Over the last years, huge resources of biological and medical data have become available for research. This data offers great chances for machine learning applications in health care, e.g. for precision medicine, but is also challenging to analyze. Typical challenges include a large number of possibly correlated featur…
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20 results for “epigenetics”
Proposes spBART for risk prediction using epigenetic signatures and covariates.
problem Complex high-dimensional epigenetic data and low-dimensional covariates for risk prediction.
method Semi-parametric Bayesian Additive Regression Trees (spBART) with cross-validation for variable selection.
result Achieves strong out-of-sample discrimination (AUC = 0.96) in held-out validation set.
A Deep Autoencoder System for Differentiation of Cancer Types Based on DNA Methylation Stateq-bio.QM
A Deep Autoencoder based content retrieval algorithm is proposed for prediction and differentiation of cancer types based on the presence of epigenetic patterns of DNA methylation identified in genetic regions known as CpG islands. The developed deep learning system uses a CpG island state classification sub-system to …
Bayesian method selects important covariates in modal regression.
problem Bayesian modal regression with heavy-tailed responses.
method Expectation-maximization algorithm for parameter estimation; test statistic for variable selection.
result Efficacy of the proposed method in identifying important covariates.
Novel U-learning method for predicting continuous outcomes from high-dimensional data.
problem Challenges in making valid inferences on predictions from high-dimensional inputs.
method U-learning via combinatory multi-subsampling for ensemble predictions and confidence intervals.
result Valid inferences on predictions from Lasso and neural networks.
With the wealth of high-throughput sequencing data generated by recent large-scale consortia, predictive gene expression modelling has become an important tool for integrative analysis of transcriptomic and epigenetic data. However, sequencing data-sets are characteristically large, and previously modelling frameworks …
In this paper we propose network methodology to infer prognostic cancer biomarkers based on the epigenetic pattern DNA methylation. Epigenetic processes such as DNA methylation reflect environmental risk factors, and are increasingly recognised for their fundamental role in diseases such as cancer. DNA methylation is a…
DNA Methylation has been the most extensively studied epigenetic mark. Usually a change in the genotype, DNA sequence, leads to a change in the phenotype, observable characteristics of the individual. But DNA methylation, which happens in the context of CpG (cytosine and guanine bases linked by phosphate backbone) dinu…
The research reported in this paper identifies the epigenetic biomarker (methylation beta pattern) of breast cancer. Many cancers are triggered by abnormal gene expression levels caused by aberrant methylation of CpG sites in the DNA. In order to develop early diagnostics of cancer-causing methylations and to develop a…
In this study, we tested the interaction effect of multimodal datasets using a novel method called the kernel method for detecting higher order interactions among biologically relevant mulit-view data. Using a semiparametric method on a reproducing kernel Hilbert space (RKHS), we used a standard mixed-effects linear mo…
The paper proposes a method to integrate prior information into penalized regression.
problem Improving predictive performance in high-dimensional tasks with prior information.
method Integrating multiple sources of prior information into penalized regression.
result The method improves predictive performance, as shown by simulations and applications.
We present a Bayesian hierarchical multi-view mixture model termed Symphony that simultaneously learns clusters of cells representing cell types and their underlying gene regulatory networks by integrating data from two views: single-cell gene expression data and paired epigenetic data, which is informative of gene-gen…
Learning Massive-scale Partial Correlation Networks in Clinical Multi-omics Studies with HP-ACCORDstat.ML
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 -penalized empirical risk.
result Estimates partial correlation network from dual-omic liver cancer data.
Study improves cancer classification using gene selection and projection methods.
problem Overfitting in high-dimensional microarray datasets for cancer classification.
method FSWOR technique, random projection, Kendall test, ensemble classifiers, LDA projection, Naïve Bayes.
result Achieved a test score of 96%, significantly outperforming existing methods.
As datasets grow richer, an important challenge is to leverage the full features in the data to maximize the number of useful discoveries while controlling for false positives. We address this problem in the context of multiple hypotheses testing, where for each hypothesis, we observe a p-value along with a set of feat…
FL-Sailer enables federated learning for scATAC-seq data, reducing dimensionality and noise.
problem Privacy-preserving federated learning for ultra-high dimensional, sparse, and heterogeneous scATAC-seq data.
method FL-Sailer integrates adaptive leverage score sampling and an invariant VAE architecture.
result FL-Sailer converges to an approximate solution with bounded error, surpassing centralized methods.
Designing RNA molecules has garnered recent interest in medicine, synthetic biology, biotechnology and bioinformatics since many functional RNA molecules were shown to be involved in regulatory processes for transcription, epigenetics and translation. Since an RNA's function depends on its structural properties, the RN…
Computational methods that predict differential gene expression from histone modification signals are highly desirable for understanding how histone modifications control the functional heterogeneity of cells through influencing differential gene regulation. Recent studies either failed to capture combinatorial effects…
Sparse multi-view matrix factorisation: a multivariate approach to multiple tissue comparisonsstat.ML
Gene expression levels in a population vary extensively across tissues. Such heterogeneity is caused by genetic variability and environmental factors, and is expected to be linked to disease development. The abundance of experimental data now enables the identification of features of gene expression profiles that are s…
GOAL algorithm reduces and rotates feature space for small data classification.
problem Challenges in identifying important features for classification in small data settings.
method GOAL algorithm reduces and rotates feature space in a lower-dimensional gauge, providing an analytically tractable solution.
result GOAL algorithm outperforms state-of-the-art ML tools in synthetic and real-world applications.