Method detects airway dilatation with high accuracy.
problem Detecting airway dilatation in lung diseases like IPF.
method Probabilistic model of abrupt relative variations, Bayesian Changepoint Detection.
result Model detects airway dilatation with 2.5mm accuracy.
Project aims to diagnose and track IPF disease using deep learning.
problem Diagnosing and tracking IPF disease in lung images.
method Developed a deep learning model for identifying honeycombing and ground glass patterns in HRCT lung images.
result Deep learning model achieved high accuracy in identifying specific lung regions.
New insights into using IPF for inferring dynamic networks from marginals.
problem Inferring dynamic networks from time-aggregated adjacency matrices and time-varying marginals.
method Identifying a generative network model and establishing its maximum likelihood estimates via IPF, with convergence guarantees for sparse data.
result IPF provides principled estimation of dynamic networks from marginals under certain conditions, with structure-dependent error bounds and guaranteed convergence for sparse data.
Iterative Proportional Fitting (IPF), combined with EM, is commonly used as an algorithm for likelihood maximization in undirected graphical models. In this paper, we present two iterative algorithms that generalize upon IPF. The first one is for likelihood maximization in discrete chain factor graphs, which we define …
A new method for fast, non-iterative graphical model estimation.
problem Scalability issues in iterative proportional fitting for high-dimensional data.
method Non-iterative approach for positive definite graphical model estimation.
result The proposed method outperforms state-of-the-art methods in high-dimensional settings.
PFs and iPFs learn principal manifolds for efficient density estimation.
problem Understanding the geometric structure of normalizing flows.
method Characterize flows using principal manifolds and contours.
result PFs and iPFs can learn principal manifolds and perform density estimation.
A framework estimates categorical distributions under constraints, ensuring generality and uniqueness.
problem Estimating categorical distributions summarizing sample data under marginal constraints.
method Theoretical framework + Iterative Proportional Fitting (IPF) to estimate the distribution.
result A unique categorical distribution of Maximum Entropy under marginal constraints exists and is estimated.
CMCD sampler connects transport and variational inference for efficient sampling.
problem Efficient sampling and generative modeling in Bayesian computation.
method Developed a principled framework using divergences on path space, CMCD sampler with adaptive dynamics.
result CMCD sampler outperforms competing approaches across various experiments.
New method solves tree-structured Schrödinger Bridge problems.
problem Computing Schrödinger Bridge between tree-structured distributions.
method Iterative Markovian Fitting (IMF) procedure for tree-structured costs.
result Extends IMF to tree-structured Schrödinger Bridge problems.
DPVis integrates HMMs into visualizations for disease progression analysis.
problem Challenges in interpreting HMMs for disease progression modeling.
method Design study with clinical experts, visualizations of HMM parameters and outcomes.
result DPVis successfully evaluates and summarizes disease progression models.
SS3M learns disease phenotypes from few labels.
problem Lack of supervised data for disease phenotyping.
method Semi-Supervised Mixed Membership Model (SS3M).
result SS3M learns interpretable disease phenotypes.
Bayesian hypergraph inference models disease pathways from EHR data.
problem Modeling rare diseases influenced by shared risk factors.
method Bayesian hypergraph inference framework reframing multi-disease modeling.
result Interpretable disease pathways and well-calibrated uncertainty quantification.
System recommends disease treatments based on big data and cloud computing.
problem Inaccurate disease classification and treatment recommendations due to complex symptoms and multi-pathogenesis.
method DPCA for disease-symptom clustering, Apriori for D-D and D-T rules, parallel Apache Spark implementation.
result Effective disease-symptom clustering and accurate treatment recommendations for inexperienced doctors.
Model learns disease self-representations for drug repositioning.
problem Drug repositioning for disease treatment.
method Enforces proximity in disease self-representations to preserve human phenome network structure.
result Method outperforms state-of-the-art approaches and produces biologically interpretable disease self-representations.
Bayesian model identifies health disparities in disease progression.
problem Health disparities bias disease progression models.
method Interpretable Bayesian model accounting for three disparities.
result Model identifies and corrects for health disparities.
