Differentiating the intrinsic subtypes of breast cancer is crucial for deciding the best treatment strategy. Deep learning can predict the subtypes from genetic information more accurately than conventional statistical methods, but to date, deep learning has not been directly utilized to examine which genes are associa…
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48 results for “subtypes”
Study identifies five AD subtypes using graph diffusion and similarity learning.
problem Identifying homogeneous AD subtypes to improve diagnosis and treatment.
method Unsupervised clustering with graph diffusion and similarity learning.
result Five distinct AD subtypes identified with significant differences in biomarkers and clinical features.
Identifying cancer subtypes in glioblastoma by combining genomic, transcriptomic and epigenomic dataq-bio.GN
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…
Improving Patient Subtyping on Longitudinal Data using Representations from Mamba-based Architecturecs.LG
Study proposes a model to improve patient subtyping from EHR data.
problem Challenges in subtyping temporal EHR datasets.
method Self-supervised Mamba-based model for learning EHR representations.
result Model outperforms baseline models in EHR data subtyping.
Identification of disease subtypes and corresponding biomarkers can substantially improve clinical diagnosis and treatment selection. Discovering these subtypes in noisy, high dimensional biomedical data is often impossible for humans and challenging for machines. We introduce a new approach to facilitate the discovery…
Patient subtyping based on temporal observations can lead to significantly nuanced subtyping that acknowledges the dynamic characteristics of diseases. Existing methods for subtyping trajectories treat the evolution of clinical observations as a homogeneous process or employ data available at regular intervals. In real…
While developing their software, professional object-oriented (OO) software developers keep in their minds an image of the subtyping relation between types in their software. The goal of this paper is to present an observation about the graph of the subtyping relation in Java, namely the observation that, after the add…
Unsupervised method selects genes for tumor subtype discovery.
problem High-dimensional tumor gene expression data with noisy variables and heterogeneity.
method Autoencoders for latent space learning, Multiple Kernel Learning for feature selection, clustering.
result Lower redundancy and better clustering performance compared to benchmarks.
In many applications, multivariate samples may harbor previously unrecognized heterogeneity at the level of conditional independence or network structure. For example, in cancer biology, disease subtypes may differ with respect to subtype-specific interplay between molecular components. Then, both subtype discovery and…
Icentia11K: An Unsupervised Representation Learning Dataset for Arrhythmia Subtype Discoveryq-bio.QM
We release the largest public ECG dataset of continuous raw signals for representation learning containing 11 thousand patients and 2 billion labelled beats. Our goal is to enable semi-supervised ECG models to be made as well as to discover unknown subtypes of arrhythmia and anomalous ECG signal events. To this end, we…
An interpretable multiple kernel learning approach for the discovery of integrative cancer subtypesstat.ML
Due to the complexity of cancer, clustering algorithms have been used to disentangle the observed heterogeneity and identify cancer subtypes that can be treated specifically. While kernel based clustering approaches allow the use of more than one input matrix, which is an important factor when considering a multidimens…
Alzheimer's disease (AD) is a degenerative brain disease impairing a person's ability to perform day to day activities. The clinical manifestations of Alzheimer's disease are characterized by heterogeneity in age, disease span, progression rate, impairment of memory and cognitive abilities. Due to these variabilities, …
Bayesian outcome-guided multi-view mixture models with applications in molecular precision medicinestat.ME
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.
MAGIC uncovers disease heterogeneity across brain scales.
problem Understanding distinct subtypes of brain diseases at different spatial scales.
method Multi-scale Heterogeneity Analysis and Clustering (MAGIC) using semi-supervised clustering.
result Two main subtypes of AD identified with distinct atrophy patterns.
New framework distinguishes lung cancer subtypes using MALDI mass spectrometry.
problem Distinguishing between adenocarcinoma and squamous cell carcinoma subtypes in lung cancer.
method Supervised topological data analysis on MALDI mass spectrometry imaging data.
result The proposed framework successfully classifies lung cancer subtypes with competitive results.
Smile-GANs clusters brain MRI scans to reveal disease subtypes and progression.
problem Understanding disease heterogeneity in brain MRI scans.
method Generative Adversarial Networks (GANs) for semi-supervised clustering.
result Discovered four subtypes of Alzheimer's and prodromal phases, with two progressive pathways.
