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.
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.
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…
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.
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…
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…
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.
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…
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…
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.
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…
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.
JigSaw discovers high-order interactions from random forests.
problem Identifying complex interactions in biological data.
method Random forest structure analysis to find high-order interactions.
result JigSaw can explain outcomes in heart disease and breast cancer.
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.
Developed a multiway classification method for sparse data.
problem Classification of multiway arrays with sparsity.
method Extended Distance Weighted Discrimination (DWD) to multiway context, accounting for sparsity.
result Improves classification accuracy in multiway structured data.
Graph auto-encoder predicts unobserved node features from biological networks and omics data.
problem Integrating biological networks and continuous node features for better prediction.
method Graph neural networks and feature auto-encoders trained on feature reconstruction.
result Graph feature auto-encoder outperforms auto-encoders trained on graph reconstruction for predicting unobserved node features.
Pipeline integrates cross-sectional and longitudinal multi-omics data for IBD research.
problem Integrating diverse data types from the same individuals for disease understanding.
method Statistical and deep learning methods for variable selection, feature extraction, and joint integration.
result Identified microbial pathways, metabolites, and genes discriminating IBD status.
Study invariant measures on measured laminations for subgroups of mapping class group.
problem Classify invariant Radon measures on space of measured laminations for subgroups of mapping class group.
method Geometric approach, focusing on recurrent measured laminations, explicitly constructing ergodic measures.
result Show uniquely ergodic for divergence-type subgroups, generalize results for full mapping class group.
New set-valued star-shaped risk measures introduced for better risk assessment.
problem Improving risk assessment in financial contexts.
method Developed new set-valued star-shaped risk measures and proved their representation theorems.
result Set-valued star-shaped risk measures can be represented as unions of set-valued convex risk measures.
The Bergman measure converges to the Zhang measure on a hybrid space.
problem Proving convergence of Bergman measures to Zhang measure.
method Analyzing convergence on a hybrid space and metrized curve complex.
result Bergman measure converges to Zhang measure on a hybrid space.
Bayesian approach to robust risk measures under model uncertainty.
problem Representing robust risk measures as a single probability measure.
method Introducing two types of risk measures and analyzing their relation to robust risk measures.
result Robust risk measures can be represented by a mixture probability measure, a Bayesian approach.
The paper studies dynamic star-shaped risk measures and their representation.
problem Representing dynamic star-shaped risk measures and their properties.
method Representation theorems for dynamic monetary and star-shaped risk measures.
result Dynamic star-shaped risk measures can be represented as the lower envelope of a family of dynamic convex risk measures.
Introduces Star-Shaped deviation measures for risk analysis.
problem Risk measurement and analysis in finance.
method Characterizes Star-Shaped deviation measures through acceptance sets and convex deviation measures.
result Exposes the relationship between Star-Shaped risk measures and deviation measures.
Transformers can interpolate between arbitrary measures.
problem Understanding the expressive power of Transformers as measure-to-measure maps.
method Provided an explicit choice of parameters for a single Transformer to match N arbitrary input measures to N arbitrary target measures.
result A single Transformer can interpolate between arbitrary measures.
Classifies invariant measures on specific character varieties.
problem Classifying invariant probability measures on character varieties.
method Measure disintegration along transverse Lagrangian tori fibrations.
result Ergodic measures are either counting measures on finite orbits or Liouville measures.
Paper characterizes star-shaped risk measures and their properties.
problem Characterizing risk measures in the presence of liquidity risk and competitive delegation.
method Characterization of star-shaped risk measures, study of their properties.
result Star-shaped risk measures include all practically used risk measures.
Paper compares fairness measures and feature importance measures using SHAP.
problem Comparing fairness measures and feature importance measures.
method Focus on SHAP, a game-theoretic measure of feature importance.
result Results for unfairness-prone datasets.
Paper introduces quasi-logconvex risk measures and their properties.
problem Characterizing and understanding new risk measures.
method Characterization through dual representation and properties of acceptance sets.
result Established dual representation and taxonomy of quasi-logconvex risk measures.
Submodularity is studied for convex risk measures, including Expected Shortfall.
problem Characterizing submodularity in convex risk measures.
method Analyzing submodularity properties of law-invariant coherent risk measures, including Expected Shortfall and Value-at-Risk.
result AES is submodular only when it reduces to ES, and empirical analysis shows AES violations are less frequent than VaR and ES violations.
