A locally-built, LLM-digested index of recent arXiv papers in quant finance, geometry/topology, and statistical ML — keyword search served straight from SQLite on this machine.
Paper identifies key CpG methylation sites for breast cancer.
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…
Many researches demonstrated that the DNA methylation, which occurs in the context of a CpG, has strong correlation with diseases, including cancer. There is a strong interest in analyzing the DNA methylation data to find how to distinguish different subtypes of the tumor. However, the conventional statistical methods …
Study uses DNA methylation data to predict suicidal and non-suicidal deaths.
New model improves DNA methylation data analysis.
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…
We consider learning parameters of Binomial Hidden Markov Models, which may be used to model DNA methylation data. The standard algorithm for the problem is EM, which is computationally expensive for sequences of the scale of the mammalian genome. Recently developed spectral algorithms can learn parameters of latent va…
Graph Canonical Correlation Analysis improves CCA for multiomics datasets.
Novel U-learning method for predicting continuous outcomes from high-dimensional data.
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…
We present a nonparametric Bayesian method for disease subtype discovery in multi-dimensional cancer data. Our method can simultaneously analyse a wide range of data types, allowing for both agreement and disagreement between their underlying clustering structure. It includes feature selection and infers the most likel…
Kernel and Multiple Kernel Canonical Correlation Analysis (CCA) are employed to classify schizophrenic and healthy patients based on their SNPs, DNA Methylation and fMRI data. Kernel and Multiple Kernel CCA are popular methods for finding nonlinear correlations between high-dimensional datasets. Data was gathered from …
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…
Study uses NMF to reduce cancer microarray data dimensions.
New method disentangles hidden data structures using HSIC and supervision.
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 …
CLARITY compares dissimilar datasets, identifying structural and relationship inconsistencies.
iDeepViewLearn combines deep learning and feature selection for multiview learning.
GIDS reduces high-dimensional response and predictor spaces, improving interpretability and computational efficiency.
Omics-GAN uses GANs to generate synthetic multi-omics data for improved disease prediction.
Sparse Canonical Correlation Analysis (CCA) has received considerable attention in high-dimensional data analysis to study the relationship between two sets of random variables. However, there has been remarkably little theoretical statistical foundation on sparse CCA in high-dimensional settings despite active methodo…
We introduce a novel Bayesian hybrid matrix factorisation model (HMF) for data integration, based on combining multiple matrix factorisation methods, that can be used for in- and out-of-matrix prediction of missing values. The model is very general and can be used to integrate many datasets across different entity type…
Motivation: In this paper we present the latest release of EBIC, a next-generation biclustering algorithm for mining genetic data. The major contribution of this paper is adding support for big data, making it possible to efficiently run large genomic data mining analyses. Additional enhancements include integration wi…
Exclusive Lasso improves survival prediction in cancer datasets.
Motivation: Modelling methods that find structure in data are necessary with the current large volumes of genomic data, and there have been various efforts to find subsets of genes exhibiting consistent patterns over subsets of treatments. These biclustering techniques have focused on one data source, often gene expres…
Imaging genetic research has essentially focused on discovering unique and co-association effects, but typically ignoring to identify outliers or atypical objects in genetic as well as non-genetics variables. Identifying significant outliers is an essential and challenging issue for imaging genetics and multiple source…
The medical research facilitates to acquire a diverse type of data from the same individual for particular cancer. Recent studies show that utilizing such diverse data results in more accurate predictions. The major challenge faced is how to utilize such diverse data sets in an effective way. In this paper, we introduc…
It is well known that in a supervised classification setting when the number of features is smaller than the number of observations, Fisher's linear discriminant rule is asymptotically Bayes. However, there are numerous modern applications where classification is needed in the high-dimensional setting. Naive implementa…
Modern medicine requires generalised approaches to the synthesis and integration of multimodal data, often at different biological scales, that can be applied to a variety of evidence structures, such as complex disease analyses and epidemiological models. However, current methods are either slow and expensive, or inef…
Proposes a copula-based model for multi-view clustering with directional dependency.
ASCEND discovers causal relationships in multi-omics data by leveraging known hierarchical structure.
Paper introduces MGLasso for multiscale graph inference in clustering and network analysis.
MOTGNN integrates multi-omics data for disease classification with improved accuracy and interpretability.
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…
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 …
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…
New method detects RNA modifications without prior training, revealing novel sites.