We study information theoretic methods for ranking biomarkers. In clinical trials there are two, closely related, types of biomarkers: predictive and prognostic, and disentangling them is a key challenge. Our first step is to phrase biomarker ranking in terms of optimizing an information theoretic quantity. This formal…
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48 results for “Prognostic biomarkers”
A method to explain disease transformation using biomarker covariance matrices.
problem Understanding disease transformation from a healthy baseline.
method Modeling healthy and disease states of biomarker covariance matrices to characterize perturbations.
result Disease perturbs the biomarker covariance structure, allowing for mechanistic explanations and individual patient prognosis.
New method identifies predictive biomarkers for subgroup analysis.
problem Identifying predictive biomarkers from large covariates.
method Generalized penalized regression with overlapped group penalties.
result Asymptotically consistent method for sparse, interpretable models.
In this paper we propose network methodology to infer prognostic cancer biomarkers based on the epigenetic pattern DNA methylation. Epigenetic processes such as DNA methylation reflect environmental risk factors, and are increasingly recognised for their fundamental role in diseases such as cancer. DNA methylation is a…
Identifying measurable genetic indicators (or biomarkers) of a specific condition of a biological system is a key element of precision medicine. Indeed it allows to tailor diagnostic, prognostic and treatment choice to individual characteristics of a patient. In machine learning terms, biomarker discovery can be framed…
Study identifies biomarkers for lung cancer in female non-smokers.
problem Identifying prognostic biomarkers for stage III NSCLC in non-smoking females.
method Gene expression profiling and XGBoost machine learning algorithm.
result Top biomarkers validated in literature, with AUC score of 0.835.
Background: Predictive, stable and interpretable gene signatures are generally seen as an important step towards a better personalized medicine. During the last decade various methods have been proposed for that purpose. However, one important obstacle for making gene signatures a standard tool in clinics is the typica…
Bayesian Semi-nonnegative Tri-matrix Factorization to Identify Pathways Associated with Cancer Typesstat.ML
Bayesian model identifies cancer pathways using genomic data.
problem Identifying altered pathways associated with specific cancer types.
method Bayesian semi-nonnegative tri-matrix factorization incorporating biological prior knowledge.
result Pathways identified can be used as prognostic biomarkers.
Stein-Encoder isolates genetic signals in multi-modal biomedical data.
problem Integration of high-dimensional genomic data with clinical data obscures genetic predictive impact.
method White-box supervised framework using Stein's method and residualization.
result Stein-Encoder improves predictive accuracy and reveals specific biological mechanisms.
Towards Unsupervised Cancer Subtyping: Predicting Prognosis Using A Histologic Visual Dictionarycs.CV
Paper proposes clustering model for ICC based on histologic patterns.
problem Challenges in grading rare cancers like ICC due to small sample sizes and difficulty in extracting patterns.
method Unsupervised deep convolutional autoencoder clustering model trained on 246 ICC digitized slides.
result Three clusters significantly associated with recurrence-free survival in Cox-proportional hazard models.
A brain signature predicts future Alzheimer's dementia in MCI patients.
problem Hard to predict which MCI patients will progress to Alzheimer's dementia.
method Identified a brain signature using machine learning in dementia patients, validated in MCI.
result 90% of MCI individuals with the signature progressed to dementia within 3 years.
Bayesian method improves clinical trial efficiency.
problem Increase treatment effect estimates in clinical trials.
method Combines prognostic covariate adjustment with a Bayesian framework.
result Substantial increase in statistical power with controlled type I error.
Enhances PHM solutions by augmenting scarce multivariate time series data.
problem Data scarcity in failure prognostics.
method Extends autoregressive models for data augmentation.
result Significantly improves PHM solution performance.
A Federated Data Fusion-Based Prognostic Model for Applications with Multi-Stream Incomplete Signalsstat.ML
A federated model predicts failures using multi-stream incomplete data.
problem Insufficient data for reliable prognostic models in multi-stream applications.
method Federated data fusion, multivariate functional principal component analysis, (log)-location-scale regression model, federated algorithm.
result Performance is as good as classic non-federated models and better than individual models.
Increasing the efficiency of randomized trial estimates via linear adjustment for a prognostic scorestat.ML
Improves trial efficiency by adjusting for historical prognostic scores.
problem Reducing statistical uncertainty in randomized trial estimates.
method Linear covariate adjustment using a prognostic model trained on historical data.
result Prognostic covariate adjustment achieves minimum variance and reduces mean-squared error.
New method detects biomarker-treatment interactions in clinical trials.
problem Detecting interactions between high-dimensional biomarkers and treatments in randomized trials.
method Two-stage penalized regression screening using ridge regression for multivariate screening.
result Ridge regression screening provides greater power than traditional methods in correlated data.
