Related papers: Knowledge Graph Completion to Predict Polypharmacy…

Drug discovery remains a slow and expensive process that involves many steps, from detecting the target structure to obtaining approval from the Food and Drug Administration (FDA), and is often riddled with safety concerns. Accurate…

Knowledge graphs are a versatile framework to encode richly structured data relationships, but it can be challenging to combine these graphs with unstructured data. Methods for retrofitting pre-trained entity representations to the…

In pharmaceutical R&D, predicting the efficacy of a pharmaceutical in treating a particular disease prior to clinical testing or any real-world use has been challenging. In this paper, we propose a flexible and modular machine…

Social recommendation leverages social information to solve data sparsity and cold-start problems in traditional collaborative filtering methods. However, most existing models assume that social effects from friend users are static and…

We introduced a methodology to efficiently exploit natural-language expressed biomedical knowledge for repurposing existing drugs towards diseases for which they were not initially intended. Leveraging on developments in Computational…

This work presents the use of graph learning for the prediction of multi-step experimental outcomes for applications across experimental research, including material science, chemistry, and biology. The viability of geometric learning for…

Biomedical datasets are often modeled as knowledge graphs (KGs) because they capture the multi-relational, heterogeneous, and dynamic natures of biomedical systems. KG completion (KGC), can, therefore, help researchers make predictions to…

Understanding how small molecules perturb gene expression is essential for uncovering drug mechanisms, predicting off-target effects, and identifying repurposing opportunities. While prior deep learning frameworks have integrated multimodal…

Recent recommender system advancements have focused on developing sequence-based and graph-based approaches. Both approaches proved useful in modeling intricate relationships within behavioral data, leading to promising outcomes in…

Finding out the differences and commonalities between the knowledge of two parties is an important task. Such a comparison becomes necessary, when one party wants to determine how much it is worth to acquire the knowledge of the second…

Identification and verification of molecular properties such as side effects is one of the most important and time-consuming steps in the process of molecule synthesis. For example, failure to identify side effects before submission to…

Multi-hop reasoning approaches over knowledge graphs infer a missing relationship between entities with a multi-hop rule, which corresponds to a chain of relationships. We extend existing works to consider a generalized form of multi-hop…

Graph neural networks (GNNs) demonstrate great performance in compound property and activity prediction due to their capability to efficiently learn complex molecular graph structures. However, two main limitations persist including…

Thanks to the increasing availability of drug-drug interactions (DDI) datasets and large biomedical knowledge graphs (KGs), accurate detection of adverse DDI using machine learning models becomes possible. However, it remains largely an…

Drug-drug interactions (DDIs) represent a critical challenge in pharmacology, often leading to adverse drug reactions with significant implications for patient safety and healthcare outcomes. While graph-based methods have achieved strong…

Predicting and discovering drug-drug interactions (DDIs) using machine learning has been studied extensively. However, most of the approaches have focused on text data or textual representation of the drug structures. We present the first…

Graph neural networks are widely used to learn global representations of graphs, which are then used for regression or classification tasks. Typically, the graphs in such data sets are connected, i.e. each training sample consists of a…

Knowledge graphs (KGs) are gaining prominence in Healthcare AI, especially in drug discovery and pharmaceutical research as they provide a structured way to integrate diverse information sources, enhancing AI system interpretability. This…

Extensive adoption of electronic health records (EHRs) offers opportunities for their use in various downstream clinical analyses. To accomplish this purpose, enriching an EHR cohort with external knowledge (e.g., standardized medical…

Accurate prediction of drug-drug interactions (DDI) is crucial for medication safety and effective drug development. However, existing methods often struggle to capture structural information across different scales, from local functional…