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"cancer detection": models, code, and papers

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) 

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.


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) 

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 

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:

* Under review 

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 

A system on chip for melanoma detection using FPGA-based SVM classifier

Sep 30, 2021
Shereen Afifi, Hamid GholamHosseini, Roopak Sinha

Support Vector Machine (SVM) is a robust machine learning model that shows high accuracy with different classification problems, and is widely used for various embedded applications. However , implementation of embedded SVM classifiers is challenging, due to the inherent complicated computations required. This motivates implementing the SVM on hardware platforms for achieving high performance computing at low cost and power consumption. Melanoma is the most aggressive form of skin cancer that increases the mortality rate. We aim to develop an optimized embedded SVM classifier dedicated for a low-cost handheld device for early detection of melanoma at the primary healthcare. In this paper, we propose a hardware/software co-design for implementing the SVM classifier onto FPGA to realize melanoma detection on a chip. The implemented SVM on a recent hybrid FPGA (Zynq) platform utilizing the modern UltraFast High-Level Synthesis design methodology achieves efficient melanoma classification on chip. The hardware implementation results demonstrate classification accuracy of 97.9%, and a significant hardware acceleration rate of 21 with only 3% resources utilization and 1.69W for power consumption. These results show that the implemented system on chip meets crucial embedded system constraints of high performance and low resources utilization, power consumption, and cost, while achieving efficient classification with high classification accuracy.

* A system on chip for melanoma detection using FPGA-based SVM classifier, Microprocessors and Microsystems 65(2019) pp.57-68 
* Journal paper, 13 pages, 3 figures, 9 tables 

Effect of Channel Geometry and Flow Rates in Hydrodynamic Focusing on Impedance Detection of Circulating Tumor Cells

Mar 08, 2022
Hassan Raji, Iraj Dehghan Hamani

Cells, other than their biological properties, have different electric and physical properties. In an impedance cytometer, cells should pass one by one in the detection region where pairs of electrodes are located. When cells are located between electrodes, the impedance changes, and this can be indicative of the presence of a cell. This is basically because the electric properties of cells are different from the medium between the electrodes which is important in determining the impedance. One of the most important aspects which influence the performance of an impedance cytometer performance is the microchannel design. In this work, in the first step, the microchannel was designed in a way to have the best detection in the impedance cytometer. In this regard, hydrodynamic focusing was selected to focus the population of cells entering from the inlet of the main channel. To find the optimal parameters of the microchannel, different geometry for the channel itself, along with flow rates and other parameters related to sheath flow were simulated. In the next step, impedance was measured in COMSOL for White blood cells, MCF7, and MDA-MB-231 breast cancer cells. The results show that by measuring the impedance of cells using the optimized channel design, CTCs can be successfully differentiated from WBCs.


PFA-ScanNet: Pyramidal Feature Aggregation with Synergistic Learning for Breast Cancer Metastasis Analysis

May 03, 2019
Zixu Zhao, Huangjing Lin, Hao Chen, Pheng Ann Heng

Automatic detection of cancer metastasis from whole slide images (WSIs) is a crucial step for following patient staging as well as prognosis. However, recent convolutional neural network (CNN) based approaches are struggling with the trade-off between accuracy and computation cost due to the difficulty in processing large-scale gigapixel images. To address this challenge, we propose a novel deep neural network, namely Pyramidal Feature Aggregation ScanNet (PFA-ScanNet) with pyramidal feature aggregation in both top-down and bottom-up paths. The discrimination capability of our detector is increased by leveraging the merit of contextual and spatial information from multi-scale features with larger receptive fields and less parameters. We also develop an extra decoder branch to synergistically learn the semantic information along with the detector, significantly improving the performance in recognizing the metastasis. Furthermore, a high-efficiency inference mechanism is designed with dense pooling layers, which allows dense and fast scanning for gigapixel WSI analysis. Our approach achieved the state-of-the-art FROC score of 89.1% on the Camelyon16 dataset, as well as competitive kappa score of 0.905 on the Camelyon17 leaderboard. In addition, our proposed method shows leading speed advantage over the state-of-the-art methods, which makes automatic analysis of breast cancer metastasis more applicable in the clinical usage.


SOMPS-Net : Attention based social graph framework for early detection of fake health news

Nov 22, 2021
Prasannakumaran D, Harish Srinivasan, Sowmiya Sree S, Sri Gayathri Devi I, Saikrishnan S, Vineeth Vijayaraghavan

Fake news is fabricated information that is presented as genuine, with intention to deceive the reader. Recently, the magnitude of people relying on social media for news consumption has increased significantly. Owing to this rapid increase, the adverse effects of misinformation affect a wider audience. On account of the increased vulnerability of people to such deceptive fake news, a reliable technique to detect misinformation at its early stages is imperative. Hence, the authors propose a novel graph-based framework SOcial graph with Multi-head attention and Publisher information and news Statistics Network (SOMPS-Net) comprising of two components - Social Interaction Graph (SIG) and Publisher and News Statistics (PNS). The posited model is experimented on the HealthStory dataset and generalizes across diverse medical topics including Cancer, Alzheimer's, Obstetrics, and Nutrition. SOMPS-Net significantly outperformed other state-of-the-art graph-based models experimented on HealthStory by 17.1%. Further, experiments on early detection demonstrated that SOMPS-Net predicted fake news articles with 79% certainty within just 8 hours of its broadcast. Thus the contributions of this work lay down the foundation for capturing fake health news across multiple medical topics at its early stages.