New method interprets deep embeddings for diabetes patient clustering.
problem Interpreting deep embeddings for disease progression.
method Patient clustering approach using deep embeddings.
result Clinically meaningful insights into diabetes progression patterns.
Study develops a dynamic risk model for COVID-19 mortality using UK Biobank data.
problem Developing tools to monitor high-risk patients during the COVID-19 pandemic.
method Data-driven random forest classification model using baseline characteristics and symptoms.
result Model predicts COVID-19 mortality with excellent performance (AUC: 0.91), identifying novel predictors.
Secure linear regression at speed of plaintext methods.
problem Secure multiparty linear regression and feature selection.
method Distributed algorithms combining geometric ideas.
result Efficient and secure genome-wide association studies.
Automatically computes reference ranges for UK Biobank cardiac data.
problem Improving healthcare by discovering patterns in large-scale population data.
method Fully automatic pipeline for 3D cardiac MR image analysis.
result Statistically significant agreement between manual and automatic indexes.
Stochastic encoding improves gender classification of brain networks from UK Biobank data.
problem Complexity and bias in interpreting deep learning models of brain connectivity.
method Stochastic encoding in ensemble of CNNs, multivariate balancing algorithm.
result AUROC of 0.8459, with resting-state data more accurate than task data.
New methods improve genetic studies of complex diseases.
problem Improving genetic studies of complex diseases using high-dimensional clinical data.
method Evaluation of unsupervised disentangled representation learning methods (autoencoders, VAE, beta-VAE, FactorVAE) for genetic association studies.
result FactorVAEs and beta-VAEs outperform standard VAEs and non-variational autoencoders in genetic studies of asthma and COPD.
Study analyzes how blood pressure impacts cardiac health.
problem Impact of blood pressure on cardiac function.
method Combines deep learning and variational autoencoder for interpretable biomarkers.
result Identifies key factors and patterns of cardiac adaptation.
Federated learning improves bioinformatics by sharing data legally.
problem Lack of access to diverse data in bioinformatics.
method Combines data from multiple institutions legally.
result Federated learning accelerates clinical discovery and robust exploration.
We propose a method based on deep learning to perform cardiac segmentation on short axis MRI image stacks iteratively from the top slice (around the base) to the bottom slice (around the apex). At each iteration, a novel variant of U-net is applied to propagate the segmentation of a slice to the adjacent slice below it…
Method tackles missing covariates in large-scale datasets.
problem Cross-population missing data problem in large-scale datasets.
method Augmented transfer regression learning method combining importance-weighted estimating equations and imputation terms.
result Estimator is n1/2-consistent and asymptotically normal, attaining semiparametric efficiency bound under correct specification. Framework for imputing missing heart data to simulate brain-heart interactions.
problem Lack of multi-modal patient data representing heart and brain processes.
method Probabilistic framework for joint cardiac data imputation and mechanistic model personalization.
result Accurate imputation of missing cardiac features in incomplete datasets.
New method clusters disease subtypes from model explanations.
problem Discovering disease subtypes in noisy, high-dimensional data.
method Train classifier, extract explanations, cluster in explanation space.
result Cluster analysis on model explanations outperforms classical methods.
With the maturation of metabolomics science and proliferation of biobanks, clinical metabolic profiling is an increasingly opportunistic frontier for advancing translational clinical research. Automated Machine Learning (AutoML) approaches provide exciting opportunity to guide feature selection in agnostic metabolic pr…
Study compares estimators for causal mediation analysis with multiple mediators.
problem Estimating causal effects through multiple mediators in observational studies.
method Parametric and non-parametric estimators, including multiply robust and double machine learning approaches.
result Advanced estimators perform well across various settings and real data.
Bayesian meta-learning improves health prediction models across similar diseases.
problem Inter- and intra-task variability in healthcare predictions due to disease heterogeneity and patient differences.
method Bayesian meta-learning approach that models task similarity to mitigate negative transfer and improve generalizability.
result Significant generalizability improvements in stroke prediction tasks using electronic health record data.
Digital risk scores predict depression and anxiety over 10 years.
problem Identifying individuals at risk of depression and anxiety.
method Developed a 10-year predictive algorithm using UKB cohort, selecting predictors via Cox proportional hazards model and DeepSurv.
result Highly discriminating models for depression and anxiety were developed.
Modeling how individuals evolve over time is a fundamental problem in the natural and social sciences. However, existing datasets are often cross-sectional with each individual observed only once, making it impossible to apply traditional time-series methods. Motivated by the study of human aging, we present an interpr…
At this moment, databanks worldwide contain brain images of previously unimaginable numbers. Combined with developments in data science, these massive data provide the potential to better understand the genetic underpinnings of brain diseases. However, different datasets, which are stored at different institutions, can…
Ensemble models provide more accurate feature importance estimates than single models.
problem Inaccurate variable importance estimates due to model instability and stochasticity.
method Theoretical analysis and validation on benchmarks and real data.
result Ensembling at the model level reduces excess risk and provides more accurate variable-importance estimates.
Paper develops conformalized survival analysis method for better prediction.
problem Survival analysis models often misspecify and require strong assumptions.
method Uses conformal prediction to wrap around any survival prediction algorithm.
result Lower predictive bounds provide guaranteed coverage without strong assumptions.
Develops methods for GWAS of high dimensional phenotypes using summary statistics.
problem Lack of methods to model pleiotropy in multi-phenotype GWAS.
method Bayesian inference model using summary statistics, fast computation, and biologically informed priors.
result Demonstrates utility in metabolite GWAS with interpretable pathway-level inference.