A federated learning framework improves RUL prognosis for aircraft engines without sharing data.
problem Limited run-to-failure data samples for accurate RUL prognosis.
method Federated learning framework, decentralized validation, and robust aggregation methods.
result The federated learning framework leads to more accurate RUL prognosis for five out of six airlines.
Deep learning improves AD diagnosis and prognosis from neuroimaging data.
problem Early detection and accurate classification of Alzheimer's disease.
method Deep learning models applied to neuroimaging data for AD diagnosis and prognosis.
result Deep learning models can achieve high accuracy in AD diagnosis and prognosis.
Optimizes biomarker selection for cost-effective treatment rules.
problem Incorporating multiple biomarkers in treatment selection rules can be costly and reduce model performance.
method Developed procedures for estimating linear and nonlinear combinations of biomarkers using 0-norm penalized weighted classification.
result Demonstrated the importance of feature selection and marker cost in treatment selection rules.
Paper proposes a tensor data model for incomplete imaging data.
problem Prognostics models for incomplete imaging data.
method Supervised tensor dimension reduction with TTF supervision and optimization.
result Model effectively extracts low-dimensional features from incomplete data.
Prognostic scores improve logistic regression analysis in RCTs with binary outcomes.
problem Non-collapsibility in logistic regression analysis of RCTs with binary endpoints.
method Prognostic score adjustment using AI predictions to address non-collapsibility.
result Prognostic score adjustment increases power or reduces sample size for estimating conditional odds ratios.
Neural network models improve ROC curve evaluation of biomarkers, focusing on age's role in physical activity-mortality association.
problem Improving biomarker evaluation using machine learning for complex relationships.
method Proposes neural network-based covariate-adjusted ROC modeling.
result Age has distinct effects on mortality outcomes when physical activity is measured as total activity time.
New biomarker predicts MRgFUS treatment outcome without contrast agents.
problem Inaccurate assessment of treated tissue viability after MRgFUS.
method Deep learning on noncontrast multiparametric MRI images, voxel-wise registration.
result Predicted follow-up NPV with DICE coefficient 0.71, outperforming current standard.
Novel approach uses textual representation for early fault detection in multivariate time-series data.
problem Early detection of incipient faults in complex systems with multiple interacting components.
method Data-driven machine learning approach employing a novel textual representation of multivariate temporal sensor observations.
result The approach outperforms existing methods in prediction accuracy, lead time, and interpretability.
RIF prioritizes predictive biomarkers for precision medicine.
problem Lack of tools to select and prioritize predictive biomarkers.
method Random Interaction Forest (RIF) method.
result RIF outperformed conventional methods in various simulation scenarios and clinical trials.
CBMs improve interpretability in RUL prediction for aircraft engines.
problem Lack of interpretability in deep learning models for asset prognostics.
method Concept Bottleneck Models (CBMs) for RUL prediction.
result CBMs achieve comparable or superior performance to black-box models while being more interpretable.
Super-resolution improves MRI resolution and accuracy for biomarker assessment.
problem Inadequate SNR for accurate quantification in high-resolution MRI.
method Utilized deep learning super-resolution to maintain SNR for T2 relaxation time biomarkers while generating high-resolution images.
result Super-resolution successfully maintains high-resolution and accurate biomarkers for MRI.
Graph Neural Network identifies ASD biomarkers from fMRI data.
problem Finding biomarkers for Autism Spectrum Disorder (ASD).
method Graph Neural Network (GNN) for analyzing task-fMRI brain networks, 2-stage pipeline to interpret feature importance.
result GNN achieves high accuracy in identifying ASD biomarkers and reveals their association with social behaviors.
Proposes a federated learning approach for industrial asset failure prediction.
problem Lack of data and privacy concerns in industrial prognostics.
method Two-stage federated learning: dimension reduction and parameter estimation.
result Validated the approach using simulated and real data.
DKT transfers biomarker information between neurodegenerative diseases.
problem Estimating biomarker trajectories in rare neurodegenerative diseases with limited data.
method DKT is a joint-disease generative model that transfers biomarker progressions from common neurodegenerative diseases to rare ones.
result DKT estimates plausible multimodal biomarker trajectories in rare diseases like PCA using only unimodal data.
This paper improves federated learning for industrial predictive analytics by accommodating client heterogeneity.
problem Traditional federated models assume homogeneity in degradation processes, which doesn't apply to industrial settings.
method Personalized federated prognostic model using proximal gradient descent algorithm for joint parameter estimation.
result The proposed model enhances performance and provides comprehensive failure time distributions.
