Benchmarking Peptide-Protein Affinity Prediction Across Peptide and Target Shifts

arXiv:2608.30175 · cs.LG, q-bio.QM · Submitted 2026-08-31 · Read on arXiv

cs.LG, q-bio.QM

Submitted: 2026-08-31

Updated: 2026-08-31

Comments: 11 pages, 6 figures, 2 tables

License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/

Terminology

• Benchmark — 16× in this paper · explained in 2 episodes
• Adaptation — 15× in this paper · explained in 1 episode
• Generalization — 7× in this paper · explained in 13 episodes
• Fine-Tuning — 6× in this paper · explained in 5 episodes
• Embeddings — 4× in this paper · explained in 2 episodes
• Trace — 3× in this paper · explained in 2 episodes
• Transformer — 3× in this paper · explained in 2 episodes
• Benchmarking — 2× in this paper · explained in 3 episodes
• Calibration — 2× in this paper · explained in 7 episodes
• Generalizability — 2× in this paper · explained in 6 episodes
• Ablation — 1× in this paper · explained in 1 episode
• Consistency — 1× in this paper · explained in 3 episodes
• Distribution Shift — 1× in this paper · explained in 5 episodes
• Foundation Model — 1× in this paper · explained in 3 episodes
• Foundation Models — 1× in this paper · explained in 7 episodes
• Latent Space — 1× in this paper · explained in 7 episodes
• LoRA Adapters — 1× in this paper · explained in 3 episodes
• Low-Rank Adaptation (LoRA) — 1× in this paper · explained in 9 episodes
• Sample Efficiency — 1× in this paper · explained in 4 episodes
• Support Vector Regression (SVR) — 1× in this paper · explained in 2 episodes

Sources

• ChemBERTa-2: Towards Chemical Foundation Models
• HELM-BERT: A Transformer for Medium-sized Peptide Property Prediction
• LoRA: Low-Rank Adaptation of Large Language Models

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