Multi-task Collaborative Pre-training and Individual-adaptive-tokens Fine-tuning: A Unified Framework for Brain Representation Learning

Structural magnetic resonance imaging (sMRI) provides accurate estimates of the brain's structural organization and learning invariant brain representations from sMRI is an enduring issue in neuroscience. Previous deep representation learning models ignore the fact that the brain, as the core of human cognitive activity, is distinct from other organs whose primary attribute is anatomy. Therefore, capturing the semantic structure that dominates interindividual cognitive variability is key to accurately representing the brain. Given that this high-level semantic information is subtle, distributed, and interdependently latent in the brain structure, sMRI-based models need to capture fine-grained details and understand how they relate to the overall global structure. However, existing models are optimized by simple objectives, making features collapse into homogeneity and worsening simultaneous representation of fine-grained information and holistic semantics, causing a lack of biological plausibility and interpretation of cognition. Here, we propose MCIAT, a unified framework that combines Multi-task Collaborative pre-training and Individual-Adaptive-Tokens fine-tuning. Specifically, we first synthesize restorative learning, age prediction auxiliary learning and adversarial learning as a joint proxy task for deep semantic representation learning. Then, a mutual-attention-based token selection method is proposed to highlight discriminative features. The proposed MCIAT achieves state-of-the-art diagnosis performance on the ADHD-200 dataset compared with several sMRI-based approaches and shows superior generalization on the MCIC and OASIS datasets. Moreover, we studied 12 behavioral tasks and found significant associations between cognitive functions and MCIAT-established representations, which verifies the interpretability of our proposed framework.