The Evaluation Gap in Medicine, AI and LLMs: Navigating Elusive Ground Truth & Uncertainty via a Probabilistic Paradigm

• URL: http://arxiv.org/abs/2601.05500v1
• Date: Fri, 09 Jan 2026 03:19:37 GMT
• Title: The Evaluation Gap in Medicine, AI and LLMs: Navigating Elusive Ground Truth & Uncertainty via a Probabilistic Paradigm
• Authors: Aparna Elangovan, Lei Xu, Mahsa Elyasi, Ismail Akdulum, Mehmet Aksakal, Enes Gurun, Brian Hur, Saab Mansour, Ravid Shwartz Ziv, Karin Verspoor, Dan Roth,
• Abstract summary: We introduce a probabilistic paradigm to theoretically explain how high certainty in ground truth answers is almost always necessary for even an expert to achieve high scores.<n>We thus bring forth the concepts of expected accuracy and expected F1 to estimate the score an expert human or system can achieve given ground truth answer variability.
• Score: 49.287792149338976
• License: http://creativecommons.org/licenses/by/4.0/
• Abstract: Benchmarking the relative capabilities of AI systems, including Large Language Models (LLMs) and Vision Models, typically ignores the impact of uncertainty in the underlying ground truth answers from experts. This ambiguity is particularly consequential in medicine where uncertainty is pervasive. In this paper, we introduce a probabilistic paradigm to theoretically explain how high certainty in ground truth answers is almost always necessary for even an expert to achieve high scores, whereas in datasets with high variation in ground truth answers there may be little difference between a random labeller and an expert. Therefore, ignoring uncertainty in ground truth evaluation data can result in the misleading conclusion that a non-expert has similar performance to that of an expert. Using the probabilistic paradigm, we thus bring forth the concepts of expected accuracy and expected F1 to estimate the score an expert human or system can achieve given ground truth answer variability. Our work leads to the recommendation that when establishing the capability of a system, results should be stratified by probability of the ground truth answer, typically measured by the agreement rate of ground truth experts. Stratification becomes critical when the overall performance drops below a threshold of 80%. Under stratified evaluation, performance comparison becomes more reliable in high certainty bins, mitigating the effect of the key confounding factor -- uncertainty.

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