DKT transfers biomarker information between neurodegenerative diseases.
problem Estimating biomarker trajectories in rare neurodegenerative diseases with limited data.
method DKT is a joint-disease generative model that transfers biomarker progressions from common neurodegenerative diseases to rare ones.
result DKT estimates plausible multimodal biomarker trajectories in rare diseases like PCA using only unimodal data.
Paper uses GANs for efficient rare disease detection.
problem Efficient detection of rare diseases with limited labeled data.
method Semi-supervised learning with GANs.
result Best precision-recall scores compared to baseline techniques.
This research uses machine learning to identify Alzheimer's disease subtypes and predict progression.
problem Heterogeneity in Alzheimer's disease clinical manifestations and progression rate limit personalized care and treatment planning.
method Unsupervised and supervised machine learning approaches applied to ADNI data.
result Identification of patient subtypes and prediction of disease progression zones.
Bayesian meta-learning predicts Alzheimer's disease progression.
problem Predicting individual Alzheimer's disease progression from limited data.
method Bayesian meta-learning approach that dynamically predicts disease score distributions.
result Bayesian meta-learner outperforms single-task models and deterministic meta-learners, especially for long-term predictions.
VGAE learns gene-disease associations from networks, predicting disease-genes.
problem Predicting gene-disease associations from disease-gene networks.
method Introducing VGAE, a variational graph auto-encoder for disease-gene prediction.
result VGAE and C-VGAE outperform baseline methods in disease-gene prediction.
Elucidating the genetic basis of human diseases is a central goal of genetics and molecular biology. While traditional linkage analysis and modern high-throughput techniques often provide long lists of tens or hundreds of disease gene candidates, the identification of disease genes among the candidates remains time-con…
Deep Belief Network predicts lncRNA-disease associations with high accuracy.
problem Accurately identifying lncRNA-disease associations to understand lncRNA functionality and disease mechanism.
method Proposes a DBN-based model using heterogeneous networks and DBN for feature learning.
result Obtained AUC of 0.96 and AUPR of 0.967 on standard dataset.
Enhances disease progression modeling using LLMs for complex brain connectivity.
problem Inaccurate predictions of disease spread due to oversimplified brain connectivity models.
method Uses LLMs to synthesize multi-modal relationships and learn disease trajectories from longitudinal data.
result Superior prediction accuracy and interpretability compared to traditional methods.
For many complex diseases, there is a wide variety of ways in which an individual can manifest the disease. The challenge of personalized medicine is to develop tools that can accurately predict the trajectory of an individual's disease, which can in turn enable clinicians to optimize treatments. We represent an indivi…
A method to explain disease transformation using biomarker covariance matrices.
problem Understanding disease transformation from a healthy baseline.
method Modeling healthy and disease states of biomarker covariance matrices to characterize perturbations.
result Disease perturbs the biomarker covariance structure, allowing for mechanistic explanations and individual patient prognosis.
Modeling disease progression in irregularly observed patients.
problem Irregular patient observation in healthcare databases.
method Continuous-time hidden Markov model with generalized linear model.
result Interpretable model of healthcare utilization events.
Paper predicts multiple types of miRNA-disease associations using tensor decomposition.
problem Predicting miRNA-disease associations, especially multi-type ones.
method Represented miRNA-disease-type triplets as a tensor and used Tensor Decomposition methods.
result Tensor Decomposition methods improve a recent baseline by up to 38% in top-1 F1.
The technique of Formal Concept Analysis is applied to a dataset describing the traits of rodents, with the goal of identifying zoonotic disease carriers,or those species carrying infections that can spillover to cause human disease. The concepts identified among these species together provide rules-of-thumb about the …
Paper uses TDA for automated Parkinson's disease classification and severity assessment.
problem Manual diagnosis of neurological diseases is time-consuming and inaccurate.
method Combines Topological Data Analysis (TDA) with machine learning on postural shift data.
result Proposes a stable and accurate method for classifying Parkinson's disease.
Proposes Ada-Sit method for mortality prediction of rare diseases.
problem Data insufficiency and clinical diversity of rare diseases make mortality prediction hard.
method Initialization-sharing multi-task learning method (Ada-Sit) for fast adaptation to similar tasks.
result Experimental results show the proposed model is effective for mortality prediction of diverse rare diseases.
