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.
Deep Belief Network predicts lncRNA-disease associations with high accuracy.
Graph network predicts circRNA-disease associations using multi-source similarity features.
MicroRNAs (miRNAs) play crucial roles in multifarious biological processes associated with human diseases. Identifying potential miRNA-disease associations contributes to understanding the molecular mechanisms of miRNA-related diseases. Most of the existing computational methods mainly focus on predicting whether a miR…
Disease-gene prediction (DGP) refers to the computational challenge of predicting associations between genes and diseases. Effective solutions to the DGP problem have the potential to accelerate the therapeutic development pipeline at early stages via efficient prioritization of candidate genes for various diseases. In…
Given genetic variations and various phenotypical traits, such as Magnetic Resonance Imaging (MRI) features, we consider two important and related tasks in biomedical research: i)to select genetic and phenotypical markers for disease diagnosis and ii) to identify associations between genetic and phenotypical data. Thes…
Motivation: The rapid growth of diverse biological data allows us to consider interactions between a variety of objects, such as genes, chemicals, molecular signatures, diseases, pathways and environmental exposures. Often, any pair of objects--such as a gene and a disease--can be related in different ways, for example…
For precision medicine and personalized treatment, we need to identify predictive markers of disease. We focus on Alzheimer's disease (AD), where magnetic resonance imaging scans provide information about the disease status. By combining imaging with genome sequencing, we aim at identifying rare genetic markers associa…
Medical researchers are coming to appreciate that many diseases are in fact complex, heterogeneous syndromes composed of subpopulations that express different variants of a related complication. Time series data extracted from individual electronic health records (EHR) offer an exciting new way to study subtle differen…
Sparse GFA identifies disease factors in FTD subgroups.
HAMN combines CF models to improve drug repositioning.
Imaging fluorescent disease biomarkers in tissues and skin is a non-invasive method to screen for health conditions. We report an automated process that combines intraoral fluorescent porphyrin biomarker imaging, clinical examinations and machine learning for correlation of systemic health conditions with periodontal d…
One primary task of population health analysis is the identification of risk factors that, for some subpopulation, have a significant association with some health condition. Examples include finding lifestyle factors associated with chronic diseases and finding genetic mutations associated with diseases in precision he…
Bayesian hypergraph inference models disease pathways from EHR data.
Most approaches to machine learning from electronic health data can only predict a single endpoint. Here, we present an alternative that uses unsupervised deep learning to simulate detailed patient trajectories. We use data comprising 18-month trajectories of 44 clinical variables from 1908 patients with Mild Cognitive…
Common complex diseases are likely influenced by the interplay of hundreds, or even thousands, of genetic variants. Converging evidence shows that genetic variants with low marginal effects (LME) play an important role in disease development. Despite their potential significance, discovering LME genetic variants and as…
Identifies patient-specific root causes of disease using structural equation models.
Genome-wide association studies (GWASs) aim to detect genetic risk factors for complex human diseases by identifying disease-associated single-nucleotide polymorphisms (SNPs). The traditional SNP-wise approach along with multiple testing adjustment is over-conservative and lack of power in many GWASs. In this article, …
It is crucial to provide compatible treatment schemes for a disease according to various symptoms at different stages. However, most classification methods might be ineffective in accurately classifying a disease that holds the characteristics of multiple treatment stages, various symptoms, and multi-pathogenesis. More…
Rare diseases affecting 350 million individuals are commonly associated with delay in diagnosis or misdiagnosis. To improve those patients' outcome, rare disease detection is an important task for identifying patients with rare conditions based on longitudinal medical claims. In this paper, we present a deep learning m…
2 Diabetes is a leading worldwide public health concern, and its increasing prevalence has significant health and economic importance in all nations. The condition is a multifactorial disorder with a complex aetiology. The genetic determinants remain largely elusive, with only a handful of identified candidate genes. G…
Study improves CAD diagnosis accuracy by selecting significant features.
