Bandit algorithms optimize treatment decisions for precision medicine.
problem Optimizing treatment decisions for individual patients based on genetic or molecular profiling.
method Contextual bandit algorithms that consider patient characteristics.
result Bandit algorithms are useful for mobile health and digital phenotyping.
This paper reviews random forest methods for analyzing longitudinal data in precision medicine.
problem Analyzing longitudinal data for precision medicine.
method Extensions of random forest for longitudinal data analysis.
result Categorization of random forest methods for different data structures and repeated measurements.
There is tremendous interest in precision medicine as a means to improve patient outcomes by tailoring treatment to individual characteristics. An individualized treatment rule formalizes precision medicine as a map from patient information to a recommended treatment. A treatment rule is defined to be optimal if it max…
AI-enabled precision medicine promises a transformational improvement in healthcare outcomes by enabling data-driven personalized diagnosis, prognosis, and treatment. However, the well-known "curse of dimensionality" and the clustered structure of biomedical data together interact to present a joint challenge in the hi…
Recent exploration of optimal individualized decision rules (IDRs) for patients in precision medicine has attracted a lot of attention due to the heterogeneous responses of patients to different treatments. In the existing literature of precision medicine, an optimal IDR is defined as a decision function mapping from t…
Proposes a federated transfer learning method to improve precision medicine models for underrepresented populations.
problem Underrepresentation of minorities in precision medicine research leads to underperforming risk prediction models.
method Two-way federated transfer learning strategy integrating diverse populations and healthcare institutions.
result Improves risk prediction models for underrepresented populations, reducing performance gaps.
We provide additional statistical background for the methodology developed in the clinical analysis of knee osteoarthritis in "A Precision Medicine Approach to Develop and Internally Validate Optimal Exercise and Weight Loss Treatments for Overweight and Obese Adults with Knee Osteoarthritis" (Jiang et al. 2020). Jiang…
Traditional medicine typically applies one-size-fits-all treatment for the entire patient population whereas precision medicine develops tailored treatment schemes for different patient subgroups. The fact that some factors may be more significant for a specific patient subgroup motivates clinicians and medical researc…
Study uses LLMs to create personalized treatment plans for rare gynecological tumors.
problem Suboptimal management and poor prognosis due to low incidence and heterogeneity of rare gynecological tumors.
method Developed a digital twin system using LLMs to integrate clinical and biomarker data.
result LLM-enabled digital twins efficiently model individual patient trajectories and identify potential treatment options.
Causal ML methods failed to validate their personalized treatment effects in two large trials.
problem Validating causal machine learning methods for personalized treatment effects in precision medicine.
method Assessed 17 mainstream causal heterogeneity ML methods using two large randomized controlled trials.
result None of the ML methods reliably validated their performance, internal or external, showing significant discrepancies between training and test data.
In this paper, we propose a new deep feature selection method based on deep architecture. Our method uses stacked auto-encoders for feature representation in higher-level abstraction. We developed and applied a novel feature learning approach to a specific precision medicine problem, which focuses on assessing and prio…
The paper predicts diseases using both clinical and genomics data.
problem Clinical predictions using genomics data are not common.
method Integrated clinical and genomics datasets, machine learning, Principal Component Analysis for feature selection.
result 73% accuracy in predicting 75 disease classes.
Proposes an interpretable machine learning framework for multi-arm HTE estimation.
problem Challenges in estimating heterogeneous treatment effects in multi-arm settings.
method Rule-based ensemble approach for HTE estimation in multi-arm trials.
result Achieved lower bias and higher estimation accuracy compared to existing methods.
Method controls treatment risk in learning beneficial allocations.
problem Learning beneficial treatment allocations with risk control in precision medicine.
method Proposes a certifiable learning method that controls treatment risk with finite samples in the partially identified setting.
result Illustrates method using both simulated and real data.
Stein-Encoder isolates genetic signals in multi-modal biomedical data.
problem Integration of high-dimensional genomic data with clinical data obscures genetic predictive impact.
method White-box supervised framework using Stein's method and residualization.
result Stein-Encoder improves predictive accuracy and reveals specific biological mechanisms.