Feature selection is an important and challenging task in high dimensional clustering. For example, in genomics, there may only be a small number of genes that are differentially expressed, which are informative to the overall clustering structure. Existing feature selection methods, such as Sparse K-means, rarely tack…
Diverse applications - particularly in tumour subtyping - have demonstrated the importance of integrative clustering techniques for combining information from multiple data sources. Cluster-Of-Clusters Analysis (COCA) is one such approach that has been widely applied in the context of tumour subtyping. However, the pro…
Towards multiple kernel principal component analysis for integrative analysis of tumor samplesstat.ML
Personalized treatment of patients based on tissue-specific cancer subtypes has strongly increased the efficacy of the chosen therapies. Even though the amount of data measured for cancer patients has increased over the last years, most cancer subtypes are still diagnosed based on individual data sources (e.g. gene exp…
Model learns to select relevant clinical variables for disease subtype prediction from small data.
problem Few-shot disease subtype prediction from small genomic data.
method Meta learning Prototypical Network with feature selection and sample reweighting.
result Superior performance in predicting disease subtypes and identifying genes.
Bioinformatics tools have been developed to interpret gene expression data at the gene set level, and these gene set based analyses improve the biologists' capability to discover functional relevance of their experiment design. While elucidating gene set individually, inter gene sets association is rarely taken into co…
Deep learning has demonstrated success in health risk prediction especially for patients with chronic and progressing conditions. Most existing works focus on learning disease Network (StageNet) model to extract disease stage information from patient data and integrate it into risk prediction. StageNet is enabled by (1…
Cluster analysis aims at separating patients into phenotypically heterogenous groups and defining therapeutically homogeneous patient subclasses. It is an important approach in data-driven disease classification and subtyping. Acute coronary syndrome (ACS) is a syndrome due to sudden decrease of coronary artery blood f…
UCSL combines clustering with supervised learning to discover interpretable subtypes.
problem Discovering interpretable subtypes in datasets relevant to supervised tasks.
method UCSL (Unsupervised Clustering driven by Supervised Learning) framework integrating clustering and supervised learning.
result UCSL achieves +1.9 points in balanced accuracy for psychiatric diseases clustering.
More than two thirds of mental health problems have their onset during childhood or adolescence. Identifying children at risk for mental illness later in life and predicting the type of illness is not easy. We set out to develop a platform to define subtypes of childhood social-emotional development using longitudinal,…
The ability to accurately classify disease subtypes is of vital importance, especially in oncology where this capability could have a life saving impact. Here we report a classification between two subtypes of non-small cell lung cancer, namely Adeno- carcinoma vs Squamous cell carcinoma. The data consists of approxima…
We investigate the use of self-tracking data and unsupervised mixed-membership models to phenotype endometriosis. Endometriosis is a systemic, chronic condition of women in reproductive age and, at the same time, a highly enigmatic condition with no known biomarkers to monitor its progression and no established staging…
Precision medicine aims for personalized prognosis and therapeutics by utilizing recent genome-scale high-throughput profiling techniques, including next-generation sequencing (NGS). However, translating NGS data faces several challenges. First, NGS count data are often overdispersed, requiring appropriate modeling. Se…
Explaining Deep Learning for ECG Analysis: Building Blocks for Auditing and Knowledge Discoveryeess.SP
Study examines XAI methods for ECG analysis to improve model transparency.
problem Lack of transparency in deep learning models for ECG analysis.
method Investigates post-hoc XAI methods for local and global perspectives, establishes sanity checks, and demonstrates knowledge discovery.
result Quantitative evidence supports expert rules for sensible attribution methods and demonstrates XAI's utility for knowledge discovery.
The rapid development of high-throughput technologies has enabled the generation of data from biological or disease processes that span multiple layers, like genomic, proteomic or metabolomic data, and further pertain to multiple sources, like disease subtypes or experimental conditions. In this work, we propose a gene…
Clustering analysis is one of the most widely used statistical tools in many emerging areas such as microarray data analysis. For microarray and other high-dimensional data, the presence of many noise variables may mask underlying clustering structures. Hence removing noise variables via variable selection is necessary…
VICatMix: variational Bayesian clustering and variable selection for discrete biomedical datastat.ML
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.
