A new robust scaling approach improves downstream metabolomics analysis.
problem Challenges in choosing scaling techniques for metabolomics data.
method Introduces a weighted scaling approach robust to outliers.
result The proposed method outperforms traditional scaling techniques in both outlier-free and outlier-present datasets.
Motivation: Untargeted metabolomics comprehensively characterizes small molecules and elucidates activities of biochemical pathways within a biological sample. Despite computational advances, interpreting collected measurements and determining their biological role remains a challenge. Results: To interpret measurement…
This work presents MeKDDaM-SAGA, computer-aided automation software for implementing a novel knowledge discovery and data mining process model that was designed for performing justifiable, traceable and reproducible metabolomics data analysis. The process model focuses on achieving metabolomics analytical objectives an…
QC-ST and CoCo methods correct batch effects in metabolomics data.
problem Batch effects in metabolomics data obscure biological variations.
method QC-ST for simultaneous detection of QC samples' mean vectors and covariance matrices, CoCo for covariance correction.
result QC-ST and CoCo improve batch effect correction in metabolomics datasets.
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…
Bayesian GAMs improve predictive performance for high-dimensional data.
problem Sparse regularization in GAMs leads to excess shrinkage and difficulty in selecting nonlinear effects.
method Developed a novel spike-and-slab LASSO prior and scalable EM-Coordinate Descent algorithm.
result Improved predictive and computational performance compared to existing models.
GEMSS discovers multiple sparse solutions in high-dimensional data.
problem Identifying multiple sparse feature combinations in high-dimensional, underdetermined systems.
method GEMSS (Gaussian Ensemble for Multiple Sparse Solutions) uses a structured spike-and-slab prior, mixture of Gaussians, and Jaccard-based penalty to optimize a single objective function via stochastic gradient descent.
result GEMSS consistently outperforms five feature selection methods on 128 experiments and real-world datasets.
BSFP method reveals latent patterns in multi-omic data for predicting lung function in HIV-associated OLD.
problem Limited understanding of multi-omic molecular phenomena and clinical outcomes in obstructive lung disease.
method Bayesian Simultaneous Factorization and Prediction (BSFP) method for multi-omic data, accommodating imputation and full posterior inference.
result BSFP reveals distinct clusters of patients with OLD and multi-omic patterns related to lung function decline.
In systems biology, it is common to measure biochemical entities at different levels of the same biological system. One of the central problems for the data fusion of such data sets is the heterogeneity of the data. This thesis discusses two types of heterogeneity. The first one is the type of data, such as metabolomic…
This paper extends compositional data analysis using graph signal processing.
problem Traditional log-ratios between all variables are not suitable for specific variable relationships.
method Linking compositional data analysis with graph signal processing, it considers only selected log-ratios.
result The approach retains desirable properties of scale invariance and compositional coherence.
ProJIVE integrates multiple data types to explain joint and individual variation.
problem Integrating multiple types of data on the same subjects.
method Probabilistic EM algorithm for JIVE framework.
result ProJIVE learns biologically meaningful courses of variation and improves accuracy.
The rapid development of high-throughput technologies has enabled the generation of data from biological or disease processes that span multiple layers, like genomic, proteomic or metabolomic data, and further pertain to multiple sources, like disease subtypes or experimental conditions. In this work, we propose a gene…
Scalable methods integrate multiview data for clinical outcomes.
problem Jointly associate and predict outcomes from multiple data sources.
method Randomized Fourier bases for nonlinear mappings, view-independent low-dimensional representations.
result Identified molecular signatures for COVID-19 status and severity.
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.
iDeepViewLearn combines deep learning and feature selection for multiview learning.
problem Learning nonlinear relationships in data from multiple complementary views.
method Combines deep learning flexibility with statistical feature selection using deep neural networks and graph Laplacian regularization.
result Identifies genes and CpG sites that differentiate between breast cancer survivors and non-survivors.
In the Pioneer 100 (P100) Wellness Project (Price and others, 2017), multiple types of data are collected on a single set of healthy participants at multiple timepoints in order to characterize and optimize wellness. One way to do this is to identify clusters, or subgroups, among the participants, and then to tailor pe…
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.
engGNN combines external and generated graphs to improve disease classification and biomarker discovery.
problem Challenges in integrating omics data due to high dimensionality and small sample sizes.
method Dual-graph framework that integrates external biological networks with data-driven generated graphs.
result engGNN outperforms state-of-the-art methods in disease classification and biomarker discovery.
Selective prediction framework reduces errors in molecular structure identification from MS/MS.
problem High-stakes applications require reliable molecular structure identification from MS/MS data.
method Selective prediction framework using risk-coverage tradeoff and uncertainty quantification.
result First-order confidence measures and retrieval-level aleatoric uncertainty achieve strong risk-coverage tradeoffs.
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…
Bayesian models link multiview data to outcomes.
problem Inferring relationships between diverse data types and outcomes.
method Developed two factor regression models: JFR and JAFAR.
result Improved prediction of clinical outcomes from multi-omics data.
BOOOM optimizes orthonormal matrices without needing gradients.
problem Optimizing over the Stiefel manifold in non-convex, non-smooth settings.
method Global Givens rotation-based parametrization and Recursive Modified Pattern Search.
result BOOOM achieves strong performance across various optimization problems.
A new approach to the sparse Canonical Correlation Analysis (sCCA)is proposed with the aim of discovering interpretable associations in very high-dimensional multi-view, i.e.observations of multiple sets of variables on the same subjects, problems. Inspired by the sparse PCA approach of Journee et al. (2010), we also s…