This work uses Sylvester normalizing flows for more accurate metabolite quantification in MRS.
problem Challenges in accurate metabolite quantification in MRS due to spectral overlap, low SNR, and artifacts.
method Bayesian inference framework with physics-informed Sylvester normalizing flows.
result Accurate metabolite quantification, well-calibrated uncertainties, and insights into parameter correlations and multi-modal distributions.
Study compares data-driven vs model-based MRS quantification strategies, focusing on resilience to out-of-distribution effects.
problem Resilience to out-of-distribution effects in data-driven MRS quantification.
method Compared three data-driven strategies (supervised regression, self-supervised learning, test-time adaptation) against model-based fitting tools.
result Test-time adaptation proved most resilient to out-of-distribution effects, while self-supervised learning achieved intermediate performance.
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.
We extend multi-way, multivariate ANOVA-type analysis to cases where one covariate is the view, with features of each view coming from different, high-dimensional domains. The different views are assumed to be connected by having paired samples; this is a common setup in recent bioinformatics experiments, of which we a…
Translating potential disease biomarkers between multi-species 'omics' experiments is a new direction in biomedical research. The existing methods are limited to simple experimental setups such as basic healthy-diseased comparisons. Most of these methods also require an a priori matching of the variables (e.g., genes o…
rags2ridges simplifies graphical modeling of high-dimensional data.
problem Graphical modeling of high-dimensional precision matrices.
method Modular framework for extraction, visualization, and analysis of Gaussian graphical models.
result Provides a one-stop-shop for graphical modeling of high-dimensional precision matrices.
This work demonstrates the execution of a novel process model for knowledge discovery and data mining for metabolomics (MeKDDaM). It aims to illustrate MeKDDaM process model applicability using four different real-world applications and to highlight its strengths and unique features. The demonstrated applications provi…
High-dimensional linear classifiers, such as the support vector machine (SVM) and distance weighted discrimination (DWD), are commonly used in biomedical research to distinguish groups of subjects based on a large number of features. However, their use is limited to applications where a single vector of features is mea…
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…
New datasets support supervised learning for fungal BGC discovery.
problem Lack of labeled data for fungal BGCs.
method Developed new publicly available datasets for supervised learning.
result Supervised learning outperforms data-driven methods in fungal BGC prediction.
This study assesses the reproducibility of 1H-MRS scans across different vendors and sessions.
problem Lack of harmonization in magnetic resonance spectroscopy protocols among vendors.
method Analysis of CV and ICC for within- and between-sessions, and correlation coefficients for across machines.
result Metabolite concentrations are highly reproducible across different vendors and sessions.
CogMol designs novel drug-like molecules for SARS-CoV-2 targets.
problem Designing efficient drugs for novel viral proteins.
method End-to-end framework combining VAE, controlled sampling, and predictors.
result Highly selective and affinity molecules for SARS-CoV-2 targets.
Reduced-rank method improves least-squares regression under output regularity.
problem Least-squares regression with infinite dimensional outputs.
method Reduced-rank method for solving least-squares problems with output regularity assumptions.
result Learning bounds and improved statistical performance compared to full-rank method.
HistNetQ improves quantification tasks by optimizing loss functions and eliminating label requirements.
problem Quantification of class prevalence in bags of examples.
method Permutation-invariant Histograms and deep neural networks.
result HistNetQ outperforms other quantification methods and optimizes custom loss functions.
Quantification is a supervised learning task that consists in predicting, given a set of classes C and a set D of unlabelled items, the prevalence (or relative frequency) p(c|D) of each class c in C. Quantification can in principle be solved by classifying all the unlabelled items and counting how many of them have bee…
Fortuna simplifies uncertainty quantification in deep learning.
problem Improving uncertainty estimates in deep learning models.
method Supports various calibration techniques including conformal prediction and scalable Bayesian inference.
result Simplifies benchmarking and builds robust AI systems.
\emph{Sentiment Quantification} (i.e., the task of estimating the relative frequency of sentiment-related classes -- such as \textsf{Positive} and \textsf{Negative} -- in a set of unlabelled documents) is an important topic in sentiment analysis, as the study of sentiment-related quantities and trends across a populati…
PUMA interprets metabolomics data to predict pathway activity and assign chemical identities.
problem Interpreting metabolomics data to determine biochemical pathway activities.
method Generative probabilistic modeling using stochastic sampling.
result PUMA predicts pathway activity and assigns chemical identities to metabolites.
