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…
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48 results for “Prostate Cancer”
Study evaluates data augmentation methods for prostate cancer detection in MRI.
problem Limited data for prostate cancer detection in MRI.
method Static application of five augmentation techniques (rotation, flip, crop, translation) to MRI dataset.
result Rotation method improved 2D slice-based AUC to 0.85.
Proposes a multi-resolution model for prostate cancer classification using mpMRI.
problem Improving voxel-wise classification of prostate cancer using multi-parametric MRI data.
method Multi-resolution Super Learner framework combining local base learners at multiple resolutions and spatial Gaussian kernel smoothing.
result Enhanced voxel-wise classification of prostate cancer status and clinical significance.
A novel deep learning architecture (XmasNet) based on convolutional neural networks was developed for the classification of prostate cancer lesions, using the 3D multiparametric MRI data provided by the PROSTATEx challenge. End-to-end training was performed for XmasNet, with data augmentation done through 3D rotation a…
Automated Prostate Cancer Diagnosis Based on Gleason Grading Using Convolutional Neural Networkeess.IV
CNN-based prostate cancer grading improves accuracy and efficiency.
problem Manual Gleason grading by pathologists is time-consuming and prone to errors.
method Patch-Based Image Reconstruction (PBIR), Distribution Correction (DC), Quadratic Weighted Mean Square Error (QWMSE).
result Achieved superior expert-level performance (0.8885 quadratic-weighted kappa coefficient).
We estimate treatment cost-savings from early cancer diagnosis. For breast, lung, prostate and colorectal cancers and melanoma, which account for more than 50% of new incidences projected in 2017, we combine published cancer treatment cost estimates by stage with incidence rates by stage at diagnosis. We extrapolate to…
New method for causal inference in survival outcomes using RDD.
problem Censoring in time-to-event analyses.
method Nonparametric approach with doubly robust censoring corrections.
result Higher efficiency and robustness to misspecification.
Radiological imaging of the prostate is becoming more popular among researchers and clinicians in searching for diseases, primarily cancer. Scans might be acquired with different equipment or at different times for prognosis monitoring, with patient movement between scans, resulting in multiple datasets that need to be…
Survival analysis has been developed and applied in the number of areas including manufacturing, finance, economics and healthcare. In healthcare domain, usually clinical data are high-dimensional, sparse and complex and sometimes there exists few amount of time-to-event (labeled) instances. Therefore building an accur…
Accurate and robust cell nuclei classification is the cornerstone for a wider range of tasks in digital and Computational Pathology. However, most machine learning systems require extensive labeling from expert pathologists for each individual problem at hand, with no or limited abilities for knowledge transfer between…
Develops platforms to analyze social media data for human behavior and emotions.
problem Understanding human behavior and emotions from social media data.
method Self-structuring incremental machine learning, event detection, natural language processing.
result Captured salient topics and events from social media data, validated against news.
Recent years have witnessed a significant increase in the online sharing of medical information, with videos representing a large fraction of such online sources. Previous studies have however shown that more than half of the health-related videos on platforms such as YouTube contain misleading information and biases. …
Optimal cutoff interval for risk scores improves binary classification accuracy.
problem Improving binary classification accuracy with abstention.
method Determines optimal cutoff interval for risk scores, refraining from decisions outside this interval.
result Minimizes classification margin and maximizes accuracy within the interval.
Prediction of Cancer Microarray and DNA Methylation Data using Non-negative Matrix Factorizationq-bio.QM
Study uses NMF to reduce cancer microarray data dimensions.
problem High dimensionality of cancer microarray data hinders understanding.
method Used Non-negative Matrix Factorization (NMF) for dimensionality reduction.
result NMF achieves 98% classification accuracy.
We propose a Bayesian model that predicts recovery curves based on information available before the disruptive event. A recovery curve of interest is the quantified sexual function of prostate cancer patients after prostatectomy surgery. We illustrate the utility of our model as a pre-treatment medical decision aid, pr…
The paper develops a method to learn cost-optimal sequential testing policies from retrospective data.
problem Learning cost-optimal sequential decision policies from retrospective data with missing test results.
method Doubly robust Q-learning framework with path-specific inverse probability weights.
result The method reduces testing cost without compromising predictive accuracy.
