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"cancer detection": models, code, and papers

Skin Lesion Segmentation and Classification with Deep Learning System

Feb 16, 2019
Devansh Bisla, Anna Choromanska, Jennifer A. Stein, David Polsky, Russell Berman

Melanoma is one of the ten most common cancers in the US. Early detection is crucial for survival, but often the cancer is diagnosed in the fatal stage. Deep learning has the potential to improve cancer detection rates, but its applicability to melanoma detection is compromised by the limitations of the available skin lesion databases, which are small, heavily imbalanced, and contain images with occlusions. We propose a complete deep learning system for lesion segmentation and classification that utilizes networks specialized in data purification and augmentation. It contains the processing unit for removing image occlusions and the data generation unit for populating scarce lesion classes, or equivalently creating virtual patients with pre-defined types of lesions. We empirically verify our approach and show superior performance over common baselines.


Properties Of Winning Tickets On Skin Lesion Classification

Aug 25, 2020
Sherin Muckatira

Skin cancer affects a large population every year -- automated skin cancer detection algorithms can thus greatly help clinicians. Prior efforts involving deep learning models have high detection accuracy. However, most of the models have a large number of parameters, with some works even using an ensemble of models to achieve good accuracy. In this paper, we investigate a recently proposed pruning technique called Lottery Ticket Hypothesis. We find that iterative pruning of the network resulted in improved accuracy, compared to that of the unpruned network, implying that -- the lottery ticket hypothesis can be applied to the problem of skin cancer detection and this hypothesis can result in a smaller network for inference. We also examine the accuracy across sub-groups -- created by gender and age -- and it was found that some sub-groups show a larger increase in accuracy than others.

* 11 pages, 11 figures, presented at WiCV workshop at ECCV 2020 

Preprocessing for Automating Early Detection of Cervical Cancer

Aug 11, 2011
Abhishek Das, Avijit Kar, Debasis Bhattacharyya

Uterine Cervical Cancer is one of the most common forms of cancer in women worldwide. Most cases of cervical cancer can be prevented through screening programs aimed at detecting precancerous lesions. During Digital Colposcopy, colposcopic images or cervigrams are acquired in raw form. They contain specular reflections which appear as bright spots heavily saturated with white light and occur due to the presence of moisture on the uneven cervix surface and. The cervix region occupies about half of the raw cervigram image. Other parts of the image contain irrelevant information, such as equipment, frames, text and non-cervix tissues. This irrelevant information can confuse automatic identification of the tissues within the cervix. Therefore we focus on the cervical borders, so that we have a geometric boundary on the relevant image area. Our novel technique eliminates the SR, identifies the region of interest and makes the cervigram ready for segmentation algorithms.

* 15th International Conference on Information Visualisation (Track: 8th International Conference BioMedical Visualization) at London, UK (IEEE Computer Society) 

Colorectal Polyp Segmentation by U-Net with Dilation Convolution

Dec 26, 2019
Xinzi Sun, Pengfei Zhang, Dechun Wang, Yu Cao, Benyuan Liu

Colorectal cancer (CRC) is one of the most commonly diagnosed cancers and a leading cause of cancer deaths in the United States. Colorectal polyps that grow on the intima of the colon or rectum is an important precursor for CRC. Currently, the most common way for colorectal polyp detection and precancerous pathology is the colonoscopy. Therefore, accurate colorectal polyp segmentation during the colonoscopy procedure has great clinical significance in CRC early detection and prevention. In this paper, we propose a novel end-to-end deep learning framework for the colorectal polyp segmentation. The model we design consists of an encoder to extract multi-scale semantic features and a decoder to expand the feature maps to a polyp segmentation map. We improve the feature representation ability of the encoder by introducing the dilated convolution to learn high-level semantic features without resolution reduction. We further design a simplified decoder which combines multi-scale semantic features with fewer parameters than the traditional architecture. Furthermore, we apply three post processing techniques on the output segmentation map to improve colorectal polyp detection performance. Our method achieves state-of-the-art results on CVC-ClinicDB and ETIS-Larib Polyp DB.

