System automates identification of cancer drug repurposing from PubMed.
problem Manual extraction of cancer drug repurposing evidence from scientific publications is infeasible.
method NLP pipeline including querying, filtering, entity extraction, classification, and study type classification.
result Automated system extracts cancer drug repurposing evidence from PubMed abstracts.
BB-FDR boosts power and controls FDR in multi-experiment studies.
problem Analyzing large-scale, multi-experiment studies for statistical significance.
method Empirical-Bayes method using deep neural networks and black box models.
result BB-FDR outperforms competing methods in discovering significant outcomes and selecting key variables.
Generative model tailors anticancer drugs based on transcriptomic data.
problem Designing effective anticancer drugs considering genetic profiles.
method RL framework using pretrained VAEs to generate compounds conditioned on transcriptomic data.
result Generative model produces molecules with high predicted inhibitory effects.
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. New method predicts cancer drug rankings based on genomic data.
problem Selecting the right drugs for cancer patients.
method pLETORg method that predicts drug ranking structures using latent vectors.
result pLETORg significantly outperforms state-of-the-art methods in prioritizing new sensitive drugs.
Deep learning predicts synergistic drug combinations from multi-omics data.
problem Predicting effective drug combinations to overcome cancer drug resistance.
method AuDNNsynergy model integrating gene expression, copy number, genetic mutation data and drug properties.
result AuDNNsynergy model outperforms state-of-the-art approaches.
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.
Model predicts drug response in tumors using genomic profiles.
problem Challenges in translating genomic insights to tumor-specific drug response predictions.
method Deep neural network (DNN) model trained on mutation and expression profiles of cancer cell lines.
result Achieved mean squared error of 1.96 for predicting IC50 values of 265 drugs.
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…
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. Improved drug response prediction using ensemble learning and gene expression signatures.
problem Predicting chemotherapeutic response of cancer cells to drugs.
method Combining machine learning methods and drug-induced gene expression signatures for improved performance.
result Ensemble method improves drug activity prediction accuracy.
Dr.S recommends cancer drugs based on genomic data.
problem Personalizing cancer treatments using genomic information.
method Machine learning to identify optimal drug-gene associations.
result Developed a Drug Recommendation System (Dr.S) for cancer cell lines.
PDBAL targets experiments for probabilistic models to maximize insights.
problem Designing experiments to yield valuable insights efficiently.
method Combines user-specified risk function with probabilistic model to adaptively choose designs.
result PDBAL consistently outperforms standard approaches in simulations and real-world drug screen data.
Generative model designs drug combinations for improved efficacy and reduced side effects.
problem Designing effective drug combinations to overcome resistance and reduce side effects.
method Developed a deep generative model using HVGAE and a novel reward system.
result Network-principled drug combinations show reduced toxicity and potential for new strategies.
NetBiTE predicts drug sensitivity and identifies biomarkers in cancer.
problem Predicting drug sensitivity and identifying biomarkers in cancer.
method NetBiTE combines prior knowledge and gene expression data using a biased tree ensemble approach.
result NetBiTE outperforms RF in predicting IC50 drug sensitivity for drugs targeting membrane receptor pathways.
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.
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…
Improved anti-cancer drug sensitivity prediction using REFINED CNN ensemble learning.
problem Challenges in predicting anti-cancer drug sensitivity for individual cell lines.
method Using REFINED CNN, which represents high-dimensional vectors as compact 2D images with spatial correlations, and building ensembles of these models.
result Ensemble approaches significantly improve drug sensitivity prediction performance compared to single models.
Collaborative filtering predicts drug responses from gene expression data.
problem Predicting drug responses from large gene expression datasets with limited samples.
method Low-rank matrix factorization and latent linear regression.
result The proposed method outperforms state-of-the-art methods in predicting drug-gene associations.
Study improves drug synergy prediction using ensemble learning.
problem Predicting drug synergy in complex diseases.
method Investigated different compound representations and proposed an ensemble model.
result Ensemble model outperforms baseline models.
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…
Model predicts eligibility of cancer patients for clinical trials.
problem Clinical trials exclude many patients based on comorbidities and age.
method Deep neural networks trained on clinical trial protocols and free-texts.
result Model accurately predicts eligibility of clinical trial statements.
Improved differentially private drug sensitivity prediction using compact representations.
problem Challenges in differentially private machine learning with genomic data.
method Representation learning using variational autoencoders, PCA, and random projection.
result Variational autoencoders provide the most accurate predictions for differentially private drug sensitivity prediction.
Proposes a new method using GANs for testing conditional independence.
problem High-dimensional conditional independence testing in statistics and machine learning.
method Double GANs framework to learn conditional distributions, then construct a test statistic.
result The test statistic is doubly robust and has asymptotic power approaching one.
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.
Novel model predicts anticancer compound sensitivity with high accuracy and interpretability.
problem Predicting anticancer compound sensitivity with high accuracy and interpretability.
method Multimodal attention-based convolutional encoder using SMILES, gene expression profiles, and protein-protein interaction networks.
result The model significantly outperforms baseline models and demonstrates high interpretability.
