Evaluation of Large Language Models for an AI Chat Assistant Focused on Pumas and Pharmacometrics

Abstract

The Large Language Model (LLM) landscape is constantly changing, with new models emerging rapidly and outperforming established benchmarks. For professionals working on LLM applications, this means constantly being aware of top-performing LLMs that can replace current LLMs in their internal AI applications; an LLM that is considered the optimal choice in a scientist’s current AI architecture cannot be assumed to remain the optimal choice as models constantly evolve. At PumasAI, while building AskPumas, a Retrieval Augmented Generation (RAG) based AI chat assistant focused on Pumas and pharmacometric-related inquiries, we noticed the importance of finding a structure to assess numerous LLMs. The motivation behind this research is to establish a framework to evaluate LLMs and select and rank them based on different criteria. This paper will explore the methodologies of our evaluation criteria, how this has served in helping select the ideal LLM for AskPumas, and how our established framework can serve as a guide for developers who seek to find the optimal LLM for their domain-specific AI application. Using this framework, we identified gpt-5-chat , gemini models, qwen3-max , and grok-4-fast as top-performing LLMs for AskPumas. The differences among the highest-ranked models are small (~1-2%), suggesting that we identified sets of strong candidates for AskPumas, rather than a single definitive winner. Overall, we conclude that model selection for domain RAG applications should be treated as a modular process that considers trade-offs between metric weights and insights from embedding-based clustering, so AskPumas can adapt its priorities as the LLM landscape evolves.