SurvMixClust clusters survival data and predicts individual survival curves.
problem Integrating clustering into survival analysis for precision medicine.
method SurvMixClust learns latent representations for clustering and predicts survival functions using a mixture of non-parametric experts.
result SurvMixClust creates balanced clusters with distinct survival curves, outperforming clustering baselines and competing with non-clustering models in predictive accuracy.
AI enhances personalized drug development and decision-making in pharma.
problem Traditional drug development lacks personalized treatment plans.
method Application of AI in drug discovery, clinical trials, and post-marketing assessment.
result AI improves personalized medicine, optimizing health outcomes.
The complexity of human cancer often results in significant heterogeneity in response to treatment. Precision medicine offers potential to improve patient outcomes by leveraging this heterogeneity. Individualized treatment rules (ITRs) formalize precision medicine as maps from the patient covariate space into the space…
RL algorithms with medical integration improve personalized treatment recommendations.
problem Developing effective personalized treatment strategies for chronic diseases.
method Integrating medical knowledge into RL algorithms for DTR.
result Enhanced treatment recommendations with increased confidence.
Predicting the efficacy of a drug for a given individual, using high-dimensional genomic measurements, is at the core of precision medicine. However, identifying features on which to base the predictions remains a challenge, especially when the sample size is small. Incorporating expert knowledge offers a promising alt…
DWTS uses observational data to improve clinical trial efficiency.
problem Lack of definitive conclusions from randomized clinical trials due to insufficient patient cohorts and confounding biases.
method DWTS combines observational data with randomized clinical trials using Doubly Debiased LASSO (DDL) to identify reliable covariates.
result DWTS reduces cumulative regret in clinical trials compared to standard methods.
Study improves LLMs for PPI analysis by addressing uncertainty.
problem Uncertainty in LLM predictions for PPIs.
method Fine-tuned LLaMA-3 and BioMedGPT models, LoRA ensembles, Bayesian LoRA for UQ.
result Competitive PPI identification performance across diverse disease contexts.
Estimates individualized treatment effects using shared RBF-net neurons.
problem Identifying differential treatment effects based on covariates.
method Non-parametric radial basis function (RBF)-nets with shared hidden neurons in a Bayesian framework.
result Demonstrated through simulations and real data, the method identifies interesting treatment effects.
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.
The ubiquitous availability of wearable sensors is responsible for driving the Internet-of-Things but is also making an impact on sport sciences and precision medicine. While human activity recognition from smartphone data or other types of inertial measurement units (IMU) has evolved to one of the most prominent daily…
Adapts randomization for single unit time-series data for optimal treatment.
problem Statistical methods for precision medicine in single unit time-series data.
method Adaptive sequential design, nonparametric model, double robust structure, efficient influence function.
result Valid inference for mean target parameter based on single sample.
SAFER improves personalized treatment recommendations for dynamic clinical contexts.
problem Personalized treatment optimization in evolving clinical contexts with safety concerns.
method Integrates structured EHR and clinical notes, uses conformal prediction for safe recommendations.
result SAFER outperforms state-of-the-art baselines in recommendation metrics and mortality rates.
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.
The field of precision medicine aims to tailor treatment based on patient-specific factors in a reproducible way. To this end, estimating an optimal individualized treatment regime (ITR) that recommends treatment decisions based on patient characteristics to maximize the mean of a pre-specified outcome is of particular…
CEDAR efficiently analyzes distributed EHR data without sharing patient-level info.
problem Analyzing patient-level data from multiple EHRs databases without sharing raw data.
method Tackles by turning problem into missing data, incorporating posterior samples.
result Improves efficiency and privacy of parameter estimates in sparse regressions.
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.
New method uses SHAP for biomarker identification in CATE models.
problem Identifying predictive biomarkers from observational data.
method Surrogate estimation approach using SHAP values for CATE meta-learners.
result SHAP accurately identifies biomarkers in high-dimensional data.
This paper reviews methods for discovering patient subgroups from EHR data.
problem Discovering subgroups of patients and co-occurring medical conditions from EHR data.
method Low-rank data approximation methods like matrix and tensor decompositions.
result These methods provide transparent and interpretable insights into patient phenotypes.
