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"cancer detection": models, code, and papers

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

Oct 22, 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.

  
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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) 
  
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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.

  
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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.

  
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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 
  
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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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Unsupervised Contrastive Learning based Transformer for Lung Nodule Detection

Apr 30, 2022
Chuang Niu, Ge Wang

Early detection of lung nodules with computed tomography (CT) is critical for the longer survival of lung cancer patients and better quality of life. Computer-aided detection/diagnosis (CAD) is proven valuable as a second or concurrent reader in this context. However, accurate detection of lung nodules remains a challenge for such CAD systems and even radiologists due to not only the variability in size, location, and appearance of lung nodules but also the complexity of lung structures. This leads to a high false-positive rate with CAD, compromising its clinical efficacy. Motivated by recent computer vision techniques, here we present a self-supervised region-based 3D transformer model to identify lung nodules among a set of candidate regions. Specifically, a 3D vision transformer (ViT) is developed that divides a CT image volume into a sequence of non-overlap cubes, extracts embedding features from each cube with an embedding layer, and analyzes all embedding features with a self-attention mechanism for the prediction. To effectively train the transformer model on a relatively small dataset, the region-based contrastive learning method is used to boost the performance by pre-training the 3D transformer with public CT images. Our experiments show that the proposed method can significantly improve the performance of lung nodule screening in comparison with the commonly used 3D convolutional neural networks.

  
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Deep Learning Based Decision Support for Medicine -- A Case Study on Skin Cancer Diagnosis

Mar 02, 2021
Adriano Lucieri, Andreas Dengel, Sheraz Ahmed

Early detection of skin cancers like melanoma is crucial to ensure high chances of survival for patients. Clinical application of Deep Learning (DL)-based Decision Support Systems (DSS) for skin cancer screening has the potential to improve the quality of patient care. The majority of work in the medical AI community focuses on a diagnosis setting that is mainly relevant for autonomous operation. Practical decision support should, however, go beyond plain diagnosis and provide explanations. This paper provides an overview of works towards explainable, DL-based decision support in medical applications with the example of skin cancer diagnosis from clinical, dermoscopic and histopathologic images. Analysis reveals that comparably little attention is payed to the explanation of histopathologic skin images and that current work is dominated by visual relevance maps as well as dermoscopic feature identification. We conclude that future work should focus on meeting the stakeholder's cognitive concepts, providing exhaustive explanations that combine global and local approaches and leverage diverse modalities. Moreover, the possibility to intervene and guide models in case of misbehaviour is identified as a major step towards successful deployment of AI as DL-based DSS and beyond.

  
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