Exploratory cancer drug studies test multiple tumor cell lines against multiple candidate drugs. The goal in each paired (cell line, drug) experiment is to map out the dose-response curve of the cell line as the dose level of the drug increases. We propose Bayesian Tensor Filtering (BTF), a hierarchical Bayesian model …
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48 results for “drug dosing”
SDF-Bayes finds safe drug combinations safely, balancing optimism and caution.
problem Finding safe drug combinations in clinical trials with multiple drugs and patient heterogeneity.
method SDF-Bayes uses Bayesian statistics to choose the most likely MTD while ensuring safety constraints.
result SDF-Bayes outperforms existing methods in both accuracy and safety for drug combination trials.
C3T-Budget optimizes drug efficacy in dose-finding trials with budget and safety constraints.
problem Heterogeneous patient populations and budget constraints make dose-finding clinical trials challenging.
method Contextual constrained clinical trial algorithm that maximizes drug efficacy while learning subgroup responses.
result Demonstrates efficient budget usage and balanced learning-treatment trade-off in simulated trials.
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.
Counterfactual harmcs.AI
Proposes a new method to measure and avoid harm in machine learning decisions.
problem Measuring and avoiding harm in machine learning algorithms.
method Formal definition of harm and benefit using causal models, counterfactual objective functions.
result Demonstrates that standard machine learning methods can lead to harmful policies under distributional shifts.
Permutation invariant multi-output Gaussian Processes for drug combination prediction in cancerq-bio.QM
Develops a scalable model for drug combination prediction in cancer.
problem Accurate prediction of drug combinations for cancer treatment.
method Permutation invariant multi-output Gaussian Processes with variational approximation and deep generative model.
result Model efficiently borrows information across drug combinations and provides uncertainty quantification.
The challenge in controlling stochastic systems in which low-probability events can set the system on catastrophic trajectories is to develop a robust ability to respond to such events without significantly compromising the optimality of the baseline control policy. This paper presents CelluDose, a stochastic simulatio…
Proposes a method for generating prediction intervals in dose-response models using conformal prediction.
problem Uncertainty quantification in continuous treatments for personalized healthcare decisions.
method Causal dose-response problem framed as covariate shift, using weighted conformal prediction with propensity estimation and kernel functions.
result Demonstrates the significance of covariate shift assumptions for robust prediction intervals.
This Perspective provides examples of current and future applications of deep learning in pharmacogenomics, including: (1) identification of novel regulatory variants located in noncoding domains and their function as applied to pharmacoepigenomics; (2) patient stratification from medical records; and (3) prediction of…
Paper introduces IC-index to evaluate interaction prediction methods.
problem Evaluate interaction prediction methods using IC-index.
method IC-index measures interaction direction prediction performance.
result IC-index complements existing prediction performance estimators.
Objective: Anemia is a frequent comorbidity in hemodialysis patients that can be successfully treated by administering erythropoiesis-stimulating agents (ESAs). ESAs dosing is currently based on clinical protocols that often do not account for the high inter- and intra-individual variability in the patient's response. …
Profiling cellular phenotypes from microscopic imaging can provide meaningful biological information resulting from various factors affecting the cells. One motivating application is drug development: morphological cell features can be captured from images, from which similarities between different drug compounds appli…
Kernel method optimizes personalized dose rules for patients.
problem Finding optimal individualized dose rules for patients.
method Kernel assisted learning method for estimating optimal dose rules.
result The method identifies the optimal individualized dose rule and produces favorable outcomes.
Shared Keyboard: An improved Bayesian design for phase I clinical trials via Beta kernel processstat.AP
Shared Keyboard design improves phase I clinical trials by borrowing information across doses.
problem Interim decisions based on current dose data may overlook signals from neighboring doses.
method Bayesian model-assisted design using Beta kernel process with kernel-weighted pseudo-counts.
result Significant improvements in identifying maximum tolerated dose and safety.
Proposes a framework for automated radiation therapy treatment planning with uncertainty quantification.
problem Quantifying uncertainties in dose-related quantities for automated treatment planning.
method Three-step pipeline: feature extraction, dose statistic prediction, and dose mimicking.
result Probabilistic treatment plans agree better with clinical counterparts than non-probabilistic ones.
New method estimates optimal dose intervals for personalized treatment.
problem Learning optimal dose intervals from observational data.
method Probability dose interval (PDI) method using DC algorithm.
result Consistent policy with risk converging to best-in-class at root-n rate.
