Foundation and Large-Scale AI Models in Neuroscience: A Comprehensive Review

Abstract: The advent of large-scale AI models has a transformative effect on neuroscience research, which represents a paradigm shift from the traditional computational methods through the facilitation of end-to-end learning from raw brain signals and neural data. In this paper, we explore the transformative effects of large-scale AI models on five major neuroscience domains: neuroimaging and data processing, brain-computer interfaces and neural decoding, molecular neuroscience and genomic modeling, clinical assistance and translational frameworks, and disease-specific applications across neurological and psychiatric disorders. These models are demonstrated to address major computational neuroscience challenges, including multimodal neural data integration, spatiotemporal pattern interpretation, and the derivation of translational frameworks for clinical deployment. Moreover, the interaction between neuroscience and AI has become increasingly reciprocal, as biologically informed architectural constraints are now incorporated to develop more interpretable and computationally efficient models. This review highlights both the notable promise of such technologies and key implementation considerations, with particular emphasis on rigorous evaluation frameworks, effective domain knowledge integration, and comprehensive ethical guidelines for clinical use. Finally, a systematic listing of critical neuroscience datasets used to derive and validate large-scale AI models across diverse research applications is provided.