# Purely Agent-Driven Black-Box Optimization for Biological Design

arXiv: https://arxiv.org/abs/2601.22382 · HTML: https://mlsanity.com/paper/2601.22382/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Placed in Medical and scientific domain agents, one of 16 directions in LLM agents and tool use.
- Builds on 4 of its 73 references that are in the map.
- First posted on arXiv 29 Jan 2026.

## Placed in

- LLM agents and tool use / [Medical and scientific domain agents](https://mlsanity.com/agents/medical-and-scientific-domain-agents/)

## Builds on (most cited first, 4 of 4)

- [A Tutorial on Bayesian Optimization](https://mlsanity.com/paper/1807.02811/) (2018)
- [Augmenting Genetic Algorithms with Deep Neural Networks for Exploring the Chemical Space](https://mlsanity.com/paper/1909.11655/) (2019)
- [High-Dimensional Bayesian Optimisation with Variational Autoencoders and Deep Metric Learning](https://mlsanity.com/paper/2106.03609/) (2021)
- [Accelerating Scientific Discovery with Autonomous Goal-evolving Agents](https://mlsanity.com/paper/2512.21782/) (2025)

## Built on by (most cited first, 3 of 3)

- [Information-Dense Synthesis for Molecular Discovery](https://mlsanity.com/paper/2610.08495/) (2026)
- [A Closer Look at Agentic BBO: Benchmarking LLM Agents for Black-Box Optimization](https://mlsanity.com/paper/2610.12183/) (2026)
- [Autonomous Science Bench: Evaluating AI Agents for Autonomous Scientific Discovery](https://mlsanity.com/paper/2610.18449/) (2026)

## Abstract (arXiv)

Many key challenges in biological design -- such as small-molecule drug discovery, antimicrobial peptide development, and protein engineering -- can be framed as black-box optimization over vast, complex structured spaces. Existing methods rely mainly on raw structural data and struggle to exploit the rich scientific literature. While large language models (LLMs) have been added to these pipelines, they have been confined to narrow roles within structure-centered optimizers. We instead cast biological black-box optimization as an agent-driven, language-based reasoning process. We introduce Purely Agent-driven BLack-box Optimization (PABLO), a hierarchical agentic system that uses scientific LLMs pretrained on chemistry and biology literature to generate and iteratively refine biological candidates. On both the standard GuacaMol molecular design and antimicrobial peptide optimization tasks, PABLO achieves state-of-the-art performance, substantially improving sample efficiency and final objective values over established baselines. Compared to prior optimization methods that incorporate LLMs, PABLO achieves competitive token usage per run despite relying on LLMs throughout the optimization loop. Beyond raw performance, the agentic formulation offers key advantages for realistic design: it naturally incorporates semantic task descriptions, retrieval-augmented domain knowledge, and complex constraints. In follow-up in vitro validation, PABLO-optimized peptides showed strong activity against drug-resistant pathogens, underscoring the practical potential of PABLO for therapeutic discovery.