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.
hyperSBINN improves drug cardiosafety assessment by efficiently modeling cardiac action potentials.
problem Complexity and limited data in modeling cardiac effects of drugs.
method Combining meta-learning with SBINNs to solve parameterized cardiac action potential models.
result hyperSBINN outperforms traditional solvers in speed and accuracy for predicting APD90 values.
RAMBO optimizes multi-regime problems by discovering and modeling distinct energy basins.
problem Multi-regime problems in molecular conformation and drug discovery.
method Dirichlet Process Mixture of Gaussian Processes with adaptive hyperparameters and concentration parameters.
result Consistent improvements over state-of-the-art on multi-regime objectives.
The paper clusters PK curves using ML, finding it useful for identifying similar patterns.
problem Improving drug development and patient outcomes through ML in pharmacogenomics.
method Unsupervised clustering of PK curves using various dissimilarity measures.
result Euclidean distance is most suitable for clustering PK curves, and clustering can validate pharmacogenomic results.
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.
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 …
New method predicts drug interactions from drug images.
problem Predicting drug interactions from molecular structures.
method Siamese neural network using drug structure images.
result First work predicting DDIs from drug images.
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.
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 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.
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.
Text classification on drug SMILES strings yields competitive drug type classification results.
problem Classifying drug types using conventional text classification methods.
method Treated drug SMILES as sentences and applied basic NLP methods for classification.
result Competitive drug type classification results achieved.
We present the Network-based Biased Tree Ensembles (NetBiTE) method for drug sensitivity prediction and drug sensitivity biomarker identification in cancer using a combination of prior knowledge and gene expression data. Our devised method consists of a biased tree ensemble that is built according to a probabilistic bi…
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.
Computational Drug Repositioning (CDR) is the task of discovering potential new indications for existing drugs by mining large-scale heterogeneous drug-related data sources. Leveraging the patient-level temporal ordering information between numeric physiological measurements and various drug prescriptions provided in E…
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.
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.
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.
STNN-DDI predicts drug interactions using substructure-aware neural networks.
problem Predicting drug-drug interactions (DDIs) to avoid side effects in poly-drug treatments.
method Designing a novel Substructure-ware Tensor Neural Network (STNN-DDI) that learns a 3-D tensor of substructure-substructure interactions.
result Significant improvement in AUC, AUPR, Accuracy, and Precision compared to state-of-the-art models.
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.
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.
Drug resistance is still a major challenge in cancer therapy. Drug combination is expected to overcome drug resistance. However, the number of possible drug combinations is enormous, and thus it is infeasible to experimentally screen all effective drug combinations considering the limited resources. Therefore, computat…
Drug-drug interactions (DDIs) are a major cause of preventable hospitalizations and deaths. Predicting the occurrence of DDIs helps drug safety professionals allocate investigative resources and take appropriate regulatory action promptly. Traditional DDI prediction methods predict DDIs based on the similarity between …
Designing a new drug is a lengthy and expensive process. As the space of potential molecules is very large (10^23-10^60), a common technique during drug discovery is to start from a molecule which already has some of the desired properties. An interdisciplinary team of scientists generates hypothesis about the required…
CASTER predicts drug interactions using chemical substructures.
problem Identifying potential drug-drug interactions during drug design.
method CASTER uses sequential pattern mining, auto-encoding, and dictionary learning to predict DDIs.
result CASTER outperformed state-of-the-art models and provided interpretable predictions.
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.
Paper proposes a new method for predicting drug interactions using adversarial autoencoders.
problem Predicting drug interactions to prevent adverse events.
method Introduces adversarial autoencoders based on Wasserstein distances and Gumbel-Softmax relaxation to generate high-quality negative samples.
result Significant improvements in link prediction and DDI classification tasks.
Survey on risk-aware multi-armed bandits for better decision-making.
problem Risk measures in multi-armed bandits for better decision-making.
method Review of existing research, definition of risk-aware bandit problems, and algorithms for minimizing regret and identifying best arms.
result Consolidation and summarization of existing research on risk measures in multi-armed bandits.
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 …
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. Paper proposes an inductive RGCN for few-shot link prediction in drug-repurposing.
problem Predicting rare interactions in drug-repurposing for novel diseases.
method Proposes an inductive RGCN to learn relation embeddings for few-shot learning.
result Significantly outperforms state-of-the-art models in few-shot learning tasks.
GEFA predicts drug-target affinity using graph neural networks.
problem Accurate prediction of drug-target interactions for rapid drug repurposing.
method GEFA (Graph Early Fusion Affinity) is a novel graph-in-graph neural network with attention mechanism.
result GEFA effectively models drug-target interactions, demonstrating the effectiveness of pre-trained protein embedding and nested graph representation.
The biological processes involved in a drug's mechanisms of action are oftentimes dynamic, complex and difficult to discern. Time-course gene expression data is a rich source of information that can be used to unravel these complex processes, identify biomarkers of drug sensitivity and predict the response to a drug. H…
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.
Proposes a self-attention-based method for drug-target interaction prediction.
problem Interpreting machine learning models for drug-target interactions.
method Self-attention-based multi-view representation learning approach.
result Competitive prediction performance with biologically interpretable results.
Visualizes deep generative models for drug design.
problem Limited visualization tools for deep generative models in drug discovery.
method Proposes a visualization framework for deep graph generative models.
result Interactive visualization and molecular optimization tools.
Understanding the phenotypic drug response on cancer cell lines plays a vital rule in anti-cancer drug discovery and re-purposing. The Genomics of Drug Sensitivity in Cancer (GDSC) database provides open data for researchers in phenotypic screening to test their models and methods. Previously, most research in these ar…
Deep learning predicts drug side-effects from molecular graphs.
problem Predicting drug side-effects from molecular structures.
method Recurrent Graph Neural Networks for multi-class multi-label graph-focused classification.
result Improved classification capability compared to previous methods.
Proposes a multi-view architecture for drug-target interaction prediction.
problem Representing compound-target pairs in deep learning models.
method Integrates differentiable and predefined molecular descriptors using an adversarial multi-view architecture.
result Demonstrates potential of the proposed approach on clinically relevant datasets.
Complex or co-existing diseases are commonly treated using drug combinations, which can lead to higher risk of adverse side effects. The detection of polypharmacy side effects is usually done in Phase IV clinical trials, but there are still plenty which remain undiscovered when the drugs are put on the market. Such acc…
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.
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…
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…
TIP model improves POSE prediction with less resources.
problem Predicting polypharmacy side effects from drug-protein interactions.
method TIP model operates on three subgraphs for progressive representation learning.
result Improves accuracy by 7%+, time efficiency by 83imes, and space efficiency by 3imes. 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.