Personalized medicine has become an important part of medicine, for instance predicting individual drug responses based on genomic information. However, many current statistical methods are not tailored to this task, because they overlook the individual heterogeneity of patients. In this paper, we look at personalized …
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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.
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…
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…
Expands statistical background for knee osteoarthritis treatment models.
problem Developing optimal exercise and weight loss treatments for knee osteoarthritis.
method Precision medicine models and jackknife cross-validation method.
result Jackknife estimator provides consistent value function estimation.
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…
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…
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.
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.
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…
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.
Targeting Underrepresented Populations in Precision Medicine: A Federated Transfer Learning Approachstat.ML
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.
AI in Pharma for Personalized Sequential Decision-Making: Methods, Applications and Opportunitiesstat.ME
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.
CAPITAL algorithm identifies optimal patient subgroups for better treatment.
problem Identify maximum number of patients benefiting from better treatment.
method Constrained Policy Tree Search (CAPITAL) algorithm to find optimal subgroup selection rule (SSR).
result Maximizes the number of patients with enhanced treatment effects.
Bayesian outcome-guided multi-view mixture models with applications in molecular precision medicinestat.ME
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.
In medicine, visualizing chromosomes is important for medical diagnostics, drug development, and biomedical research. Unfortunately, chromosomes often overlap and it is necessary to identify and distinguish between the overlapping chromosomes. A segmentation solution that is fast and automated will enable scaling of co…
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.
Large Language Models-Enabled Digital Twins for Precision Medicine in Rare Gynecological Tumorscs.CL
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…
Network medicine predicts repurposable drugs for COVID-19.
problem Identifying effective drugs for SARS-CoV-2 infections quickly.
method Artificial intelligence, network diffusion, and network proximity algorithms.
result A multimodal approach combining predictions from multiple algorithms outperforms individual methods.
Paper proposes federated offline RL for personalized medicine.
problem Privacy constraints and heterogeneity in healthcare data.
method Multi-site Markov decision process model and first federated policy optimization algorithm.
result The proposed algorithm achieves comparable suboptimality to centralized RL.
Scientific investigations that incorporate next generation sequencing involve analyses of high-dimensional data where the need to organize, collate and interpret the outcomes are pressingly important. Currently, data can be collected at the microbiome level leading to the possibility of personalized medicine whereby tr…
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.
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.
Statistical Learning for Heterogeneous Treatment Effects: Pretraining, Prognosis, and Predictionstat.ML
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.
Personalized medicine aims at identifying best treatments for a patient with given characteristics. It has been shown in the literature that these methods can lead to great improvements in medicine compared to traditional methods prescribing the same treatment to all patients. Subgroup identification is a branch of per…
Paper uses stats to predict treatment choice based on illness probability.
problem Improving treatment decision-making in personalized medicine.
method Statistical decision theory with maximum regret evaluation.
result Estimates illness probability for better treatment choice.
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.
Bayesian CNN estimates uncertainty in bone age prediction.
problem Uncertainty quantification in age estimation models.
method Variational Inference for Bayesian CNNs.
result Model uncertainty distinguished from data uncertainty.
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.
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…
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.
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…
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.
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.
Medical Knowledge Integration into Reinforcement Learning Algorithms for Dynamic Treatment Regimesstat.ME
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.
3D dataset for intracranial aneurysms aids deep learning applications.
problem Lack of 3D medical datasets for deep learning.
method Developed an open-access 3D dataset, IntrA, for intracranial aneurysms.
result Demonstrated the challenges and performance of 3D medical datasets.
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…
Do we know if a short selling ban or a Tobin Tax result in more stable asset prices? Or do they in fact make things worse? Just like medicine regulatory measures in financial markets aim at improving an already complex system. And just like medicine these interventions can cause side effects which are even harder to as…
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…
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.
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…
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.
Automated medical prognosis has gained interest as artificial intelligence evolves and the potential for computer-aided medicine becomes evident. Nevertheless, it is challenging to design an effective system that, given a patient's medical history, is able to predict probable future conditions. Previous works, mostly c…
MSBM extends SB for multi-marginal trajectory inference.
problem Trajectory inference from multiple discrete snapshots.
method Multi-Marginal Schrödinger Bridge Matching (MSBM) using iterative Markovian fitting (IMF).
result MSBM effectively captures complex trajectories and respects intermediate distributions.