Bayesian meta learning improves uncertainty quantification in regression.
problem Trusting uncertainty quantification in Bayesian regression.
method Trust-Bayes framework for Bayesian meta learning, optimizing for trustworthy uncertainty quantification.
result Lower bounds and sample complexity for trustworthy uncertainty quantification are characterized.
In high-dimensional data, structured noise caused by observed and unobserved factors affecting multiple target variables simultaneously, imposes a serious challenge for modeling, by masking the often weak signal. Therefore, (1) explaining away the structured noise in multiple-output regression is of paramount importanc…
Bayesian uncertainty quantification is flawed, according to new research.
problem Flawed interpretation of Bayesian uncertainty quantification.
method Discussion of Bayesian updating and optimization-based perspective, proposing measures of quality.
result Bayesian uncertainty quantification is not coherent with optimization-based perspective.
A new KDE-based method improves multiclass quantification.
problem Quantifying class prevalence in multiclass settings.
method Kernel Density Estimation (KDE) for multivariate densities.
result KDEy method yields superior quantification performance.
Geometry-aware KDE model improves multiclass quantification.
problem Accurately estimating class prevalence for label shift adaptation.
method Log-ratio representations and Aitchison geometry for compositional data, shrinkage regularization.
result Competitive with state-of-the-art quantifiers, often improving over standard KDE-based baselines.
New GP-based method improves uncertainty quantification for causal functions.
problem Challenges in quantifying uncertainty for causal effects, especially for entire functions.
method GP-based approach using inner-product of observational functions in RKHS, with tractable posterior moments and calibration.
result Improves uncertainty quantification while maintaining causal effect estimation performance.
Unified taxonomy for ML uncertainty in physics, validated.
problem Uncertainty quantification in machine learning for physics.
method Unified taxonomy, principled validation tools.
result Illustrated validation tools with examples.
Proposes PQ, a more precise Bayesian quantifier for prevalence estimation.
problem Uncertainty quantification in prevalence estimation.
method Bayesian quantification methods, focusing on precision and coverage.
result PQ provides more precise and well-calibrated uncertainty quantification.
Bayesian neural network models improve uncertainty quantification in multivariate regression.
problem Uncertainty quantification in multivariate regression models with heteroscedastic noise.
method Proposes Bayesian Last Layer neural network models and EM algorithms for parameter learning.
result Capable of disentangling aleatoric and epistemic uncertainty.
Novel framework for uncertainty quantification in metric spaces.
problem Uncertainty quantification in regression models with metric responses.
method Developed algorithms for large datasets, agnostic to predictive models, with asymptotic and non-asymptotic guarantees.
result Asymptotic and non-asymptotic guarantees for special cases, demonstrated in clinical applications.
Quantification is the task of estimating, given a set σ of unlabelled items and a set of classes C={c1,…,c∣C∣}, the prevalence (or `relative frequency') in σ of each class ci∈C. While quantification may in principle be solved by classifying each item in σ and…
Proposes measures for uncertainty quantification using proper scoring rules.
problem Uncertainty quantification for prediction tasks.
method Decomposes proper scoring rules into divergence and entropy components, tailoring uncertainty quantification to specific tasks.
result Flexibility in uncertainty quantification improves performance in selective prediction and active learning.
Develops a framework for inferring causal relationships in networked data with uncertainty quantification.
problem Extracting reliable inference from complex Hawkes network data with uncertainty.
method Statistical inference framework based on maximum likelihood estimation and concentration inequalities of continuous-time martingales.
result Provides a non-asymptotic confidence set for uncertainty quantification.
Optimizes sampling for faster convergence in Bayesian experimental design and uncertainty quantification.
problem Efficiently selecting samples for faster convergence in Bayesian experimental design and uncertainty quantification.
method Output-weighted acquisition functions leveraging likelihood ratio to guide sampling towards relevant regions.
result Superiority of the proposed method in uncertainty quantification and rare event identification.
New BNN architectures reduce computational cost for uncertainty quantification.
problem High computational cost in Bayesian neural networks.
method Partial trace-class Bayesian neural networks (PaTraC BNNs).
result Comparable uncertainty quantification with fewer parameters.
