Rare diseases affect a relatively small number of people, which limits investment in research for treatments and cures. Developing an efficient method for rare disease detection is a crucial first step towards subsequent clinical research. In this paper, we present a semi-supervised learning framework for rare disease …
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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.
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…
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.
In rare disease physician targeting, a major challenge is how to identify physicians who are treating diagnosed or underdiagnosed rare diseases patients. Rare diseases have extremely low incidence rate. For a specified rare disease, only a small number of patients are affected and a fractional of physicians are involve…
Simulates patient pathways to detect delayed rare disease diagnoses.
problem Delayed rare disease diagnoses in France, causing health system and patient harm.
method Probabilistic modelling of patient pathways to create an alert system.
result Alert system detects and refers wandering patients to CRMRs.
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…
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.
Enhancing spectral embedding for low-dimensional embeddings in rare disease cohorts
problem Representing clinical concepts and patients in electronic health records
method Spectral-based unsupervised learning with flexible knowledge transfer
result Outperforms competing approaches in challenging scenarios
In this work, we present our various contributions to the objective of building a decision support tool for the diagnosis of rare diseases. Our goal is to achieve a state of knowledge where the uncertainty about the patient's disease is below a predetermined threshold. We aim to reach such states while minimizing the a…
We introduce Disease Knowledge Transfer (DKT), a novel technique for transferring biomarker information between related neurodegenerative diseases. DKT infers robust multimodal biomarker trajectories in rare neurodegenerative diseases even when only limited, unimodal data is available, by transferring information from …
Approach for modeling EHR data with rare features, improving prediction and interpretation.
problem Challenges in modeling rare binary features in EHR data.
method Tree-guided feature selection and logic aggregation for large-scale regression.
result Improved prediction and model interpretation of suicide risk in EHR data.
We link disjoint longitudinal data for rare disease patients using latent representations and mixed-effects regression.
problem Analyzing treatment switches in rare diseases with limited data and changing measurement instruments.
method We embed item values into a shared latent space using variational autoencoders and apply mixed-effects regression to quantify treatment effects.
result Our approach allows for statistical inference and quantifies the impact of treatment switches in spinal muscular atrophy.
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,…
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.
Diagnosing an inherited disease often requires identifying the pattern of inheritance in a patient's family. We represent family trees with genetic patterns of inheritance using hypergraphs and latent state space models to provide explainable inheritance pattern predictions. Our approach allows for exact causal inferen…
Proposes dynamic borrowing method for historical data in clinical trials.
problem Insufficient statistical power in rare and pediatric disease clinical trials.
method Dynamic borrowing method based on frequentist approach using similarity measures.
result Demonstrates usefulness of dynamic borrowing in reanalyzing clinical trial data.
Detection of rare variants by resequencing is important for the identification of individuals carrying disease variants. Rapid sequencing by new technologies enables low-cost resequencing of target regions, although it is still prohibitive to test more than a few individuals. In order to improve cost trade-offs, it has…
The Neyman-Pearson (NP) paradigm in binary classification seeks classifiers that achieve a minimal type II error while enforcing the prioritized type I error controlled under some user-specified level . This paradigm serves naturally in applications such as severe disease diagnosis and spam detection, where people h…
Planning the optimal time of intervention for pulmonary valve replacement surgery in patients with the congenital heart disease Tetralogy of Fallot (TOF) is mainly based on ventricular volume and function according to current guidelines. Both of these two biomarkers are most reliably assessed by segmentation of 3D card…
Massively multi-label prediction/classification problems arise in environments like health-care or biology where very precise predictions are useful. One challenge with massively multi-label problems is that there is often a long-tailed frequency distribution for the labels, which results in few positive examples for t…
Smartphone app diagnoses pulmonary diseases from chest X-rays.
problem Scarcity of training data and class imbalance issues.
method Data Augmentation Generative Adversarial Network (DAGAN) and Convolutional Siamese Network with attention mechanism.
result Achieved 99.30% and 98.40% testing accuracy on Binary/Multiclass scenarios.
Generative AI models improve clinical trial data by generating survival outcomes.
problem Generating valid survival outcomes for clinical trials with synthetic data.
method A variational autoencoder (VAE) that jointly generates mixed-type covariates and survival outcomes.
result The method outperforms GAN baselines on fidelity, utility, and privacy metrics.
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…
Study improves machine learning models for GI tract disease detection using comprehensive evaluations and cross-dataset testing.
problem Incomplete or incorrect evaluation of machine learning models for GI tract diseases.
method Comprehensive evaluations of five machine learning models using Global Features and Deep Neural Networks, introducing performance hexagons and cross-dataset testing.
result Demonstrates the need for more sophisticated performance metrics and evaluation methods to build generalizable models.