* 8 pages. ICMLA (International Conference on Machine Learning and Applications) 

VinDr-Mammo: A large-scale benchmark dataset for computer-aided diagnosis in full-field digital mammography

Mar 20, 2022
Hieu T. Nguyen, Ha Q. Nguyen, Hieu H. Pham, Khanh Lam, Linh T. Le, Minh Dao, Van Vu

Mammography, or breast X-ray, is the most widely used imaging modality to detect cancer and other breast diseases. Recent studies have shown that deep learning-based computer-assisted detection and diagnosis (CADe or CADx) tools have been developed to support physicians and improve the accuracy of interpreting mammography. However, most published datasets of mammography are either limited on sample size or digitalized from screen-film mammography (SFM), hindering the development of CADe and CADx tools which are developed based on full-field digital mammography (FFDM). To overcome this challenge, we introduce VinDr-Mammo - a new benchmark dataset of FFDM for detecting and diagnosing breast cancer and other diseases in mammography. The dataset consists of 5,000 mammography exams, each of which has four standard views and is double read with disagreement (if any) being resolved by arbitration. It is created for the assessment of Breast Imaging Reporting and Data System (BI-RADS) and density at the breast level. In addition, the dataset also provides the category, location, and BI-RADS assessment of non-benign findings. We make VinDr-Mammo publicly available on PhysioNet as a new imaging resource to promote advances in developing CADe and CADx tools for breast cancer screening.

* The manuscript is under review by Nature Scientific Data 

A Comparative Study of Gastric Histopathology Sub-size Image Classification: from Linear Regression to Visual Transformer

May 25, 2022
Weiming Hu, Haoyuan Chen, Wanli Liu, Xiaoyan Li, Hongzan Sun, Xinyu Huang, Marcin Grzegorzek, Chen Li

Gastric cancer is the fifth most common cancer in the world. At the same time, it is also the fourth most deadly cancer. Early detection of cancer exists as a guide for the treatment of gastric cancer. Nowadays, computer technology has advanced rapidly to assist physicians in the diagnosis of pathological pictures of gastric cancer. Ensemble learning is a way to improve the accuracy of algorithms, and finding multiple learning models with complementarity types is the basis of ensemble learning. The complementarity of sub-size pathology image classifiers when machine performance is insufficient is explored in this experimental platform. We choose seven classical machine learning classifiers and four deep learning classifiers for classification experiments on the GasHisSDB database. Among them, classical machine learning algorithms extract five different image virtual features to match multiple classifier algorithms. For deep learning, we choose three convolutional neural network classifiers. In addition, we also choose a novel Transformer-based classifier. The experimental platform, in which a large number of classical machine learning and deep learning methods are performed, demonstrates that there are differences in the performance of different classifiers on GasHisSDB. Classical machine learning models exist for classifiers that classify Abnormal categories very well, while classifiers that excel in classifying Normal categories also exist. Deep learning models also exist with multiple models that can be complementarity. Suitable classifiers are selected for ensemble learning, when machine performance is insufficient. This experimental platform demonstrates that multiple classifiers are indeed complementarity and can improve the efficiency of ensemble learning. This can better assist doctors in diagnosis, improve the detection of gastric cancer, and increase the cure rate.

* arXiv admin note: text overlap with arXiv:2106.02473 

Towards Reliable and Explainable AI Model for Solid Pulmonary Nodule Diagnosis

Apr 08, 2022
Chenglong Wang, Yun Liu, Fen Wang, Chengxiu Zhang, Yida Wang, Mei Yuan, Guang Yang

Lung cancer has the highest mortality rate of deadly cancers in the world. Early detection is essential to treatment of lung cancer. However, detection and accurate diagnosis of pulmonary nodules depend heavily on the experiences of radiologists and can be a heavy workload for them. Computer-aided diagnosis (CAD) systems have been developed to assist radiologists in nodule detection and diagnosis, greatly easing the workload while increasing diagnosis accuracy. Recent development of deep learning, greatly improved the performance of CAD systems. However, lack of model reliability and interpretability remains a major obstacle for its large-scale clinical application. In this work, we proposed a multi-task explainable deep-learning model for pulmonary nodule diagnosis. Our neural model can not only predict lesion malignancy but also identify relevant manifestations. Further, the location of each manifestation can also be visualized for visual interpretability. Our proposed neural model achieved a test AUC of 0.992 on LIDC public dataset and a test AUC of 0.923 on our in-house dataset. Moreover, our experimental results proved that by incorporating manifestation identification tasks into the multi-task model, the accuracy of the malignancy classification can also be improved. This multi-task explainable model may provide a scheme for better interaction with the radiologists in a clinical environment.


