Advances in Machine Learning for Directed Evolution: A Five-Year Retrospective

arXiv:2609.03046 · q-bio.BM, cs.LG · Submitted 2026-09-02 · Read on arXiv

q-bio.BM, cs.LG

Submitted: 2026-09-02

Updated: 2026-09-02

Terminology

• Generative Model — 6× in this paper · explained in 2 episodes
• Generative Models — 5× in this paper · explained in 2 episodes
• Benchmark — 4× in this paper · explained in 2 episodes
• Generative AI — 3× in this paper · explained in 2 episodes
• Downstream Tasks — 2× in this paper · explained in 2 episodes
• Foundation Model — 2× in this paper · explained in 3 episodes
• Foundation Models — 2× in this paper · explained in 7 episodes
• Resource Constraints — 2× in this paper · explained in 3 episodes
• Transfer Learning — 2× in this paper · explained in 10 episodes
• Abstraction — 1× in this paper · explained in 1 episode
• Accuracy — 1× in this paper · explained in 1 episode
• Active Learning — 1× in this paper · explained in 6 episodes
• Additivity — 1× in this paper · explained in 1 episode
• Core — 1× in this paper · explained in 2 episodes
• Generalization — 1× in this paper · explained in 13 episodes
• Generative Modeling — 1× in this paper · explained in 3 episodes
• Steering — 1× in this paper · explained in 2 episodes

Sources

• GPT-4 Technical Report
• Artificial Intelligence Index Report 2025
• Scaling and Data Saturation in Protein Language Models
• Generative AI for Controllable Protein Sequence Design: A Survey
• Scientists' Perspectives on the Potential for Generative AI in their Fields
• Foundation Models for AI-Enabled Biological Design
• Sparks of Artificial General Intelligence: Early experiments with GPT-4
• ProteinGuide: On-the-fly property guidance for protein sequence generative models
• Steering Generative Models with Experimental Data for Protein Fitness Optimization

Related papers

• Speak to a Protein: An Interactive Multimodal Co-Scientist
• Learning Topological Representations of Protein Structure and Dynamics
• p2smi: A Python Toolkit for Peptide FASTA-to-SMILES Conversion and Molecular Property Analysis
• UNAAGI: Atom-Level Diffusion for Generating Non-Canonical Amino Acid Substitutions
• Co-folding with a Soup of Representations
• Non-Markovain Quantum State Diffusion for the Tunneling in SARS-COVID-19 virus