Deep neural network improves DNA methylation data analysis.
problem Analyzing highly dimensional DNA methylation data with bounded support.
method Designing a deep neural network composed of stacked binary restricted Boltzmann machines.
result Deep features learned by the neural network perform best in cluster analysis of breast cancer DNA methylation data.
Paper identifies key CpG methylation sites for breast cancer.
problem Early detection and treatment of breast cancer.
method Used machine learning on TCGA dataset to classify cancer vs. non-cancer samples.
result Reduced model with 25 key CpG sites achieves over 94% accuracy.
Study uses DNA methylation data to predict suicidal and non-suicidal deaths.
problem Predicting suicidal and non-suicidal deaths from DNA methylation data.
method Support Vector Machines (SVM) with dimensionality reduction using PCA and t-SNE.
result t-SNE outperforms PCA in reducing data dimensionality.
New model improves DNA methylation data analysis.
problem Analyzing DNA methylation data with complex distributions.
method Doubly non-central beta (DNCB) distribution for non-negative matrix factorization.
result Improves predictive performance and yields meaningful latent representations.
CNNs classify cancer types based on DNA methylation patterns.
problem Classifying cancer types using DNA methylation data.
method Convolutional Neural Networks (CNNs) for classification.
result CNNs can classify cancer types from DNA methylation profiles.
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…
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…
Deep autoencoder predicts cancer types from DNA methylation patterns.
problem Differentiating cancer types based on DNA methylation states.
method Deep learning system with CpG island state classification and statistical methods.
result Overall Sensitivity of 88.24%, Specificity of 83.33%, Accuracy of 84.75%.
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…
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.
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.
problem High dimensionality of cancer microarray data hinders understanding.
method Used Non-negative Matrix Factorization (NMF) for dimensionality reduction.
result NMF achieves 98% classification accuracy.
New method disentangles hidden data structures using HSIC and supervision.
problem Tackles the challenge of interpreting high-dimensional data.
method Supervised Independent Subspace Principal Component Analysis (sisPCA) using HSIC.
result Identifies and separates hidden data structures effectively.
Graph Canonical Correlation Analysis improves CCA for multiomics datasets.
problem Limited ability of conventional CCA methods to incorporate structured patterns in cross-correlation matrices.
method Graph Canonical Correlation Analysis (gCCA) calculates canonical correlations based on the graph structure of cross-correlation matrices.
result gCCA outperforms competing CCA methods in simulations and multiomics dataset analysis.
CLARITY compares dissimilar datasets, identifying structural and relationship inconsistencies.
problem Integrating qualitatively different datasets from various disciplines.
method Non-parametric approach decomposing similarities into structural and relationship components.
result Identifies and interprets inconsistencies between datasets.
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.
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.
GIDS reduces high-dimensional response and predictor spaces, improving interpretability and computational efficiency.
problem Challenges in modeling interactions among high-dimensional multimodal data.
method Graph Independence Dual Screening (GIDS) framework that reduces both response and predictor dimensions.
result GIDS reduces feature space to 9,000 CpGs and 2,000 transcripts, revealing coordinated regulatory mechanisms.
Exclusive Lasso improves survival prediction in cancer datasets.
problem Enhanced survival prediction in cancer datasets with high-dimensional genomic and clinical data.
method Proposes Exclusive Lasso regularization for feature selection in Cox regression models for grouped variables.
result Demonstrates improved survival prediction performance using Exclusive Lasso compared to standard Cox regression.
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…
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…
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…
EBIC is a biclustering tool for big genomic data, achieving significant speedup.
problem Mining genetic data for high-dimensional and big data challenges.
method EBIC is a biclustering algorithm enhanced for big data, including support for missing values and integration with R.
result EBIC achieves over 6.6 fold speedup on large datasets, demonstrating high scalability.
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…
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…
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.
Paper introduces MGLasso for multiscale graph inference in clustering and network analysis.
problem Graphical models in high-dimensional data analysis need to handle clustering and sparsity simultaneously.
method MGLasso combines clustering and graph inference through a convex relaxation of k-means and hierarchical clustering. It uses CONESTA for regularization.
result MGLasso improves network interpretability by estimating graphs at multiple scales.