Causal Explainability of Machine Learning in Heart Failure Prediction from Electronic Health Recordsstat.ML
The paper investigates causal relationships in heart failure prediction using machine learning.
problem Understanding the causal relationships between clinical variables and heart failure.
method Proposes a new computational framework for causal structure discovery (CSD) of mixed-type clinical variables for binary disease outcomes.
result Feature importance from nonlinear classifiers strongly correlates with causal strength of variables, but not differentiating cause and effect.
This paper explores object detection in the small data regime, where only a limited number of annotated bounding boxes are available due to data rarity and annotation expense. This is a common challenge today with machine learning being applied to many new tasks where obtaining training data is more challenging, e.g. i…
The development of machine learning systems for the diagnosis of rare diseases is challenging mainly due the lack of data to study them. Despite this challenge, this paper proposes a system for the Computer Aided Diagnosis (CAD) of low-prevalence, congenital muscular dystrophies from confocal microscopy images. The pro…
Paper proposes an inductive RGCN for few-shot link prediction in drug-repurposing.
problem Predicting rare interactions in drug-repurposing for novel diseases.
method Proposes an inductive RGCN to learn relation embeddings for few-shot learning.
result Significantly outperforms state-of-the-art models in few-shot learning tasks.
Enhances MIL performance in scarce data scenarios using topological inductive biases.
problem Low performance of MIL in data-scarce scenarios.
method Incorporates topological inductive biases into MIL framework.
result Average performance improvements of 15.3% for synthetic datasets, 2.8% for benchmarks, and 5.5% for rare anemia classification.
New KNN test improves association analysis of high-dimensional sequencing data.
problem Challenges in using neural networks for high-dimensional sequencing data analysis.
method Kernel-based neural network (KNN) test for complex association analysis.
result KNN test outperforms SKAT in detecting non-linear and interaction effects.
Machine learning improves detection of Brugada Syndrome from ECGs.
problem Detecting Brugada Syndrome (BrS) from ECGs is challenging due to limited diagnostic criteria.
method Pipeline that reads and processes scanned ECG images, uses LSTM classifier to diagnose.
result The proposed pipeline distinguishes between ECG types and diagnoses BrS with high accuracy.
Framework harmonizes EHR data across institutions for better analysis.
problem Heterogeneity of medical codes and terminologies hinder EHR data analysis.
method MASH (Multi-source Automated Structured Hierarchy) uses neural optimal transport and learned hyperbolic embeddings to align and structure EHR data.
result MASH generates interpretable hierarchical graphs for unstructured local laboratory codes.
Image modality recognition is essential for efficient imaging workflows in current clinical environments, where multiple imaging modalities are used to better comprehend complex diseases. Emerging biomarkers from novel, rare modalities are being developed to aid in such understanding, however the availability of these …
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.
Insufficient training data and severe class imbalance are often limiting factors when developing machine learning models for the classification of rare diseases. In this work, we address the problem of classifying bone lesions from X-ray images by increasing the small number of positive samples in the training set. We …
It is common in modern prediction problems for many predictor variables to be counts of rarely occurring events. This leads to design matrices in which many columns are highly sparse. The challenge posed by such "rare features" has received little attention despite its prevalence in diverse areas, ranging from natural …
Malaria is a life-threatening disease affecting millions. Microscopy-based assessment of thin blood films is a standard method to (i) determine malaria species and (ii) quantitate high-parasitemia infections. Full automation of malaria microscopy by machine learning (ML) is a challenging task because field-prepared sli…
Disease phenotyping algorithms process observational clinical data to identify patients with specific diseases. Supervised phenotyping methods require significant quantities of expert-labeled data, while unsupervised methods may learn non-disease phenotypes. To address these limitations, we propose the Semi-Supervised …
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.
Clinical researchers use disease progression models to understand patient status and characterize progression patterns from longitudinal health records. One approach for disease progression modeling is to describe patient status using a small number of states that represent distinctive distributions over a set of obser…
Variable selection is a challenging issue in statistical applications when the number of predictors far exceeds the number of observations . In this ultra-high dimensional setting, the sure independence screening (SIS) procedure was introduced to significantly reduce the dimensionality by preserving the true mod…
A Disease Diagnosis and Treatment Recommendation System Based on Big Data Mining and Cloud Computingcs.LG
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…
Drug repositioning is an attractive cost-efficient strategy for the development of treatments for human diseases. Here, we propose an interpretable model that learns disease self-representations for drug repositioning. Our self-representation model represents each disease as a linear combination of a few other diseases…
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…
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, …
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.