Related papers: Pharmacology Knowledge Graphs: Do We Need Chemical…

Pretrained neural networks have attracted significant interest in chemistry and small molecule drug design. Embeddings from these models are widely used for molecular property prediction, virtual screening, and small data learning in…

Adverse Drug Reactions (ADRs) are a leading cause of morbidity and mortality. Existing prediction methods rely mainly on chemical similarity, machine learning on structured databases, or isolated target profiles, but often fail to integrate…

A ChatGPT-like system for drug compounds could be a game-changer in pharmaceutical research, accelerating drug discovery, enhancing our understanding of structure-activity relationships, guiding lead optimization, aiding drug repurposing,…

Pain is a complex concept that can interconnect with other concepts such as a disorder that might cause pain, a medication that might relieve pain, and so on. To fully understand the context of pain experienced by either an individual or…

Knowledge Graphs (KG) and associated Knowledge Graph Embedding (KGE) models have recently begun to be explored in the context of drug discovery and have the potential to assist in key challenges such as target identification. In the drug…

Motivation: Biomedical knowledge graphs (KGs) are crucial for drug discovery and disease understanding, yet their completion and reasoning are challenging. Knowledge Embedding (KE) methods capture global semantics but struggle with dynamic…

Advancements in neural machinery have led to a wide range of algorithmic solutions for molecular property prediction. Two classes of models in particular have yielded promising results: neural networks applied to computed molecular…

Knowledge Graph Embeddings (KGE) have become a quite popular class of models specifically devised to deal with ontologies and graph structure data, as they can implicitly encode statistical dependencies between entities and relations in a…

Machine learning on graphs is an important and ubiquitous task with applications ranging from drug design to friendship recommendation in social networks. The primary challenge in this domain is finding a way to represent, or encode, graph…

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…

Development of new drugs is an expensive and time-consuming process. Due to the world-wide SARS-CoV-2 outbreak, it is essential that new drugs for SARS-CoV-2 are developed as soon as possible. Drug repurposing techniques can reduce the time…

Explainable Graph Neural Networks (GNNs) have been developed and applied to drug-protein binding prediction to identify the key chemical structures in a drug that have active interactions with the target proteins. However, the key…

Machine learning, particularly graph learning, is gaining increasing recognition for its transformative impact across various fields. One such promising application is in the realm of molecule design and discovery, notably within the…

Recommending safe and effective medication combinations from electronic health records (EHRs) is a core clinical AI problem, yet it remains difficult because patient trajectories are long, noisy, and clinically heterogeneous. Existing…

This paper designs and implements an explainable recommendation model that integrates knowledge graphs with structure-aware attention mechanisms. The model is built on graph neural networks and incorporates a multi-hop neighbor aggregation…

Predicting interactions among heterogenous graph structured data has numerous applications such as knowledge graph completion, recommendation systems and drug discovery. Often times, the links to be predicted belong to rare types such as…

Recent advances and achievements of artificial intelligence (AI) as well as deep and graph learning models have established their usefulness in biomedical applications, especially in drug-drug interactions (DDIs). DDIs refer to a change in…

Several generative models with elaborate training and sampling procedures have been proposed to accelerate structure-based drug design (SBDD); however, their empirical performance turns out to be suboptimal. We seek to better understand…

Off-the-shelf biomedical embeddings obtained from the recently released various pre-trained language models (such as BERT, XLNET) have demonstrated state-of-the-art results (in terms of accuracy) for the various natural language…

Accurate drug target affinity prediction can improve drug candidate selection, accelerate the drug discovery process, and reduce drug production costs. Previous work focused on traditional fingerprints or used features extracted based on…