The paper advocates for interpretable, accountable, reproducible machine learning in medicine.
problem Black box models in medicine lack transparency and regulatory approval.
method Intrinsically interpretable modeling approaches and collaborative learning paradigms.
result Interpretable machine learning models can support clinical decisions and gain regulatory approval.
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.
This paper considers the use of Machine Learning (ML) in medicine by focusing on the main problem that this computational approach has been aimed at solving or at least minimizing: uncertainty. To this aim, we point out how uncertainty is so ingrained in medicine that it biases also the representation of clinical pheno…
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.
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.
POSL predicts dynamic convection volumes in hemodiafiltration patients.
problem Continuous, personalised predictions in personalised medicine.
method Adapted POSL to dynamically predict convection volumes using combinations of parametric regressions and machine learning.
result POSL outperformed candidate learners in predicting convection volumes with lower errors and better calibration.
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.
PDX studies help personalize cancer treatment.
problem Precision medicine in cancer treatment.
method Machine learning methods for estimating optimal ITRs from PDX data.
result Superlearner approach combining multiple ITRs improves personalized treatment recommendations.
Risk prediction is central to both clinical medicine and public health. While many machine learning models have been developed to predict mortality, they are rarely applied in the clinical literature, where classification tasks typically rely on logistic regression. One reason for this is that existing machine learning…
R package for machine learning in survival analysis.
problem Limited machine learning interfaces for survival analysis.
method Provides a comprehensive machine learning interface for survival analysis.
result Systematic infrastructure for survival modeling and evaluation.
The issue of disagreements amongst human experts is a ubiquitous one in both machine learning and medicine. In medicine, this often corresponds to doctor disagreements on a patient diagnosis. In this work, we show that machine learning models can be trained to give uncertainty scores to data instances that might result…
The paper proposes a method to estimate heterogeneous treatment effects using pretraining strategies.
problem Estimating conditional average treatment effects (CATE) in the presence of many covariates.
method The approach leverages prognostic factors that also predict treatment effect heterogeneity, using the R-learner framework.
result The proposed method improves estimation accuracy and power for detecting treatment effect heterogeneity.
Causal ML predicts treatment outcomes, aiding personalized medicine.
problem Predicting individualized treatment effects for personalized medicine.
method Flexible, data-driven methods using causal inference with clinical trial and real-world data.
result Causal ML allows for estimating individualized treatment effects.
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 guide introduces machine learning for medical data analysis.
problem Handling large, complex datasets in healthcare.
method Explains common machine learning algorithms and tasks.
result Illustrates machine learning applications in healthcare.
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.
Automates feature extraction for IMU-based activity recognition.
problem Manual feature engineering is time-consuming and limits IMU-based applications.
method FRESH algorithm for automated feature extraction.
result Workflow automates feature extraction from synchronized IMU sensors.
Generative models create personalized patient health simulations.
problem Creating accurate digital twins for personalized medicine.
method Neural network architecture for conditional generative models of clinical trajectories.
result Same architecture generates accurate twins across 13 indications.
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.
Improved aggregation methods learn from all ICU events without preprocessing for better patient risk analysis.
problem Lack of efficient methods to dynamically assess patient status in ICU.
method Improved aggregation methods for a deep learning architecture that learns from all events without preprocessing.
result Models achieve strong performance (AUROC 0.87) in patient mortality classification.
The quality of machine translation is rapidly evolving. Today one can find several machine translation systems on the web that provide reasonable translations, although the systems are not perfect. In some specific domains, the quality may decrease. A recently proposed approach to this domain is neural machine translat…
Many of the current scientific advances in the life sciences have their origin in the intensive use of data for knowledge discovery. In no area this is so clear as in bioinformatics, led by technological breakthroughs in data acquisition technologies. It has been argued that bioinformatics could quickly become the fiel…
Machine learning models trained on indirect data labels can fail on real-world examples.
problem Validity issues in machine learning when target labels are indirectly defined.
method Identification of problematic datasets and models using a general procedure.
result Machine learning models trained on indirect data labels will fail on real-world examples.
Fourier-transform infra-red (FTIR) spectra of samples from 7 plant species were used to explore the influence of preprocessing and feature extraction on efficiency of machine learning algorithms. Wavelet Tensor Train (WTT) and Discrete Wavelet Transforms (DWT) were compared as feature extraction techniques for FTIR dat…
In biological research machine learning algorithms are part of nearly every analytical process. They are used to identify new insights into biological phenomena, interpret data, provide molecular diagnosis for diseases and develop personalized medicine that will enable future treatments of diseases. In this paper we (1…
New report on machine learning visualization techniques and trends.
problem Improving trust in machine learning models through visualization.
method Analysis of peer-reviewed articles on machine learning visualization techniques.
result Rapid growth in machine learning visualization techniques over the past three years.
