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"cancer detection": models, code, and papers

Accurate Prostate Cancer Detection and Segmentation on Biparametric MRI using Non-local Mask R-CNN with Histopathological Ground Truth

Oct 28, 2020
Zhenzhen Dai, Ivan Jambor, Pekka Taimen, Milan Pantelic, Mohamed Elshaikh, Craig Rogers, Otto Ettala, Peter Boström, Hannu Aronen, Harri Merisaari, Ning Wen

Purpose: We aimed to develop deep machine learning (DL) models to improve the detection and segmentation of intraprostatic lesions (IL) on bp-MRI by using whole amount prostatectomy specimen-based delineations. We also aimed to investigate whether transfer learning and self-training would improve results with small amount labelled data. Methods: 158 patients had suspicious lesions delineated on MRI based on bp-MRI, 64 patients had ILs delineated on MRI based on whole mount prostatectomy specimen sections, 40 patients were unlabelled. A non-local Mask R-CNN was proposed to improve the segmentation accuracy. Transfer learning was investigated by fine-tuning a model trained using MRI-based delineations with prostatectomy-based delineations. Two label selection strategies were investigated in self-training. The performance of models was evaluated by 3D detection rate, dice similarity coefficient (DSC), 95 percentile Hausdrauff (95 HD, mm) and true positive ratio (TPR). Results: With prostatectomy-based delineations, the non-local Mask R-CNN with fine-tuning and self-training significantly improved all evaluation metrics. For the model with the highest detection rate and DSC, 80.5% (33/41) of lesions in all Gleason Grade Groups (GGG) were detected with DSC of 0.548[0.165], 95 HD of 5.72[3.17] and TPR of 0.613[0.193]. Among them, 94.7% (18/19) of lesions with GGG > 2 were detected with DSC of 0.604[0.135], 95 HD of 6.26[3.44] and TPR of 0.580[0.190]. Conclusion: DL models can achieve high prostate cancer detection and segmentation accuracy on bp-MRI based on annotations from histologic images. To further improve the performance, more data with annotations of both MRI and whole amount prostatectomy specimens are required.

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Local image registration a comparison for bilateral registration mammography

Aug 12, 2013
José M. Celaya-Padilla, Juan Rodriguez-Rojas, Victor Trevino, José G. Gerardo Tamez-Pena

Early tumor detection is key in reducing the number of breast cancer death and screening mammography is one of the most widely available and reliable method for early detection. However, it is difficult for the radiologist to process with the same attention each case, due the large amount of images to be read. Computer aided detection (CADe) systems improve tumor detection rate; but the current efficiency of these systems is not yet adequate and the correct interpretation of CADe outputs requires expert human intervention. Computer aided diagnosis systems (CADx) are being designed to improve cancer diagnosis accuracy, but they have not been efficiently applied in breast cancer. CADx efficiency can be enhanced by considering the natural mirror symmetry between the right and left breast. The objective of this work is to evaluate co-registration algorithms for the accurate alignment of the left to right breast for CADx enhancement. A set of mammograms were artificially altered to create a ground truth set to evaluate the registration efficiency of DEMONs, and SPLINE deformable registration algorithms. The registration accuracy was evaluated using mean square errors, mutual information and correlation. The results on the 132 images proved that the SPLINE deformable registration over-perform the DEMONS on mammography images.

* 9 pages, Submitted to The 9th International Seminar on Medical Information Processing and Analysis (formerly International Seminar on Medical Image Processing and Analysis) (pending approval) 
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Detection and Demarcation of Tumor using Vector Quantization in MRI images

Jan 23, 2010
H. B. Kekre, Tanuja K. Sarode, Saylee M. Gharge

Segmenting a MRI images into homogeneous texture regions representing disparate tissue types is often a useful preprocessing step in the computer-assisted detection of breast cancer. That is why we proposed new algorithm to detect cancer in mammogram breast cancer images. In this paper we proposed segmentation using vector quantization technique. Here we used Linde Buzo-Gray algorithm (LBG) for segmentation of MRI images. Initially a codebook of size 128 was generated for MRI images. These code vectors were further clustered in 8 clusters using same LBG algorithm. These 8 images were displayed as a result. This approach does not leads to over segmentation or under segmentation. For the comparison purpose we displayed results of watershed segmentation and Entropy using Gray Level Co-occurrence Matrix along with this method.

