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.
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.
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.
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.
New methods predict drug interactions using drug co-medication patterns and graph matching.
problem Predicting adverse drug reactions from drug combinations.
method Developed novel kernels over drug combinations using support vector machines and graph matching to measure similarities.
result Achieved an AUC of 0.912 on a real-world dataset.
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.
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.
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.
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.
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 …
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.
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.
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.
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. Novel GNN predicts drug-target interactions using protein-ligand 3D structures.
problem Accurate prediction of drug-target interactions for in silico drug design.
method 3D structure-embedded graph representations and distance-aware graph attention algorithm with gate augmentation.
result Our model outperforms docking and other deep learning methods in virtual screening and pose prediction.
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.
The task of drug-target interaction prediction holds significant importance in pharmacology and therapeutic drug design. In this paper, we present FRnet-DTI, an auto encoder and a convolutional classifier for feature manipulation and drug target interaction prediction. Two convolutional neural neworks are proposed wher…
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.
The use of drug combinations, termed polypharmacy, is common to treat patients with complex diseases and co-existing conditions. However, a major consequence of polypharmacy is a much higher risk of adverse side effects for the patient. Polypharmacy side effects emerge because of drug-drug interactions, in which activi…
HiGraphDTI learns drug and target representations from molecular graphs to predict DTIs.
problem Inaccurate drug-target interaction prediction due to insufficient chemical information extraction.
method Hierarchical graph representation learning to extract chemical information from atoms, motifs, and molecules.
result HiGraphDTI outperforms state-of-the-art methods in DTI prediction and interaction interpretation.
Interactive learning framework for various settings.
problem Various interactive learning settings.
method Adapted active learning algorithm for interactive structure discovery.
result Noise-tolerant algorithm with favorable query complexity.
New method improves graph neural networks by considering different types of relations in sampling.
problem Current graph neural networks ignore relation types in biomedical graphs, leading to suboptimal performance.
method Proposes relation-dependent sampling for multi-relational graphs to balance relation frequency and importance.
result State-of-the-art graph neural networks achieve better accuracy and efficiency with relation-dependent sampling.
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 identification of novel drug-target (DT) interactions is a substantial part of the drug discovery process. Most of the computational methods that have been proposed to predict DT interactions have focused on binary classification, where the goal is to determine whether a DT pair interacts or not. However, protein-l…
DeepPurpose simplifies DL for DTI prediction.
problem Accurate prediction of drug-target interactions.
method Comprehensive deep learning library with 15 compound and protein encoders and 50 neural architectures.
result State-of-the-art performance on benchmark datasets.
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.
ISAAC audits deep models for drug-target interactions, revealing structural differences.
problem Deep models for DTI often use irrelevant features, making them hard to evaluate.
method ISAAC uses intervention-based structural auditing to evaluate model sensitivity.
result ISAAC reveals significant structural differences in DTI models' reasoning.
Predict drug-drug side effects using co-attention neural network.
problem Early detection of polypharmacy side effects in drug combinations.
method Co-attention neural network architecture for DDI prediction.
result State-of-the-art results on predicting side effects from drug types and structures.
The occurrence of drug-drug-interactions (DDI) from multiple drug dispensations is a serious problem, both for individuals and health-care systems, since patients with complications due to DDI are likely to reenter the system at a costlier level. We present a large-scale longitudinal study (18 months) of the DDI phenom…
Background. Drug-drug interaction (DDI) is a major cause of morbidity and mortality. [...] Biomedical literature mining can aid DDI research by extracting relevant DDI signals from either the published literature or large clinical databases. However, though drug interaction is an ideal area for translational research, …
In silico drug-target interaction (DTI) prediction is an important and challenging problem in biomedical research with a huge potential benefit to the pharmaceutical industry and patients. Most existing methods for DTI prediction including deep learning models generally have binary endpoints, which could be an oversimp…
Much recent research aims to identify evidence for Drug-Drug Interactions (DDI) and Adverse Drug reactions (ADR) from the biomedical scientific literature. In addition to this "Bibliome", the universe of social media provides a very promising source of large-scale data that can help identify DDI and ADR in ways that ha…
In this study, we intend to solve a mutual information problem in interacting molecules of any type, such as proteins, nucleic acids, and small molecules. Using machine learning techniques, we accurately predict pairwise interactions, which can be of medical and biological importance. Graphs are are useful in this prob…
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.
NucleusDiff models atomic nuclei interactions to prevent separation violations in drug design.
problem Maintaining minimum pairwise distance between atoms to avoid separation violations in drug design.
method Enforces distance constraint between atomic nuclei and manifolds in a diffusion model.
result Reduces separation violations by up to 100.00% and enhances binding affinity by up to 22.16%.
Recent progress in deep learning is revolutionizing the healthcare domain including providing solutions to medication recommendations, especially recommending medication combination for patients with complex health conditions. Existing approaches either do not customize based on patient health history, or ignore existi…
The understanding of the type of inhibitory interaction plays an important role in drug design. Therefore, researchers are interested to know whether a drug has competitive or non-competitive interaction to particular protein targets. Method: to analyze the interaction types we propose factorization method Macau which …
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.
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. 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…
Drug-drug interaction (DDI) is a major cause of morbidity and mortality and a subject of intense scientific interest. Biomedical literature mining can aid DDI research by extracting evidence for large numbers of potential interactions from published literature and clinical databases. Though DDI is investigated in domai…
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.
Drug similarity has been studied to support downstream clinical tasks such as inferring novel properties of drugs (e.g. side effects, indications, interactions) from known properties. The growing availability of new types of drug features brings the opportunity of learning a more comprehensive and accurate drug similar…
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.
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.
A fast algorithm speeds up training of pairwise kernels.
problem Training pairwise kernels efficiently for large datasets.
method Generalized vec trick for Kronecker product kernels.
result Pairwise kernels can be expressed as sums of Kronecker products.
Improved drug-protein interaction prediction using FTL method.
problem Predicting drug-protein interactions from noisy data with uncertain labels.
method Filtered Transfer Learning (FTL) method that fine-tunes a deep neural network across multiple tiers of data confidence.
result FTL method outperforms deep neural networks trained on single confidence ranges.