Model predicts anti-cancer drug responses using gene and molecular data.
problem Expensive and time-consuming cancer drug discovery and tailoring.
method Uses variational autoencoders and multi-layer perceptrons to encode gene expression and drug data.
result High average R2 of 0.83 and 0.845 in predicting drug responses for breast and pan-cancer cell lines, respectively. Bayesian model for cancer drug studies maps dose-response curves.
problem Mapping dose-response curves in cancer drug studies.
method Bayesian Tensor Filtering (BTF) with low-dimensional embeddings and structured shrinkage priors.
result BTF outperforms state-of-the-art methods in cancer drug studies.
A key goal of computational personalized medicine is to systematically utilize genomic and other molecular features of samples to predict drug responses for a previously unseen sample. Such predictions are valuable for developing hypotheses for selecting therapies tailored for individual patients. This is especially va…
We present two deep generative models based on Variational Autoencoders to improve the accuracy of drug response prediction. Our models, Perturbation Variational Autoencoder and its semi-supervised extension, Drug Response Variational Autoencoder (Dr.VAE), learn latent representation of the underlying gene states befor…
The study of high-throughput genomic profiles from a pharmacogenomics viewpoint has provided unprecedented insights into the oncogenic features modulating drug response. A recent screening of ~1,000 cancer cell lines to a collection of anti-cancer drugs illuminated the link between genotypes and vulnerability. However,…
Motivation: Analysis of relationships of drug structure to biological response is key to understanding off-target and unexpected drug effects, and for developing hypotheses on how to tailor drug thera-pies. New methods are required for integrated analyses of a large number of chemical features of drugs against the corr…
REP predicts drug response at every stage of treatment using time-course gene expression data.
problem Lack of dynamic drug response prediction from time-course gene expression data.
method REP framework that predicts drug response values at every stage of a long-term treatment using recursive structure and tensor completion.
result REP can estimate drug response at any stage of a given treatment from initial gene expression levels.
Personalized time series models improve drug response prediction.
problem Fitting time series models to cohorts ignoring individual variation.
method Multi-task learning applied to time series data with and without control inputs.
result Improved predictive accuracy and uncertainty estimation.
ChemCPA predicts cellular responses to novel drugs using transfer learning.
problem Scaling high-throughput screens to measure cellular responses for many drugs is costly and challenging.
method ChemCPA, a new encoder-decoder architecture combined with transfer learning.
result Training on existing bulk RNA HTS datasets improves generalization performance, reducing the need for extensive single-cell screens.
Predicting the response of cancer cells to drugs is an important problem in pharmacogenomics. Recent efforts in generation of large scale datasets profiling gene expression and drug sensitivity in cell lines have provided a unique opportunity to study this problem. However, one major challenge is the small number of sa…
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…
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.
Chemotherapeutic response of cancer cells to a given compound is one of the most fundamental information one requires to design anti-cancer drugs. Recent advances in producing large drug screens against cancer cell lines provided an opportunity to apply machine learning methods for this purpose. In addition to cytotoxi…
Paper introduces tCNNS model for predicting drug cell line interactions.
problem Predicting phenotypic drug responses on cancer cell lines.
method tCNNS model using SMILES format for drugs and cancer cell lines.
result Achieves 0.84 for R2 and 0.92 for Rp. A new model uses GPs and latent force models to predict patient responses to drugs.
problem Challenges in modeling short-term effects of drugs on patient physiology.
method Hybrid Gaussian process with latent force model for joint modeling of patient physiology and drug effects.
result The model accurately predicts patient responses to three common drugs, showing competitive performance.
Classifying chemicals according to putative modes of action (MOAs) is of paramount importance in the context of risk assessment. However, current methods are only able to handle a very small proportion of the existing chemicals. We address this issue by proposing an integrative deep learning architecture that learns a …
PKB framework boosts genomic data analysis by integrating pathway knowledge.
problem Boosting discovery power and connecting new findings with biological mechanisms in genomic data.
method Pathway-based Kernel Boosting (PKB) framework integrating clinical and pathway information for prediction of various outcomes.
result PKB substantially outperforms other methods in predicting drug response and cancer survival.
Proposes a method to estimate drug sensitivity uncertainty using deep regression forests.
problem Lack of confidence intervals in deep learning models for critical tasks.
method Uses Deep Regression Forests to estimate variance and uncertainty for drug sensitivity prediction.
result Improves efficiency and coverage of uncertainty estimates for drug sensitivity predictions.
Automated scoring engines are increasingly being used to score the free-form text responses that students give to questions. Such engines are not designed to appropriately deal with responses that a human reader would find alarming such as those that indicate an intention to self-harm or harm others, responses that all…
Deep neural networks (DNNs) achieve state-of-the-art results in a variety of domains. Unfortunately, DNNs are notorious for their non-interpretability, and thus limit their applicability in hypothesis-driven domains such as biology and healthcare. Moreover, in the resource-constraint setting, it is critical to design t…
Generative model learns to create molecules with multiple properties using interpretable substructures.
problem Creating molecules with multiple chemical properties is challenging.
method Compose molecules from substructures identified as responsible for each property, using graph generative models.
result Significant improvements in accuracy, diversity, and novelty of generated compounds over state-of-the-art baselines.
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.
Enhances high-throughput imaging of microtubule networks, improving clarity and consistency.
problem Fluorescence noise obscures microtubule structures in high-throughput imaging.
method CycleGAN learning to enhance low-resolution images of microtubule networks.
result CycleGAN effectively identifies microtubules with high accuracy (0.93+ AUC-ROC).
