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"cancer detection": models, code, and papers

Abnormality Detection in Mammography using Deep Convolutional Neural Networks

Mar 05, 2018
Pengcheng Xi, Chang Shu, Rafik Goubran

Breast cancer is the most common cancer in women worldwide. The most common screening technology is mammography. To reduce the cost and workload of radiologists, we propose a computer aided detection approach for classifying and localizing calcifications and masses in mammogram images. To improve on conventional approaches, we apply deep convolutional neural networks (CNN) for automatic feature learning and classifier building. In computer-aided mammography, deep CNN classifiers cannot be trained directly on full mammogram images because of the loss of image details from resizing at input layers. Instead, our classifiers are trained on labelled image patches and then adapted to work on full mammogram images for localizing the abnormalities. State-of-the-art deep convolutional neural networks are compared on their performance of classifying the abnormalities. Experimental results indicate that VGGNet receives the best overall accuracy at 92.53\% in classifications. For localizing abnormalities, ResNet is selected for computing class activation maps because it is ready to be deployed without structural change or further training. Our approach demonstrates that deep convolutional neural network classifiers have remarkable localization capabilities despite no supervision on the location of abnormalities is provided.

* 6 pages 
  
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Detecting Pancreatic Adenocarcinoma in Multi-phase CT Scans via Alignment Ensemble

Apr 03, 2020
Yingda Xia, Qihang Yu, Wei Shen, Yuyin Zhou, Elliot K. Fishman, Alan L. Yuille

Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers among population. Screening for PDACs in dynamic contrast-enhanced CT is beneficial for early diagnose. In this paper, we investigate the problem of automated detecting PDACs in multi-phase (arterial and venous) CT scans. Multiple phases provide more information than single phase, but they are unaligned and inhomogeneous in texture, making it difficult to combine cross-phase information seamlessly. We study multiple phase alignment strategies, i.e., early alignment (image registration), late alignment (high-level feature registration) and slow alignment (multi-level feature registration), and suggest an ensemble of all these alignments as a promising way to boost the performance of PDAC detection. We provide an extensive empirical evaluation on two PDAC datasets and show that the proposed alignment ensemble significantly outperforms previous state-of-the-art approaches, illustrating strong potential for clinical use.

* The first two authors contributed equally to this work 
  
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Classification of breast cancer histology images using transfer learning

Feb 26, 2018
Sulaiman Vesal, Nishant Ravikumar, AmirAbbas Davari, Stephan Ellmann, Andreas Maier

Breast cancer is one of the leading causes of mortality in women. Early detection and treatment are imperative for improving survival rates, which have steadily increased in recent years as a result of more sophisticated computer-aided-diagnosis (CAD) systems. A critical component of breast cancer diagnosis relies on histopathology, a laborious and highly subjective process. Consequently, CAD systems are essential to reduce inter-rater variability and supplement the analyses conducted by specialists. In this paper, a transfer-learning based approach is proposed, for the task of breast histology image classification into four tissue sub-types, namely, normal, benign, \textit{in situ} carcinoma and invasive carcinoma. The histology images, provided as part of the BACH 2018 grand challenge, were first normalized to correct for color variations resulting from inconsistencies during slide preparation. Subsequently, image patches were extracted and used to fine-tune Google`s Inception-V3 and ResNet50 convolutional neural networks (CNNs), both pre-trained on the ImageNet database, enabling them to learn domain-specific features, necessary to classify the histology images. The ResNet50 network (based on residual learning) achieved a test classification accuracy of 97.50% for four classes, outperforming the Inception-V3 network which achieved an accuracy of 91.25%.

* 8 pages, Submitted to 15th International Conference on Image Analysis and Recognition (ICAIR 2018) 
  
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Automated pulmonary nodule detection using 3D deep convolutional neural networks

Mar 23, 2019
Hao Tang, Daniel R. Kim, Xiaohui Xie

Early detection of pulmonary nodules in computed tomography (CT) images is essential for successful outcomes among lung cancer patients. Much attention has been given to deep convolutional neural network (DCNN)-based approaches to this task, but models have relied at least partly on 2D or 2.5D components for inherently 3D data. In this paper, we introduce a novel DCNN approach, consisting of two stages, that is fully three-dimensional end-to-end and utilizes the state-of-the-art in object detection. First, nodule candidates are identified with a U-Net-inspired 3D Faster R-CNN trained using online hard negative mining. Second, false positive reduction is performed by 3D DCNN classifiers trained on difficult examples produced during candidate screening. Finally, we introduce a method to ensemble models from both stages via consensus to give the final predictions. By using this framework, we ranked first of 2887 teams in Season One of Alibaba's 2017 TianChi AI Competition for Healthcare.

* 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018) 
  
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Fake News Detection by means of Uncertainty Weighted Causal Graphs

Feb 04, 2020
Eduardo C. Garrido-Merchán, Cristina Puente, Rafael Palacios

Society is experimenting changes in information consumption, as new information channels such as social networks let people share news that do not necessarily be trust worthy. Sometimes, these sources of information produce fake news deliberately with doubtful purposes and the consumers of that information share it to other users thinking that the information is accurate. This transmission of information represents an issue in our society, as can influence negatively the opinion of people about certain figures, groups or ideas. Hence, it is desirable to design a system that is able to detect and classify information as fake and categorize a source of information as trust worthy or not. Current systems experiment difficulties performing this task, as it is complicated to design an automatic procedure that can classify this information independent on the context. In this work, we propose a mechanism to detect fake news through a classifier based on weighted causal graphs. These graphs are specific hybrid models that are built through causal relations retrieved from texts and consider the uncertainty of causal relations. We take advantage of this representation to use the probability distributions of this graph and built a fake news classifier based on the entropy and KL divergence of learned and new information. We believe that the problem of fake news is accurately tackled by this model due to its hybrid nature between a symbolic and quantitative methodology. We describe the methodology of this classifier and add empirical evidence of the usefulness of our proposed approach in the form of synthetic experiments and a real experiment involving lung cancer.