SMURF-THP improves Transformer Hawkes process models by providing uncertainty quantification.
problem Uncertainty quantification for Transformer Hawkes process predictions.
method Score matching for learning the score function of event arrival times.
result SMURF-THP outperforms likelihood-based methods in confidence calibration.
Generative models improve image reconstruction and uncertainty quantification.
problem Bayesian inverse problems, especially image reconstruction from noisy and incomplete data.
method Data-driven priors and computationally tractable posterior analysis.
result Efficient uncertainty quantification without retraining for different corruption types.
Uncertainty Toolbox aids in assessing and improving uncertainty quantification in machine learning.
problem Disparate evaluation metrics and implementations hinder direct comparison of uncertainty quantification results.
method Provides an open-source Python library for assessing, visualizing, and improving uncertainty quantification.
result Facilitates more accurate and comparable uncertainty quantification across different works.
The paper analyzes uncertainty quantification in sparse Gaussian process regression with a Brownian motion prior.
problem Analyzing uncertainty in sparse Gaussian process regression with a Brownian motion prior.
method Theoretical guarantees and limitations for pointwise credible sets are derived for a rescaled Brownian motion prior with a sparse variational Gaussian process method.
result Theoretical characterization of asymptotic frequentist coverage for credible sets, distinguishing conservative and overconfident cases.
A new method quantifies a specific class without labeled data.
problem Quantifying unknown or large number of classes with limited data.
method One-class Quantification (OCQ) and Passive Aggressive Threshold (PAT).
result PAT is the fastest and most accurate algorithm for quantification.
New method quantifies uncertainty at class level for better decision-making.
problem Improving cost-sensitive decision-making in classification tasks.
method Label-wise decomposition of uncertainty measures based on non-categorical metrics.
result Proposed measures adhere to desirable properties and improve uncertainty quantification.
Classification is the task of predicting the class labels of objects based on the observation of their features. In contrast, quantification has been defined as the task of determining the prevalences of the different sorts of class labels in a target dataset. The simplest approach to quantification is Classify & Count…
NCP improves deep classifier uncertainty quantification efficiency.
problem Uncertainty quantification for deep classifiers in high-stake applications.
method Neighborhood Conformal Prediction (NCP) algorithm.
result NCP produces smaller prediction sets than traditional CP methods.
New framework for robust uncertainty quantification in strategic settings.
problem Machine learning model predictions can be strategically altered by informed agents.
method Strategic Conformal Prediction framework
result Theoretical guarantees and experimental validation show remarkable effectiveness.
A method constructs a stochastic surrogate from dimensionality reduction results for high-dimensional uncertainty quantification.
problem High-dimensional uncertainty quantification with physics-based models.
method Constructs a stochastic surrogate model from dimensionality reduction results.
result Preserves convenience of sequential dimensionality reduction and Gaussian process regression while overcoming limitations.
New method improves calibration of BayesCG for better uncertainty quantification.
problem Bayesian conjugate gradient method's poor calibration limits its utility.
method Randomized postiteration strategy to enhance posterior calibration.
result The method improves the distribution of posterior errors and enhances uncertainty quantification.
SVGP KAN integrates uncertainty quantification into Kolmogorov-Arnold networks.
problem Uncertainty quantification in scientific machine learning models.
method Sparse variational Gaussian process inference with Kolmogorov-Arnold topology.
result Demonstrated ability to distinguish aleatoric and epistemic uncertainty in various scientific applications.
The paper studies uncertainty quantification and exploration in RL, providing methods and results.
problem Fundamental questions about inference and error quantification in RL remain open.
method The paper fills the literature gap by studying central limit theorem behaviors of Q-values and value functions.
result Explicitly identified closed-form expressions of asymptotic variances for Q-values and value functions.
CP-ROC bands improve graph classification accuracy and uncertainty quantification.
problem Uncertainty quantification and robustness to distributional shifts in graph classification.
method Conditional Prediction ROC (CP-ROC) bands for graph classification, developed for TGNNs and adaptable to GNNs.
result Statistically guaranteed coverage for CP-ROC under local exchangeability condition, improving prediction reliability.
Study benchmarks uncertainty quantification in chest X-ray classification.
problem Reliable uncertainty quantification for medical AI models.
method Evaluation of 13 uncertainty quantification methods on MIMIC-CXR-JPG dataset.
result Insights into effectiveness and disentanglement of epistemic and aleatoric uncertainties.