PFArena: Benchmarking Language Models for Protein Modification

arXiv:2609.28921 · cs.AI, q-bio.BM · Submitted 2026-09-24 · Read on arXiv

cs.AI, q-bio.BM

Submitted: 2026-09-24

Updated: 2026-09-24

Code: https://github.com/RomeroLab/BioDesignBench

Terminology

• Benchmark — 28× in this paper · explained in 2 episodes
• Alignment — 19× in this paper · explained in 1 episode
• Core — 8× in this paper · explained in 2 episodes
• Test-time Scaling — 7× in this paper · explained in 2 episodes
• Accuracy — 6× in this paper · explained in 1 episode
• Aggregation — 6× in this paper · explained in 1 episode
• Consistency — 6× in this paper · explained in 3 episodes
• Hallucination — 5× in this paper · explained in 3 episodes
• Abundance — 4× in this paper · explained in 1 episode
• Adaptation — 4× in this paper · explained in 1 episode
• Benchmarking — 4× in this paper · explained in 3 episodes
• Additivity — 2× in this paper · explained in 1 episode
• Failure Modes — 2× in this paper · explained in 3 episodes
• Generative Model — 2× in this paper · explained in 2 episodes
• Generative Models — 2× in this paper · explained in 2 episodes
• Institute for AI Industry Research — 2× in this paper
• Large Language Models (LLMs) — 2× in this paper · explained in 6 episodes
• Action Space — 1× in this paper · explained in 1 episode
• Adam — 1× in this paper · explained in 2 episodes
• Agentic System — 1× in this paper · explained in 2 episodes
• Agentic Workflows — 1× in this paper · explained in 1 episode
• Borda Fusion and Reciprocal Rank Fusion — 1× in this paper
• Fine-Tuning — 1× in this paper · explained in 5 episodes
• Generalization — 1× in this paper · explained in 13 episodes
• Representation Learning — 1× in this paper · explained in 2 episodes
• Robustness — 1× in this paper · explained in 5 episodes
• Transferability — 1× in this paper · explained in 4 episodes
• Transformer — 1× in this paper · explained in 2 episodes

Sources

• Kimi K3: Open Frontier Intelligence
• AMix-2: Establishing Protein as a Native Modality in Large Language Models
• Large Language Model is Secretly a Protein Sequence Optimizer

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