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"cancer detection": models, code, and papers

Towards Confident Detection of Prostate Cancer using High Resolution Micro-ultrasound

Jul 21, 2022
Mahdi Gilany, Paul Wilson, Amoon Jamzad, Fahimeh Fooladgar, Minh Nguyen Nhat To, Brian Wodlinger, Purang Abolmaesumi, Parvin Mousavi

MOTIVATION: Detection of prostate cancer during transrectal ultrasound-guided biopsy is challenging. The highly heterogeneous appearance of cancer, presence of ultrasound artefacts, and noise all contribute to these difficulties. Recent advancements in high-frequency ultrasound imaging - micro-ultrasound - have drastically increased the capability of tissue imaging at high resolution. Our aim is to investigate the development of a robust deep learning model specifically for micro-ultrasound-guided prostate cancer biopsy. For the model to be clinically adopted, a key challenge is to design a solution that can confidently identify the cancer, while learning from coarse histopathology measurements of biopsy samples that introduce weak labels. METHODS: We use a dataset of micro-ultrasound images acquired from 194 patients, who underwent prostate biopsy. We train a deep model using a co-teaching paradigm to handle noise in labels, together with an evidential deep learning method for uncertainty estimation. We evaluate the performance of our model using the clinically relevant metric of accuracy vs. confidence. RESULTS: Our model achieves a well-calibrated estimation of predictive uncertainty with area under the curve of 88$\%$. The use of co-teaching and evidential deep learning in combination yields significantly better uncertainty estimation than either alone. We also provide a detailed comparison against state-of-the-art in uncertainty estimation.

  

Detecting Scatteredly-Distributed, Small, andCritically Important Objects in 3D OncologyImaging via Decision Stratification

May 27, 2020
Zhuotun Zhu, Ke Yan, Dakai Jin, Jinzheng Cai, Tsung-Ying Ho, Adam P Harrison, Dazhou Guo, Chun-Hung Chao, Xianghua Ye, Jing Xiao, Alan Yuille, Le Lu

Finding and identifying scatteredly-distributed, small, and critically important objects in 3D oncology images is very challenging. We focus on the detection and segmentation of oncology-significant (or suspicious cancer metastasized) lymph nodes (OSLNs), which has not been studied before as a computational task. Determining and delineating the spread of OSLNs is essential in defining the corresponding resection/irradiating regions for the downstream workflows of surgical resection and radiotherapy of various cancers. For patients who are treated with radiotherapy, this task is performed by experienced radiation oncologists that involves high-level reasoning on whether LNs are metastasized, which is subject to high inter-observer variations. In this work, we propose a divide-and-conquer decision stratification approach that divides OSLNs into tumor-proximal and tumor-distal categories. This is motivated by the observation that each category has its own different underlying distributions in appearance, size and other characteristics. Two separate detection-by-segmentation networks are trained per category and fused. To further reduce false positives (FP), we present a novel global-local network (GLNet) that combines high-level lesion characteristics with features learned from localized 3D image patches. Our method is evaluated on a dataset of 141 esophageal cancer patients with PET and CT modalities (the largest to-date). Our results significantly improve the recall from $45\%$ to $67\%$ at $3$ FPs per patient as compared to previous state-of-the-art methods. The highest achieved OSLN recall of $0.828$ is clinically relevant and valuable.

* 14 pages, 4 Figures 
  

Improving the diagnosis of breast cancer based on biophysical ultrasound features utilizing machine learning

