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"cancer detection": models, code, and papers

Deep Learning for fully automatic detection, segmentation, and Gleason Grade estimation of prostate cancer in multiparametric Magnetic Resonance Images

Mar 24, 2021
Oscar J. Pellicer-Valero, José L. Marenco Jiménez, Victor Gonzalez-Perez, Juan Luis Casanova Ramón-Borja, Isabel Martín García, María Barrios Benito, Paula Pelechano Gómez, José Rubio-Briones, María José Rupérez, José D. Martín-Guerrero

The emergence of multi-parametric magnetic resonance imaging (mpMRI) has had a profound impact on the diagnosis of prostate cancers (PCa), which is the most prevalent malignancy in males in the western world, enabling a better selection of patients for confirmation biopsy. However, analyzing these images is complex even for experts, hence opening an opportunity for computer-aided diagnosis systems to seize. This paper proposes a fully automatic system based on Deep Learning that takes a prostate mpMRI from a PCa-suspect patient and, by leveraging the Retina U-Net detection framework, locates PCa lesions, segments them, and predicts their most likely Gleason grade group (GGG). It uses 490 mpMRIs for training/validation, and 75 patients for testing from two different datasets: ProstateX and IVO (Valencia Oncology Institute Foundation). In the test set, it achieves an excellent lesion-level AUC/sensitivity/specificity for the GGG$\geq$2 significance criterion of 0.96/1.00/0.79 for the ProstateX dataset, and 0.95/1.00/0.80 for the IVO dataset. Evaluated at a patient level, the results are 0.87/1.00/0.375 in ProstateX, and 0.91/1.00/0.762 in IVO. Furthermore, on the online ProstateX grand challenge, the model obtained an AUC of 0.85 (0.87 when trained only on the ProstateX data, tying up with the original winner of the challenge). For expert comparison, IVO radiologist's PI-RADS 4 sensitivity/specificity were 0.88/0.56 at a lesion level, and 0.85/0.58 at a patient level. Additional subsystems for automatic prostate zonal segmentation and mpMRI non-rigid sequence registration were also employed to produce the final fully automated system. The code for the ProstateX-trained system has been made openly available at https://github.com/OscarPellicer/prostate_lesion_detection. We hope that this will represent a landmark for future research to use, compare and improve upon.

  
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Multiscale Detection of Cancerous Tissue in High Resolution Slide Scans

Oct 01, 2020
Qingchao Zhang, Coy D. Heldermon, Corey Toler-Franklin

We present an algorithm for multi-scale tumor (chimeric cell) detection in high resolution slide scans. The broad range of tumor sizes in our dataset pose a challenge for current Convolutional Neural Networks (CNN) which often fail when image features are very small (8 pixels). Our approach modifies the effective receptive field at different layers in a CNN so that objects with a broad range of varying scales can be detected in a single forward pass. We define rules for computing adaptive prior anchor boxes which we show are solvable under the equal proportion interval principle. Two mechanisms in our CNN architecture alleviate the effects of non-discriminative features prevalent in our data - a foveal detection algorithm that incorporates a cascade residual-inception module and a deconvolution module with additional context information. When integrated into a Single Shot MultiBox Detector (SSD), these additions permit more accurate detection of small-scale objects. The results permit efficient real-time analysis of medical images in pathology and related biomedical research fields.

* 14 pages, 7 figures, 2 tables 
  
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Wavelet based approach for tissue fractal parameter measurement: Pre cancer detection

Mar 21, 2015
Sabyasachi Mukhopadhyay, Nandan K. Das, Soham Mandal, Sawon Pratiher, Asish Mitra, Asima Pradhan, Nirmalya Ghosh, Prasanta K. Panigrahi

In this paper, we have carried out the detail studies of pre-cancer by wavelet coherency and multifractal based detrended fluctuation analysis (MFDFA) on differential interference contrast (DIC) images of stromal region among different grades of pre-cancer tissues. Discrete wavelet transform (DWT) through Daubechies basis has been performed for identifying fluctuations over polynomial trends for clear characterization and differentiation of tissues. Wavelet coherence plots are performed for identifying the level of correlation in time scale plane between normal and various grades of DIC samples. Applying MFDFA on refractive index variations of cervical tissues, we have observed that the values of Hurst exponent (correlation) decreases from healthy (normal) to pre-cancer tissues. The width of singularity spectrum has a sudden degradation at grade-I in comparison of healthy (normal) tissue but later on it increases as cancer progresses from grade-II to grade-III.

  
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Detection and Attention: Diagnosing Pulmonary Lung Cancer from CT by Imitating Physicians

Dec 14, 2017
Ning Li, Haopeng Liu, Bin Qiu, Wei Guo, Shijun Zhao, Kungang Li, Jie He

This paper proposes a novel and efficient method to build a Computer-Aided Diagnoses (CAD) system for lung nodule detection based on Computed Tomography (CT). This task was treated as an Object Detection on Video (VID) problem by imitating how a radiologist reads CT scans. A lung nodule detector was trained to automatically learn nodule features from still images to detect lung nodule candidates with both high recall and accuracy. Unlike previous work which used 3-dimensional information around the nodule to reduce false positives, we propose two simple but efficient methods, Multi-slice propagation (MSP) and Motionless-guide suppression (MLGS), which analyze sequence information of CT scans to reduce false negatives and suppress false positives. We evaluated our method in open-source LUNA16 dataset which contains 888 CT scans, and obtained state-of-the-art result (Free-Response Receiver Operating Characteristic score of 0.892) with detection speed (end to end within 20 seconds per patient on a single NVidia GTX 1080) much higher than existing methods.

