Research map / Probabilistic and scientific modeling / Molecules and proteins
Fast End-to-End Learning on Protein Surfaces
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Measured effects reported in the paper
| What was changed | Where | Measured | Effect |
|---|---|---|---|
| Use dMaSIF with 3 convolution layers instead of MaSIF-site | Binding site identification · Binding site identification | ROC-AUC: 0.85 -> 0.87 | Helped |
| Use dMaSIF with 3 convolution layers instead of MaSIF-site | Binding site identification · Binding site identification | forward-pass time per protein: 164 ms vs. 36 ms | Helped |
| Use dMaSIF instead of MaSIF-site | Binding site identification · Binding site identification | memory per protein: 1492 MB/protein -> 132 MB/protein | Helped |
| Use dMaSIF-search instead of MaSIF-search | Protein interaction prediction · Protein interaction prediction | ROC-AUC: 0.81 -> 0.82 | Helped |
| Use dMaSIF-search instead of MaSIF-search | Protein interaction prediction · Protein interaction prediction | inference time: 727 ± 403 ms vs. 17.5±6.7 ms | Helped |
| Add geometric curvatures to learned chemical features (ablation) | dMaSIF · Binding site identification | ROC-AUC | No clear effect |
Closest papers by meaning
- AtomSurf: Surface Representation for Learning on Protein Structures (ICLR 2025 · similarity 0.90)
- Evaluating Representation Learning on the Protein Structure Universe (ICLR 2024 · similarity 0.89)
- Generalized Implicit Neural Representations for Dynamic Molecular Surface Modeling (AAAI 2025 · similarity 0.87)
- Pre-Training Protein Bi-level Representation Through Span Mask Strategy On 3D Protein Chains (ICML 2024 · similarity 0.87)
- Pushing the Limits of All-Atom Geometric Graph Neural Networks: Pre-Training, Scaling, and Zero-Shot Transfer (ICLR 2025 · similarity 0.87)
- Full-Atom Peptide Design with Geometric Latent Diffusion (NeurIPS 2024 · similarity 0.85)
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