Detection and Localization of Robotic Tools in Robot-Assisted Surgery Videos Using Deep Neural Networks for Region Proposal and Detection

Jul 29, 2020
Duygu Sarikaya, Jason J. Corso, Khurshid A. Guru

Video understanding of robot-assisted surgery (RAS) videos is an active research area. Modeling the gestures and skill level of surgeons presents an interesting problem. The insights drawn may be applied in effective skill acquisition, objective skill assessment, real-time feedback, and human-robot collaborative surgeries. We propose a solution to the tool detection and localization open problem in RAS video understanding, using a strictly computer vision approach and the recent advances of deep learning. We propose an architecture using multimodal convolutional neural networks for fast detection and localization of tools in RAS videos. To our knowledge, this approach will be the first to incorporate deep neural networks for tool detection and localization in RAS videos. Our architecture applies a Region Proposal Network (RPN), and a multi-modal two stream convolutional network for object detection, to jointly predict objectness and localization on a fusion of image and temporal motion cues. Our results with an Average Precision (AP) of 91% and a mean computation time of 0.1 seconds per test frame detection indicate that our study is superior to conventionally used methods for medical imaging while also emphasizing the benefits of using RPN for precision and efficiency. We also introduce a new dataset, ATLAS Dione, for RAS video understanding. Our dataset provides video data of ten surgeons from Roswell Park Cancer Institute (RPCI) (Buffalo, NY) performing six different surgical tasks on the daVinci Surgical System (dVSS R ) with annotations of robotic tools per frame.

* IEEE Transactions on Medical Imaging 36 (2017) 1542-1549 

Dynamic hardware system for cascade SVM classification of melanoma

Dec 10, 2021
Shereen Afifi, Hamid GholamHosseini, Roopak Sinha

Melanoma is the most dangerous form of skin cancer, which is responsible for the majority of skin cancer-related deaths. Early diagnosis of melanoma can significantly reduce mortality rates and treatment costs. Therefore, skin cancer specialists are using image-based diagnostic tools for detecting melanoma earlier. We aim to develop a handheld device featured with low cost and high performance to enhance early detection of melanoma at the primary healthcare. But, developing this device is very challenging due to the complicated computations required by the embedded diagnosis system. Thus, we aim to exploit the recent hardware technology in reconfigurable computing to achieve a high-performance embedded system at low cost. Support vector machine (SVM) is a common classifier that shows high accuracy for classifying melanoma within the diagnosis system and is considered as the most compute-intensive task in the system. In this paper, we propose a dynamic hardware system for implementing a cascade SVM classifier on FPGA for early melanoma detection. A multi-core architecture is proposed to implement a two-stage cascade classifier using two classifiers with accuracies of 98% and 73%. The hardware implementation results were optimized by using the dynamic partial reconfiguration technology, where very low resource utilization of 1% slices and power consumption of 1.5 W were achieved. Consequently, the implemented dynamic hardware system meets vital embedded system constraints of high performance and low cost, resource utilization, and power consumption, while achieving efficient classification with high accuracy.

* Neural Computing & Applications 32 (2020) pp.1777-1788 
* Journal paper, 9 pages, 4 figures, 4 tables 

Feasibility of Colon Cancer Detection in Confocal Laser Microscopy Images Using Convolution Neural Networks

Dec 05, 2018
Nils Gessert, Lukas Wittig, Daniel Drömann, Tobias Keck, Alexander Schlaefer, David B. Ellebrecht

Histological evaluation of tissue samples is a typical approach to identify colorectal cancer metastases in the peritoneum. For immediate assessment, reliable and real-time in-vivo imaging would be required. For example, intraoperative confocal laser microscopy has been shown to be suitable for distinguishing organs and also malignant and benign tissue. So far, the analysis is done by human experts. We investigate the feasibility of automatic colon cancer classification from confocal laser microscopy images using deep learning models. We overcome very small dataset sizes through transfer learning with state-of-the-art architectures. We achieve an accuracy of 89.1% for cancer detection in the peritoneum which indicates viability as an intraoperative decision support system.

* Accepted at BVM Workshop 2019