We analyze large, multi-dimensional, sparse counting data sets, finding unsupervised groups to provide unique insights into genetic data. We create gene and biological pathway groups based on patients' variants to find common risk factors for four common types of cancer (breast, lung, prostate, and colorectal) and auti…
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…
Estimating heterogeneous survival treatment effect in observational data using machine learningstat.AP
Study improves machine learning for estimating survival treatment effects.
problem Estimating heterogeneous survival treatment effects in observational data.
method Flexible machine learning methods in the counterfactual framework, including AFT-BART-NP.
result AFT-BART-NP consistently yields best performance in terms of bias, precision, and frequentist coverage.
We describe an adversarial learning approach to constrain convolutional neural network training for image registration, replacing heuristic smoothness measures of displacement fields often used in these tasks. Using minimally-invasive prostate cancer intervention as an example application, we demonstrate the feasibilit…
The purpose of this paper is to construct confidence intervals for the regression coefficients in the Fine-Gray model for competing risks data with random censoring, where the number of covariates can be larger than the sample size. Despite strong motivation from biomedical applications, a high-dimensional Fine-Gray mo…
DP synthetic data may inflate statistical test results, caution advised.
problem Inflated Type I errors in statistical tests on DP-synthetic data.
method Evaluation of Mann-Whitney U test, t-test, chi-squared test, and median test on DP-synthetic data generated from real-world and simulated datasets using various DP-synthetic data generation methods.
result A large portion of evaluation results showed inflated Type I errors, especially at low privacy levels.
A deep learning-based method for prostate segmentation in T2-weighted magnetic resonance imagingeess.IV
We propose a novel automatic method for accurate segmentation of the prostate in T2-weighted magnetic resonance imaging (MRI). Our method is based on convolutional neural networks (CNNs). Because of the large variability in the shape, size, and appearance of the prostate and the scarcity of annotated training data, we …
The outcome of a functional genomics pipeline is usually a partial list of genomic features, ranked by their relevance in modelling biological phenotype in terms of a classification or regression model. Due to resampling protocols or just within a meta-analysis comparison, instead of one list it is often the case that …
Penalized regression models are popularly used in high-dimensional data analysis to conduct variable selection and model fitting simultaneously. Whereas success has been widely reported in literature, their performances largely depend on the tuning parameters that balance the trade-off between model fitting and model s…
Over the past decades, statisticians and machine-learning researchers have developed literally thousands of new tools for the reduction of high-dimensional data in order to identify the variables most responsible for a particular trait. These tools have applications in a plethora of settings, including data analysis in…
Histopathology tissue samples are widely available in two states: paraffin-embedded unstained and non-paraffin-embedded stained whole slide RGB images (WSRI). Hematoxylin and eosin stain (H&E) is one of the principal stains in histology but suffers from several shortcomings related to tissue preparation, staining proto…
Proposes a two-stage method for estimating heterogeneous treatment effects using gradient boosting trees.
problem Estimating heterogeneous treatment effects in randomized clinical trials with high-dimensional predictive markers.
method Two-stage statistical learning procedure using gradient boosting trees (XGBoost) to estimate main effects and HTE.
result Improves efficiency in estimating heterogeneous treatment effects through nonparametric function estimation.
Prostate motion modelling using biomechanically-trained deep neural networks on unstructured nodescs.LG
Deep neural networks predict prostate motion from MR images.
problem Predicting prostate motion during ultrasound-guided interventions.
method Biomechanically-trained deep neural networks on unstructured nodes.
result Trained networks yield near real-time inference with 0.017 mm error.
Machine learning methods are used to discover complex nonlinear relationships in biological and medical data. However, sophisticated learning models are computationally unfeasible for data with millions of features. Here we introduce the first feature selection method for nonlinear learning problems that can scale up t…
Spatially-aware metrics improve uncertainty evaluation in segmentation.
problem Uncertainty evaluation metrics treat voxels independently, ignoring spatial context.
method Proposed three spatially aware metrics incorporating structural and boundary information.
result Improved alignment with clinically important factors and better discrimination between uncertainty patterns.
