13 accepted papers
Protein design is revolutionizing biotechnology, yet existing approaches struggle to balance structural foldability with functional performance. Structure-based models excel at generating stable protein backbones but often overlook critical functional properties, while protein language models captur
Molecular structure generation from mass spectrometry is fundamental for understanding cellular metabolism and discovering novel compounds. Although tandem mass spectrometry (MS/MS) enables the high-throughput acquisition of fragment fingerprints, these spectra often reflect higher-order interaction
Understanding genotype-phenotype relationships is pivotal for advancing biomedical research, drug discovery, and precision medicine. With the rise of high-throughput cellular imaging, it is essential to tightly integrate high-content cellular morphology with structured biological knowledge to extrac
Drug-drug interaction (DDI) prediction is pivotal for drug safety and clinical decision-making. Recently, subgraph-based methods utilizing knowledge graphs (KGs) and domain information have achieved promising results by extracting informative subgraphs for DDI prediction. However, existing subgraph
Spatial transcriptomics (ST) links gene expression to tissue architecture and enables predicting spatial expression from H&E-stained whole-slide images (WSIs). However, existing spot- or slide-level predictors focus on single-spot features or pairwise relations, failing to capture high-order, many-t
Predicting changes in binding free energy ($\Delta\Delta G$) is essential for understanding protein-protein interactions, which are critical in drug design and protein engineering. However, existing methods often rely on pre-trained knowledge and heuristic features, limiting their ability to accurat…
Diffusion-based molecular graph generative models have achieved significant success in template-free, single-step retrosynthesis prediction. However, these models typically generate reactants from scratch, often overlooking the fact that the scaffold of a product molecule typically remains unchanged…
While Graph Neural Networks and Transformers have shown promise in predicting molecular properties, they struggle with directly modeling complex many-body interactions. Current methods often approximate interactions like three- and four-body terms in message passing, while attention-based models, de…
Virtual Screening (VS) is vital for drug discovery but struggles with low hit rates and high computational costs. While Active Learning (AL) has shown promise in improving the efficiency of VS, traditional methods rely on inflexible and handcrafted heuristics, limiting adaptability in complex chemic…
Ribonucleic acid (RNA) binds to molecules to achieve specific biological functions. While generative models are advancing biomolecule design, existing methods for designing RNA that target specific ligands face limitations in capturing RNA’s conformational flexibility, ensuring structural validity,…
Illuminating the interconnections between drugs and genes is an important topic in drug development and precision medicine. Currently, computational predictions of drug-gene interactions mainly focus on the binding interactions without considering other relation types like agonist, antagonist, etc.…
Illuminating interactions between proteins and small drug molecules is a long-standing challenge in the field of drug discovery. Despite the importance of understanding these interactions, most previous works are limited by hand-designed scoring functions and insufficient conformation sampling. The…
Constructing appropriate representations of molecules lies at the core of numerous tasks such as material science, chemistry, and drug designs. Recent researches abstract molecules as attributed graphs and employ graph neural networks (GNN) for molecular representation learning, which have made rema…