A Unified Geometric Space for Topological Alignment Between Transformer-Based Models and Human Brain Networks

Convolutional neural networks (CNNs) and vision transformers are both used to model the human visual system, but whether the two architectures diverge at a specific point in network depth is unclear. We compared six CNNs and two vision transformers by computing the Pearson correlation (r) between each model's predicted and measured EEG response at every layer or block, in ten participants viewing 200 natural images. For the transformer models, we also tested four token representations, from the classification (CLS) token alone to CLS combined with all patch tokens. CNNs showed strongest correspondence at the earliest layers, weakening at deeper layers, particularly later in the post-stimulus response. Transformers instead sustained strong correspondence at their deepest blocks, though not at their earliest ones. This advantage depended on token representation: pooled representations gave weaker peak correlations (r approx 0.48-0.51) than representations retaining all patch tokens (r=0.640 for CLIP-ViT-B/32, r=0.656 for DINOv2-ViT-B/14). Controlled comparisons showed architecture, not training objective, drove this effect: MoCo-v1 and ResNet-50 (matched architecture) performed nearly identically (r=0.673, 0.670), whereas CLIP-RN50 and CLIP-ViT-B/32 (matched objective) diverged until patch tokens were preserved. We propose that CNN training's classification bottleneck compresses brain-relevant information at depth, unlike transformers' self-attention and non-classification objectives. A spatial topography analysis showed a common occipital-dominant pattern across all models, indicating these differences reflect signal strength and persistence rather than distinct brain regions. Patch-preserving transformer representations sustain brain-predictive correspondence where CNNs collapse.

Visual perception depends on top-down goals and bottom-up sensory mechanisms. Vision-language models implement both, allowing us to treat each component as a separable hypothesis about what drives where we look. We compared spatial attention maps from six vision-language models against human fixation heatmaps recorded on 200 images during two tasks (general description and social captioning). The six models spanned a 2$\times$2 factorial of CNN vs.\ ViT encoders crossed with LSTM vs.\ Transformer decoders, plus Molmo 7B-D and Qwen3.5 9B. We found that both decoder and encoder architecture shaped alignment, but decoder choice dominated. LSTM vs.\ Transformer decoders increased alignment by 40--50 percentage points (80--87% vs.\ 40--59% of the human noise ceiling). In contrast, CNN vs.\ ViT encoders contributed a secondary 5--20 point advantage depending on decoder family, with CNN-LSTM the most aligned model overall (85--87%). Despite their alignment advantage, LSTM-decoder attention maps were spatially diffuse and minimally task-differentiated; ViT-Transformer, the weakest in alignment, showed the sharpest spatial concentration and strongest task differentiation. A hemispatial-neglect simulation confirmed that ablating attention impacted LSTM decoders more than Transformer decoders. In an exploratory extension using TRIBE-simulated synthetic neural responses, fixation alignment and neural relevance dissociate: CNN-Transformer attention maps better predicted synthetic brain activity despite lower fixation alignment, with attention maps best predicting early visual cortex. Together, top-down and bottom-up components trade off what they predict in behavioral and synthetic neural data.

Neural networks encode inputs as high-dimensional vectors, known as representations, that capture how models process data by encoding task-relevant structure and semantics. Representation alignment refers to the degree to which different models, layers, or training conditions produce similar representations for the same inputs, with important implications for model interpretation, selection, and robustness analysis. Existing approaches to measure alignment primarily rely on geometric properties, such as neighborhood and cluster similarity, offering limited insight into the global organization of representations. In this work, we present TopoAlign, a topology-aware framework for visually comparing model representations from a structural perspective. Leveraging mapper graphs from topological data analysis, TopoAlign jointly analyzes graphs constructed from representations of shared inputs across different models or layers. The framework supports a top-down comparative workflow: it first performs global structure alignment via joint force-directed optimization to produce coordinated graph layouts; it then identifies local correspondences through automated detection of structurally matching regions, visualized with Bubble Sets; and finally it enables fine-grained pattern inspection through motif-based queries and membrane-inspired visualizations. We demonstrate TopoAlign through case studies on language and multimodal models, complemented by expert feedback. Our results show that TopoAlign provides meaningful insights into representation structure and alignment from a topological perspective.