With the rapid development of high-throughput technologies, parallel acquisition of large-scale drug-informatics data provides huge opportunities to improve pharmaceutical research and development. One significant application is the purpose prediction of small molecule compounds, aiming to specify therapeutic propertie…
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48 results for “Therapeutic Drugs”
Study repurposes open data to find potential COVID-19 drugs.
problem Developing effective treatments for COVID-19.
method Deep learning network-based approach using large scientific corpus.
result Identified 41 repurposable drugs for COVID-19.
Machine learning identifies potential drugs for COVID-19.
problem Finding effective treatments for COVID-19.
method Trained neural network models on virus protein sequences and antiviral drugs.
result Identified potential drug candidates for treating COVID-19.
FREED++: Improving RL Agents for Fragment-Based Molecule Generation by Thorough Reproductionq-bio.BM
Improved RL model for fragment-based molecule generation.
problem Generating molecules with high docking scores.
method Thorough reproduction, scrutiny, and improvement of the FREED model.
result The improved model produces molecules with superior docking scores.
Manifold-Constrained Nucleus-Level Denoising Diffusion Model for Structure-Based Drug Designq-bio.QM
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%.
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…
More than 200 generic drugs approved by the U.S. Food and Drug Administration for non-cancer indications have shown promise for treating cancer. Due to their long history of safe patient use, low cost, and widespread availability, repurposing of generic drugs represents a major opportunity to rapidly improve outcomes f…
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.
Model predicts VKA dosage for Indian patients, aiding in safe medication.
problem Safe and accurate dosing of VKA drugs for Indian patients.
method Support Vector Machine (SVM) Regression model trained on patient data.
result Predicted dosages closely match actual dosages.
Optimal algorithm selects biological models without prior info.
problem Determining the correct biological model without prior knowledge.
method Systems biology models and likelihood-free inference.
result Improved model selection performance over conventional methods.
New models suggest molecules that are often unfeasible to synthesize.
problem Models suggest molecules that are difficult to synthesize.
method Used a computer-aided synthesis planning program to analyze synthesizability of molecules generated by state-of-the-art models.
result State-of-the-art models generate molecules that are often unfeasible to synthesize.
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,…
Drug Discovery under Covariate Shift with Domain-Informed Prior Distributions over Functionsq-bio.BM
Q-SAVI model improves drug discovery accuracy with prior knowledge of chemical space.
problem Challenges in drug discovery due to covariate shift and limited labeled data.
method Probabilistic model with domain-informed prior distributions over functions.
result Q-SAVI outperforms state-of-the-art techniques in predictive accuracy and calibration.
Study improves neural network calibration for drug discovery.
problem Improper calibration of neural network predictions in drug discovery.
method Compared different metrics for model hyperparameter tuning and proposed Bayesian Linear Probing (BLP) method.
result Bayesian Linear Probing (BLP) improves model calibration and accuracy.
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…
Framework designs antiviral drugs using deep learning and RL.
problem Designing effective antiviral drugs for SARS-CoV-2.
method Deep learning framework with conditional molecular generator and RL.
result Framework generates more antiviral ligands than a VAE baseline.
CGD improves diffusion models' out-of-distribution generalization.
problem Reliable sampling from high-value regions beyond training data.
method Context-guided diffusion (CGD) using unlabeled data and smoothness constraints.
result Substantial performance gains across various diffusion processes.
AI in Pharma for Personalized Sequential Decision-Making: Methods, Applications and Opportunitiesstat.ME
AI enhances personalized drug development and decision-making in pharma.
problem Traditional drug development lacks personalized treatment plans.
method Application of AI in drug discovery, clinical trials, and post-marketing assessment.
result AI improves personalized medicine, optimizing health outcomes.
New methods use RL and DA to improve dosing precision and reduce side effects.
problem Improving precision and safety of anticancer drug dosing.
method Bayesian data assimilation and reinforcement learning.
result Significantly reduces incidence of severe side effects.
Automated digital twin discovery from biological data improves drug discovery and personalized medicine.
problem Developing reliable digital twins from noisy, incomplete biological data.
method Symbolic and sparse regression, Bayesian frameworks, deep learning, and large language models.
result Sparse regression generally outperforms symbolic regression, especially with Bayesian frameworks.
An efficient graph generative model for navigating ultra-large combinatorial synthesis librariesq-bio.QM
CSLVAE generates large chemical libraries efficiently.
problem Navigating ultra-large combinatorial synthesis libraries.
method Hierarchically-organized database with molecular encoder and decoder.
result Generates valid molecular graphs without autoregression.