Jul 13, 2022
Jihye Baek, Avice M. O'Connell, Kevin J. Parker

The improved diagnostic accuracy of ultrasound breast examinations remains an important goal. In this study, we propose a biophysical feature based machine learning method for breast cancer detection to improve the performance beyond a benchmark deep learning algorithm and to furthermore provide a color overlay visual map of the probability of malignancy within a lesion. This overall framework is termed disease specific imaging. Previously, 150 breast lesions were segmented and classified utilizing a modified fully convolutional network and a modified GoogLeNet, respectively. In this study multiparametric analysis was performed within the contoured lesions. Features were extracted from ultrasound radiofrequency, envelope, and log compressed data based on biophysical and morphological models. The support vector machine with a Gaussian kernel constructed a nonlinear hyperplane, and we calculated the distance between the hyperplane and data point of each feature in multiparametric space. The distance can quantitatively assess a lesion, and suggest the probability of malignancy that is color coded and overlaid onto B mode images. Training and evaluation were performed on in vivo patient data. The overall accuracy for the most common types and sizes of breast lesions in our study exceeded 98.0% for classification and 0.98 for an area under the receiver operating characteristic curve, which is more precise than the performance of radiologists and a deep learning system. Further, the correlation between the probability and BI RADS enables a quantitative guideline to predict breast cancer. Therefore, we anticipate that the proposed framework can help radiologists achieve more accurate and convenient breast cancer classification and detection.

  

Application of Graph Based Features in Computer Aided Diagnosis for Histopathological Image Classification of Gastric Cancer

May 17, 2022
Haiqing Zhang, Chen Li, Shiliang Ai, Haoyuan Chen, Yuchao Zheng, Yixin Li, Xiaoyan Li, Hongzan Sun, Xinyu Huang, Marcin Grzegorzek

The gold standard for gastric cancer detection is gastric histopathological image analysis, but there are certain drawbacks in the existing histopathological detection and diagnosis. In this paper, based on the study of computer aided diagnosis system, graph based features are applied to gastric cancer histopathology microscopic image analysis, and a classifier is used to classify gastric cancer cells from benign cells. Firstly, image segmentation is performed, and after finding the region, cell nuclei are extracted using the k-means method, the minimum spanning tree (MST) is drawn, and graph based features of the MST are extracted. The graph based features are then put into the classifier for classification. In this study, different segmentation methods are compared in the tissue segmentation stage, among which are Level-Set, Otsu thresholding, watershed, SegNet, U-Net and Trans-U-Net segmentation; Graph based features, Red, Green, Blue features, Grey-Level Co-occurrence Matrix features, Histograms of Oriented Gradient features and Local Binary Patterns features are compared in the feature extraction stage; Radial Basis Function (RBF) Support Vector Machine (SVM), Linear SVM, Artificial Neural Network, Random Forests, k-NearestNeighbor, VGG16, and Inception-V3 are compared in the classifier stage. It is found that using U-Net to segment tissue areas, then extracting graph based features, and finally using RBF SVM classifier gives the optimal results with 94.29%.

  

The impact of using voxel-level segmentation metrics on evaluating multifocal prostate cancer localisation

Mar 31, 2022
Wen Yan, Qianye Yang, Tom Syer, Zhe Min, Shonit Punwani, Mark Emberton, Dean C. Barratt, Bernard Chiu, Yipeng Hu

Dice similarity coefficient (DSC) and Hausdorff distance (HD) are widely used for evaluating medical image segmentation. They have also been criticised, when reported alone, for their unclear or even misleading clinical interpretation. DSCs may also differ substantially from HDs, due to boundary smoothness or multiple regions of interest (ROIs) within a subject. More importantly, either metric can also have a nonlinear, non-monotonic relationship with outcomes based on Type 1 and 2 errors, designed for specific clinical decisions that use the resulting segmentation. Whilst cases causing disagreement between these metrics are not difficult to postulate. This work first proposes a new asymmetric detection metric, adapting those used in object detection, for planning prostate cancer procedures. The lesion-level metrics is then compared with the voxel-level DSC and HD, whereas a 3D UNet is used for segmenting lesions from multiparametric MR (mpMR) images. Based on experimental results we report pairwise agreement and correlation 1) between DSC and HD, and 2) between voxel-level DSC and recall-controlled precision at lesion-level, with Cohen's [0.49, 0.61] and Pearson's [0.66, 0.76] (p-values}<0.001) at varying cut-offs. However, the differences in false-positives and false-negatives, between the actual errors and the perceived counterparts if DSC is used, can be as high as 152 and 154, respectively, out of the 357 test set lesions. We therefore carefully conclude that, despite of the significant correlations, voxel-level metrics such as DSC can misrepresent lesion-level detection accuracy for evaluating localisation of multifocal prostate cancer and should be interpreted with caution.