Develops methods for near-optimal personalized treatment recommendations.
problem Assigning optimal treatments to patients based on individual characteristics.
method Outcome weighted learning framework to estimate near-optimal alternative individualized treatment recommendations (A-ITR).
result Consistency of proposed methods and upper bound for risk between optimal and estimated recommendations.
Develops a weighting framework to generalize ITRs from source to target populations.
problem Challenges in generalizing ITRs from a source population to a target population with differing characteristics.
method A robust sample weighting framework using a reproducing kernel Hilbert space to balance covariates and improve ITR learning methods.
result Improves ITR estimation for the target population compared to other weighting methods.
Proposes a two-stage method for estimating heterogeneous treatment effects using gradient boosting trees.
problem Estimating heterogeneous treatment effects in randomized clinical trials with high-dimensional predictive markers.
method Two-stage statistical learning procedure using gradient boosting trees (XGBoost) to estimate main effects and HTE.
result Improves efficiency in estimating heterogeneous treatment effects through nonparametric function estimation.
Framework integrates mental disorder measurements for personalized treatment.
problem Optimizing treatment for mental disorders with latent mental states and heterogeneity.
method Measurement theory and multi-layer neural network for complex treatment effects.
result Learned treatment policies outperform alternatives on heterogeneous treatment effects.
A new method models individual survival curves using conditional normalizing flows.
problem Precise per-individual predictions in survival analysis.
method Conditional normalizing flows for flexible and individualized survival distributions.
result Efficient estimation of individual survival curves without overfitting.
DeepCoDA provides personalized interpretability for complex health data.
problem Interpreting complex health data, especially compositional data, is challenging.
method DeepCoDA framework for high-dimensional compositional data, personalized interpretability through patient-specific weights.
result DeepCoDA maintains state-of-the-art performance and provides coherent, personalized interpretations.
Paper tackles gene mutation prediction for HCC using multi-instance multi-label learning.
problem Gene mutation prediction in hepatocellular carcinoma for personalized treatments.
method Multi-instance multi-label learning with oversampling for data imbalance.
result Proposed approach shows superiority in gene mutation prediction.
New methods use RL and DA to improve dosing precision and reduce side effects.
problem Improving precision and safety of anticancer drug dosing.
method Bayesian data assimilation and reinforcement learning.
result Significantly reduces incidence of severe side effects.
Users of a personalised recommendation system face a dilemma: recommendations can be improved by learning from data, but only if the other users are willing to share their private information. Good personalised predictions are vitally important in precision medicine, but genomic information on which the predictions are…
Predicting drug-target interactions (DTI) is an essential part of the drug discovery process, which is an expensive process in terms of time and cost. Therefore, reducing DTI cost could lead to reduced healthcare costs for a patient. In addition, a precisely learned molecule representation in a DTI model could contribu…
Bayesian models link multiview data to outcomes.
problem Inferring relationships between diverse data types and outcomes.
method Developed two factor regression models: JFR and JAFAR.
result Improved prediction of clinical outcomes from multi-omics data.
AI improves precision health through adaptive interventions.
problem Improving healthcare through personalized and dynamic treatments.
method Reinforcement learning (RL) for adaptive interventions in digital health.
result RL shows promise in dynamic healthcare problems.
A new method estimates treatment effects across multiple studies considering differences.
problem Estimating treatment effects across multiple studies with varying conditions.
method The multi-study R-learner framework that accounts for between-study heterogeneity.
result The multi-study R-learner is more efficient and normal than existing methods in the presence of heterogeneity.
The paper integrates AI and expert knowledge to optimize radiotherapy decisions.
problem Optimizing radiation dose planning considering patient-specific information.
method Integrating Gaussian process models with deep neural networks to quantify uncertainty.
result Improves AI model performance and guides clinical decision making.
Recently, deep learning has been advancing the state of the art in artificial intelligence to a new level, and humans rely on artificial intelligence techniques more than ever. However, even with such unprecedented advancements, the lack of explanation regarding the decisions made by deep learning models and absence of…