SoftBlobGIN combines ESM-2 representations with protein contact graphs via a lightweight GNN and differentiable substructure pooling to achieve 92.8% accuracy on enzyme classification, raise binding-site AUROC to 0.983, and generate auditable structural explanations without retraining the language模型
arXiv preprint arXiv:2203.06125 , year=
4 Pith papers cite this work. Polarity classification is still indexing.
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Pith papers citing it
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2026 4verdicts
UNVERDICTED 4representative citing papers
Yeti is a compact tokenizer for protein structures that delivers strong codebook use, token diversity, and reconstruction while enabling from-scratch multimodal generation of plausible sequences and structures with 10x fewer parameters than ESM3.
L3-PPI reformulates PPI pair classification as graph classification over a prompt graph with controlled virtual L3 paths to inject the biological interaction prior and boost performance on existing models.
PRIME is a five-level hierarchical equivariant graph model for proteins that uses physics-informed deterministic operators to exchange information across scales and achieves state-of-the-art results on fold classification and reaction class prediction.
citing papers explorer
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Structural Interpretations of Protein Language Model Representations via Differentiable Graph Partitioning
SoftBlobGIN combines ESM-2 representations with protein contact graphs via a lightweight GNN and differentiable substructure pooling to achieve 92.8% accuracy on enzyme classification, raise binding-site AUROC to 0.983, and generate auditable structural explanations without retraining the language模型
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Yeti: A compact protein structure tokenizer for reconstruction and multi-modal generation
Yeti is a compact tokenizer for protein structures that delivers strong codebook use, token diversity, and reconstruction while enabling from-scratch multimodal generation of plausible sequences and structures with 10x fewer parameters than ESM3.
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Learning the Interaction Prior for Protein-Protein Interaction Prediction: A Model-Agnostic Approach
L3-PPI reformulates PPI pair classification as graph classification over a prompt graph with controlled virtual L3 paths to inject the biological interaction prior and boost performance on existing models.
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PRIME: Protein Representation via Physics-Informed Multiscale Equivariant Hierarchies
PRIME is a five-level hierarchical equivariant graph model for proteins that uses physics-informed deterministic operators to exchange information across scales and achieves state-of-the-art results on fold classification and reaction class prediction.