  

Overcoming the limitations of patch-based learning to detect cancer in whole slide images

Dec 01, 2020
Ozan Ciga, Tony Xu, Sharon Nofech-Mozes, Shawna Noy, Fang-I Lu, Anne L. Martel

Whole slide images (WSIs) pose unique challenges when training deep learning models. They are very large which makes it necessary to break each image down into smaller patches for analysis, image features have to be extracted at multiple scales in order to capture both detail and context, and extreme class imbalances may exist. Significant progress has been made in the analysis of these images, thanks largely due to the availability of public annotated datasets. We postulate, however, that even if a method scores well on a challenge task, this success may not translate to good performance in a more clinically relevant workflow. Many datasets consist of image patches which may suffer from data curation bias; other datasets are only labelled at the whole slide level and the lack of annotations across an image may mask erroneous local predictions so long as the final decision is correct. In this paper, we outline the differences between patch or slide-level classification versus methods that need to localize or segment cancer accurately across the whole slide, and we experimentally verify that best practices differ in both cases. We apply a binary cancer detection network on post neoadjuvant therapy breast cancer WSIs to find the tumor bed outlining the extent of cancer, a task which requires sensitivity and precision across the whole slide. We extensively study multiple design choices and their effects on the outcome, including architectures and augmentations. Furthermore, we propose a negative data sampling strategy, which drastically reduces the false positive rate (7% on slide level) and improves each metric pertinent to our problem, with a 15% reduction in the error of tumor extent.

  

Going Deeper through the Gleason Scoring Scale: An Automatic end-to-end System for Histology Prostate Grading and Cribriform Pattern Detection

May 21, 2021
Julio Silva-Rodríguez, Adrián Colomer, María A. Sales, Rafael Molina, Valery Naranjo

The Gleason scoring system is the primary diagnostic and prognostic tool for prostate cancer. In recent years, with the development of digitisation devices, the use of computer vision techniques for the analysis of biopsies has increased. However, to the best of the authors' knowledge, the development of algorithms to automatically detect individual cribriform patterns belonging to Gleason grade 4 has not yet been studied in the literature. The objective of the work presented in this paper is to develop a deep-learning-based system able to support pathologists in the daily analysis of prostate biopsies. The methodological core of this work is a patch-wise predictive model based on convolutional neural networks able to determine the presence of cancerous patterns. In particular, we train from scratch a simple self-design architecture. The cribriform pattern is detected by retraining the set of filters of the last convolutional layer in the network. From the reconstructed prediction map, we compute the percentage of each Gleason grade in the tissue to feed a multi-layer perceptron which provides a biopsy-level score.mIn our SICAPv2 database, composed of 182 annotated whole slide images, we obtained a Cohen's quadratic kappa of 0.77 in the test set for the patch-level Gleason grading with the proposed architecture trained from scratch. Our results outperform previous ones reported in the literature. Furthermore, this model reaches the level of fine-tuned state-of-the-art architectures in a patient-based four groups cross validation. In the cribriform pattern detection task, we obtained an area under ROC curve of 0.82. Regarding the biopsy Gleason scoring, we achieved a quadratic Cohen's Kappa of 0.81 in the test subset. Shallow CNN architectures trained from scratch outperform current state-of-the-art methods for Gleason grades classification.

