Survey examines challenges and tools for integrating multiple types of omics data.
problem Integrating multiple types of omics data for healthcare applications.
method Categorizes fusion approaches, collects open-source tools, explores datasets.
result Identifies challenges and gaps in multimodal learning for multi-omics.
Omics-GAN uses GANs to generate synthetic multi-omics data for improved disease prediction.
problem Limited sample sizes, noise, and heterogeneity in multi-omics data reduce predictive power.
method Omics-GAN is a GAN-based framework that generates high-quality synthetic multi-omics profiles.
result Synthetic datasets consistently improved prediction accuracy compared to original omics profiles.
Different aspects of a clinical sample can be revealed by multiple types of omics data. Integrated analysis of multi-omics data provides a comprehensive view of patients, which has the potential to facilitate more accurate clinical decision making. However, omics data are normally high dimensional with large number of …
BayReL learns molecular interactions across multi-omics data.
problem Inferring meaningful interactions across diverse molecular data types.
method BayReL uses Bayesian representation learning with graph models to integrate multi-omics data.
result BayReL outperforms existing methods in inferring molecular interactions.
MOTGNN integrates multi-omics data for disease classification with improved accuracy and interpretability.
problem Challenges in integrating multi-omics data due to high dimensionality, heterogeneity, and lack of reliable interaction networks.
method MOTGNN uses XGBoost for graph construction, modality-specific GNNs for representation learning, and a deep feedforward network for cross-omics integration.
result MOTGNN outperforms state-of-the-art baselines by 5-10% in accuracy, ROC-AUC, and F1-score across three real-world disease datasets.
MKL-based models outperform complex multi-omics integrative approaches.
problem Integrating diverse omics data sources.
method Supervised multiple kernel learning with different kernel fusion strategies.
result MKL-based models outperform more complex architectures.
Multi-omic data provides multiple views of the same patients. Integrative analysis of multi-omic data is crucial to elucidate the molecular underpinning of disease etiology. However, multi-omic data has the "big p, small N" problem (the number of features is large, but the number of samples is small), it is challenging…
RobKMR improves robustness in multi-omics data analysis for osteoporosis biomarker discovery.
problem Sensitivity to adversarial outliers and lack of comprehensive multi-omics data integration.
method RobKMR, a non-linear M-estimator-based approach using robust kernel centered Gram matrix and robust score test.
result Selected biomarkers (DKK1, MTND5, FASTKD2) significantly bond with four drugs for osteoporosis.
Study evaluates multi-omics data's role in predicting cancer survival.
problem Determining the usefulness of multi-omics data for predicting disease outcomes.
method 5-fold cross-validation with 12 prediction methods applied to 18 cancer datasets.
result Multi-omics data generally improves prediction performance, but not consistently.
Improved logistic regression for multi-omics data improves prediction and variable selection.
problem Predicting binary class labels from multi-omics datasets with varying characteristics.
method Two-step penalized logistic regression with separate variable selection for each data layer.
result Our approach selects more relevant predictors and achieves comparable prediction performance.
The potential benefits of applying machine learning methods to -omics data are becoming increasingly apparent, especially in clinical settings. However, the unique characteristics of these data are not always well suited to machine learning techniques. These data are often generated across different technologies in dif…
Estimates complex dependency structures in multi-omics data.
problem Graphical model estimation from multi-omics data with scalability and consistency.
method Pseudolikelihood-based graphical model framework with ℓ1-penalized empirical risk. result Estimates partial correlation network from dual-omic liver cancer data.
MoReL models multi-omics data to find hidden molecular interactions.
problem Heterogeneous multi-omics data with varying quality and structure.
method Fused Gromov-Wasserstein (FGW) regularization in a deep Bayesian generative model.
result Enhanced performance in inferring meaningful interactions from real-world datasets.
A new hybrid federated learning algorithm for combining clinical and omics data.
problem Combining clinical and omics data in federated learning settings.
method Reformulated Kernel Regularized Least Squares algorithm for hybrid federated learning.
result Validation of two variants of the hybrid algorithm on well-established datasets.