* IJEST Volume 1 Issue 2 2009 59-66 
* 8 Pages 
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A Precision Diagnostic Framework of Renal Cell Carcinoma on Whole-Slide Images using Deep Learning

Oct 26, 2021
Jialun Wu, Haichuan Zhang, Zeyu Gao, Xinrui Bao, Tieliang Gong, Chunbao Wang, Chen Li

Diagnostic pathology, which is the basis and gold standard of cancer diagnosis, provides essential information on the prognosis of the disease and vital evidence for clinical treatment. Tumor region detection, subtype and grade classification are the fundamental diagnostic indicators for renal cell carcinoma (RCC) in whole-slide images (WSIs). However, pathological diagnosis is subjective, differences in observation and diagnosis between pathologists is common in hospitals with inadequate diagnostic capacity. The main challenge for developing deep learning based RCC diagnostic system is the lack of large-scale datasets with precise annotations. In this work, we proposed a deep learning-based framework for analyzing histopathological images of patients with renal cell carcinoma, which has the potential to achieve pathologist-level accuracy in diagnosis. A deep convolutional neural network (InceptionV3) was trained on the high-quality annotated dataset of The Cancer Genome Atlas (TCGA) whole-slide histopathological image for accurate tumor area detection, classification of RCC subtypes, and ISUP grades classification of clear cell carcinoma subtypes. These results suggest that our framework can help pathologists in the detection of cancer region and classification of subtypes and grades, which could be applied to any cancer type, providing auxiliary diagnosis and promoting clinical consensus.

* BIBM 2021 accepted, 9 pages including reference, 3 figures and 1 table 
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Detecting Deficient Coverage in Colonoscopies

Jan 26, 2020
Daniel Freedman, Yochai Blau, Liran Katzir, Amit Aides, Ilan Shimshoni, Danny Veikherman, Tomer Golany, Ariel Gordon, Greg Corrado, Yossi Matias, Ehud Rivlin

Colorectal Cancer (CRC) is a global health problem, resulting in 900K deaths per year. Colonoscopy is the tool of choice for preventing CRC, by detecting polyps before they become cancerous, and removing them. However, colonoscopy is hampered by the fact that endoscopists routinely miss an average of 22-28% of polyps. While some of these missed polyps appear in the endoscopist's field of view, others are missed simply because of substandard coverage of the procedure, i.e. not all of the colon is seen. This paper attempts to rectify the problem of substandard coverage in colonoscopy through the introduction of the C2D2 (Colonoscopy Coverage Deficiency via Depth) algorithm which detects deficient coverage, and can thereby alert the endoscopist to revisit a given area. More specifically, C2D2 consists of two separate algorithms: the first performs depth estimation of the colon given an ordinary RGB video stream; while the second computes coverage given these depth estimates. Rather than compute coverage for the entire colon, our algorithm computes coverage locally, on a segment-by-segment basis; C2D2 can then indicate in real-time whether a particular area of the colon has suffered from deficient coverage, and if so the endoscopist can return to that area. Our coverage algorithm is the first such algorithm to be evaluated in a large-scale way; while our depth estimation technique is the first calibration-free unsupervised method applied to colonoscopies. The C2D2 algorithm achieves state of the art results in the detection of deficient coverage: it is 2.4 times more accurate than human experts.

