Confidence Calibration for Multimodal LLMs: An Empirical Study through Medical VQA

Multimodal large language models (MLLMs) applied to Medical Visual Question Answering (VQA) tend to produce overconfident outputs regardless of actual correctness, and existing verbalized confidence calibration methods, developed primarily for text only LLMs, do not account for the multimodal nature of medical image understanding. This work proposes a training based framework that finetunes MLLMs to improve their calibration using a composite loss function combining a Brier style calibration term, an anchor regularizer that prevents confidence collapse toward extreme values, a contrastive image text alignment term, and a KL based model stabilization term. The alignment signal is derived from a $2 \times 2$ factorial perturbation design that crosses image presence with text integrity, probing the reliance of the model on visual modality input versus language priors. Finally, a top K KL divergence regularizer is used to protect the answering ability of the model during finetuning. Across three Medical VQA benchmarks and two architectures (MedGemma 4B IT and Qwen2 VL 7B Instruct), our method reduces calibration error by 60% or more, and improves discrimination by 26% or more, while preserving predictive accuracy. On average across benchmarks, the technique outperforms prompting based, sampling based, and training based approaches, and ablation experiments confirm that each component of the loss function is indeed necessary for improving the calibration. All code for the experiments is publicly available.

Reinforcement Fine-Tuning (RFT) has enabled medical Multimodal Large Language Models (MLLMs) to produce Chain-of-Thought (CoT) reasoning for visual question answering, yet these models suffer from $\textit{confidence miscalibration}$---a systematic gap between expressed certainty and actual diagnostic accuracy that undermines clinical trust. We propose $\textbf{CARE}$, a $\textbf{C}$onfidence-$\textbf{A}$ware medical $\textbf{RE}$asoning framework that jointly optimizes accuracy and calibration through a dual-stage pipeline. First, a scalable Medical-CoT synthesis provides structured cold-start data for Supervised Fine-Tuning. Second, Group Relative Policy Optimization (GRPO) with a novel $\textbf{Confidence-Aware Reward (CAR)}$ mechanism ties the model's confidence to diagnostic correctness within the reward signal. Across three Medical VQA benchmarks, $\textbf{CARE}$ achieves the highest diagnostic accuracy while obtaining the lowest Expected Calibration Error and Hallucination Rate, establishing a foundation for trustworthy clinical decision support. Our code is available at https://github.com/anotherbricki/CARE.

Multimodal Large Language Models (MLLMs) have demonstrated exceptional capabilities in various perception and reasoning tasks. Despite this success, ensuring their reliability in practical deployment necessitates robust confidence estimation. Prior works have predominantly focused on text-only LLMs, often relying on computationally expensive self-consistency sampling. In this paper, we extend this to multimodal settings and conduct a comprehensive evaluation of MLLMs' response confidence estimation. Our analysis reveals a significant instinct-reflection misalignment: the model's implicit token-level support frequently diverges from its verbal self-assessment confidence. To address this misalignment, we propose a monotone confidence fusion framework to merge dual-channel signals and cross-channel consistency to estimate correctness. Subsequently, an order-preserving mean alignment step is applied to correct global bias, which improves calibration while preserving the risk-coverage trade-off for selective prediction. Experiments on diverse open-source and closed-source MLLMs show that our method consistently yields more reliable confidence estimates and improves both calibration and failure prediction. Code will be available at https://github.com/Yunkaidang/Instinct-vs.-Reflection.