# What an Autonomous Agent Discovers About Molecular Transformer Design: Does It Transfer?

arXiv: https://arxiv.org/abs/2603.28015 · HTML: https://mlsanity.com/paper/2603.28015/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 19 of its 28 references that are in the map.
- First posted on arXiv 30 Mar 2026.

## Builds on (most cited first, 19 of 19)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Llama 2: Open Foundation and Fine-Tuned Chat Models](https://mlsanity.com/paper/2307.09288/) (2023)
- [Scaling Laws for Neural Language Models](https://mlsanity.com/paper/2001.08361/) (2020)
- [Self-Refine: Iterative Refinement with Self-Feedback](https://mlsanity.com/paper/2303.17651/) (2023)
- [Training Compute-Optimal Large Language Models](https://mlsanity.com/paper/2203.15556/) (2022)
- [GLU Variants Improve Transformer](https://mlsanity.com/paper/2002.05202/) (2020)
- [GQA: Training Generalized Multi-Query Transformer Models from Multi-Head Checkpoints](https://mlsanity.com/paper/2305.13245/) (2023)
- [The FineWeb Datasets: Decanting the Web for the Finest Text Data at Scale](https://mlsanity.com/paper/2406.17557/) (2024)
- [The AI Scientist: Towards Fully Automated Open-Ended Scientific Discovery](https://mlsanity.com/paper/2408.06292/) (2024)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [Language Modeling with Gated Convolutional Networks](https://mlsanity.com/paper/1612.08083/) (2016)
- [BOHB: Robust and Efficient Hyperparameter Optimization at Scale](https://mlsanity.com/paper/1807.01774/) (2018)
- [ChemBERTa: Large-Scale Self-Supervised Pretraining for Molecular Property Prediction](https://mlsanity.com/paper/2010.09885/) (2020)
- [Large-Scale Chemical Language Representations Capture Molecular Structure and Properties](https://mlsanity.com/paper/2106.09553/) (2021)
- [Evolution through Large Models](https://mlsanity.com/paper/2206.08896/) (2022)
- [EvoPrompting: Language Models for Code-Level Neural Architecture Search](https://mlsanity.com/paper/2302.14838/) (2023)
- [LLMatic: Neural Architecture Search via Large Language Models and Quality Diversity Optimization](https://mlsanity.com/paper/2306.01102/) (2023)
- [IMPROVE: Iterative Model Pipeline Refinement and Optimization Leveraging LLM Experts](https://mlsanity.com/paper/2502.18530/) (2025)
- [LM-Searcher: Cross-domain Neural Architecture Search with LLMs via Unified Numerical Encoding](https://mlsanity.com/paper/2509.05657/) (2025)

## Abstract (arXiv)

Deep learning models for drug-like molecules and proteins overwhelmingly reuse transformer architectures designed for natural language, yet whether molecular sequences benefit from different designs has not been systematically tested. We deploy autonomous architecture search via an agent across three sequence types (SMILES, protein, and English text as control), running 3,106 experiments on a single GPU. For SMILES, architecture search is counterproductive: tuning learning rates and schedules alone outperforms the full search (p = 0.001). For natural language, architecture changes drive 81% of improvement (p = 0.009). Proteins fall between the two. Surprisingly, although the agent discovers distinct architectures per domain (p = 0.004), every innovation transfers across all three domains with <1% degradation, indicating that the differences reflect search-path dependence rather than fundamental biological requirements. We release a decision framework and open-source toolkit for molecular modeling teams to choose between autonomous architecture search and simple hyperparameter tuning.