  

Detection of prostate cancer in whole-slide images through end-to-end training with image-level labels

Jun 05, 2020
Hans Pinckaers, Wouter Bulten, Jeroen van der Laak, Geert Litjens

Prostate cancer is the most prevalent cancer among men in Western countries, with 1.1 million new diagnoses every year. The gold standard for the diagnosis of prostate cancer is a pathologists' evaluation of prostate tissue. To potentially assist pathologists deep-learning-based cancer detection systems have been developed. Many of the state-of-the-art models are patch-based convolutional neural networks, as the use of entire scanned slides is hampered by memory limitations on accelerator cards. Patch-based systems typically require detailed, pixel-level annotations for effective training. However, such annotations are seldom readily available, in contrast to the clinical reports of pathologists, which contain slide-level labels. As such, developing algorithms which do not require manual pixel-wise annotations, but can learn using only the clinical report would be a significant advancement for the field. In this paper, we propose to use a streaming implementation of convolutional layers, to train a modern CNN (ResNet-34) with 21 million parameters end-to-end on 4712 prostate biopsies. The method enables the use of entire biopsy images at high-resolution directly by reducing the GPU memory requirements by 2.4 TB. We show that modern CNNs, trained using our streaming approach, can extract meaningful features from high-resolution images without additional heuristics, reaching similar performance as state-of-the-art patch-based and multiple-instance learning methods. By circumventing the need for manual annotations, this approach can function as a blueprint for other tasks in histopathological diagnosis. The source code to reproduce the streaming models is available at https://github.com/DIAGNijmegen/pathology-streaming-pipeline .

  

A New Cervical Cytology Dataset for Nucleus Detection and Image Classification (Cervix93) and Methods for Cervical Nucleus Detection

Nov 23, 2018
Hady Ahmady Phoulady, Peter R. Mouton

Analyzing Pap cytology slides is an important tasks in detecting and grading precancerous and cancerous cervical cancer stages. Processing cytology images usually involve segmenting nuclei and overlapping cells. We introduce a cervical cytology dataset that can be used to evaluate nucleus detection, as well as image classification methods in the cytology image processing area. This dataset contains 93 real image stacks with their grade labels and manually annotated nuclei within images. We also present two methods: a baseline method based on a previously proposed approach, and a deep learning method, and compare their results with other state-of-the-art methods. Both the baseline method and the deep learning method outperform other state-of-the-art methods by significant margins. Along with the dataset, we publicly make the evaluation code and the baseline method available to download for further benchmarking.

* 5 pages, 6 figures, conference 
  

A deep learning algorithm for reducing false positives in screening mammography

Apr 13, 2022
Stefano Pedemonte, Trevor Tsue, Brent Mombourquette, Yen Nhi Truong Vu, Thomas Matthews, Rodrigo Morales Hoil, Meet Shah, Nikita Ghare, Naomi Zingman-Daniels, Susan Holley, Catherine M. Appleton, Jason Su, Richard L. Wahl

Screening mammography improves breast cancer outcomes by enabling early detection and treatment. However, false positive callbacks for additional imaging from screening exams cause unnecessary procedures, patient anxiety, and financial burden. This work demonstrates an AI algorithm that reduces false positives by identifying mammograms not suspicious for breast cancer. We trained the algorithm to determine the absence of cancer using 123,248 2D digital mammograms (6,161 cancers) and performed a retrospective study on 14,831 screening exams (1,026 cancers) from 15 US and 3 UK sites. Retrospective evaluation of the algorithm on the largest of the US sites (11,592 mammograms, 101 cancers) a) left the cancer detection rate unaffected (p=0.02, non-inferiority margin 0.25 cancers per 1000 exams), b) reduced callbacks for diagnostic exams by 31.1% compared to standard clinical readings, c) reduced benign needle biopsies by 7.4%, and d) reduced screening exams requiring radiologist interpretation by 41.6% in the simulated clinical workflow. This work lays the foundation for semi-autonomous breast cancer screening systems that could benefit patients and healthcare systems by reducing false positives, unnecessary procedures, patient anxiety, and expenses.

  
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