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"cancer detection": models, code, and papers

Accurate and Robust Pulmonary Nodule Detection by 3D Feature Pyramid Network with Self-supervised Feature Learning

Jul 25, 2019
Jingya Liu, Liangliang Cao, Oguz Akin, Yingli Tian

Accurate detection of pulmonary nodules with high sensitivity and specificity is essential for automatic lung cancer diagnosis from CT scans. Although many deep learning-based algorithms make great progress for improving the accuracy of nodule detection, the high false positive rate is still a challenging problem which limits the automatic diagnosis in routine clinical practice. Moreover, the CT scans collected from multiple manufacturers may affect the robustness of Computer-aided diagnosis (CAD) due to the differences in intensity scales and machine noises. In this paper, we propose a novel self-supervised learning assisted pulmonary nodule detection framework based on a 3D Feature Pyramid Network (3DFPN) to improve the sensitivity of nodule detection by employing multi-scale features to increase the resolution of nodules, as well as a parallel top-down path to transit the high-level semantic features to complement low-level general features. Furthermore, a High Sensitivity and Specificity (HS2) network is introduced to eliminate the false positive nodule candidates by tracking the appearance changes in continuous CT slices of each nodule candidate on Location History Images (LHI). In addition, in order to improve the performance consistency of the proposed framework across data captured by different CT scanners without using additional annotations, an effective self-supervised learning schema is applied to learn spatiotemporal features of CT scans from large-scale unlabeled data. The performance and robustness of our method are evaluated on several publicly available datasets with significant performance improvements. The proposed framework is able to accurately detect pulmonary nodules with high sensitivity and specificity and achieves 90.6% sensitivity with 1/8 false positive per scan which outperforms the state-of-the-art results 15.8% on LUNA16 dataset.

* 15 pages, 8 figures, 5 tables, under review by Medical Image Analysis. arXiv admin note: substantial text overlap with arXiv:1906.03467 

Adversarial Networks for Prostate Cancer Detection

Nov 28, 2017
Simon Kohl, David Bonekamp, Heinz-Peter Schlemmer, Kaneschka Yaqubi, Markus Hohenfellner, Boris Hadaschik, Jan-Philipp Radtke, Klaus Maier-Hein

The large number of trainable parameters of deep neural networks renders them inherently data hungry. This characteristic heavily challenges the medical imaging community and to make things even worse, many imaging modalities are ambiguous in nature leading to rater-dependant annotations that current loss formulations fail to capture. We propose employing adversarial training for segmentation networks in order to alleviate aforementioned problems. We learn to segment aggressive prostate cancer utilizing challenging MRI images of 152 patients and show that the proposed scheme is superior over the de facto standard in terms of the detection sensitivity and the dice-score for aggressive prostate cancer. The achieved relative gains are shown to be particularly pronounced in the small dataset limit.


Response monitoring of breast cancer on DCE-MRI using convolutional neural network-generated seed points and constrained volume growing

Nov 22, 2018
Bas H. M. van der Velden, Bob D. de Vos, Claudette E. Loo, Hugo J. Kuijf, Ivana Isgum, Kenneth G. A. Gilhuijs

Response of breast cancer to neoadjuvant chemotherapy (NAC) can be monitored using the change in visible tumor on magnetic resonance imaging (MRI). In our current workflow, seed points are manually placed in areas of enhancement likely to contain cancer. A constrained volume growing method uses these manually placed seed points as input and generates a tumor segmentation. This method is rigorously validated using complete pathological embedding. In this study, we propose to exploit deep learning for fast and automatic seed point detection, replacing manual seed point placement in our existing and well-validated workflow. The seed point generator was developed in early breast cancer patients with pathology-proven segmentations (N=100), operated shortly after MRI. It consisted of an ensemble of three independently trained fully convolutional dilated neural networks that classified breast voxels as tumor or non-tumor. Subsequently, local maxima were used as seed points for volume growing in patients receiving NAC (N=10). The percentage of tumor volume change was evaluated against semi-automatic segmentations. The primary cancer was localized in 95% of the tumors at the cost of 0.9 false positive per patient. False positives included focally enhancing regions of unknown origin and parts of the intramammary blood vessels. Volume growing from the seed points showed a median tumor volume decrease of 70% (interquartile range: 50%-77%), comparable to the semi-automatic segmentations (median: 70%, interquartile range 23%-76%). To conclude, a fast and automatic seed point generator was developed, fully automating a well-validated semi-automatic workflow for response monitoring of breast cancer to neoadjuvant chemotherapy.

* This work has been accepted for SPIE Medical Imaging 2019, Computer-Aided Diagnosis conference, Paper 10950-12 

SCPM-Net: An Anchor-free 3D Lung Nodule Detection Network using Sphere Representation and Center Points Matching

Apr 12, 2021
Xiangde Luo, Tao Song, Guotai Wang, Jieneng Chen, Yinan Chen, Kang Li, Dimitris N. Metaxas, Shaoting Zhang

Automatic and accurate lung nodule detection from 3D Computed Tomography scans plays a vital role in efficient lung cancer screening. Despite the state-of-the-art performance obtained by recent anchor-based detectors using Convolutional Neural Networks, they require predetermined anchor parameters such as the size, number, and aspect ratio of anchors, and have limited robustness when dealing with lung nodules with a massive variety of sizes. We propose a 3D sphere representation-based center-points matching detection network (SCPM-Net) that is anchor-free and automatically predicts the position, radius, and offset of nodules without the manual design of nodule/anchor parameters. The SCPM-Net consists of two novel pillars: sphere representation and center points matching. To mimic the nodule annotation in clinical practice, we replace the conventional bounding box with the newly proposed bounding sphere. A compatible sphere-based intersection over-union loss function is introduced to train the lung nodule detection network stably and efficiently.We empower the network anchor-free by designing a positive center-points selection and matching (CPM) process, which naturally discards pre-determined anchor boxes. An online hard example mining and re-focal loss subsequently enable the CPM process more robust, resulting in more accurate point assignment and the mitigation of class imbalance. In addition, to better capture spatial information and 3D context for the detection, we propose to fuse multi-level spatial coordinate maps with the feature extractor and combine them with 3D squeeze-and-excitation attention modules. Experimental results on the LUNA16 dataset showed that our proposed SCPM-Net framework achieves superior performance compared with existing used anchor-based and anchor-free methods for lung nodule detection.