Model predicts HU response for sickle cell patients.
problem Predicting which sickle cell patients will respond to Hydroxyurea.
method Developed Deep Artificial Neural Network models.
result 92.6% accuracy in predicting HbF response.
Novel framework predicts cell responses to perturbations using GRNs.
problem Predicting cellular responses to perturbations for drug discovery and personalized therapeutics.
method Graph variational Bayesian causal inference framework with refined GRNs and robust estimator.
result Enhanced model performance and robust estimation of perturbation effects.
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.
The vast majority of current machine learning algorithms are designed to predict single responses or a vector of responses, yet many types of response are more naturally organized as matrices or higher-order tensor objects where characteristics are shared across modes. We present a new machine learning algorithm BaTFLE…
Statistical detection of a rare class of objects in a two-class classification problem can pose several challenges. Because the class of interest is rare in the training data, there is relatively little information in the known class response labels for model building. At the same time the available explanatory variabl…
We describe two recently proposed machine learning approaches for discovering emerging trends in fatal accidental drug overdoses. The Gaussian Process Subset Scan enables early detection of emerging patterns in spatio-temporal data, accounting for both the non-iid nature of the data and the fact that detecting subtle p…
Improved antibody humanness prediction using patent data.
problem Predicting the immunogenic response of antibody therapeutics.
method Multi-stage, multi-loss training process with contrastive learning and cross-entropy loss.
result The model outperforms baselines on five out of six inference tasks, improving humanness prediction.
ASD algorithm maximizes model estimates by adaptively labeling points.
problem Maximizing model estimates through adaptive labeling of points in a sequential decision-making problem.
method Formulated a general information-directed sampling (IDS) algorithm with theoretical guarantees for linear, graph, and low-rank models.
result IDS algorithm outperforms in both simulation and real-data experiments for discovering chemical reaction conditions.
GENOT matches cells across data modalities using neural OT solvers.
problem Scalability, privacy, and out-of-sample estimation issues in traditional OT solvers.
method Learn stochastic maps, parameterize OT maps, relax mass conservation, integrate quadratic solvers.
result Demonstrates significant potential for enhancing therapeutic strategies.
Combines RFs and GLMs for better accuracy and interpretable feature importance.
problem Inability to interpret random forests (RFs) due to black box nature and unstable feature importance methods.
method Reinterprets decision trees and MDI as linear regression and R² values, combining RFs and GLMs in RF+.
result MDI+ outperforms existing feature importance measures in identifying signal features and stability.
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…
The goal of personalized decision making is to map a unit's characteristics to an action tailored to maximize the expected outcome for that unit. Obtaining high-quality mappings of this type is the goal of the dynamic regime literature. In healthcare settings, optimizing policies with respect to a particular causal pat…
Accurately predicting drug responses to cancer is an important problem hindering oncologists' efforts to find the most effective drugs to treat cancer, which is a core goal in precision medicine. The scientific community has focused on improving this prediction based on genomic, epigenomic, and proteomic datasets measu…
Robust Conformalized Selection controls FDR under noisy responses.
problem Existing conformal selection methods fail to control FDR under contaminated calibration data.
method RCS framework for selective classification with valid FDR control under label contamination.
result RCS framework controls FDR and maintains power under contaminated calibration data.
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.
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.
Automated digital twin discovery from biological data improves drug discovery and personalized medicine.
problem Developing reliable digital twins from noisy, incomplete biological data.
method Symbolic and sparse regression, Bayesian frameworks, deep learning, and large language models.
result Sparse regression generally outperforms symbolic regression, especially with Bayesian frameworks.
Models predict drug interactions with high accuracy.
problem Detecting drug-drug interactions to prevent medical injuries.
method Artificial neural networks and graph similarity measures.
result Models achieve high accuracy in predicting drug interactions.
Gonogo offers tools for sensitivity experiments in R.
problem Conducting, analyzing, and simulating sensitivity experiments.
method Suite of R functions for various adaptive procedures.
result Achieving overlapping data and refining testing in distribution tails.
Estimation of individual treatment effect in observational data is complicated due to the challenges of confounding and selection bias. A useful inferential framework to address this is the counterfactual (potential outcomes) model which takes the hypothetical stance of asking what if an individual had received both tr…
Method learns drug-disease representations for repositioning opportunities.
problem Identifying new uses for existing drugs.
method Multi-relation unsupervised graph embedding model.
result Superior prediction performance in repositioning opportunities.
Bi-GNN models drug interactions using a bi-level graph approach.
problem Predicting drug-drug interactions using machine learning.
method Bi-level graph neural networks that consider both interaction graph and representation graphs of drugs.
result Bi-GNN model improves DDI prediction accuracy compared to existing methods.
GENN predicts drug interactions by modeling correlations between link labels.
problem Predicting drug-drug interactions with consideration of link type correlations.
method GENN uses graph energy neural networks to model link type correlations in DDI prediction.
result GENN outperforms baseline models by 13.77% and 5.01% in PR-AUC on two real-world datasets.
HAMN combines CF models to improve drug repositioning.
problem Efficient drug repositioning with cold start problem.
method Hybrid Attentional Memory Network (HAMN) integrating memory and attention mechanisms.
result HAMN outperforms other models in drug repositioning tasks.
A neural network predicts drug interactions using attention mechanisms.
problem Predicting drug-drug interactions from massive combinations of drugs.
method Siamese self-attention multi-modal neural network integrating drug characteristics.
result The model achieves AUPR scores ranging from 0.77 to 0.92 on various benchmark datasets.