Creating large scale high-quality annotations is a known challenge in medical imaging. In this work, based on the CycleGAN algorithm, we propose leveraging annotations from one modality to be useful in other modalities. More specifically, the proposed algorithm creates highly realistic synthetic CT images (SynCT) from …
Estimating causal effects for survival outcomes in the high-dimensional setting is an extremely important topic for many biomedical applications as well as areas of social sciences. We propose a new orthogonal score method for treatment effect estimation and inference that results in asymptotically valid confidence int…
CausalMix generates synthetic data with causal controls for mixed-type tables.
problem Synthetic data for causal inference with mixed-type and multimodal tabular data.
method CausalMix combines Gaussian latent priors with data-type-specific decoders for control over overlap, confounding, and treatment effect heterogeneity.
result CausalMix achieves state-of-the-art distributional metrics and stable causal control.
Bayesian neural networks improve uncertainty quantification with unlabelled data.
problem Over-confidence in predictions on covariate-shifted data.
method Approximate Bayesian inference using posterior regularisation with pseudo-labels from unlabelled data.
result Significant improvement in uncertainty quantification accuracy on covariate-shifted data.
Model predicts anti-cancer drug responses using gene and molecular data.
problem Expensive and time-consuming cancer drug discovery and tailoring.
method Uses variational autoencoders and multi-layer perceptrons to encode gene expression and drug data.
result High average of 0.83 and 0.845 in predicting drug responses for breast and pan-cancer cell lines, respectively.
We present a novel method for extracting cancer signatures by applying statistical risk models (http://ssrn.com/abstract=2732453) from quantitative finance to cancer genome data. Using 1389 whole genome sequenced samples from 14 cancers, we identify an "overall" mode of somatic mutational noise. We give a prescription …
Cardiotoxicity related to cancer therapies has become a serious issue, diminishing cancer treatment outcomes and quality of life. Early detection of cancer patients at risk for cardiotoxicity before cardiotoxic treatments and providing preventive measures are potential solutions to improve cancer patients's quality of …
Lung cancer is one of the death threatening diseases among human beings. Early and accurate detection of lung cancer can increase the survival rate from lung cancer. Computed Tomography (CT) images are commonly used for detecting the lung cancer.Using a data set of thousands of high-resolution lung scans collected from…
With the increased affordability and availability of whole-genome sequencing, large-scale and high-throughput gene expression is widely used to characterize diseases, including cancers. However, establishing specificity in cancer diagnosis using gene expression data continues to pose challenges due to the high dimensio…
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.
Machine learning accurately diagnoses cancer from whole genome sequencing data.
problem Accurate cancer diagnosis at all stages.
method Novel MLAC (Machine Learning Against Cancer) method using next-gen RNA sequencing.
result Perfect precision, sensitivity, and specificity achieved for most tumor types.
Neural networks improve cancer risk prediction from family history data.
problem Improving cancer risk prediction from family history data using machine learning.
method Developed and trained neural network models on large pedigrees to predict hereditary cancers.
result Neural networks can achieve nearly optimal prediction performance and outperform traditional models in misreported data.
Over the past decades, both critical care and cancer care have improved substantially. Due to increased cancer-specific survival, we hypothesized that both the number of cancer patients admitted to the ICU and overall survival have increased since the millennium change. MIMIC-III, a freely accessible critical care data…
Using Apple Machine Learning Algorithms to Detect and Subclassify Non-Small Cell Lung Cancerq-bio.QM
Lung cancer continues to be a major healthcare challenge with high morbidity and mortality rates among both men and women worldwide. The majority of lung cancer cases are of non-small cell lung cancer type. With the advent of targeted cancer therapy, it is imperative not only to properly diagnose but also sub-classify …
We present *K-means clustering algorithm and source code by expanding statistical clustering methods applied in https://ssrn.com/abstract=2802753 to quantitative finance. *K-means is statistically deterministic without specifying initial centers, etc. We apply *K-means to extracting cancer signatures from genome data w…
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…
Accurately predicting drug responses to cancer is an important problem hindering oncologists' efforts to find the most effective drugs to treat cancer, which is a core goal in precision medicine. The scientific community has focused on improving this prediction based on genomic, epigenomic, and proteomic datasets measu…