* 8 pages, 8 figures, 5 tables 
  
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Understanding the Mechanism of Deep Learning Framework for Lesion Detection in Pathological Images with Breast Cancer

Mar 04, 2019
Wei-Wen Hsu, Chung-Hao Chen, Chang Hoa, Yu-Ling Hou, Xiang Gao, Yun Shao, Xueli Zhang, Jingjing Wang, Tao He, Yanghong Tai

The computer-aided detection (CADe) systems are developed to assist pathologists in slide assessment, increasing diagnosis efficiency and reducing missing inspections. Many studies have shown such a CADe system with deep learning approaches outperforms the one using conventional methods that rely on hand-crafted features based on field-knowledge. However, most developers who adopted deep learning models directly focused on the efficacy of outcomes, without providing comprehensive explanations on why their proposed frameworks can work effectively. In this study, we designed four experiments to verify the consecutive concepts, showing that the deep features learned from pathological patches are interpretable by domain knowledge of pathology and enlightening for clinical diagnosis in the task of lesion detection. The experimental results show the activation features work as morphological descriptors for specific cells or tissues, which agree with the clinical rules in classification. That is, the deep learning framework not only detects the distribution of tumor cells but also recognizes lymphocytes, collagen fibers, and some other non-cell structural tissues. Most of the characteristics learned by the deep learning models have summarized the detection rules that can be recognized by the experienced pathologists, whereas there are still some features may not be intuitive to domain experts but discriminative in classification for machines. Those features are worthy to be further studied in order to find out the reasonable correlations to pathological knowledge, from which pathological experts may draw inspirations for exploring new characteristics in diagnosis.

* v1 
  
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Convolutional Neural Networks for the segmentation of microcalcification in Mammography Imaging

Sep 11, 2018
Gabriele Valvano, Gianmarco Santini, Nicola Martini, Andrea Ripoli, Chiara Iacconi, Dante Chiappino, Daniele Della Latta

Cluster of microcalcifications can be an early sign of breast cancer. In this paper we propose a novel approach based on convolutional neural networks for the detection and segmentation of microcalcification clusters. In this work we used 283 mammograms to train and validate our model, obtaining an accuracy of 98.22% in the detection of preliminary suspect regions and of 97.47% in the segmentation task. Our results show how deep learning could be an effective tool to effectively support radiologists during mammograms examination.

* 13 pages, 7 figures 
  
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CELNet: Evidence Localization for Pathology Images using Weakly Supervised Learning

Sep 16, 2019
Yongxiang Huang, Albert C. S. Chung

Despite deep convolutional neural networks boost the performance of image classification and segmentation in digital pathology analysis, they are usually weak in interpretability for clinical applications or require heavy annotations to achieve object localization. To overcome this problem, we propose a weakly supervised learning-based approach that can effectively learn to localize the discriminative evidence for a diagnostic label from weakly labeled training data. Experimental results show that our proposed method can reliably pinpoint the location of cancerous evidence supporting the decision of interest, while still achieving a competitive performance on glimpse-level and slide-level histopathologic cancer detection tasks.

* Accepted for MICCAI 2019 
  
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Beyond Visual Image: Automated Diagnosis of Pigmented Skin Lesions Combining Clinical Image Features with Patient Data

Jan 25, 2022
José G. M. Esgario, Renato A. Krohling

kin cancer is considered one of the most common type of cancer in several countries. Due to the difficulty and subjectivity in the clinical diagnosis of skin lesions, Computer-Aided Diagnosis systems are being developed for assist experts to perform more reliable diagnosis. The clinical analysis and diagnosis of skin lesions relies not only on the visual information but also on the context information provided by the patient. This work addresses the problem of pigmented skin lesions detection from smartphones captured images. In addition to the features extracted from images, patient context information was collected to provide a more accurate diagnosis. The experiments showed that the combination of visual features with context information improved final results. Experimental results are very promising and comparable to experts.

* 33 pages, 11 figures 
  
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Dense Fully Convolutional Network for Skin Lesion Segmentation

Jun 05, 2018
Ebrahim Nasr-Esfahani, Shima Rafiei, Mohammad H. Jafari, Nader Karimi, James S. Wrobel, S. M. Reza Soroushmehr, Shadrokh Samavi, Kayvan Najarian

Lesion segmentation in skin images is an important step in computerized detection of skin cancer. Melanoma is known as one of the most life threatening types of this cancer. Existing methods often fall short of accurately segmenting lesions with fuzzy boarders. In this paper, a new class of fully convolutional network is proposed, with new dense pooling layers for segmentation of lesion regions in non-dermoscopic images. Unlike other existing convolutional networks, this proposed network is designed to produce dense feature maps. This network leads to highly accurate segmentation of lesions. The produced dice score here is 91.6% which outperforms state-of-the-art algorithms in segmentation of skin lesions based on the Dermquest dataset.

  
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Attention U-Net Based Adversarial Architectures for Chest X-ray Lung Segmentation

Mar 23, 2020
Gusztáv Gaál, Balázs Maga, András Lukács

Chest X-ray is the most common test among medical imaging modalities. It is applied for detection and differentiation of, among others, lung cancer, tuberculosis, and pneumonia, the last with importance due to the COVID-19 disease. Integrating computer-aided detection methods into the radiologist diagnostic pipeline, greatly reduces the doctors' workload, increasing reliability and quantitative analysis. Here we present a novel deep learning approach for lung segmentation, a basic, but arduous task in the diagnostic pipeline. Our method uses state-of-the-art fully convolutional neural networks in conjunction with an adversarial critic model. It generalized well to CXR images of unseen datasets with different patient profiles, achieving a final DSC of 97.5% on the JSRT dataset.

* 7 pages, 4 figures 
  
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