Exploring Modularity of Agentic Systems for Drug Discovery (2506.22189v1)

Abstract: Large-LLMs and agentic systems present exciting opportunities to accelerate drug discovery and design. In this study, we critically examine the modularity of LLM-based agentic systems for drug discovery, i.e., whether parts of the agentic system such as the LLM are interchangeable, a topic that has received limited attention in drug discovery applications. We compare the performance of different LLMs and the effectiveness of tool-calling agents versus code-generating agents in this domain. Our case study, comparing performance in orchestrating tools for chemistry and drug discovery using an LLM-as-a-judge score, shows that Claude-3.5-Sonnet, Claude-3.7-Sonnet and GPT-4o outperform alternative LLMs such as Llama-3.1-8B, Llama-3.1-70B, GPT-3.5-Turbo, and Nova-Micro. Although we confirm that code-generating agents outperform the tool-calling ones on average, we show that this is highly question and model dependent. Furthermore, the impact of replacing system prompts is dependent on the specific question asked and the model used, underscoring that -- even in this particular domain -- one cannot just replace LLMs without considering prompt re-engineering. Our study highlights the necessity of further research into the modularity of agentic systems to enable the development of stable and scalable solutions for real-world problems.