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"cancer detection": models, code, and papers

AMDet: A Tool for Mitotic Cell Detection in Histopathology Slides

Aug 08, 2021
Walt Williams, Jimmy Hall

Breast Cancer is the most prevalent cancer in the world. The World Health Organization reports that the disease still affects a significant portion of the developing world citing increased mortality rates in the majority of low to middle income countries. The most popular protocol pathologists use for diagnosing breast cancer is the Nottingham grading system which grades the proliferation of tumors based on 3 major criteria, the most important of them being mitotic cell count. The way in which pathologists evaluate mitotic cell count is to subjectively and qualitatively analyze cells present in stained slides of tissue and make a decision on its mitotic state i.e. is it mitotic or not?This process is extremely inefficient and tiring for pathologists and so an efficient, accurate, and fully automated tool to aid with the diagnosis is extremely desirable. Fortunately, creating such a tool is made significantly easier with the AutoML tool available from Microsoft Azure, however to the best of our knowledge the AutoML tool has never been formally evaluated for use in mitotic cell detection in histopathology images. This paper serves as an evaluation of the AutoML tool for this purpose and will provide a first look on how the tool handles this challenging problem. All code is available athttps://github.com/WaltAFWilliams/AMDet

  

A Search-based Neural Model for Biomedical Nested and Overlapping Event Detection

Oct 25, 2019
Kurt Espinosa, Makoto Miwa, Sophia Ananiadou

We tackle the nested and overlapping event detection task and propose a novel search-based neural network (SBNN) structured prediction model that treats the task as a search problem on a relation graph of trigger-argument structures. Unlike existing structured prediction tasks such as dependency parsing, the task targets to detect DAG structures, which constitute events, from the relation graph. We define actions to construct events and use all the beams in a beam search to detect all event structures that may be overlapping and nested. The search process constructs events in a bottom-up manner while modelling the global properties for nested and overlapping structures simultaneously using neural networks. We show that the model achieves performance comparable to the state-of-the-art model Turku Event Extraction System (TEES) on the BioNLP Cancer Genetics (CG) Shared Task 2013 without the use of any syntactic and hand-engineered features. Further analyses on the development set show that our model is more computationally efficient while yielding higher F1-score performance.

* Accepted at EMNLP-IJCNLP 2019 
  

FusionNet: Incorporating Shape and Texture for Abnormality Detection in 3D Abdominal CT Scans

Aug 27, 2019
Fengze Liu, Yuyin Zhou, Elliot Fishman, Alan Yuille

Automatic abnormality detection in abdominal CT scans can help doctors improve the accuracy and efficiency in diagnosis. In this paper we aim at detecting pancreatic ductal adenocarcinoma (PDAC), the most common pancreatic cancer. Taking the fact that the existence of tumor can affect both the shape and the texture of pancreas, we design a system to extract the shape and texture feature at the same time for detecting PDAC. In this paper we propose a two-stage method for this 3D classification task. First, we segment the pancreas into a binary mask. Second, a FusionNet is proposed to take both the binary mask and CT image as input and perform a binary classification. The optimal architecture of the FusionNet is obtained by searching a pre-defined functional space. We show that the classification results using either shape or texture information are complementary, and by fusing them with the optimized architecture, the performance improves by a large margin. Our method achieves a specificity of 97% and a sensitivity of 92% on 200 normal scans and 136 scans with PDAC.

* Accepted to MICCAI 2019 Workshop(MLMI)(8 pages, 3 figures) 
  

Comparison Detector: A novel object detection method for small dataset

Oct 14, 2018
Zhihong Tang, Yixiong Liang, Meng Yan, Jialin Chen, Jianfeng Liu

Though the object detection has shown great success when the training set is sufficient, there is a serious shortage of generalization in the small dataset scenario. However, we inevitably just get a small one in some application scenarios, especially medicine. In this paper, we propose Comparison detector which still maintains the end-to-end fashion in training and testing, surpassing the state-of-the-art two-stage object detection model on the small dataset. Inspired by one/few-shot learning, we replace the parameter classifier in feature pyramid network(FPN) with the comparison classifier in no-parameters or semi-parameters manner. In fact, a stronger inductive bias is added to the model to simplify the problem and reduce the dependence of data. The performance of our model is evaluated on the cervical cancer pathology test set. When training on the small dataset, it achieves a mAP 26.3% and an AR 35.7%, both improving about 20 points compared to baseline model. Moreover, Comparison detector achieves same mAP performance as the current state-of-the-art model when training on the medium dataset, and improves AR by 4 points. Our method is promising for the development of object detection in small dataset scenario.

