Differentiating the intrinsic subtypes of breast cancer is crucial for deciding the best treatment strategy. Deep learning can predict the subtypes from genetic information more accurately than conventional statistical methods, but to date, deep learning has not been directly utilized to examine which genes are associa…
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48 results for “Breast Cancer Subtype”
Paper proposes scalable method for analyzing multi-omic data.
problem Integrating high-dimensional multi-omic data for cancer subtyping.
method Mixed graphical model approach using Birth-Death MCMC algorithm.
result Our method outperforms LASSO and standard BDMCMC in computational efficiency and model selection accuracy.
We introduce a tensor-based clustering method to extract sparse, low-dimensional structure from high-dimensional, multi-indexed datasets. 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. Our cluste…
ERICA assesses replicability of cluster analysis results.
problem Lack of quantitative scrutiny for clustering results.
method ERICA: a framework to assess replicability of cluster analysis.
result Clusters are found to be replicable in synthetic data but not in real-world datasets.
A hybrid method clusters and characterizes cancer data efficiently.
problem Challenges in clustering high-dimensional biomedical data.
method Gaussian mixture with generalized factor analyzers for efficient estimation.
result Our approach outperforms existing methods with faster convergence and higher accuracy.
OPAL optimizes labeling strategy for precise inference from uncertain models.
problem Inference from uncertain machine learning models is brittle.
method OPAL learns a smooth policy to adaptively label data points based on model uncertainty.
result OPAL yields estimators with the lowest variance and achieves nominal coverage in finite samples.
Towards Unsupervised Cancer Subtyping: Predicting Prognosis Using A Histologic Visual Dictionarycs.CV
Unlike common cancers, such as those of the prostate and breast, tumor grading in rare cancers is difficult and largely undefined because of small sample sizes, the sheer volume of time needed to undertake on such a task, and the inherent difficulty of extracting human-observed patterns. One of the most challenging exa…
Bayesian outcome-guided multi-view mixture models with applications in molecular precision medicinestat.ME
Bayesian model clusters diverse 'omics data for disease subtyping.
problem Clustering diverse 'omics datasets conflates multiple structures.
method Multi-view Bayesian mixture model with semi-supervised learning.
result Identifies distinct clusters of patients for stratified medicine.
Many researches demonstrated that the DNA methylation, which occurs in the context of a CpG, has strong correlation with diseases, including cancer. There is a strong interest in analyzing the DNA methylation data to find how to distinguish different subtypes of the tumor. However, the conventional statistical methods …
Among American women, the rate of breast cancer is only second to lung cancer. An estimated 12.4% women will develop breast cancer over the course of their lifetime. The widespread use of social media across the socio-economic spectrum offers unparalleled ways to facilitate information sharing, in particular as it pert…
Prediction of Malignant & Benign Breast Cancer: A Data Mining Approach in Healthcare Applicationscs.LG
As much as data science is playing a pivotal role everywhere, healthcare also finds it prominent application. Breast Cancer is the top rated type of cancer amongst women; which took away 627,000 lives alone. This high mortality rate due to breast cancer does need attention, for early detection so that prevention can be…
The research reported in this paper identifies the epigenetic biomarker (methylation beta pattern) of breast cancer. Many cancers are triggered by abnormal gene expression levels caused by aberrant methylation of CpG sites in the DNA. In order to develop early diagnostics of cancer-causing methylations and to develop a…
The task of clustering a set of objects based on multiple sources of data arises in several modern applications. We propose an integrative statistical model that permits a separate clustering of the objects for each data source. These separate clusterings adhere loosely to an overall consensus clustering, and hence the…
This report assesses different machine learning approaches to 10-year survival prediction of breast cancer patients.