New geometric measure simplifies complex analysis.
problem Complex geometric analysis challenges.
method Geometric integration and convergence methods.
result Smallest measure satisfying Area Formula.
The paper explores non-convex risk measures and their characterizations.
problem Characterizing non-convex risk measures without convexity or weak convexity.
method Characterizes monetary risk measures as lower envelopes of families of convex or coherent risk measures, considering law-invariance and SSD-consistency.
result Unified representation theorems for law-invariant risk measures, including VaR.
The paper calculates extreme measures in continuous time conic finance.
problem Determining valuation bounds for financial claims.
method Using dynamic spectral risk measures and estimating extreme measures from market data.
result Explicit formulas for extreme measures' Radon-Nykodim derivatives and estimation methods.
Paper characterizes monotonic mean-deviation risk measures.
problem Developing consistent risk measures from mean-deviation models.
method Applying a risk-weighting function to the deviation part of a mean-deviation model.
result Characterizes monotonic mean-deviation measures as consistent risk measures.
Introduces factor risk measures to assess risk relative to multiple factors.
problem Measuring risk relative to multiple factors.
method Introduces a double-argument mapping as a risk measure to assess risk relative to a vector of factors.
result Characterizes various types of factor risk measures including distortion, quantile, linear, and coherent measures.
Dual representations for robust risk measures and uncertainty sets.
problem Characterizing continuity of robust risk measures and their uncertainty sets.
method Develop dual representations for robust risk measures and uncertainty sets based on distinct geometric assumptions.
result Two dual frameworks for consolidated uncertainty sets are complementary, not interchangeable.
A scalable approach to learning from probability measures using quantization.
problem Efficiently comparing and manipulating large sets of probability measures.
method Quantization of probability measures to a fixed support, followed by optimal transport computations.
result Consistency and convergence guarantees for quantized measures in various OT-based tasks.
Study on measurable pseudo-Anosov maps on surfaces.
problem Characterize dynamics of pseudo-Anosov maps on surfaces.
method Analyze measurable pseudo-Anosov homeomorphisms with specific properties.
result Prove transitivity, dense periodic points, sensitivity, and ergodicity.
In this paper, we propose a new method of Bayesian measurement for spectral deconvolution, which regresses spectral data into the sum of unimodal basis function such as Gaussian or Lorentzian functions. Bayesian measurement is a framework for considering not only the target physical model but also the measurement model…
The Cannon-Thurston map's pushed measures on the circle are singular with respect to sphere measures.
problem Understanding the behavior of geodesics and measures on fibered hyperbolic 3-manifolds.
method Properties of geodesics and measures on the circle and sphere are analyzed to prove singularity.
result Natural measures on the circle become singular with respect to measures on the sphere.
Risk measures for multivariate financial positions are studied in a utility-based framework. Under a certain incomplete preference relation, shortfall and divergence risk measures are defined as the optimal values of specific set minimization problems. The dual relationship between these two classes of multivariate ris…
New weighted surface area measures for convex bodies with applications.
problem Generalizing surface area measures to weighted Borel measures.
method Formulating and analyzing weighted surface area measures, proving integral formula and Bézout-type inequality.
result New integral formula for mixed measure of three bodies, generalizing Bézout-type inequality.
Standardized fairness measures for continuous risk scores using Wasserstein distance.
problem Quantifying and interpreting group disparities in continuous risk scores.
method Proposes standardized fairness measures based on Wasserstein distance for continuous scores.
result Proposed measures outperform ROC-based fairness measures by being more explicit and quantifying significant biases.
Starting with the work of Preiss on the geometry of measures, the classification of uniform measures in Rd has remained open, except for d=1 and for compactly supported measures in d=2, and for codimension 1. In this paper we study 1-dimensional measures in Rd for all d and classify unif…
Study SRB measures for Anosov actions on manifolds.
problem Characterize SRB measures for Anosov actions.
method Use Ruelle-Taylor resonances and properties of Sinai-Ruelle-Bowen measures.
result SRB measures have properties like smooth disintegrations, positive basins, and are unique under certain conditions.
We study generalizations of Reifenberg's Theorem for measures in Rn under assumptions on the Jones' β-numbers, which appropriately measure how close the support is to being contained in a subspace. Our main results, which holds for general measures without density assumptions, give effective measure bounds…
Study proposes worst+gap measure for better DG evaluation.
problem Lack of comprehensive exploration of average measure in DG evaluation.
method Introduced worst+gap measure and compared it with average measure.
result Worst+gap measure provides a more accurate approximation of true DG performance.