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"cancer detection": models, code, and papers

Perfusion imaging in deep prostate cancer detection from mp-MRI: can we take advantage of it?

Jul 06, 2022
Audrey Duran, Gaspard Dussert, Carole Lartizien

To our knowledge, all deep computer-aided detection and diagnosis (CAD) systems for prostate cancer (PCa) detection consider bi-parametric magnetic resonance imaging (bp-MRI) only, including T2w and ADC sequences while excluding the 4D perfusion sequence,which is however part of standard clinical protocols for this diagnostic task. In this paper, we question strategies to integrate information from perfusion imaging in deep neural architectures. To do so, we evaluate several ways to encode the perfusion information in a U-Net like architecture, also considering early versus mid fusion strategies. We compare performance of multiparametric MRI (mp-MRI) models with the baseline bp-MRI model based on a private dataset of 219 mp-MRI exams. Perfusion maps derived from dynamic contrast enhanced MR exams are shown to positively impact segmentation and grading performance of PCa lesions, especially the 3D MR volume corresponding to the maximum slope of the wash-in curve as well as Tmax perfusion maps. The latter mp-MRI models indeed outperform the bp-MRI one whatever the fusion strategy, with Cohen's kappa score of 0.318$\pm$0.019 for the bp-MRI model and 0.378 $\pm$ 0.033 for the model including the maximum slope with a mid fusion strategy, also achieving competitive Cohen's kappa score compared to state of the art.

* 19th IEEE International Symposium on Biomedical Imaging (ISBI), Mar 2022, Kolkata, India. pp.1-5 

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) 

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.


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 

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.


RCNN for Region of Interest Detection in Whole Slide Images

Sep 18, 2020
A Nugaliyadde, Kok Wai Wong, Jeremy Parry, Ferdous Sohel, Hamid Laga, Upeka V. Somaratne, Chris Yeomans, Orchid Foster

Digital pathology has attracted significant attention in recent years. Analysis of Whole Slide Images (WSIs) is challenging because they are very large, i.e., of Giga-pixel resolution. Identifying Regions of Interest (ROIs) is the first step for pathologists to analyse further the regions of diagnostic interest for cancer detection and other anomalies. In this paper, we investigate the use of RCNN, which is a deep machine learning technique, for detecting such ROIs only using a small number of labelled WSIs for training. For experimentation, we used real WSIs from a public hospital pathology service in Western Australia. We used 60 WSIs for training the RCNN model and another 12 WSIs for testing. The model was further tested on a new set of unseen WSIs. The results show that RCNN can be effectively used for ROI detection from WSIs.

* This paper was accepted to the 27th International Conference on Neural Information Processing (ICONIP 2020) and will be published in the Springer CCIS Series 

Mitosis Detection Under Limited Annotation: A Joint Learning Approach

Jul 02, 2020
Pushpak Pati, Antonio Foncubierta-Rodriguez, Orcun Goksel, Maria Gabrani

Mitotic counting is a vital prognostic marker of tumor proliferation in breast cancer. Deep learning-based mitotic detection is on par with pathologists, but it requires large labeled data for training. We propose a deep classification framework for enhancing mitosis detection by leveraging class label information, via softmax loss, and spatial distribution information among samples, via distance metric learning. We also investigate strategies towards steadily providing informative samples to boost the learning. The efficacy of the proposed framework is established through evaluation on ICPR 2012 and AMIDA 2013 mitotic data. Our framework significantly improves the detection with small training data and achieves on par or superior performance compared to state-of-the-art methods for using the entire training data.

* 2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI) 

A Hypersensitive Breast Cancer Detector

Jan 23, 2020
Stefano Pedemonte, Brent Mombourquette, Alexis Goh, Trevor Tsue, Aaron Long, Sadanand Singh, Thomas Paul Matthews, Meet Shah, Jason Su

Early detection of breast cancer through screening mammography yields a 20-35% increase in survival rate; however, there are not enough radiologists to serve the growing population of women seeking screening mammography. Although commercial computer aided detection (CADe) software has been available to radiologists for decades, it has failed to improve the interpretation of full-field digital mammography (FFDM) images due to its low sensitivity over the spectrum of findings. In this work, we leverage a large set of FFDM images with loose bounding boxes of mammographically significant findings to train a deep learning detector with extreme sensitivity. Building upon work from the Hourglass architecture, we train a model that produces segmentation-like images with high spatial resolution, with the aim of producing 2D Gaussian blobs centered on ground-truth boxes. We replace the pixel-wise $L_2$ norm with a weak-supervision loss designed to achieve high sensitivity, asymmetrically penalizing false positives and false negatives while softening the noise of the loose bounding boxes by permitting a tolerance in misaligned predictions. The resulting system achieves a sensitivity for malignant findings of 0.99 with only 4.8 false positive markers per image. When utilized in a CADe system, this model could enable a novel workflow where radiologists can focus their attention with trust on only the locations proposed by the model, expediting the interpretation process and bringing attention to potential findings that could otherwise have been missed. Due to its nearly perfect sensitivity, the proposed detector can also be used as a high-performance proposal generator in two-stage detection systems.

* SPIE Medical Imaging 2020