  

3D Aggregated Faster R-CNN for General Lesion Detection

Jan 29, 2020
Ning Zhang, Yu Cao, Benyuan Liu, Yan Luo

Lesions are damages and abnormalities in tissues of the human body. Many of them can later turn into fatal diseases such as cancers. Detecting lesions are of great importance for early diagnosis and timely treatment. To this end, Computed Tomography (CT) scans often serve as the screening tool, allowing us to leverage the modern object detection techniques to detect the lesions. However, lesions in CT scans are often small and sparse. The local area of lesions can be very confusing, leading the region based classifier branch of Faster R-CNN easily fail. Therefore, most of the existing state-of-the-art solutions train two types of heterogeneous networks (multi-phase) separately for the candidate generation and the False Positive Reduction (FPR) purposes. In this paper, we enforce an end-to-end 3D Aggregated Faster R-CNN solution by stacking an "aggregated classifier branch" on the backbone of RPN. This classifier branch is equipped with Feature Aggregation and Local Magnification Layers to enhance the classifier branch. We demonstrate our model can achieve the state of the art performance on both LUNA16 and DeepLesion dataset. Especially, we achieve the best single-model FROC performance on LUNA16 with the inference time being 4.2s per processed scan.

  

Multi-level colonoscopy malignant tissue detection with adversarial CAC-UNet

Jun 30, 2020
Chuang Zhu, Ke Mei, Ting Peng, Yihao Luo, Jun Liu, Ying Wang, Mulan Jin

The automatic and objective medical diagnostic model can be valuable to achieve early cancer detection, and thus reducing the mortality rate. In this paper, we propose a highly efficient multi-level malignant tissue detection through the designed adversarial CAC-UNet. A patch-level model with a pre-prediction strategy and a malignancy area guided label smoothing is adopted to remove the negative WSIs, with which to lower the risk of false positive detection. For the selected key patches by multi-model ensemble, an adversarial context-aware and appearance consistency UNet (CAC-UNet) is designed to achieve robust segmentation. In CAC-UNet, mirror designed discriminators are able to seamlessly fuse the whole feature maps of the skillfully designed powerful backbone network without any information loss. Besides, a mask prior is further added to guide the accurate segmentation mask prediction through an extra mask-domain discriminator. The proposed scheme achieves the best results in MICCAI DigestPath2019 challenge on colonoscopy tissue segmentation and classification task. The full implementation details and the trained models are available at https://github.com/Raykoooo/CAC-UNet.

* accepted by Neurocomputing; winner of the MICCAI DigestPath 2019 challenge on colonoscopy tissue segmentation and classification task 
  

Re-Identification and Growth Detection of Pulmonary Nodules without Image Registration Using 3D Siamese Neural Networks

Dec 22, 2019
Xavier Rafael-Palou, Anton Aubanell, Ilaria Bonavita, Mario Ceresa, Gemma Piella, Vicent Ribas, Miguel Ángel González Ballester

Lung cancer follow-up is a complex, error prone, and time consuming task for clinical radiologists. Several lung CT scan images taken at different time points of a given patient need to be individually inspected, looking for possible cancerogenous nodules. Radiologists mainly focus their attention in nodule size, density, and growth to assess the existence of malignancy. In this study, we present a novel method based on a 3D siamese neural network, for the re-identification of nodules in a pair of CT scans of the same patient without the need for image registration. The network was integrated into a two-stage automatic pipeline to detect, match, and predict nodule growth given pairs of CT scans. Results on an independent test set reported a nodule detection sensitivity of 94.7%, an accuracy for temporal nodule matching of 88.8%, and a sensitivity of 92.0% with a precision of 88.4% for nodule growth detection.

* 14 pages, 8 figures 
  
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