Study creates a multimodal learning framework for CVD risk prediction.
problem Predicting cardiovascular disease risk in diverse populations.
method Combines cross modal transformers, graph neural networks, and causal representation learning.
result Model predicts personalized CVD risk with causal invariance across subpopulations.
We construct genomic predictors for heritable and extremely complex human quantitative traits (height, heel bone density, and educational attainment) using modern methods in high dimensional statistics (i.e., machine learning). Replication tests show that these predictors capture, respectively, ∼40, 20, and 9 perc…
Bayesian hypergraph inference models disease pathways from EHR data.
problem Modeling rare diseases influenced by shared risk factors.
method Bayesian hypergraph inference framework reframing multi-disease modeling.
result Interpretable disease pathways and well-calibrated uncertainty quantification.
New method for mixed data types in graphical models.
problem Challenges in analyzing data with mixed variable types.
method Latent Gaussian copula models with leveraged polychoric and polyserial correlations.
result Flexible and scalable methodology for mixed data types.
ICAM creates interpretable feature attribution maps for brain images.
problem Challenges in predicting class relevance from brain images due to heterogeneity and background variation.
method A VAE-GAN framework for disentangling class relevance from background features.
result FA maps generated by ICAM outperform baseline methods and support phenotype variation exploration.
New method improves statistical inference using machine learning-imputed data.
problem Improving statistical inference with imputed data from machine learning.
method Two-phase sampling approach for Z-estimation with ML-imputed outcomes.
result Guaranteed efficiency matching or exceeding classical inference, regardless of prediction quality.
Tensor dropout improves CNN robustness and efficiency.
problem Limited generalization and robustness of deep CNNs.
method Tensor layers with low-rank structures and tensor dropout.
result Tensor dropout outperforms other methods in robustness and efficiency.
Develops a SAS approach for high-dimensional risk prediction using unlabeled data.
problem Challenges in risk modeling with EHR data due to lack of direct disease outcomes and high dimensionality.
method Surrogate Assisted Semi-supervised Learning (SAS) approach leveraging unlabeled and labeled data.
result Valid inference for predicted risk even when underlying model is dense and mis-specified.
A transfer learning method builds high-dimensional models using disparate datasets.
problem Building comprehensive prediction models with small sample sizes and limited features.
method Transfer learning approach using external data to build a reduced model and apply calibration equations.
result Proposes a penalized generalized method of moment framework for inference and one-step estimation.
New method reduces memory usage for high-dimensional variable selection.
problem Scalability issues in high-dimensional variable selection, especially in genomics.
method Adaptive sampling of null features to eliminate dummy matrix materialization.
result Reduces memory and runtime by several orders of magnitude while preserving FDR control.
Unified CCA methods for large-scale data with fast SGD algorithms.
problem Computational infeasibility of classical CCA methods for large-scale data.
method Unconstrained objective, stochastic gradient descent (SGD) algorithms.
result Significantly faster convergence and higher correlations than previous methods.
Unified normative modeling for neuroimaging phenotypes using denoising diffusion models.
problem Discarding multivariate dependence in neuroimaging pipelines.
method Denoising diffusion probabilistic models (DDPMs) with FiLM and SAINT backbones.
result Unified multivariate normative modeling with better calibration and dependence preservation.
Deep CITs test conditional independence in images, improving brain MRI scan analysis.
problem Testing conditional independence in complex, high-dimensional variables like images.
method Combines embedding maps and nonparametric CITs for feature representations.
result Valid DNCITs for brain MRI scans and behavioral traits, confirming null results.
LEARNER improves low-rank matrix estimation using source population data.
problem Improving low-rank matrix estimation in target populations with diverse data sources.
method LEARNER uses similarity in latent spaces between source and target populations to enhance estimation.
result LEARNER often outperforms benchmark methods, especially with higher signal-to-noise ratios in the source population.
Develops a Bayesian method for causal inference with partly censored time-to-event data.
problem Estimating causal effects with unobserved confounders and measurement errors in partly censored time-to-event data.
method Semiparametric Bayesian instrumental variable analysis using a two-stage Dirichlet process mixture model.
result The proposed method outperforms competing methods in simulations and real-world data analysis.
Paper develops SKPD framework for signal region detection in image regression.
problem Limited research on image region detection in high-resolution image regression.
method Sparse Kronecker Product Decomposition (SKPD) framework for matrices and tensors.
result Computed solutions converge to truth with guaranteed consistency.
Gradient-flow optimization is reinterpreted as a statistical inference problem.
problem Optimizing training duration and assessing model performance in deep learning.
method Develops a statistical framework for gradient-flow training, treating it as a random-effects model.
result Establishes asymptotic optimality for prediction and reduces reliance on validation splits.
SLOE speeds up logistic regression in high dimensions with accurate signal strength estimation.
problem Poor performance of logistic regression in high-dimensional settings.
method SLOE reparameterizes the signal strength for faster and more accurate estimation.
result SLOE provides a fast and accurate method for dimensionality correction in logistic regression.
A clinician desires to use a risk-stratification method that achieves confident risk-stratification - the risk estimates of the different patients reflect the true risks with a high probability. This allows him/her to use these risks to make accurate predictions about prognosis and decisions about screening, treatments…
Measurement noise limits the advantage of nonlinear models over linear models in biomedical prediction
problem Nonlinear models vs. linear models in biomedical prediction
method Measurement reliability
result Measurement noise blurs the population-optimal predictor