In retrospective assessments, internet news reports have been shown to capture early reports of unknown infectious disease transmission prior to official laboratory confirmation. In general, media interest and reporting peaks and wanes during the course of an outbreak. In this study, we quantify the extent to which med…
Genome-wide association studies have proven to be essential for understanding the genetic basis of disease. However, many complex traits---personality traits, facial features, disease subtyping---are inherently high-dimensional, impeding simple approaches to association mapping. We developed a nonparametric Bayesian re…
New KNN test improves association analysis of high-dimensional sequencing data.
Simulates patient pathways to detect delayed rare disease diagnoses.
Study uses machine learning and survival analysis to predict CKD progression.
JigSaw discovers high-order interactions from random forests.
ENN method uses expectile regression for genetic data analysis of complex diseases.
Graphs are widely used as a natural framework that captures interactions between individual elements represented as nodes in a graph. In medical applications, specifically, nodes can represent individuals within a potentially large population (patients or healthy controls) accompanied by a set of features, while the gr…
Novel approach combines local and global brain changes for AD prediction.
Study uses machine learning to identify IBD biomarkers from gut microbiota.
Disease prediction or classification using health datasets involve using well-known predictors associated with the disease as features for the models. This study considers multiple data components of an individual's health, using the relationship between variables to generate features that may improve the performance o…
New methods improve genetic studies of complex diseases.
After admission to emergency department (ED), patients with critical illnesses are transferred to intensive care unit (ICU) due to unexpected clinical deterioration occurrence. Identifying such unplanned ICU transfers is urgently needed for medical physicians to achieve two-fold goals: improving critical care quality a…
Modeling disease progression using irregular time intervals in EHRs.
Second generation sequencing technologies are being increasingly used for genetic association studies, where the main research interest is to identify sets of genetic variants that contribute to various phenotype. The phenotype can be univariate disease status, multivariate responses and even high-dimensional outcomes.…
A test for neural networks identifies genetic associations.
We introduce a probabilistic generative model for disentangling spatio-temporal disease trajectories from series of high-dimensional brain images. The model is based on spatio-temporal matrix factorization, where inference on the sources is constrained by anatomically plausible statistical priors. To model realistic tr…
Generative model designs drug combinations for improved efficacy and reduced side effects.
Genome-wide association studies (GWAS) have emerged as a rich source of genetic clues into disease biology, and they have revealed strong genetic correlations among many diseases and traits. Some of these genetic correlations may reflect causal relationships. We developed a method to quantify causal relationships betwe…
ECGDetect uses deep learning to detect ischemia in heart ECGs.
We propose a novel hierarchical model for multitask bipartite ranking. The proposed approach combines a matrix-variate Gaussian process with a generative model for task-wise bipartite ranking. In addition, we employ a novel trace constrained variational inference approach to impose low rank structure on the posterior m…
New method predicts AD progression using MEG brain networks.
Paper introduces a framework for diagnosing Alzheimer's disease using higher-order topological features from fMRI.
Alzheimer's disease is a major cause of dementia. Its diagnosis requires accurate biomarkers that are sensitive to disease stages. In this respect, we regard probabilistic classification as a method of designing a probabilistic biomarker for disease staging. Probabilistic biomarkers naturally support the interpretation…
In this work, we consider the problem of predicting the course of a progressive disease, such as cancer or Alzheimer's. Progressive diseases often start with mild symptoms that might precede a diagnosis, and each patient follows their own trajectory. Patient trajectories exhibit wild variability, which can be associate…
Malignant Pleural Mesothelioma (MPM) or malignant mesothelioma (MM) is an atypical, aggressive tumor that matures into cancer in the pleura, a stratum of tissue bordering the lungs. Diagnosis of MPM is difficult and it accounts for about seventy-five percent of all mesothelioma diagnosed yearly in the United States of …
Deep models improve GWAS by identifying genetic interactions.