Proposes a copula-based model for multi-view clustering with directional dependency.
problem Challenges in integrating multi-source datasets with directional dependency.
method Copula-based multi-view clustering model accounting for directional dependence.
result Ignoring directional dependence negatively impacts clustering performance.
AIME embeds multi-omics data to adjust confounders and find related features.
problem Extracting meaningful relationships between complex omics data types while accounting for confounders.
method Autoencoder-based deep learning approach that incorporates clinical confounders.
result AIME effectively adjusts for confounders and extracts biologically relevant features.
Deep learning model improves medical diagnosis and reduces patient time.
problem Ineffective and slow methods for synthesizing multimodal medical data.
method Cross-modal deep learning architecture with co-attention mechanism.
result Model outperforms previous methods by 2.35% and is 53% more efficient.
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.
OmiVAE combines variational autoencoders and a classification network to classify multi-omics data.
problem Classifying samples from high-dimensional multi-omics data.
method OmiVAE integrates variational autoencoders and a classification network to extract features and classify samples.
result OmiVAE achieved an average classification accuracy of 97.49% across 33 tumour types and normal samples.
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…
New method detects RNA modifications without prior training, revealing novel sites.
problem Detecting RNA modifications with high accuracy and sensitivity.
method Anomaly detection using nanopore raw ionic current signals and nearest neighbor comparison.
result Detects diverse RNA modifications without prior training, including a novel 2'-O-methylated site in DENV.
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…
Data preprocessing improves data quality for robust data mining.
problem Noisy and incomplete data hinders data mining models.
method Overview of data cleaning, transformation, and preprocessing methods.
result Preprocessing significantly affects data mining model performance.
Big data sets must be carefully partitioned into statistically similar data subsets that can be used as representative samples for big data analysis tasks. In this paper, we propose the random sample partition (RSP) data model to represent a big data set as a set of non-overlapping data subsets, called RSP data blocks,…
A new method for handling imbalanced big data using ensembles and smart data.
problem Imbalanced data distribution in big data scenarios.
method Smart Data driven Decision Trees Ensemble (SD_DeTE) methodology.
result SD_DeTE outperforms Random Forest in handling imbalanced binary classification problems in big data.
Prevents sensitive data generation in diffusion models using labeled and unlabeled data.
problem Generating sensitive data in diffusion models using unlabeled data.
method Positive-Unlabeled Diffusion Models, approximating ELBO with labeled and unlabeled data.
result Prevents the generation of sensitive data without compromising image quality.
Study reveals Data Shapley's inconsistent performance in data selection tasks.
problem Inconsistency of Data Shapley's performance in data selection across different settings.
method Hypothesis testing framework and identification of utility functions.
result Data Shapley's performance is no better than random selection without specific constraints.
Survey on data collection challenges in machine learning.
problem Data scarcity and need for labeled data in machine learning.
method Comprehensive study of data acquisition, labeling, and improvement techniques.
result Identification of research challenges in data collection.
PRRO generates synthetic tabular data that improves SL performance and class distribution.
problem Low SL utility of synthetic data due to class imbalance and overlooked data relationships.
method Data pruning and column reordering to optimize SL utility.
result Synthetic data generated with PRRO enhances predictive performance and class distribution.
Defines data science as a natural ecosystem with challenges and missions.
problem Challenges and missions in data science due to 5D complexities and data life cycle phases.
method Systemic and data-centric view of data science as a fusion of data universe and its challenges, formalizing a general-purpose architecture.
result Essential data science as a natural ecosystem integrating specific disciplines and high-impact applications.
Synthetic data enhances analytics but requires careful volume management.
problem Accuracy of statistical methods on synthetic data vs. raw data.
method Synthetic Data Generation for Analytics framework using tabular diffusion models.
result Error rate decreases with more synthetic data but may stabilize or increase.
DPASF stream preprocesses Big Data streams efficiently.
problem Efficient preprocessing of streaming Big Data.
method Implemented six preprocessing algorithms in Apache Flink.
result Preprocessing improves data accuracy in streaming Big Data.
This paper introduces C-DSL to improve data mining outcomes by considering context.
problem Data collection ambiguities, data imbalance, hidden biases, lack of domain info, and data incompleteness.
method Developed Context-Driven Data Science Lifecycle (C-DSL) to address data quality issues.
result Tangible improvements to data mining outcomes were achieved through C-DSL.