Spatial transcriptomics (STs) have become a valuable approach for understanding the growth and development of organisms. Despite the recent emergence of numerous ST models, accurately identifying spatial domains remains challenging owing to the trade-off between preserving local details and reducing noise. Here, we int...
Drug repositioning offers an efficient alternative to de novo drug development; however, accurately identifying potential drug-disease associations remains challenging. Existing methods do not fully exploit higher-order collaborative information at the drug-drug and disease-disease levels, and their feature fusion stra...
Hao Zhang, Jin-Can Li, Xian-Fang Tang et al.· Journal of Chemical Informat...· 0 citations
This study reviews the methodological evolution from conventional machine learning to deep learning, graph neural networks and large-scale pre-trained language models, and compares their differences in data preparation, evaluation protocols and generalization behavior, and places particular emphasis on recent advances...
GoMA-DTA is proposed, a framework integrating gene ontology (GO) functional annotations with protein semantic features with channelwise gating mechanism that uses functional semantics as anchors to dynamically recalibrate ESM-2embeddings, achieving adaptive semantic filtering.
An Xiong, Zheyu Zhou, Ya-Zi Li et al.· IEEE Transactions on Neural...· 0 citations
Accurate prediction of drug-target binding affinity (DTA) is a key task in virtual screening. However, current computational methods face a key challenge: sequence-based approaches often fail to capture critical spatial information, while structure-based models rely on computationally expensive 3D coordinates, which re...
Junlin Xu, Ye Yuan, Menglong Hu et al.· IEEE journal of biomedical a...· 0 citations
MolLingua, a token-centric, dual-modal framework designed for native molecular understanding, uses a dual-branch Residual Vector Quantization engine to discretize heterogeneous, high-dimensional spatial 2D and 3D features into compact code sequences rather than relying solely on continuous projections.
Haoyang Liu, Xikang Feng, Fei Guo et al.· IEEE journal of biomedical a...· 0 citations
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