We study the problem of finding the optimal dosage in early stage clinical trials through the multi-armed bandit lens. We advocate the use of the Thompson Sampling principle, a flexible algorithm that can accommodate different types of monotonicity assumptions on the toxicity and efficacy of the doses. For the simplest…
Determining the optimal initial dose for warfarin is a critically important task. Several factors have an impact on the therapeutic dose for individual patients, such as patients' physical attributes (Age, Height, etc.), medication profile, co-morbidities, and metabolic genotypes (CYP2C9 and VKORC1). These wide range f…
Warfarin dosing remains challenging due to narrow therapeutic index and highly individual variability. Incorrect warfarin dosing is associated with devastating adverse events. Remarkable efforts have been made to develop the machine learning based warfarin dosing algorithms incorporating clinical factors and genetic va…
A new cycleGAN architecture reduces memory and parameter requirements for low-dose CT denoising.
problem Efficient unsupervised low-dose CT denoising with minimal memory and parameter usage.
method Single switchable generator using AdaIN layers for efficient training and inference.
result The proposed method outperforms previous cycleGAN approaches with half the parameters.
SEEDA optimizes dose allocation in clinical trials to balance efficacy and safety.
problem Complex relationships between efficacy and toxicity in new drug trials.
method Adaptive clinical trial methodology that maximizes cumulative efficacy while ensuring safety constraints.
result SEEDA outperforms existing methods in finding optimal doses with higher success rates and fewer patients.
A novel dose-finding design for cancer clinical trials using level set estimation.
problem Finding the maximum tolerated dose (MTD) in phase I cancer clinical trials.
method Proposes a novel dose-finding design based on level set estimation (LSE) to determine the next dose.
result The proposed LSE design achieves higher accuracy in estimating the MTD and lower risk of overdosing compared to existing designs.
Surrogate-free machine learning-based organ dose reconstruction for pediatric abdominal radiotherapyphysics.med-ph
A ML-based method reconstructs 3D organ doses from 2D radiographs for pediatric abdominal radiotherapy.
problem Reconstructing detailed 3D dose distributions for childhood cancer survivors using limited 2D radiographs.
method Surrogate-free ML approach using 142 abdominal planning CTs, 300 artificial plans, and evolutionary algorithm.
result Accurate 3D dose reconstructions with MAEs ≤ 1.7 Gy for edge organs, validated on independent dataset.
The distribution of absorbed dose in radionuclide therapy with Lu can be approximated by convolving an image of the time-integrated activity distribution with a dose voxel kernel representing different tissue types. This fast but inaccurate approximation is unsuitable for personalised dosimetry because it negle…
Warfarin is one of the most commonly used oral blood anticoagulant agent in the world, the proper dose of Warfarin is difficult to establish not only because it is substantially variant among patients, but also adverse even severe consequences of taking an incorrect dose. Typical practice is to prescribe an initial dos…
In coronary CT angiography, a series of CT images are taken at different levels of radiation dose during the examination. Although this reduces the total radiation dose, the image quality during the low-dose phases is significantly degraded. To address this problem, here we propose a novel semi-supervised learning tech…
DoSE improves OOD detection by estimating model probability density.
problem Poor specificity of model likelihoods for OOD detection.
method DoSE uses density of states concept to avoid direct model probability comparison.
result DoSE achieves state-of-the-art performance on OOD detection benchmarks.
Estimating what would be an individual's potential response to varying levels of exposure to a treatment is of high practical relevance for several important fields, such as healthcare, economics and public policy. However, existing methods for learning to estimate counterfactual outcomes from observational data are ei…
Due to the widespread use of positron emission tomography (PET) in clinical practice, the potential risk of PET-associated radiation dose to patients needs to be minimized. However, with the reduction in the radiation dose, the resultant images may suffer from noise and artifacts that compromise diagnostic performance.…
Gaussian surrogates improve Poisson imaging performance at low doses.
problem Improving Poisson imaging performance at low doses.
method Analysis of Poisson and Gaussian surrogate reconstruction objectives under Poisson noise.
result Gaussian surrogates can achieve MSE comparable to Poisson MAP at low doses.
Develops a neural surrogate for proton dose calculation using Monte Carlo dropout uncertainty.
problem Computational demand in proton therapy workflows requiring repeated evaluations.
method Integrates Monte Carlo dropout into a neural network surrogate for fast, differentiable dose predictions and uncertainty quantification.
result Shows significant speedups over MC while retaining uncertainty information.
Model based iterative reconstruction (MBIR) algorithms for low-dose X-ray CT are computationally expensive. To address this problem, we recently proposed a deep convolutional neural network (CNN) for low-dose X-ray CT and won the second place in 2016 AAPM Low-Dose CT Grand Challenge. However, some of the texture were n…
Paper develops methods to estimate derivative of dose-response curve for continuous treatments.
problem Estimating the derivative of the dose-response curve for continuous treatments.
method Doubly robust (DR) inference method using kernel smoothing, bias-corrected IPW and DR estimators.
result Proposes novel bias-corrected IPW and DR estimators for continuous treatments.