Graph network predicts circRNA-disease associations using multi-source similarity features.
problem Identifying circRNA-disease associations is challenging and time-consuming.
method Proposes a graph convolution network framework using multi-source similarity information.
result Framework predicts circRNA-disease associations with promising results and outperforms existing methods.
Deep learning detects Crohn's disease in MRI images.
problem Detecting Crohn's disease in MRI images.
method Residual Networks for feature extraction and soft attention mechanisms for interpretability.
result Deep learning algorithms perform comparably to clinical standards with faster inference.
Alzheimer's Disease (AD) is characterized by a cascade of biomarkers becoming abnormal, the pathophysiology of which is very complex and largely unknown. Event-based modeling (EBM) is a data-driven technique to estimate the sequence in which biomarkers for a disease become abnormal based on cross-sectional data. It can…
Deep learning boosts rare disease detection from medical claims.
problem Improving diagnosis and treatment of rare diseases.
method Generative adversarial networks (GANs) and recurrent neural networks for sequence modeling.
result Accurate prediction with 0.56 PR-AUC, outperforming benchmarks.
Study compares machine learning and process-based models for predicting rice blast disease.
problem Predicting rice blast disease to support rice growers in controlling the disease.
method Compared four models: two process-based (Yoshino and WARM) and two machine learning (M5Rules and RNN).
result Machine learning models outperformed process-based models in predicting rice blast disease.
PASS model predicts disease progression with both accuracy and interpretability.
problem Balancing accurate disease prediction with clinically interpretable models.
method Phased LSTM units with attention mechanism for non-stationary state dynamics.
result PASS model achieves superior predictive accuracy and interpretable representations.
Model shows screening for infectious disease is hard but Thompson sampling works well.
problem Optimal screening policy for infectious diseases is hard to find.
method Stochastic-control model with Thompson sampling for optimal performance.
result Thompson sampling provides optimal performance guarantees in screening for infectious diseases.
Automated process links oral health to systemic conditions using machine learning.
problem Correlating oral health with systemic health conditions.
method Intraoral fluorescent biomarker imaging, machine learning segmentation, and clinical examination.
result Machine learning classifier achieved AUC of 0.677, indicating a learned association between disease signatures in images and periodontal disease.
WEST uses EHRs and expert cases to improve rare disease phenotyping.
problem Limited labeled data for rare diseases.
method Weakly supervised transformer model trained on probabilistic silver-standard labels.
result WEST outperforms existing methods in phenotype classification and subphenotyping.
Traditional disease surveillance can be augmented with a wide variety of real-time sources such as, news and social media. However, these sources are in general unstructured and, construction of surveillance tools such as taxonomical correlations and trace mapping involves considerable human supervision. In this paper,…
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…
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…
Bayesian approach models neurodegenerative diseases without clinical labels.
problem Personalized, predictive modeling of neurodegenerative diseases.
method Probabilistic programmed deep kernel learning combining Gaussian processes and neural networks.
result Surpasses deep learning in accuracy and timeliness of predicting neurodegeneration.
ENN method uses expectile regression for genetic data analysis of complex diseases.
problem Discover additional genetic variants contributing to complex diseases.
method Developed an expectile neural network (ENN) method integrating expectile regression and neural networks.
result ENN method outperforms existing expectile regression in discovering genetic variants predisposing to sub-populations.
New method uses probabilistic independence to discover disease signatures from medical records.
problem Insufficiently precise diagnosis of clinical disease leading to treatment failures.
method Unsupervised machine learning using probabilistic independence to disentangle disease patterns.
result Inferred 2000 clinical disease signatures from medical records, improving cancer prediction.
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…
The paper proposes a deep generative model for complex disease trajectories.
problem Modeling and analyzing complex disease trajectories.
method Deep generative time series approach with semi-supervised latent processes.
result The model can discover novel aspects of diseases and cluster them into new sub-types.
Improves disease progression prediction using auxiliary surrogate labels and health markers.
problem Challenges in predicting disease progression due to unknown true disease states.
method Integrates hidden Markov model with time-varying discriminative classification model.
result Significant improvement in distinguishing LBD from AD using objective markers.