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 neural network predicts drug interactions using attention mechanisms.
HiGraphDTI learns drug and target representations from molecular graphs to predict DTIs.
GEFA predicts drug-target affinity using graph neural networks.
STNN-DDI predicts drug interactions using substructure-aware neural networks.
HAMN combines CF models to improve drug repositioning.
Method learns drug-disease representations for repositioning opportunities.
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…
We study the problem of detecting adverse drug events in electronic healthcare records. The challenge in this work is to aggregate heterogeneous data types involving diagnosis codes, drug codes, as well as lab measurements. An earlier framework proposed for the same problem demonstrated promising predictive performance…
CASTER predicts drug interactions using chemical substructures.
Generative Intervention Models predict perturbation effects without knowing the underlying mechanisms.
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, …
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…
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…
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…
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…
Predicting drug-target interactions (DTI) is an essential part of the drug discovery process, which is an expensive process in terms of time and cost. Therefore, reducing DTI cost could lead to reduced healthcare costs for a patient. In addition, a precisely learned molecule representation in a DTI model could contribu…
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,…
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…
New disease drug trials use ML to predict best therapy.
Model predicts VKA dosage for Indian patients, aiding in safe medication.
GeneDisco benchmarks experimental design for drug discovery.
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…
Deep filtering improves robustness of models from noisy, sparse data.
Currently, approximately 30% of epileptic patients treated with antiepileptic drugs (AEDs) remain resistant to treatment (known as refractory patients). This project seeks to understand the underlying similarities in refractory patients vs. other epileptic patients, identify features contributing to drug resistance acr…
A new drug embedding method using hierarchical drug relations and chemical structures.
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.
Graph-augmented CNN predicts drug interactions with high accuracy.
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.
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.
Text classification on drug SMILES strings yields competitive drug type classification results.
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.
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…
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…
Dr.S recommends cancer drugs based on genomic data.
Network medicine predicts repurposable drugs for COVID-19.
MAT uses attention mechanism for molecule property prediction.
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…
Generative model designs drug combinations for improved efficacy and reduced side effects.
Paper proposes a new method for predicting drug interactions using adversarial autoencoders.
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.
Paper proposes an inductive RGCN for few-shot link prediction in drug-repurposing.
Improves drug properties using a novel LLM and reinforcement learning.