BIDIFAC+ factorizes linked matrices for cancer studies.
problem Integrating multiple omics platforms across various cancer types.
method Flexible approach to simultaneous factorization and decomposition of linked matrices using BIDIFAC+.
result Identifies shared and specific modes of variability across multiple omics platforms and cancer types.
AI framework uses multi-omics data to personalize cancer treatment suggestions.
problem Leveraging AI for personalized cancer treatment based on complex patient characteristics.
method Modular machine learning framework trained on diverse multi-omics technologies.
result Superior performance in personalized counterfactual treatment suggestions.
Convolutional Neural Networks (CNNs) are a popular deep learning architecture widely applied in different domains, in particular in classifying over images, for which the concept of convolution with a filter comes naturally. Unfortunately, the requirement of a distance (or, at least, of a neighbourhood function) in the…
ASCEND discovers causal relationships in multi-omics data by leveraging known hierarchical structure.
problem Causal inference in high-dimensional multi-omics data, especially when ignoring the hierarchical structure.
method Two-tiered divide-and-conquer strategy with ancestral conditioning sets.
result Achieves polynomial-time complexity and accurately recovers ancestral relationships.
scICML integrates multi-omics data from single cells using co-clustering.
problem High noise and sparsity in multi-omics data from single cells.
method Information-theoretic co-clustering-based multi-view learning.
result Improves clustering performance and provides biological insights.
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.
GmGM models multi-axis data for faster analysis.
problem Efficiently modeling multi-axis data across multiple tensors.
method Generalizes Gaussian Graphical Model to learn sparse graph representations across shared axes.
result Achieves significant speedup (order of magnitude) for large multi-modal datasets.
In this work, a machine learning approach for identifying the multi-omics metabolic regulatory control circuits inside the pathways is described. Therefore, the identification of bacterial metabolic pathways that are more regulated than others in term of their multi-omics follows from the analysis of these circuits . T…
Study evaluates consistency of feature attribution in deep learning for multi-omics data.
problem Challenges in interpretability of deep learning models in biological research.
method Investigation of Shapley Additive Explanations (SHAP) on multi-view deep learning models applied to multi-omics data.
result SHAP rankings are sensitive to architecture and random initialization, suggesting caution.
In the integrative analyses of omics data, it is often of interest to extract data representation from one data type that best reflect its relations with another data type. This task is traditionally fulfilled by linear methods such as canonical correlation analysis (CCA) and partial least squares (PLS). However, infor…
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.
Bayesian Cox model identifies biomarkers from multi-omics data.
problem Produce interpretable survival prognosis from multi-omics data.
method Penalized semiparametric Bayesian Cox model with graph-structured selection priors.
result Model identifies new biomarkers and improves survival prediction.
New model identifies cell-specific genes for cancer prognosis.
problem No statistical model to integrate multiscale cancer data.
method Bayesian generalized promotion time cure models (GPTCMs).
result Improves cancer prognosis by identifying cell-specific genes.
We developed OmicsMapNet approach to take advantage of existing deep leaning frameworks to analyze high-dimensional omics data as 2-dimensional images. The omics data of individual samples were first rearranged into 2D images in which molecular features related in functions, ontologies, or other relationships were orga…
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.
Paper proposes scalable method for analyzing multi-omic data.
problem Integrating high-dimensional multi-omic data for cancer subtyping.
method Mixed graphical model approach using Birth-Death MCMC algorithm.
result Our method outperforms LASSO and standard BDMCMC in computational efficiency and model selection accuracy.
VICatMix clusters categorical biomedical data efficiently and selects relevant variables.
problem Efficient clustering of high-dimensional categorical biomedical data.
method Variational Bayesian finite mixture model with variational inference.
result Improves clustering accuracy and variable selection on noisy, high-dimensional data.
OMIC improves matrix completion with orthonormal side information and nuclear-norm regularization.
problem Matrix completion with improved interpretability and adaptability.
method OMIC combines orthonormal side information and nuclear-norm regularization, optimized by a converging algorithm.
result OMIC outperforms state-of-the-art methods in synthetic and real-world datasets.