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…
Omics-GAN uses GANs to generate synthetic multi-omics data for improved disease prediction.
problem Limited sample sizes, noise, and heterogeneity in multi-omics data reduce predictive power.
method Omics-GAN is a GAN-based framework that generates high-quality synthetic multi-omics profiles.
result Synthetic datasets consistently improved prediction accuracy compared to original omics profiles.
Bayesian framework for analyzing heterogeneous covariance data with a novel MoE-Wishart model.
problem Analyzing complex multivariate systems with varying covariance structures.
method Comprehensive Bayesian framework using mixture-of-experts Wishart model with predictor-dependent mixture weights.
result Accurate subpopulation recovery and estimation in heterogeneous covariance scenarios.
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.
New method uses machine learning to estimate drug parameters in brain models.
problem Estimating unknown parameters in complex brain drug models.
method Physics-Informed Neural Networks (PINNs) for inverse problem solving.
result Accurate parameter estimation leads to precise drug concentration profiles.
New DTI model using self-attention molecule representation outperforms state-of-the-art.
problem Predicting drug-target interactions to reduce costs and improve personalized medicine.
method Proposes a new molecule representation using self-attention and a new DTI model.
result Our DTI model outperforms state-of-the-art by up to 4.9% points in precision-recall.
Improves drug properties using a novel LLM and reinforcement learning.
problem Optimizing drug properties while retaining chemical stability.
method Structured Policy Optimization (SPO) for fine-tuning a large language model.
result Enhanced drug properties across multiple target objectives.
Study uses machine learning to predict heart failure in cancer patients.
problem Early detection of cancer patients at risk for cardiotoxicity.
method Examined four machine learning algorithms on 143,199 cancer patients.
result Gradient boosting model achieved best AUC score of 0.9077.
Network Elastic Net identifies smoking-specific gene expression for lung cancer prognosis.
problem Identifying smoking-specific gene expression biomarkers in lung cancer prognosis.
method Introduces Network Elastic Net, a method that clusters and regresses on graphs based on smoking behavior.
result Shows efficacy of clusters in identifying cancer stages using gene expression and smoking behavior.
Motivation: Driver (epi)genomic alterations underlie the positive selection of cancer subpopulations, which promotes drug resistance and relapse. Even though substantial heterogeneity is witnessed in most cancer types, mutation accumulation patterns can be regularly found and can be exploited to reconstruct predictive …
MuLFA predicts drug interactions more accurately than existing methods.
problem Improving drug safety by predicting drug interactions.
method Proposes MuLFA, a factorization autoencoder that models nonlinear interactions between drug pairs.
result MuLFA outperforms state-of-the-art methods in predicting drug interactions.
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.
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.
A new method learns graph-level features for drug properties predication.
problem Predicting drug efficacy and toxicity from molecular graphs.
method Introducing a dummy super node connected to all nodes and modifying graph operations to learn graph-level features.
result The method improves molecular properties predication performance on MoleculeNet.
Machine learning predicts biologic therapy outcomes in psoriasis patients.
problem Predicting long-term biologic therapy outcomes in psoriasis patients.
method Machine learning algorithms were used to predict drug discontinuation and treatment duration.
result Machine learning models accurately predict outcomes with high diagnostic accuracy and low MAE.
Personalized treatment of patients based on tissue-specific cancer subtypes has strongly increased the efficacy of the chosen therapies. Even though the amount of data measured for cancer patients has increased over the last years, most cancer subtypes are still diagnosed based on individual data sources (e.g. gene exp…
Paper predicts medication non-adherence in cancer patients using ML.
problem Predicting and understanding medication non-adherence in cancer patients.
method Developed ML models to predict non-adherence, fine-tuned by oncologists.
result Improved support for cancer patients through ML risk scores.
New algorithms find all ε-good arms in stochastic bandits.
problem Finding all arms with means above a specified threshold in stochastic bandits.
method Two algorithms introduced to identify all ε-good arms.
result Demonstrated great empirical performance on large datasets.
Machine learning models improve cancer type classification accuracy.
problem Early and accurate cancer diagnosis is challenging due to high costs and biological marker limitations.
method Assessed five machine learning algorithms for 17 cancer types using RNA-seq data.
result Ensemble algorithms achieve 100% accuracy in 14 out of 17 cancer types.
AI detects oral pre-cancerous lesions with high accuracy.
problem Manual screening of oral cavity cancer is expensive and lacks specialists.
method Deep convolutional neural networks (DCNNs) using transfer learning.
result DCNN models achieve high accuracy in distinguishing between benign and pre-cancerous tongue lesions.
A novel feature representation method for non-image based features.
problem Inability of Convolutional Neural Networks for non-image based features or features without spatial correlations.
method REFINED: Representation of Features as Images with Neighborhood Dependencies.
result Higher prediction accuracy compared to existing methodologies.
ERP improves drug discovery by balancing molecule generation quality and efficiency.
problem Generating valid and optimal molecules from large language models.
method Entropy-Reinforced Planning (ERP) for Transformer Decoding.
result ERP outperforms current state-of-the-art algorithms by 1-5 percent on SARS-CoV-2 and human cancer cell targets.