A locally-built, LLM-digested index of recent arXiv papers in quant finance, geometry/topology, and statistical ML — keyword search served straight from SQLite on this machine.
A new drug embedding method using hierarchical drug relations and chemical structures.
HiGraphDTI learns drug and target representations from molecular graphs to predict DTIs.
Improved drug-protein interaction prediction using FTL method.
Bi-GNN models drug interactions using a bi-level graph approach.
New method improves graph neural networks by considering different types of relations in sampling.
Drug-Drug Interactions (DDIs) Extraction refers to the efforts to generate hand-made or automatic tools to extract embedded information from text and literature in the biomedical domain. Because of restrictions in hand-made efforts and their lower speed, Machine-Learning, or Deep-Learning approaches have become more po…
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 …
Method learns drug-disease representations for repositioning opportunities.
Generative model designs drug combinations for improved efficacy and reduced side effects.
Graph-augmented CNN predicts drug interactions with high accuracy.
Deep convolutional neural networks comprise a subclass of deep neural networks (DNN) with a constrained architecture that leverages the spatial and temporal structure of the domain they model. Convolutional networks achieve the best predictive performance in areas such as speech and image recognition by hierarchically …
Opioid overdose rates have reached an epidemic level and state-level policy innovations have followed suit in an effort to prevent overdose deaths. State-level drug law is a set of policies that may reinforce or undermine each other, and analysts have a limited set of tools for handling the policy collinearity using st…
Paper proposes an inductive RGCN for few-shot link prediction in drug-repurposing.
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…
Text classification on drug SMILES strings yields competitive drug type classification results.
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…
A model learns symptom-drug relations for PD patients.
Improved 3D generative models for drug design reduce bias and enhance data efficiency.
Learning from small data sets is critical in many practical applications where data collection is time consuming or expensive, e.g., robotics, animal experiments or drug design. Meta learning is one way to increase the data efficiency of learning algorithms by generalizing learned concepts from a set of training tasks …
Deep learning predicts drug side-effects from molecular graphs.
Architectures for sparse hierarchical representation learning have recently been proposed for graph-structured data, but so far assume the absence of edge features in the graph. We close this gap and propose a method to pool graphs with edge features, inspired by the hierarchical nature of chemistry. In particular, we …
Multi-output Gaussian processes (GPs) are a flexible Bayesian nonparametric framework that has proven useful in jointly modeling the physiological states of patients in medical time series data. However, capturing the short-term effects of drugs and therapeutic interventions on patient physiological state remains chall…
Drug repositioning is an attractive cost-efficient strategy for the development of treatments for human diseases. Here, we propose an interpretable model that learns disease self-representations for drug repositioning. Our self-representation model represents each disease as a linear combination of a few other diseases…
A new model designs molecular latent vectors for drug discovery.
The polypharmacy side effect prediction problem considers cases in which two drugs taken individually do not result in a particular side effect; however, when the two drugs are taken in combination, the side effect manifests. In this work, we demonstrate that multi-relational knowledge graph completion achieves state-o…
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…
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…
DESMILES uses deep learning to improve drug discovery by optimizing molecule properties.
New neural network predicts accurate protein complex structures.
GEN tackles few-shot out-of-graph link prediction in evolving multi-relational graphs.
Paper tackles multi-task learning for molecular property prediction with limited data.
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 …
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.
New method uses spectral geometry to improve matrix completion with geometric relations.
GeneDisco benchmarks experimental design for drug discovery.
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…
CSLVAE generates large chemical libraries efficiently.
CardiGraphormer uses SSL and GNNs to improve drug discovery.
RobKMR improves robustness in multi-omics data analysis for osteoporosis biomarker discovery.
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…
Hierarchical NMF organizes COVID-19 literature into a searchable tree.
HIRM models noisy, sparse, heterogeneous relational data using hierarchical clustering and Dirichlet processes.
Framework designs antiviral drugs using deep learning and RL.
Predicting and discovering drug-drug interactions (DDIs) is an important problem and has been studied extensively both from medical and machine learning point of view. Almost all of the machine learning approaches have focused on text data or textual representation of the structural data of drugs. We present the first …
Dr.S recommends cancer drugs based on genomic data.
A neural network predicts drug interactions using attention mechanisms.
STNN-DDI predicts drug interactions using substructure-aware neural networks.