* Compliance with internal requirements 
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Colonoscopy Polyp Detection and Classification: Dataset Creation and Comparative Evaluations

Apr 22, 2021
Kaidong Li, Mohammad I. Fathan, Krushi Patel, Tianxiao Zhang, Cuncong Zhong, Ajay Bansal, Amit Rastogi, Jean S. Wang, Guanghui Wang

Colorectal cancer (CRC) is one of the most common types of cancer with a high mortality rate. Colonoscopy is the preferred procedure for CRC screening and has proven to be effective in reducing CRC mortality. Thus, a reliable computer-aided polyp detection and classification system can significantly increase the effectiveness of colonoscopy. In this paper, we create an endoscopic dataset collected from various sources and annotate the ground truth of polyp location and classification results with the help of experienced gastroenterologists. The dataset can serve as a benchmark platform to train and evaluate the machine learning models for polyp classification. We have also compared the performance of eight state-of-the-art deep learning-based object detection models. The results demonstrate that deep CNN models are promising in CRC screening. This work can serve as a baseline for future research in polyp detection and classification.

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SVM Classifier on Chip for Melanoma Detection

Aug 26, 2021
Shereen Afifi, Hamid GholamHosseini, Roopak Sinha

Support Vector Machine (SVM) is a common classifier used for efficient classification with high accuracy. SVM shows high accuracy for classifying melanoma (skin cancer) clinical images within computer-aided diagnosis systems used by skin cancer specialists to detect melanoma early and save lives. We aim to develop a medical low-cost handheld device that runs a real-time embedded SVM- based diagnosis system for use in primary care for early detection of melanoma. In this paper, an optimized SVM classifier is implemented onto a recent FPGA platform using the latest design methodology to be embedded into the proposed device for realizing online efficient melanoma detection on a single system on chip/device. The hardware implementation results demonstrate a high classification accuracy of 97.9% and a significant acceleration factor of 26 from equivalent software implementation on an embedded processor, with 34% of resources utilization and 2 watts for power consumption. Consequently, the implemented system meets crucial embedded systems constraints of high performance and low cost, resources utilization and power consumption, while achieving high classification accuracy.

* Proceedings of the 39th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC2017). Jeju, Korea (South), IEEE Computer Society Press, pp.270-274 
* Conference paper, 5 pages, 4 figures, 1 tables 
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Deep learning approach for breast cancer diagnosis

Mar 10, 2020
Essam A. Rashed, M. Samir Abou El Seoud

Breast cancer is one of the leading fatal disease worldwide with high risk control if early discovered. Conventional method for breast screening is x-ray mammography, which is known to be challenging for early detection of cancer lesions. The dense breast structure produced due to the compression process during imaging lead to difficulties to recognize small size abnormalities. Also, inter- and intra-variations of breast tissues lead to significant difficulties to achieve high diagnosis accuracy using hand-crafted features. Deep learning is an emerging machine learning technology that requires a relatively high computation power. Yet, it proved to be very effective in several difficult tasks that requires decision making at the level of human intelligence. In this paper, we develop a new network architecture inspired by the U-net structure that can be used for effective and early detection of breast cancer. Results indicate a high rate of sensitivity and specificity that indicate potential usefulness of the proposed approach in clinical use.

* ICSIE '19: Proceedings of the 2019 8th International Conference on Software and Information Engineering 
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DiagSet: a dataset for prostate cancer histopathological image classification

May 09, 2021
Michał Koziarski, Bogusław Cyganek, Bogusław Olborski, Zbigniew Antosz, Marcin Żydak, Bogdan Kwolek, Paweł Wąsowicz, Andrzej Bukała, Jakub Swadźba, Piotr Sitkowski

Cancer diseases constitute one of the most significant societal challenges. In this paper we introduce a novel histopathological dataset for prostate cancer detection. The proposed dataset, consisting of over 2.6 million tissue patches extracted from 430 fully annotated scans, 4675 scans with assigned binary diagnosis, and 46 scans with diagnosis given independently by a group of histopathologists, can be found at Furthermore, we propose a machine learning framework for detection of cancerous tissue regions and prediction of scan-level diagnosis, utilizing thresholding and statistical analysis to abstain from the decision in uncertain cases. During the experimental evaluation we identify several factors negatively affecting the performance of considered models, such as presence of label noise, data imbalance, and quantity of data, that can serve as a basis for further research. The proposed approach, composed of ensembles of deep neural networks operating on the histopathological scans at different scales, achieves 94.6% accuracy in patch-level recognition, and is compared in a scan-level diagnosis with 9 human histopathologists.

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