability threshold, detection and segmentation performance was assessed on a per metastasis basis. The area under the ROC-curve (AUC), averaged across all patients, was 0.98. The AUC in the subgroups was 0.99, 0.97, and 0.97 for patients having 1-3, 4-10, and >10 metastases, respectively. Using an average optimal probability threshold determined by the development set, precision, recall, and Dice-score were 0.79, 0.53, and 0.79, respectively. At the same probability threshold, the network showed an average false positive rate of 8.3/patient (no lesion-size limit) and 3.4/patient (10 mm3 lesion size limit). In conclusion, a deep learning approach using multi-sequence MRI can aid in the detection and segmentation of brain metastases.

  
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A Novel Low-Complexity Framework in Ultra-Wideband Imaging for Breast Cancer Detection

Sep 08, 2017
Yasaman Ettefagh, Mohammad Hossein Moghaddam, Saeed Vahidian

In this research work, a novel framework is pro- posed as an efficient successor to traditional imaging methods for breast cancer detection in order to decrease the computational complexity. In this framework, the breast is devided into seg- ments in an iterative process and in each iteration, the one having the most probability of containing tumor with lowest possible resolution is selected by using suitable decision metrics. After finding the smallest tumor-containing segment, the resolution is increased in the detected tumor-containing segment, leaving the other parts of the breast image with low resolution. Our framework is applied on the most common used beamforming techniques, such as delay and sum (DAS) and delay multiply and sum (DMAS) and according to simulation results, our framework can decrease the computational complexity significantly for both DAS and DMAS without imposing any degradation on accuracy of basic algorithms. The amount of complexity reduction can be determined manually or automatically based on two proposed methods that are described in this framework.

  
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Encoding Clinical Priori in 3D Convolutional Neural Networks for Prostate Cancer Detection in bpMRI

Nov 03, 2020
Anindo Saha, Matin Hosseinzadeh, Henkjan Huisman

We hypothesize that anatomical priors can be viable mediums to infuse domain-specific clinical knowledge into state-of-the-art convolutional neural networks (CNN) based on the U-Net architecture. We introduce a probabilistic population prior which captures the spatial prevalence and zonal distinction of clinically significant prostate cancer (csPCa), in order to improve its computer-aided detection (CAD) in bi-parametric MR imaging (bpMRI). To evaluate performance, we train 3D adaptations of the U-Net, U-SEResNet, UNet++ and Attention U-Net using 800 institutional training-validation scans, paired with radiologically-estimated annotations and our computed prior. For 200 independent testing bpMRI scans with histologically-confirmed delineations of csPCa, our proposed method of encoding clinical priori demonstrates a strong ability to improve patient-based diagnosis (upto 8.70% increase in AUROC) and lesion-level detection (average increase of 1.08 pAUC between 0.1-1.0 false positive per patient) across all four architectures.

* Accepted to Medical Imaging Meets NeurIPS Workshop of the 34th Conference on Neural Information Processing Systems (NeurIPS 2020) 
  
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ScanNet: A Fast and Dense Scanning Framework for Metastatic Breast Cancer Detection from Whole-Slide Images

Jul 30, 2017
Huangjing Lin, Hao Chen, Qi Dou, Liansheng Wang, Jing Qin, Pheng-Ann Heng

Lymph node metastasis is one of the most significant diagnostic indicators in breast cancer, which is traditionally observed under the microscope by pathologists. In recent years, computerized histology diagnosis has become one of the most rapidly expanding fields in medical image computing, which alleviates pathologists' workload and reduces misdiagnosis rate. However, automatic detection of lymph node metastases from whole slide images remains a challenging problem, due to the large-scale data with enormous resolutions and existence of hard mimics. In this paper, we propose a novel framework by leveraging fully convolutional networks for efficient inference to meet the speed requirement for clinical practice, while reconstructing dense predictions under different offsets for ensuring accurate detection on both micro- and macro-metastases. Incorporating with the strategies of asynchronous sample prefetching and hard negative mining, the network can be effectively trained. Extensive experiments on the benchmark dataset of 2016 Camelyon Grand Challenge corroborated the efficacy of our method. Compared with the state-of-the-art methods, our method achieved superior performance with a faster speed on the tumor localization task and surpassed human performance on the WSI classification task.

