A General Harness for Protein Foundation Model Fitness Prediction

arXiv:2609.34654 · cs.AI, q-bio.QM · Submitted 2026-09-28 · Read on arXiv

cs.AI, q-bio.QM

Submitted: 2026-09-28

Updated: 2026-09-28

Code: https://github.com/ai4protein/VenusREM-Harness

Terminology

• Benchmark — 65× in this paper · explained in 2 episodes
• AUC — 30× in this paper · explained in 2 episodes
• Calibration — 28× in this paper · explained in 7 episodes
• Abundance — 23× in this paper · explained in 1 episode
• RAG — 18× in this paper · explained in 3 episodes
• Alignment — 15× in this paper · explained in 1 episode
• Aggregation — 13× in this paper · explained in 1 episode
• Provenance — 7× in this paper · explained in 3 episodes
• Ablation — 6× in this paper · explained in 1 episode
• Trace — 6× in this paper · explained in 2 episodes
• Adam — 5× in this paper · explained in 2 episodes
• Foundation Model — 5× in this paper · explained in 3 episodes
• Consistency — 4× in this paper · explained in 3 episodes
• Foundation Models — 4× in this paper · explained in 7 episodes
• Transformer — 4× in this paper · explained in 2 episodes
• Fine-Tuning — 3× in this paper · explained in 5 episodes
• Generative Model — 3× in this paper · explained in 2 episodes
• Accuracy — 2× in this paper · explained in 1 episode
• Generative Models — 2× in this paper · explained in 2 episodes
• Representation Learning — 2× in this paper · explained in 2 episodes
• alpha — 2× in this paper · explained in 1 episode
• Adaptation — 1× in this paper · explained in 1 episode
• Additivity — 1× in this paper · explained in 1 episode
• Benchmarking — 1× in this paper · explained in 3 episodes
• Computational Biology — 1× in this paper · explained in 2 episodes
• Core — 1× in this paper · explained in 2 episodes
• Cross-Model Transfer — 1× in this paper · explained in 2 episodes
• Data Provenance — 1× in this paper · explained in 2 episodes
• Elias — 1× in this paper · explained in 2 episodes
• Frozen model — 1× in this paper · explained in 3 episodes
• Generalization — 1× in this paper · explained in 13 episodes
• Generative AI — 1× in this paper · explained in 2 episodes
• Large Language Model (LLM) — 1× in this paper · explained in 3 episodes
• Mixture of Experts — 1× in this paper · explained in 2 episodes
• Model-Agnostic — 1× in this paper · explained in 2 episodes
• Multi-agent Collaboration — 1× in this paper · explained in 2 episodes
• Tokenization — 1× in this paper · explained in 2 episodes

Sources

• RITA: a Study on Scaling Up Generative Protein Sequence Models
• ViroGym: Realistic Large-Scale Benchmarks for Evaluating Viral Proteins

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