Breast cancer is the most frequently reported cancer type among the women around the globe and beyond that it has the second highest female fatality rate among all cancer types. Despite all the progresses made in prevention and early intervention, early prognosis and survival prediction rates are still unsatisfactory. …
We trained and evaluated a localization-based deep CNN for breast cancer screening exam classification on over 200,000 exams (over 1,000,000 images). Our model achieves an AUC of 0.919 in predicting malignancy in patients undergoing breast cancer screening, reducing the error rate of the baseline (Wu et al., 2019a) by …
Identifying cancer subtypes in glioblastoma by combining genomic, transcriptomic and epigenomic dataq-bio.GN
We present a nonparametric Bayesian method for disease subtype discovery in multi-dimensional cancer data. Our method can simultaneously analyse a wide range of data types, allowing for both agreement and disagreement between their underlying clustering structure. It includes feature selection and infers the most likel…
An interpretable multiple kernel learning approach for the discovery of integrative cancer subtypesstat.ML
Due to the complexity of cancer, clustering algorithms have been used to disentangle the observed heterogeneity and identify cancer subtypes that can be treated specifically. While kernel based clustering approaches allow the use of more than one input matrix, which is an important factor when considering a multidimens…
Microwave-based breast cancer detection has been proposed as a complementary approach to compensate for some drawbacks of existing breast cancer detection techniques. Among the existing microwave breast cancer detection methods, machine learning-type algorithms have recently become more popular. These focus on detectin…
Radiologist-level Performance by Using Deep Learning for Segmentation of Breast Cancers on MRI Scanscs.LG
Deep learning network matches radiologists in breast cancer segmentation.
problem Automating radiologist-level cancer segmentation from breast MRI.
method 3D U-Net architecture trained on 382,290 breast scans, compared to 255,500 benign cases.
result Network performance matched radiologists' on 2D segmentation of breast cancers.
Unified framework improves gene prioritization in disease studies.
problem Identifying genes involved in diseases using heterogeneous biological data.
method Network propagation-based gene prioritization with integrated biological information.
result Significant improvements in prioritizing genes not identified by traditional methods.
Towards multiple kernel principal component analysis for integrative analysis of tumor samplesstat.ML
Personalized treatment of patients based on tissue-specific cancer subtypes has strongly increased the efficacy of the chosen therapies. Even though the amount of data measured for cancer patients has increased over the last years, most cancer subtypes are still diagnosed based on individual data sources (e.g. gene exp…
Deep learning predicts breast cancer with high accuracy from patient data.
problem Early detection of breast cancer from patient data.
method Feature selection and k-fold Monte Carlo cross-validation using deep learning.
result Deep learning model effectively distinguishes between cancer and healthy patients.
New framework distinguishes lung cancer subtypes using MALDI mass spectrometry.
problem Distinguishing between adenocarcinoma and squamous cell carcinoma subtypes in lung cancer.
method Supervised topological data analysis on MALDI mass spectrometry imaging data.
result The proposed framework successfully classifies lung cancer subtypes with competitive results.
An algorithm reduces breast cancer detection data complexity using effect sizes.
problem Improving accuracy in breast cancer detection.
method Statistical feature selection and SVM classifier with linear kernel.
result SVM classifier achieved over 90% accuracy.
DDSTN improves breast cancer diagnosis by leveraging imbalanced ultrasound modalities.
problem Imbalanced ultrasound modalities in diagnosing breast cancer.
method Integrates LUPI and MMD into a deep transfer learning framework.
result Outperforms state-of-the-art algorithms in BUS-based CAD.
Copula-based fusion improves breast cancer risk stratification.
problem Combining clinical and genomic risk scores using simple rules fails to capture their joint relationship.
method Used copulas to model the joint relationship between clinical and genomic risk scores.
result Copula-based fusion improves risk stratification, identifying subgroups with the worst prognosis.
Paper optimizes sparse feature selection for cancer detection using GSVP and SVM.
problem Sparse feature selection for cancer detection.
method Regularized GSVP with proximal gradient descent, feature selection via SVM.
result Near-perfect balanced accuracy with few selected features.
Breast density classification is an essential part of breast cancer screening. Although a lot of prior work considered this problem as a task for learning algorithms, to our knowledge, all of them used small and not clinically realistic data both for training and evaluation of their models. In this work, we explore the…
In order to investigate the breast cancer prediction problem on the aging population with the grades of DCIS, we conduct a tree augmented naive Bayesian network experiment trained and tested on a large clinical dataset including consecutive diagnostic mammography examinations, consequent biopsy outcomes and related can…
Deep object detection improves mitotic nucleus detection in breast cancer biopsies.
problem Challenges in automated mitotic nucleus detection in breast cancer histopathological images.
method Adapted Mask R-CNN for deep object detection, initially selects candidate regions with maximum recall, refines them with multi-object loss function.
result Improved discrimination ability (F-score of 0.86) and significant precision (0.86) for mitotic nuclei compared to two-stage models.