Bayesian model clusters diverse 'omics data for disease subtyping.
problem Clustering diverse 'omics datasets conflates multiple structures.
method Multi-view Bayesian mixture model with semi-supervised learning.
result Identifies distinct clusters of patients for stratified medicine.
CR-UOT improves matching of heterogeneous single-cell omics profiles.
problem Matching nonnegative finite Radon measures across heterogeneous spaces.
method Cost-regularized unbalanced optimal transport (CR-UOT) framework.
result CR-UOT improves alignment of heterogeneous single-cell omics profiles.
This paper reviews random forest methods for analyzing longitudinal data in precision medicine.
problem Analyzing longitudinal data for precision medicine.
method Extensions of random forest for longitudinal data analysis.
result Categorization of random forest methods for different data structures and repeated measurements.
Random forest hyperparameters affect variable selection in omics studies.
problem Impact of hyperparameters on variable selection in random forests.
method Two simulation studies using theoretical and empirical data.
result Hyperparameters influence variable selection more than the splitting strategy and sample fraction.
New Gromov-Wasserstein metric controls rigidity and incorporates prior knowledge.
problem Inflexible Gromov-Wasserstein distance and lack of feature alignment.
method Augmented Gromov-Wasserstein distance with feature alignments and prior knowledge.
result Improved performance in single-cell multi-omic alignment and transfer learning.
For precision medicine and personalized treatment, we need to identify predictive markers of disease. We focus on Alzheimer's disease (AD), where magnetic resonance imaging scans provide information about the disease status. By combining imaging with genome sequencing, we aim at identifying rare genetic markers associa…
A novel criterion selects optimal distance metrics for cell profile analysis.
problem Determining the most accurate distance metric for high-dimensional cell profiles.
method Generalized proposition and corollaries to evaluate and select distance metrics.
result Wasserstein and cosine similarity metrics are optimal for general cases.
Bayesian model predicts iron deficiency from multi-source multi-way molecular data.
problem Predicting iron deficiency in rhesus monkeys from multi-source multi-way molecular data.
method Developed a Bayesian approach with a linear model incorporating multi-way dependence and varying signal sizes across sources.
result Model accurately classifies iron deficiency in monkeys and outperforms simpler models.
A method for identifying joint and individual subspaces from multi-view data.
problem Unclear conditions for reliably identifying joint and individual subspaces from noisy, high-dimensional measurements.
method Rigorously quantifies conditions based on signal rank, principal angles, and noise levels. Characterizes spectrum perturbations of product of projection matrices.
result Estimates joint and individual subspaces more accurately than existing approaches in simulations and real-world applications.
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…
Drug resistance is still a major challenge in cancer therapy. Drug combination is expected to overcome drug resistance. However, the number of possible drug combinations is enormous, and thus it is infeasible to experimentally screen all effective drug combinations considering the limited resources. Therefore, computat…
A unique challenge in predictive model building for omics data has been the small number of samples (n) versus the large amount of features (p). This "n≪p" property brings difficulties for disease outcome classification using deep learning techniques. Sparse learning by incorporating external gene network info…
Unified method for discovering biclusters and triclusters in longitudinal data.
problem High-dimensional, sparsely sampled, irregularly observed longitudinal data.
method Tri-SfSVD, a unified sparse functional Singular Value Decomposition framework.
result Identified localized structures at the subject, subject-feature, and subject-feature-time levels.
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.
A new method for combining multiple data views in supervised learning.
problem Combining multiple data views in supervised learning, especially in biology and medicine.
method Cooperative learning combines squared error loss with an agreement penalty to encourage predictions from different data views to agree.
result Cooperative learning achieves higher predictive accuracy on simulated and real multiomics data.
We introduce Block Sparse Canonical Correlation Analysis which estimates multiple pairs of canonical directions (together a "block") at once, resulting in significantly improved orthogonality of the sparse directions which, we demonstrate, translates to more interpretable solutions. Our approach builds on the sparse CC…