A Pontryagin class obstruction for purely electric and purely magnetic Weyl curvature tensorsmath.DG
The study finds obstructions for certain Weyl curvature tensors on manifolds.
problem Can manifolds admit metrics with purely electric or magnetic Weyl tensors?
method Analyzes algebraic curvature tensors and their Pontryagin classes on scalar product spaces.
result Obstructions to the existence of metrics with PE or PM Weyl tensors in top-degree cohomology.
Viral sequence classification is an important task in pathogen detection, epidemiological surveys and evolutionary studies. Statistical learning methods are widely used to classify and identify viral sequences in samples from environments. These methods face several challenges associated with the nature and properties …
Multi-view data, that is matched sets of measurements on the same subjects, have become increasingly common with advances in multi-omics technology. Often, it is of interest to find associations between the views that are related to the intrinsic class memberships. Existing association methods cannot directly incorpora…
We consider the problem of jointly estimating multiple inverse covariance matrices from high-dimensional data consisting of distinct classes. An -penalized maximum likelihood approach is employed. The suggested approach is flexible and generic, incorporating several other -penalized estimators as specia…
Modeling disease progression using irregular time intervals in EHRs.
problem Challenges in analyzing temporal data from EHRs.
method Developed a Markovian generative model using EHR data.
result Model accurately recovers underlying disease progression patterns from irregular time intervals.
OPAL optimizes labeling strategy for precise inference from uncertain models.
problem Inference from uncertain machine learning models is brittle.
method OPAL learns a smooth policy to adaptively label data points based on model uncertainty.
result OPAL yields estimators with the lowest variance and achieves nominal coverage in finite samples.
Towards Unsupervised Cancer Subtyping: Predicting Prognosis Using A Histologic Visual Dictionarycs.CV
Unlike common cancers, such as those of the prostate and breast, tumor grading in rare cancers is difficult and largely undefined because of small sample sizes, the sheer volume of time needed to undertake on such a task, and the inherent difficulty of extracting human-observed patterns. One of the most challenging exa…
The study examines Cox models for lifetime loan default risk, addressing biased estimates by incorporating recurrent events.
problem Ignoring recurrent default events in Cox models leads to biased and inaccurate PD estimates.
method Investigates and compares different Cox models (Andersen-Gill and Prentice-Williams-Peterson) for lifetime loan default risk.
result The Andersen-Gill model underperforms compared to the Prentice-Williams-Person model and the time to first default model.
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.
Deep Representation Learning of Electronic Health Records to Unlock Patient Stratification at Scaleq-bio.QM
Deep learning model creates patient representations for scalable EHR-based stratification.
problem Challenges in summarizing and representing patient data from EHRs prevent scalable stratification analysis.
method Unsupervised framework based on deep learning (ConvAE) using word embeddings, CNNs, and autoencoders.
result ConvAE significantly outperformed baselines in clustering diverse patient cohorts, identifying clinically relevant subtypes.
We introduce a new discriminant analysis method (Empirical Discriminant Analysis or EDA) for binary classification in machine learning. Given a dataset of feature vectors, this method defines an empirical feature map transforming the training and test data into new data with components having Gaussian empirical distrib…
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 …
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…
Multiple Sclerosis (MS) is a neurodegenerative disorder characterized by a complex set of clinical assessments. We use an unsupervised machine learning model called a Conditional Restricted Boltzmann Machine (CRBM) to learn the relationships between covariates commonly used to characterize subjects and their disease pr…
Combining Bayesian nonparametrics and a forward model selection strategy, we construct parsimonious Bayesian deep networks (PBDNs) that infer capacity-regularized network architectures from the data and require neither cross-validation nor fine-tuning when training the model. One of the two essential components of a PB…
The task of clustering a set of objects based on multiple sources of data arises in several modern applications. We propose an integrative statistical model that permits a separate clustering of the objects for each data source. These separate clusterings adhere loosely to an overall consensus clustering, and hence the…