Deep Reprogramming Distillation for Medical Foundation Models
Authors: Siyuan Du, Yuhang Zhou, Haolin Li, Jiangchao Yao, Haishuai Wang, Hui Lin, Ya Zhang, Yanfeng Wang
Abstract
Medical foundation models pre-trained on large-scale datasets have shown powerful versatile performance. However, when adapting medical foundation models for specific medical scenarios, it remains the inevitable challenge due to the gap induced by the discrepancy between pre-training and downstream tasks, the real-world computation, and speed constraints. Relevant techniques that probably handle this challenge more or less suffer from some intrinsic limitations. For example, knowledge distillation (KD) assumes that teacher and student models share the same task, training strategy, and model structure family, while prevalent parameter-efficient fine-tuning (PEFT) fails to achieve personalized and lightweight deployment. Even the combination of PEFT and KD still struggles to resolve model structures and training strategies inconsistencies between teacher and student models, leading to inefficient knowledge transfer. In this study, we propose a novel framework called Deep Reprogramming Distillation (DRD) to combat the general adaptation challenge. Specifically, DRD introduces the novel reprogramming module that on the one side overcomes the domain and task discrepancy between pretraining and downstream scenarios, and on the other side builds the student-friendly efficient distillation from foundation models to lightweight downstream models. Furthermore, to mitigate variability under different training conditions, we design a centered kernel alignment (CKA) distillation method to promote robust knowledge transfer. Empirical results show that DRD surpasses previous PEFT and KD methods across 18 medical downstream tasks under different foundation models, covering various scenarios including 2D/3D classification and 2D/3D segmentation.
In the context of resource-constrained environments such as embedded systems, adapting reduced-size foundation models to downstream tasks has become increasingly popular. This has recently motivated the emerging setting of task-specific distillation, where a larger and a smaller version of the same foundation model are both adapted to the same downstream task, with the goal of transferring knowledge from the former to the latter. Recent work has demonstrated the benefits of using a larger version of the same foundation model to assist the adaptation of a smaller one. Typically, the larger model (teacher) is first adapted via fine-tuning or linear probing before its knowledge is distilled into the smaller model (student). While fine-tuning the teacher often increases its performance, recent work showed that probing it leads to better knowledge distillation to the student. Our findings show that this is mainly due to a mis-alignment in feature representation between the teacher and the student which occurs during the teacher's fine-tuning. Inspired by existing efforts to preserve previously learned knowledge, we first propose leveraging low-rank adaptation, resulting in better feature alignment and therefore better knowledge transfer. Drawing from this insight, we further enhance the feature alignment through a parameter-sharing strategy of the adapters between the two encoders during joint training. Our proposed method, SLAD, shows better feature alignment between the teacher and student, which results in increased performance for not only the student but also the teacher model, while being 2x faster to train than fine-tuning. Through extensive experiments on multiple classification and segmentation datasets, we demonstrate the improved accuracy and transfer efficiency of our method, achieving state-of-the-art performance in the task-specific distillation framework.
Tabular foundation models (TFMs) achieve strong performance on health datasets, but their inference cost and infrastructure requirements limit practical use. We study whether their predictive behavior can be transferred to lightweight tabular models through knowledge distillation. Since in-context TFMs condition on the training set at inference time, naive distillation can introduce context leakage; we address this with stratified out-of-fold teacher labeling. Across 19 healthcare datasets, 6 TFM teachers, 4 student families, and several multi-teacher ensembles, we find that distilled students retain at least 90% of teacher AUC, outperforming teachers in some cases, while running at least 26× faster on CPU and preserving calibration and fairness critical for health applications. Moreover, multi-teacher averaging does not consistently improve over the best single teacher. Leakage-aware distillation is thus a viable route for bringing TFM-quality predictions into inference-constrained health settings.
Accurate 3D medical segmentation is limited by anatomical variability and high computational costs. While knowledge distillation (KD) offers a route for model compression, conventional methods often fail to preserve complex structures and are overwhelmed by background noise. We propose Displacement-Preserving Relational Distillation (DPRD), which distills latent anatomical trajectories via vector based alignment to preserve the orientation and relative scale of the teacher's manifold, and prevents signal dilution by anchoring distillation in task-relevant structures. Integrated into nnU-Net, DPRD outperforms established baselines on ISLES 2022 and AMOS 2022 benchmarks. Notably, on the AMOS dataset, DPRD achieves a Dice score of 85.46%, edging out the high-capacity MedNeXt teacher while significantly reducing boundary errors. Despite utilizing only ~5% of the teacher's parameters and ~3% of its FLOPs, our approach maintains high structural consistency. This provides a robust, efficient solution for deploying high performance segmenters in resource-constrained clinical environments. Code: https://github.com/ClinicaAlpha/DPRD-3D-MedSeg