* An extension of this paper (MICCAI2020 early accept), the first two authors contributed equally. Code: 

Depth Reconstruction and Computer-Aided Polyp Detection in Optical Colonoscopy Video Frames

Sep 10, 2016
Saad Nadeem, Arie Kaufman

We present a computer-aided detection algorithm for polyps in optical colonoscopy images. Polyps are the precursors to colon cancer. In the US alone, more than 14 million optical colonoscopies are performed every year, mostly to screen for polyps. Optical colonoscopy has been shown to have an approximately 25% polyp miss rate due to the convoluted folds and bends present in the colon. In this work, we present an automatic detection algorithm to detect these polyps in the optical colonoscopy images. We use a machine learning algorithm to infer a depth map for a given optical colonoscopy image and then use a detailed pre-built polyp profile to detect and delineate the boundaries of polyps in this given image. We have achieved the best recall of 84.0% and the best specificity value of 83.4%.

* **The title has been modified to highlight the contributions more clearly. The original title is: "Computer-Aided Detection of Polyps in Optical Colonoscopy Images". Keywords: Machine learning, computer-aided detection, segmentation, endoscopy, colonoscopy, videos, polyp, detection, medical imaging, depth maps, 3D, reconstruction, computed tomography, virtual colonoscopy, colorectal cancer, SPIE Medical Imaging, 2016 

Sparse Autoencoder for Unsupervised Nucleus Detection and Representation in Histopathology Images

Apr 10, 2017
Le Hou, Vu Nguyen, Dimitris Samaras, Tahsin M. Kurc, Yi Gao, Tianhao Zhao, Joel H. Saltz

Histopathology images are crucial to the study of complex diseases such as cancer. The histologic characteristics of nuclei play a key role in disease diagnosis, prognosis and analysis. In this work, we propose a sparse Convolutional Autoencoder (CAE) for fully unsupervised, simultaneous nucleus detection and feature extraction in histopathology tissue images. Our CAE detects and encodes nuclei in image patches in tissue images into sparse feature maps that encode both the location and appearance of nuclei. Our CAE is the first unsupervised detection network for computer vision applications. The pretrained nucleus detection and feature extraction modules in our CAE can be fine-tuned for supervised learning in an end-to-end fashion. We evaluate our method on four datasets and reduce the errors of state-of-the-art methods up to 42%. We are able to achieve comparable performance with only 5% of the fully-supervised annotation cost.


Improving Specificity in Mammography Using Cross-correlation between Wavelet and Fourier Transform

Jan 29, 2022
Liuhua Zhang

Breast cancer is in the most common malignant tumor in women. It accounted for 30% of new malignant tumor cases. Although the incidence of breast cancer remains high around the world, the mortality rate has been continuously reduced. This is mainly due to recent developments in molecular biology technology and improved level of comprehensive diagnosis and standard treatment. Early detection by mammography is an integral part of that. The most common breast abnormalities that may indicate breast cancer are masses and calcifications. Previous detection approaches usually obtain relatively high sensitivity but unsatisfactory specificity. We will investigate an approach that applies the discrete wavelet transform and Fourier transform to parse the images and extracts statistical features that characterize an image's content, such as the mean intensity and the skewness of the intensity. A naive Bayesian classifier uses these features to classify the images. We expect to achieve an optimal high specificity.


DenseNet for Breast Tumor Classification in Mammographic Images

Jan 24, 2021
Yuliana Jim茅nez Gaona, Mar铆a Jos茅 Rodriguez-Alvarez, Hector Espin贸 Morat贸, Darwin Castillo Malla, Vasudevan Lakshminarayanan

Breast cancer is the most common invasive cancer in women, and the second main cause of death. Breast cancer screening is an efficient method to detect indeterminate breast lesions early. The common approaches of screening for women are tomosynthesis and mammography images. However, the traditional manual diagnosis requires an intense workload by pathologists, who are prone to diagnostic errors. Thus, the aim of this study is to build a deep convolutional neural network method for automatic detection, segmentation, and classification of breast lesions in mammography images. Based on deep learning the Mask-CNN (RoIAlign) method was developed to features selection and extraction; and the classification was carried out by DenseNet architecture. Finally, the precision and accuracy of the model is evaluated by cross validation matrix and AUC curve. To summarize, the findings of this study may provide a helpful to improve the diagnosis and efficiency in the automatic tumor localization through the medical image classification.

* to be submitted to The 2nd International Conference on Medical Imaging and Computer-Aided Diagnosis (MICAD2021) 

Perineural Invasion Detection in Multiple Organ Cancer Based on Deep Convolutional Neural Network

Oct 23, 2021
Ramin Nateghi, Fattaneh Pourakpour

Perineural invasion (PNI) by malignant tumor cells has been reported as an independent indicator of poor prognosis in various cancers. Assessment of PNI in small nerves on glass slides is a labor-intensive task. In this study, we propose an algorithm to detect the perineural invasions in colon, prostate, and pancreas cancers based on a convolutional neural network (CNN).