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.
Provides a compendium of data sources for various applications.
problem Lack of comprehensive data sources for data science, machine learning, and AI.
method Compilation of diverse data sources across multiple application areas.
result A comprehensive list of data sources for data scientists and machine learning experts.
YouTube presents an unprecedented opportunity to explore how machine learning methods can improve healthcare information dissemination. We propose an interdisciplinary lens that synthesizes machine learning methods with healthcare informatics themes to address the critical issue of developing a scalable algorithmic sol…
New meta-learners estimate time-varying treatment effects without model assumptions.
problem Estimating treatment effects over time in personalized medicine.
method Model-agnostic meta-learners for weighted pseudo-outcome regressions.
result Comprehensive theoretical analysis and practical insights for choosing meta-learners.
Myriad offers a testbed for integrating machine learning and trajectory optimization.
problem Real-world trajectory optimization challenges.
method JAX-based testbed with machine learning and trajectory optimization integration.
result End-to-end learning and planning with neural ODEs.
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.
MPSTime uses matrix-product states for efficient time-series ML.
problem Learning complex correlations in time-series data.
method Developed an MPS-based algorithm for joint probability distribution learning.
result MPSTime efficiently learns time-series probability distributions.
Proposes MRIV framework for unbiased CATE estimation using binary IVs.
problem Bias in estimating CATEs due to unobserved confounders.
method Multiply robust machine learning framework (MRIV) for binary IVs.
result MRIV yields multiple robust convergence rates and outperforms existing methods.
Federated Learning solves privacy and data distribution challenges in machine learning.
problem Privacy concerns and distributed data in machine learning.
method Federated Learning framework to handle privacy and distributed data.
result Solves privacy and data distribution challenges in machine learning.
Optimizes personalized medicine prediction by individual tuning.
problem Predicting individual drug responses using genomic information.
method Introduces a new ridge estimator and tuning parameter calibration scheme.
result Optimal in terms of oracle inequalities, fast, and highly effective.
The medical field stands to see significant benefits from the recent advances in deep learning. Knowing the uncertainty in the decision made by any machine learning algorithm is of utmost importance for medical practitioners. This study demonstrates the utility of using Bayesian LSTMs for classification of medical time…
Private RL algorithm with privacy guarantees for personalized medicine decisions.
problem Privacy-preserving reinforcement learning for personalized medicine decisions.
method Developed a private optimism-based RL algorithm using joint differential privacy (JDP).
result Achieved strong PAC and regret bounds with a privacy guarantee.
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…
New technologies have enabled the investigation of biology and human health at an unprecedented scale and in multiple dimensions. These dimensions include a myriad of properties describing genome, epigenome, transcriptome, microbiome, phenotype, and lifestyle. No single data type, however, can capture the complexity of…
Develops methods to learn optimal treatment regimes using causal tree methods.
problem Lack of methods for estimating treatment effects and handling complex patient data.
method Causal tree and causal forest methods for estimating heterogeneous treatment effects.
result Outperforms state-of-the-art baselines in cumulative regret and percentage of optimal decisions.
Representation learning improves EHR data for healthcare tasks.
problem Transforming EHR data into useful representations for machine learning.
method Deep learning and disentangling underlying factors from EHR data.
result Better representations improve machine learning performance in healthcare.
The current flood of information in all areas of machine learning research, from computer vision to reinforcement learning, has made it difficult to make aggregate scientific inferences. It can be challenging to distill a myriad of similar papers into a set of useful principles, to determine which new methodologies to …
Framework assesses variable importance for heterogeneous treatment effects.
problem High-risk domains need reliable methods to assess treatment effect heterogeneity.
method Inferential framework based on Shapley values and semiparametric theory.
result Valid inference on variable importance for heterogeneous treatment effects.
In this work, we investigate the importance of ethnicity in colorectal cancer survivability prediction using machine learning techniques and the SEER cancer incidence database. We compare model performances for 2-year survivability prediction and feature importance rankings between Hispanic, White, and mixed patient po…
Machine learning confound removal biases results, leading to misleading predictions.
problem Common confound removal methods in machine learning lead to misleading predictions.
method Featurewise removal of confound variance by linear regression before applying ML.
result This common deconfounding approach can leak information, amplifying null or moderate effects.
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 show how to learn low-dimensional representations (embeddings) of patient visits from the corresponding electronic health record (EHR) where International Classification of Diseases (ICD) diagnosis codes are removed. We expect that these embeddings will be useful for the construction of predictive statistical models…