fMRI Encoding and Decoding with LLMs: Input Embeddings vs. Hidden State Representations

Abstract

Systematically comparing how linguistic representations relate to brain activity has become an important topic in the field of computational neuroscience. Prior studies have mainly relied on contextual hidden states combined with linear regression, leaving open questions about the role of static input embeddings and the benefits of nonlinear mappings. In this study, we compare input embeddings and hidden states from multiple language model families (BERT, GPT-2, and LLaMA) within both encoding frameworks, which map text features to brain responses, and decoding frameworks, which reconstruct linguistic features from brain activity. We benchmarked voxel-wise ridge regression against bidirectional long short-term memory (BiLSTMs) models, using repeat-split cross-validation and explainable variance normalization on functional magnetic resonance imaging (fMRI) data from three subjects. Our analyses demonstrate that input embeddings, despite being context-invariant, remain competitive and, in some cases, outperform hidden states, while BiLSTMs provide modest but region-specific improvements over ridge regression. Fine-grained voxel-level results further revealed distinct cortical distributions of stable versus context-dependent features. Together, these findings clarify the trade-off between predictive performance and interpretability and highlight that input embeddings offer a strong and interpretable baseline for representational alignment between language models and brain activity.