  
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Analysing the Extent of Misinformation in Cancer Related Tweets

Apr 02, 2020
Rakesh Bal, Sayan Sinha, Swastika Dutta, Rishabh Joshi, Sayan Ghosh, Ritam Dutt

Twitter has become one of the most sought after places to discuss a wide variety of topics, including medically relevant issues such as cancer. This helps spread awareness regarding the various causes, cures and prevention methods of cancer. However, no proper analysis has been performed, which discusses the validity of such claims. In this work, we aim to tackle the misinformation spread in such platforms. We collect and present a dataset regarding tweets which talk specifically about cancer and propose an attention-based deep learning model for automated detection of misinformation along with its spread. We then do a comparative analysis of the linguistic variation in the text corresponding to misinformation and truth. This analysis helps us gather relevant insights on various social aspects related to misinformed tweets.

* Proceedings of the 14th International Conference on Web and Social Media (ICWSM-20) 
  
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Fast CapsNet for Lung Cancer Screening

Jun 19, 2018
Aryan Mobiny, Hien Van Nguyen

Lung cancer is the leading cause of cancer-related deaths in the past several years. A major challenge in lung cancer screening is the detection of lung nodules from computed tomography (CT) scans. State-of-the-art approaches in automated lung nodule classification use deep convolutional neural networks (CNNs). However, these networks require a large number of training samples to generalize well. This paper investigates the use of capsule networks (CapsNets) as an alternative to CNNs. We show that CapsNets significantly outperforms CNNs when the number of training samples is small. To increase the computational efficiency, our paper proposes a consistent dynamic routing mechanism that results in $3\times$ speedup of CapsNet. Finally, we show that the original image reconstruction method of CapNets performs poorly on lung nodule data. We propose an efficient alternative, called convolutional decoder, that yields lower reconstruction error and higher classification accuracy.

  
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An AI-Augmented Lesion Detection Framework For Liver Metastases With Model Interpretability

Jul 17, 2019
Xin J. Hunt, Ralph Abbey, Ricky Tharrington, Joost Huiskens, Nina Wesdorp

Colorectal cancer (CRC) is the third most common cancer and the second leading cause of cancer-related deaths worldwide. Most CRC deaths are the result of progression of metastases. The assessment of metastases is done using the RECIST criterion, which is time consuming and subjective, as clinicians need to manually measure anatomical tumor sizes. AI has many successes in image object detection, but often suffers because the models used are not interpretable, leading to issues in trust and implementation in the clinical setting. We propose a framework for an AI-augmented system in which an interactive AI system assists clinicians in the metastasis assessment. We include model interpretability to give explanations of the reasoning of the underlying models.

* 4 pages, 2 figures, 2019 KDD Workshop on Applied Data Science for Healthcare 
  
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Weakly Supervised Multi-Task Learning for Cell Detection and Segmentation

Oct 27, 2019
Alireza Chamanzar, Yao Nie

Cell detection and segmentation is fundamental for all downstream analysis of digital pathology images. However, obtaining the pixel-level ground truth for single cell segmentation is extremely labor intensive. To overcome this challenge, we developed an end-to-end deep learning algorithm to perform both single cell detection and segmentation using only point labels. This is achieved through the combination of different task orientated point label encoding methods and a multi-task scheduler for training. We apply and validate our algorithm on PMS2 stained colon rectal cancer and tonsil tissue images. Compared to the state-of-the-art, our algorithm shows significant improvement in cell detection and segmentation without increasing the annotation efforts.

  
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