Breast cancer is the most common cancer and is the leading cause of cancer death among women worldwide. Detection of breast cancer, while it is still small and confined to the breast, provides the best chance of effective treatment. Computer Aided Detection (CAD) systems that detect cancer from mammograms will help in …
Deep neural networks have introduced significant advancements in the field of machine learning-based analysis of digital pathology images including prostate tissue images. With the help of transfer learning, classification and segmentation performance of neural network models have been further increased. However, due t…
Breast Cancer Histopathology Image Classification and Localization using Multiple Instance Learningcs.CV
A-MIL improves histopathology image classification and localization.
problem Improving diagnosis of breast cancer through better interpretation of histopathology images.
method Frame image classification as multiple instance learning, use attention-based learning for localization.
result A-MIL achieves better localization without compromising classification accuracy.
PersonalizedUS assesses breast cancer risk with local coverage guarantees.
problem Manual BI-RADS scoring leads to unnecessary biopsies and mental health burden.
method Conformal prediction for precise, personalized risk estimates.
result Local coverage guarantees with high sensitivity and specificity.
In this paper, we analyze the Wisconsin Diagnostic Breast Cancer Data using Machine Learning classification techniques, such as the SVM, Bayesian Logistic Regression (Variational Approximation), and K-Nearest-Neighbors. We describe each model, and compare their performance through different measures. We conclude that S…
We present a global optimization approach for solving the maximum a-posteriori (MAP) clustering problem under the Gaussian mixture model.Our approach can accommodate side constraints and it preserves the combinatorial structure of the MAP clustering problem by formulating it asa mixed-integer nonlinear optimization pro…
In this paper we utilize a survival analysis methodology incorporating Bayesian additive regression trees to account for nonlinear and additive covariate effects. We compare the performance of Bayesian additive regression trees, Cox proportional hazards and random survival forests models for censored survival data, usi…
Automatization of the diagnosis of any kind of disease is of great importance and it's gaining speed as more and more deep learning solutions are applied to different problems. One of such computer aided systems could be a decision support too able to accurately differentiate between different types of breast cancer hi…
Method predicts ODX scores for breast cancer patients based on clinical data.
problem Predicting ODX scores for breast cancer patients to aid decision-making.
method Distributional random forest approach using 9 clinico-pathological characteristics.
result Correctly predicted 92% of low risk and 40.2% of high risk patients.
We present a deep convolutional neural network for breast cancer screening exam classification, trained and evaluated on over 200,000 exams (over 1,000,000 images). Our network achieves an AUC of 0.895 in predicting whether there is a cancer in the breast, when tested on the screening population. We attribute the high …
Precision medicine aims for personalized prognosis and therapeutics by utilizing recent genome-scale high-throughput profiling techniques, including next-generation sequencing (NGS). However, translating NGS data faces several challenges. First, NGS count data are often overdispersed, requiring appropriate modeling. Se…
Improved breast cancer screening with a fast, memory-efficient model.
problem Classifying high-resolution breast cancer screening images.
method Extends globally-aware multiple instance classifier to handle image-level labels.
result Achieves AUC of 0.93 in classifying malignant findings, outperforming existing methods.
Radiologists typically compare a patient's most recent breast cancer screening exam to their previous ones in making informed diagnoses. To reflect this practice, we propose new neural network models that compare pairs of screening mammograms from the same patient. We train and evaluate our proposed models on over 665,…
Objectives: Most cancer data sources lack information on metastatic recurrence. Electronic medical records (EMRs) and population-based cancer registries contain complementary information on cancer treatment and outcomes, yet are rarely used synergistically. To enable detection of metastatic breast cancer (MBC), we appl…
High predictive performance and ease of use and interpretability are important requirements for the applicability of a computer-aided diagnosis (CAD) to human reading studies. We propose a CAD system specifically designed to be more comprehensible to the radiologist reviewing screening breast MRI studies. Multiparametr…
Study assesses deep neural networks' robustness in mammogram images.
problem Understanding deep neural networks' robustness in mammogram images for breast cancer screening.
method Measuring sensitivity to four perturbations and analyzing low-pass filtering effects.
result Mammogram image classifiers are sensitive to perturbations similar to natural images, but low-pass filtering degrades clinically meaningful features.
Two new feature selection methods improve breast cancer diagnosis accuracy.
problem Improving breast cancer diagnosis accuracy and reducing dataset dimensions.
method Imperialist Competitive Algorithm (ICA) and Bat Algorithm (BA) integrated with ML algorithms.
result BA-based feature selection method outperforms other methods with 99.12% accuracy.