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Using Large Language Models (LLMs) to process graph-structured data is an active research area, yet current state-of-the-art approaches typically rely on multi-step pipelines with Graph Neural Network (GNN) encoders that compress rich…

The paper utilizes the graph embeddings generated for entities of a large biomedical database to perform link prediction to capture various new relationships among different entities. A novel node similarity measure is proposed that…

MiRNAs, due to their role in gene regulation, have paved a new pathway for pharmacology, focusing on drug development that targets miRNAs. However, traditional wet lab experiments are limited by efficiency and cost constraints, making it…

Drug repurposing is often framed as a candidate identification task, but existing approaches provide limited guidance for distinguishing biologically plausible candidates from historically well-connected ones. Here we introduce DrugKLM, a…

Goal-oriented de novo molecule design, namely generating molecules with specific property or substructure constraints, is a crucial yet challenging task in drug discovery. Existing methods, such as Bayesian optimization and reinforcement…

Large language models (LLMs) have demonstrated immense potential across various tasks. However, research for exploring and improving the capabilities of LLMs in interpreting graph structures remains limited. To address this gap, we conduct…

Textual Attributed Graphs (TAGs) are crucial for modeling complex real-world systems, yet leveraging large language models (LLMs) for TAGs presents unique challenges due to the gap between sequential text processing and graph-structured…

We address a fundamental problem in chemistry known as chemical reaction product prediction. Our main insight is that the input reactant and reagent molecules can be jointly represented as a graph, and the process of generating product…

In clinical treatment, identifying potential adverse reactions of drugs can help assist doctors in making medication decisions. In response to the problems in previous studies that features are high-dimensional and sparse, independent…

GNN-based methods have achieved excellent results as a mainstream task in drug response prediction tasks in recent years. Traditional GNN methods use only the atoms in a drug molecule as nodes to obtain the representation of the molecular…

The rise of advanced chatbots, such as ChatGPT, has sparked curiosity in the scientific community. ChatGPT is a general-purpose chatbot powered by large language models (LLMs) GPT-3.5 and GPT-4, with the potential to impact numerous fields,…

Predicting synergistic drug combinations can help accelerate discovery of cancer treatments, particularly therapies personalized to a patient's specific tumor via biopsied cells. In this paper, we propose a novel setting and models for…

Prompt learning has demonstrated impressive efficacy in the fine-tuning of multimodal large models to a wide range of downstream tasks. Nonetheless, applying existing prompt learning methods for the diagnosis of neurological disorder still…

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…

AI tasks encompass a wide range of domains and fields. While numerous AI models have been designed for specific tasks and applications, they often require considerable human efforts in finding the right model architecture, optimization…

Recently, graph neural networks (GNNs) have been shown powerful capacity at modeling structural data. However, when adapted to downstream tasks, it usually requires abundant task-specific labeled data, which can be extremely scarce in…

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…

Integrating large language models (LLMs) like ChatGPT into computer science education offers transformative potential for complex courses such as data structures and algorithms (DSA). This study examines ChatGPT as a supplementary tool for…

This paper takes an exploratory approach to examine the use of ChatGPT for pattern mining. It proposes an eight-step collaborative process that combines human insight with AI capabilities to extract patterns from known uses. The paper…

The contributions of model complexity, data volume, and feature modalities to knowledge graph-based drug repurposing remain poorly quantified under rigorous temporal validation. We constructed a pharmacology knowledge graph from ChEMBL 36…