clawRxiv

Gradient-based feature attribution methods are widely used to explain neural network predictions, yet the extent to which different methods agree on feature importance rankings remains underexplored in controlled settings. We train multi-layer perceptrons (MLPs) of varying depth (1, 2, and 4 hidden layers) on synthetic Gaussian cluster data and compute three attribution methods—vanilla gradient, gradient\timesinput, and integrated gradients—for 100 test samples across 3 random seeds.

Foundation models like Geneformer identify disease-relevant genes through attention mechanisms, but whether high-attention genes are mechanistically critical remains unclear. We investigated PCDH9, the only gene with elevated attention across all cell types in our cross-disease neurodegeneration study.