A new model improves CT image quality from low-dose scans.
problem Improving CT image quality from low-dose scans.
method Multi-layer Residual Sparsifying Transform (MRST) learning model for low-dose CT reconstruction.
result The MRST model outperforms conventional methods in maintaining subtle details.
Obtaining accurate and reliable images from low-dose computed tomography (CT) is challenging. Regression convolutional neural network (CNN) models that are learned from training data are increasingly gaining attention in low-dose CT reconstruction. This paper modifies the architecture of an iterative regression CNN, BC…
NPOD algorithm improves efficiency in estimating pharmacokinetic parameters.
problem Efficiently estimating joint distribution of model parameters in population pharmacokinetics.
method Uses gradient approach to suggest new support points, reducing evaluation time.
result Achieves similar solutions to NPAG but with significantly fewer cycles and runtime.
Controlled interventions provide the most direct source of information for learning causal effects. In particular, a dose-response curve can be learned by varying the treatment level and observing the corresponding outcomes. However, interventions can be expensive and time-consuming. Observational data, where the treat…
A new drug embedding method using hierarchical drug relations and chemical structures.
problem Learning accurate drug representations from chemical structures and hierarchies.
method Semi-supervised drug embedding using VAE in hyperbolic space.
result The method accurately places drugs in a hierarchy and predicts side-effects.
Using a Generative Adversarial Network for CT Normalization and its Impact on Radiomic Featureseess.IV
GAN normalizes CT scans for consistent radiomic feature values.
problem Variations in dose levels and slice thickness affect radiomic features sensitivity.
method Used a 3D generative adversarial network (GAN) to normalize reduced dose, thick slice images to normal dose, thinner slice images.
result GAN-based approach led to significantly smaller error in radiomic features.
Proposes estimators for complex dose-response curves using kernel methods.
problem Estimating complex dose-response curves with continuous treatments, mediators, and covariates.
method Kernel ridge regression with sequential kernel embedding technique.
result Simple estimators for mediated and time-varying dose response curves with nonasymptotic uniform rates.
Background: The problem of predicting whether a drug combination of arbitrary orders is likely to induce adverse drug reactions is considered in this manuscript. Methods: Novel kernels over drug combinations of arbitrary orders are developed within support vector machines for the prediction. Graph matching methods are …
Image denoising techniques are essential to reducing noise levels and enhancing diagnosis reliability in low-dose computed tomography (CT). Machine learning based denoising methods have shown great potential in removing the complex and spatial-variant noises in CT images. However, some residue artifacts would appear in…
Graph-augmented CNN predicts drug interactions with high accuracy.
problem Predicting drug-drug interactions (DDIs) with high accuracy.
method Combining graph CNN with an attentive pooling network to extract structural relations between drug pairs.
result Desirable performance with ROC 0.988, F1-score 0.956, and AUPR 0.986.
Selecting the right drugs for the right patients is a primary goal of precision medicine. In this manuscript, we consider the problem of cancer drug selection in a learning-to-rank framework. We have formulated the cancer drug selection problem as to accurately predicting 1). the ranking positions of sensitive drugs an…
Deep Rule Forests identifies drug-drug and drug-disease interactions causing AKI.
problem Identifying drug-drug and drug-disease interactions leading to AKI.
method Deep Rule Forests (DRF) algorithm discovering rules from multilayer tree models.
result DRF model outperforms other algorithms in prediction accuracy and interpretability.
Method bounds continuous-valued treatment effects when confounding variables are hidden.
problem Inferring causal effects of continuous treatments when hidden confounders are present.
method Novel methodology to bound average and conditional average continuous-valued treatment effects.
result Method gives tighter coverage of true dose-response curve than existing methods.
Drug-drug interactions are preventable causes of medical injuries and often result in doctor and emergency room visits. Computational techniques can be used to predict potential drug-drug interactions. We approach the drug-drug interaction prediction problem as a link prediction problem and present two novel methods fo…
CardiGraphormer: Unveiling the Power of Self-Supervised Learning in Revolutionizing Drug Discoverycs.LG
CardiGraphormer uses SSL and GNNs to improve drug discovery.
problem Challenges in drug discovery due to combinatorial chemical space and limited approved drugs.
method Combines self-supervised learning, Graph Neural Networks, and Cardinality Preserving Attention.
result Enhanced predictive performance and interpretability in drug discovery.