A new VAE model identifies and estimates treatment effects with limited overlap.
problem Identifying and estimating treatment effects when subjects with certain features belong to a single treatment group.
method Developed a latent variable model to estimate a prognostic score, which is sufficient for treatment effects. The model is a new type of VAE called β-Intact-VAE.
result The model identifies individualized treatment effects and provides TE error bounds.
An Adaptive Oversampling Learning Method for Class-Imbalanced Fault Diagnostics and Prognosticscs.LG
A new method improves fault diagnostics and prognostics for class-imbalanced data.
problem Class imbalance in industrial fault diagnostics and prognostics.
method EWMOTE: EM-based Weighted Minority Oversampling TEchnique.
result EWMOTE achieves better performance on binary and multi-class imbalance learning tasks.
Study classifies and typologizes performance metrics for ML regression, forecasting, and prognostics.
problem Improving evaluation of machine learning models in regression, forecasting, and prognostics.
method Analysis of existing metrics and development of a typology based on structure and properties.
result Proposed framework of four categories of metrics and three key components determining their structure.
This paper compares feature selection methods for biomarker discovery in toxicant-treated fish.
problem Choosing the most suitable method for biomarker discovery in toxicant exposure studies.
method Three feature selection methods: SAM, mRMR, and GeoDE are compared.
result Different methods perform better in different cases, requiring dataset-specific decisions.
This research uses cooperative game theory to interpret deep learning models for ASD biomarker discovery.
problem Understanding image features used by deep learning models for ASD biomarker discovery.
method Shapley value explanation (SVE) from cooperative game theory applied to deep learning models with graph structure optimization.
result SVE provides more accurate biomarker importance than traditional methods.
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.
Study examines survival models for ALS, focusing on proportional hazards assumption.
problem Impact of proportional hazards assumption on survival models for ALS.
method Theoretical and empirical investigation of survival forests and their variants.
result Alternative split procedures can improve model performance in non-proportional hazards situations.
Uncertainty-Calibrated Prediction of Randomly-Timed Biomarker Trajectories with Conformal Bandsstat.ML
Method predicts biomarker trajectories with uncertainty bands for Alzheimer's disease.
problem Uncertainty in biomarker predictions poses risks in clinical deployment.
method Conformal prediction for randomly-timed biomarker trajectories.
result Conformal bands achieve desired coverage and are tighter than baseline.
Proposes ConRad model for lung cancer classification using radiomics and interpretable machine learning.
problem Lack of interpretability in deep neural networks for cancer diagnosis.
method Integration of radiomics and DNN-predicted biomarkers in interpretable classifiers (ConRad).
result ConRad models outperform CNNs in five-fold cross-validation.
EBM uses high-dimensional imaging biomarkers to improve dementia progression estimation.
problem Current EBMs only use scalar biomarkers, limiting accuracy from cross-sectional data.
method Proposes nDEBM, a novel method using semi-supervised SVM on voxel-wise imaging biomarkers.
result nDEBM outperforms state-of-the-art EBM methods using regional volume biomarkers.
Self-supervised learning improves RUL prediction with limited data in fatigue damage prognosis.
problem Limited labelled data for RUL prediction in fatigue damage prognosis.
method Pre-training deep learning models on unlabelled sensor data using self-supervised learning.
result Self-supervised pre-trained models significantly outperform non-pre-trained models in RUL prediction with scarce labelled data.
Proposes a novel approach for RUL estimation of aero-engines.
problem Lack of prior knowledge for defining exact failure thresholds in dynamic environments.
method Simultaneous and dynamic prediction of continuous and discrete states within a single learning framework.
result Improves RUL estimation for aero-engines by reducing complexity.
Adaptive Shrinkage Estimation For Personalized Deep Kernel Regression In Modeling Brain Trajectoriescs.LG
Novel framework predicts brain biomarker trajectories with superior performance.
problem Challenges in estimating longitudinal brain biomarker trajectories due to variability, inconsistencies, and irregular measurements.
method Personalized deep kernel regression with Adaptive Shrinkage Estimation.
result Superior predictive performance compared to state-of-the-art models.
Proposes FMPCA for federated tensor data dimensionality reduction.
problem Integration of MPCA into federated learning.
method Federated Multilinear Principal Component Analysis (FMPCA).
result FMPCA preserves performance of traditional MPCA in federated learning.
Paper proposes ARPHMM for fault detection and prognosis in aero-engines.
problem Fault detection and prognosis in aero-engines using sensor data.
method Autoregressive Partially-hidden Markov Model (ARPHMM) with prior knowledge integration.
result Model estimates remaining useful life and degradation level.
PR-GNN identifies salient brain regions for ASD biomarkers.
problem Identifying brain regions associated with neurological disorders.
method Pooling Regularized Graph Neural Network (PR-GNN) with novel salient region selection.
result PR-GNN outperforms baseline methods in ASD classification accuracy.
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.