Non-coding RNAs (ncRNAs), which do not encode proteins, have been implicated in chemotherapy resistance in cancer treatment. Given the high costs and time requirements of traditional biological experiments, there is an increasing need for computational models to predict ncRNA-drug resistance associations. In this study, we introduce AGCLNDA, an adaptive contrastive learning method designed to uncover these associations. AGCLNDA begins by constructing a bipartite graph from existing ncRNA-drug resistance data. It then utilizes a light graph convolutional network (LightGCN) to learn vector representations for both ncRNAs and drugs. The method assesses resistance association scores through the inner product of these vectors. To tackle data sparsity and noise, AGCLNDA incorporates learnable augmented view generators and denoised view generators, which provide contrastive views for enhanced data augmentation. Comparative experiments demonstrate that AGCLNDA outperforms five other advanced methods. Case studies further validate AGCLNDA as an effective tool for predicting ncRNA-drug resistance associations.

Exploring gene-drug associations is a key step in identifying new drug candidates, but traditional experimental methods are often expensive and time-consuming. While Graph Neural Network (GNN)-based models have demonstrated effectiveness in association prediction tasks, they face challenges in the information aggregation process. Existing GNN models either treat all nodes uniformly or rely on simple attention mechanisms to assign weights to neighboring nodes, limiting their capacity to capture complex relationships and improve performance. To address these limitations, we propose a novel adaptive graph diffusion network, ADiffGDA, for gene-drug association prediction. The model begins by randomly initializing embeddings for genes and drugs, which are then updated through neighborhood information aggregation. A key feature of ADiffGDA is the incorporation of a heat kernel, enabling each node to dynamically adjust aggregation weights based on its local structure. This approach allows the model to better capture variations in node types and local neighborhood patterns. Through extensive comparative experiments, we show that ADiffGDA outperforms existing state-of-the-art methods. Furthermore, case studies validate its effectiveness as a predictive tool, offering valuable insights for future biological experiments. The code and datasets for ADiffGDA are freely available at https://github.com/one-melon/ADiffGDA.

Exploring the intricate connections between non-coding RNAs (ncRNAs) and drug resistance is crucial for understanding the molecular mechanisms behind drug resistance, identifying novel drug development targets, and uncovering key biomarkers to optimize therapeutic strategies. Traditional biological assays face significant challenges, including high costs and lengthy timelines, prompting the need for advanced computational methods to predict ncRNA-drug resistance associations. In this study, we introduce HGTRDA, a novel computational framework designed to predict potential associations between ncRNAs and drug resistance. HGTRDA leverages LightGCN to generate node representations that capture topological information from the surrounding node neighborhood. These representations are then dynamically optimized using a global hypergraph transformer to model the relationships between ncRNAs and drug resistance. To enhance the quality of the learned embeddings, HGTRDA employs self-supervised learning to fine-tune topology-aware embeddings, reducing the impact of noise and improving representation quality. The final association scores between ncRNAs and drugs are computed using an inner product method. Empirical evaluations on the ncRNADrug database demonstrate that HGTRDA outperforms six contemporary state-of-the-art methods in predicting ncRNA-drug resistance associations. Furthermore, case studies illustrate the practical utility of HGTRDA as a predictive tool in real-world scenarios. The code and dataset for HGTRDA are freely available at https://github.com/one-melon/HGTRDA.

Drug repurposing offers a viable strategy for discovering new drugs and therapeutic targets through the analysis of drug-gene interactions. However, traditional experimental methods are plagued by their costliness and inefficiency. Despite graph convolutional network (GCN)-based models' state-of-the-art performance in prediction, their reliance on supervised learning makes them vulnerable to data sparsity, a common challenge in drug discovery, further complicating model development. In this study, we propose SGCLDGA, a novel computational model leveraging graph neural networks and contrastive learning to predict unknown drug-gene associations. SGCLDGA employs GCNs to extract vector representations of drugs and genes from the original bipartite graph. Subsequently, singular value decomposition (SVD) is employed to enhance the graph and generate multiple views. The model performs contrastive learning across these views, optimizing vector representations through a contrastive loss function to better distinguish positive and negative samples. The final step involves utilizing inner product calculations to determine association scores between drugs and genes. Experimental results on the DGIdb4.0 dataset demonstrate SGCLDGA's superior performance compared with six state-of-the-art methods. Ablation studies and case analyses validate the significance of contrastive learning and SVD, highlighting SGCLDGA's potential in discovering new drug-gene associations. The code and dataset for SGCLDGA are freely available at https://github.com/one-melon/SGCLDGA.

Accurately delineating the connection between short nucleolar RNA (snoRNA) and disease is crucial for advancing disease detection and treatment. While traditional biological experimental methods are effective, they are labor-intensive, costly and lack scalability. With the ongoing progress in computer technology, an increasing number of deep learning techniques are being employed to predict snoRNA-disease associations. Nevertheless, the majority of these methods are black-box models, lacking interpretability and the capability to elucidate the snoRNA-disease association mechanism. In this study, we introduce IGCNSDA, an innovative and interpretable graph convolutional network (GCN) approach tailored for the efficient inference of snoRNA-disease associations. IGCNSDA leverages the GCN framework to extract node feature representations of snoRNAs and diseases from the bipartite snoRNA-disease graph. SnoRNAs with high similarity are more likely to be linked to analogous diseases, and vice versa. To facilitate this process, we introduce a subgraph generation algorithm that effectively groups similar snoRNAs and their associated diseases into cohesive subgraphs. Subsequently, we aggregate information from neighboring nodes within these subgraphs, iteratively updating the embeddings of snoRNAs and diseases. The experimental results demonstrate that IGCNSDA outperforms the most recent, highly relevant methods. Additionally, our interpretability analysis provides compelling evidence that IGCNSDA adeptly captures the underlying similarity between snoRNAs and diseases, thus affording researchers enhanced insights into the snoRNA-disease association mechanism. Furthermore, we present illustrative case studies that demonstrate the utility of IGCNSDA as a valuable tool for efficiently predicting potential snoRNA-disease associations. The dataset and source code for IGCNSDA are openly accessible at: https://github.com/altriavin/IGCNSDA.

Non-coding RNAs (ncRNAs) play a critical role in the occurrence and development of numerous human diseases. Consequently, studying the associations between ncRNAs and diseases has garnered significant attention from researchers in recent years. Various computational methods have been proposed to explore ncRNA-disease relationships, with Graph Neural Network (GNN) emerging as a state-of-the-art approach for ncRNA-disease association prediction. In this survey, we present a comprehensive review of GNN-based models for ncRNA-disease associations. Firstly, we provide a detailed introduction to ncRNAs and GNNs. Next, we delve into the motivations behind adopting GNNs for predicting ncRNA-disease associations, focusing on data structure, high-order connectivity in graphs and sparse supervision signals. Subsequently, we analyze the challenges associated with using GNNs in predicting ncRNA-disease associations, covering graph construction, feature propagation and aggregation, and model optimization. We then present a detailed summary and performance evaluation of existing GNN-based models in the context of ncRNA-disease associations. Lastly, we explore potential future research directions in this rapidly evolving field. This survey serves as a valuable resource for researchers interested in leveraging GNNs to uncover the complex relationships between ncRNAs and diseases.