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.
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.
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.
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.
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.
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.
Deep learning identifies transcriptomic patterns and cell types associated with SARS-CoV-2 infection and COVID-19 severity.
problem Understanding how SARS-CoV-2 varies in infecting and causing severe COVID-19.
method Developed a new approach to generating self-supervised edge features, using Graph Attention Networks (GAT) and Set Transformer.
result Achieved state-of-the-art performance in predicting disease state of individual cells using single-cell RNA sequencing 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.
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.
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.
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.
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.
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.
New method learns complex cell networks from millions of cells.
problem Existing methods fail to scale to large datasets.
method Multi-axis Gaussian graphical models.
result Method scales to millions of cells in minutes.
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.
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.
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…
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.
IndiSeek learns disentangled representations by balancing independence and completeness.
problem Learning disentangled representations with mutual information in multi-modal data.
method Combines independence-enforcing objective with a reconstruction loss that bounds conditional mutual information.
result Demonstrates effectiveness on synthetic data, CITE-seq, and real-world multi-modal benchmarks.
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.
Improves visualization of high-dimensional data by correcting misleading artifacts in neighbor embedding methods.
problem Misleading visual artifacts in t-SNE and UMAP due to lack of data-independent manifold learning interpretations.
method LOO-map framework that extends embedding maps to the entire input space, identifying and correcting map discontinuities.
result Developed point-wise diagnostic scores to detect unreliable embedding points and improve hyperparameter selection.
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.
Several modern applications require the integration of multiple large data matrices that have shared rows and/or columns. For example, cancer studies that integrate multiple omics platforms across multiple types of cancer, pan-omics pan-cancer analysis, have extended our knowledge of molecular heterogenity beyond what …
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…
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.
Kernel method embeds noisy datasets, capturing shared structures.
problem Limited power in capturing nonlinear structures, noisiness, high-dimensionality, and interpretability issues.
method Kernel spectral joint embeddings using duo-landmark integral operators.
result Consistent recovery of low-dimensional noiseless signals and convergence to eigenfunctions of integral operators.
In recent years, the advances in single-cell RNA-seq techniques have enabled us to perform large-scale transcriptomic profiling at single-cell resolution in a high-throughput manner. Unsupervised learning such as data clustering has become the central component to identify and characterize novel cell types and gene exp…
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.
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.
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.
Improved GPLVM model for single-cell RNA-seq data.
problem Lack of effective scalable models for clustering cell types in large-scale single-cell RNA-seq data.
method Introduces amortized stochastic variational Bayesian GPLVM (BGPLVM) tailored for single-cell RNA-seq.
result Matches the performance of scVI on synthetic and real-world datasets and reveals more interpretable latent structures.
Kernel testing compares cell states in single-cell data.
problem Comparing non-linear cell states in single-cell data.
method Kernel-based testing framework for non-linear distribution comparison.
result Identifies subtle population variations in cell states.
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…
SMAI framework tests and integrates single-cell data alignability.
problem Lack of a rigorous statistical test for alignability and distortion during alignment.
method Spectral manifold alignment and inference (SMAI) framework.
result SMAI outperforms existing methods in alignability testing and integration.
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.
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.
MarkerMap selects key genes for cell type analysis in single-cell RNA-seq.
problem Selecting informative genes from large single-cell RNA-seq datasets is challenging and computationally intensive.
method MarkerMap is a generative model that identifies minimal gene sets explaining cell type variability.
result MarkerMap outperforms existing methods in both supervised and unsupervised marker selection.
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.
Forest Fire Clustering discovers cell types from single-cell data.
problem Discovering cell types from large-scale single-cell sequencing data.
method Iterative label propagation and parallelized Monte Carlo simulation.
result Forest Fire Clustering outperforms state-of-the-art methods on diverse benchmarks.
NESS improves neighbor embedding for smooth cell-state transitions in single-cell data.
problem Challenges in extracting smooth, low-dimensional representations from noisy single-cell data.
method Builds on PCS framework to develop NESS, a stable machine learning approach.
result NESS consistently yields useful biological insights across diverse single-cell datasets.
New methods for visualizing multi-view data improve clustering accuracy.
problem Visualizing multi-view data for better understanding of samples.
method Extensions of manifold learning methods (t-SNE, LLE, ISOMAP) for multi-view data.
result Improved clustering accuracy of multi-view data.
Proposes CCCVAE for better single-cell clustering with cell-cell communication.
problem Improving single-cell RNA sequencing clustering by incorporating cell-cell communication.
method Integrates cell-cell communication into a variational autoencoder framework.
result Empirical results show CCCVAE outperforms standard VAEs in clustering performance.
New model generates realistic single-cell gene expression data.
problem Generating realistic single-cell gene expression profiles is challenging.
method scLDM, a latent diffusion model using Diffusion Transformers and linear interpolants.
result Superior performance in generating realistic single-cell gene expression data.
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…
Motivation: Single cell transcriptome sequencing (scRNA-Seq) has become a revolutionary tool to study cellular and molecular processes at single cell resolution. Among existing technologies, the recently developed droplet-based platform enables efficient parallel processing of thousands of single cells with direct coun…