  
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Ovarian Cancer Prediction from Ovarian Cysts Based on TVUS Using Machine Learning Algorithms

Aug 30, 2021
Laboni Akter, Nasrin Akhter

Ovarian Cancer (OC) is type of female reproductive malignancy which can be found among young girls and mostly the women in their fertile or reproductive. There are few number of cysts are dangerous and may it cause cancer. So, it is very important to predict and it can be from different types of screening are used for this detection using Transvaginal Ultrasonography (TVUS) screening. In this research, we employed an actual datasets called PLCO with TVUS screening and three machine learning (ML) techniques, respectively Random Forest KNN, and XGBoost within three target variables. We obtained a best performance from this algorithms as far as accuracy, recall, f1 score and precision with the approximations of 99.50%, 99.50%, 99.49% and 99.50% individually. The AUC score of 99.87%, 98.97% and 99.88% are observed in these Random Forest, KNN and XGB algorithms .This approach helps assist physicians and suspects in identifying ovarian risks early on, reducing ovarian malignancy-related complications and deaths.

* This paper has been published in International Conference on Big Data, IoT and Machine Learning 2021 (BIM 2021) 
  
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Reliable and Trustworthy Machine Learning for Health Using Dataset Shift Detection

Oct 26, 2021
Chunjong Park, Anas Awadalla, Tadayoshi Kohno, Shwetak Patel

Unpredictable ML model behavior on unseen data, especially in the health domain, raises serious concerns about its safety as repercussions for mistakes can be fatal. In this paper, we explore the feasibility of using state-of-the-art out-of-distribution detectors for reliable and trustworthy diagnostic predictions. We select publicly available deep learning models relating to various health conditions (e.g., skin cancer, lung sound, and Parkinson's disease) using various input data types (e.g., image, audio, and motion data). We demonstrate that these models show unreasonable predictions on out-of-distribution datasets. We show that Mahalanobis distance- and Gram matrices-based out-of-distribution detection methods are able to detect out-of-distribution data with high accuracy for the health models that operate on different modalities. We then translate the out-of-distribution score into a human interpretable CONFIDENCE SCORE to investigate its effect on the users' interaction with health ML applications. Our user study shows that the \textsc{confidence score} helped the participants only trust the results with a high score to make a medical decision and disregard results with a low score. Through this work, we demonstrate that dataset shift is a critical piece of information for high-stake ML applications, such as medical diagnosis and healthcare, to provide reliable and trustworthy predictions to the users.

* Neu 
  
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Memory-aware curriculum federated learning for breast cancer classification

Jul 06, 2021
Amelia Jiménez-Sánchez, Mickael Tardy, Miguel A. González Ballester, Diana Mateus, Gemma Piella

For early breast cancer detection, regular screening with mammography imaging is recommended. Routinary examinations result in datasets with a predominant amount of negative samples. A potential solution to such class-imbalance is joining forces across multiple institutions. Developing a collaborative computer-aided diagnosis system is challenging in different ways. Patient privacy and regulations need to be carefully respected. Data across institutions may be acquired from different devices or imaging protocols, leading to heterogeneous non-IID data. Also, for learning-based methods, new optimization strategies working on distributed data are required. Recently, federated learning has emerged as an effective tool for collaborative learning. In this setting, local models perform computation on their private data to update the global model. The order and the frequency of local updates influence the final global model. Hence, the order in which samples are locally presented to the optimizers plays an important role. In this work, we define a memory-aware curriculum learning method for the federated setting. Our curriculum controls the order of the training samples paying special attention to those that are forgotten after the deployment of the global model. Our approach is combined with unsupervised domain adaptation to deal with domain shift while preserving data privacy. We evaluate our method with three clinical datasets from different vendors. Our results verify the effectiveness of federated adversarial learning for the multi-site breast cancer classification. Moreover, we show that our proposed memory-aware curriculum method is beneficial to further improve classification performance. Our code is publicly available at: https://github.com/ameliajimenez/curriculum-federated-learning.

* Under review 
  
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Tensor clustering with algebraic constraints gives interpretable groups of crosstalk mechanisms in breast cancer

Apr 28, 2017
Anna Seigal, Mariano Beguerisse-DĂ­az, Birgit Schoeberl, Mario Niepel, Heather A. Harrington

We introduce a tensor-based clustering method to extract sparse, low-dimensional structure from high-dimensional, multi-indexed datasets. Specifically, this framework is designed to enable detection of clusters of data in the presence of structural requirements which we encode as algebraic constraints in a linear program. We illustrate our method on a collection of experiments measuring the response of genetically diverse breast cancer cell lines to an array of ligands. Each experiment consists of a cell line-ligand combination, and contains time-course measurements of the early-signalling kinases MAPK and AKT at two different ligand dose levels. By imposing appropriate structural constraints and respecting the multi-indexed structure of the data, our clustering analysis can be optimized for biological interpretation and therapeutic understanding. We then perform a systematic, large-scale exploration of mechanistic models of MAPK-AKT crosstalk for each cluster. This analysis allows us to quantify the heterogeneity of breast cancer cell subtypes, and leads to hypotheses about the mechanisms by which cell lines respond to ligands. Our clustering method is general and can be tailored to a variety of applications in science and industry.

* 22 pages, 12 figures, 4 tables 
  
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