Schizophrenia, a mental disorder that is characterized by abnormal social behavior and failure to distinguish one's own thoughts and ideas from reality, has been associated with structural abnormalities in the architecture of functional brain networks. Using various methods from network analysis, we examine the effect …
Improved antibody humanness prediction using patent data.
problem Predicting the immunogenic response of antibody therapeutics.
method Multi-stage, multi-loss training process with contrastive learning and cross-entropy loss.
result The model outperforms baselines on five out of six inference tasks, improving humanness prediction.
EGR refines and assesses protein complex structures.
problem Improving the accuracy of protein complex 3D structures for drug discovery.
method E(3)-equivariant graph neural network (GNN) for multi-task refinement and assessment.
result EGR achieves state-of-the-art performance in refining and assessing protein complexes.
Given the crucial role of microtubules for cell survival, many researchers have found success using microtubule-targeting agents in the search for effective cancer therapeutics. Understanding microtubule responses to targeted interventions requires that the microtubule network within cells can be consistently observed …
BioBO optimizes gene perturbation design using Bayesian optimization with biological priors.
problem Efficient design of genomic perturbation experiments in drug discovery.
method Integrates Bayesian optimization with multimodal gene embeddings and enrichment analysis.
result Improves labeling efficiency by 25-40% and identifies top-performing perturbations more effectively.
This abstract reviews recent methods for predicting protein-ligand binding affinity.
problem Predicting protein-ligand binding affinity for various applications in life sciences.
method Traditional and deep learning models for binding affinity prediction.
result Improved predictive performance of AI-driven models.
Accelerating Antimicrobial Discovery with Controllable Deep Generative Models and Molecular Dynamicscs.LG
New method designs antimicrobial peptides with high potency and low toxicity.
problem Designing potent antimicrobial drugs with low toxicity.
method CLaSS method using deep generative autoencoder and atomistic simulations.
result Design and synthesis of two novel AMPs with high potency and low toxicity.
GENOT matches cells across data modalities using neural OT solvers.
problem Scalability, privacy, and out-of-sample estimation issues in traditional OT solvers.
method Learn stochastic maps, parameterize OT maps, relax mass conservation, integrate quadratic solvers.
result Demonstrates significant potential for enhancing therapeutic strategies.
Microbes are everywhere, including in and on our bodies, and have been shown to play key roles in a variety of prevalent human diseases. Consequently, there has been intense interest in the design of bacteriotherapies or "bugs as drugs," which are communities of bacteria administered to patients for specific therapeuti…
BioFinBERT analyzes sentiment of biotech press releases and financial text around inflection points.
problem Analyzing sentiment of biotech press releases and financial text around inflection points.
method Finetuning BioBERT on financial datasets to create BioFinBERT for sentiment analysis.
result BioFinBERT accurately analyzes sentiment of biotech press releases and financial text around inflection points.
Predicting Cellular Responses with Variational Causal Inference and Refined Relational Informationcs.LG
Novel framework predicts cell responses to perturbations using GRNs.
problem Predicting cellular responses to perturbations for drug discovery and personalized therapeutics.
method Graph variational Bayesian causal inference framework with refined GRNs and robust estimator.
result Enhanced model performance and robust estimation of perturbation effects.
Novel method identifies proteomic risk markers for Alzheimer disease.
problem Lack of comprehensive proteomic risk markers for Alzheimer disease diagnosis.
method Deep belief network-based feature selection method using proteomic and clinical data.
result Identified an optimal subset of proteins achieving 90% accuracy in Alzheimer disease diagnosis.
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 …
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.
Novel parallel GNN predicts protein-ligand interactions with high accuracy.
problem Accurate prediction of protein-ligand interactions for drug design.
method Parallel Graph Neural Networks (GNN) integrating 3D structural data.
result GNN achieves high accuracy in predicting binary interactions and activity.
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: Unveiling the Power of Self-Supervised Learning in Revolutionizing Drug Discoverycs.LG
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.
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.
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.
Alzheimer's disease (AD) is the most common neurodegenerative disease in older people. Despite considerable efforts to find a cure for AD, there is a 99.6% failure rate of clinical trials for AD drugs, likely because AD patients cannot easily be identified at early stages. This project investigated machine learning app…
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.
Study limits of circadian synchronization under different light signals.
problem Disruption of circadian rhythms due to misalignment with external light signals.
method Matrix-free approach for locating periodic steady states, numerical continuation, bifurcation diagrams, unsupervised learning.
result Limits of circadian synchronization to external light signals of different frequency and duty cycle.
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…