No Free Swap: Protocol-Dependent Layer Redundancy in Transformers

One-shot pruning methods like Wanda and SparseGPT apply the same sparsity ratio to every layer of a transformer, ignoring known variation in layer importance. We propose PALS (Percentile-Aware Layerwise Sparsity), which adjusts per-layer sparsity based on the 99th percentile of activation magnitudes, bounded to $\pm 5\%$ around the target ratio. On LLaMA-2-7B at 50% sparsity, PALS achieves 10.96 WikiText-2 perplexity versus 12.92 for uniform Wanda (mean over 9 runs, $p < 0.001$). The benefit is architecture-dependent: LLaMA-3-8B shows marginal gains and Mistral-7B shows none. We also find that gradient-based allocation -- the seemingly more principled approach -- produces results worse than random, suggesting that gradient magnitude does not predict the impact of discrete weight removal. PALS adds negligible cost to the pruning pipeline and requires no fine-tuning.

Layer pruning removes entire Transformer decoder blocks from large language models, but introduces a mismatch between the hidden state received by the next surviving layer and the distribution it was trained to process, leading to significant performance degradation. We propose Ghosted Layers, a training-free recovery module that addresses this issue by solving a boundary activation alignment problem. Our method derives a closed-form optimal linear operator from a small calibration set to reconstruct the activation discrepancy introduced by the pruned layers. We show that this solution corresponds to the unconstrained optimum of the alignment objective, whereas existing methods are restricted to constrained solutions over limited operator subspaces. Experiments across multiple LLM backbones and pruning strategies demonstrate that our method consistently improves accuracy and perplexity over prior training-free baselines, while preserving the efficiency gains of layer pruning. Official code repository: https://github.com/daniel-eai/ghosted_layers_official_repository/.

Understanding whether deep neural networks are effectively optimized remains challenging, as training occurs in highly nonconvex landscapes and standard metrics provide limited visibility into layer-wise learning quality. This challenge is particularly acute for transformer-based language models, where training is expensive, models are often reused in frozen form, and poorly optimized layers can silently degrade performance. We propose a layer-wise peeling framework for monitoring training dynamics, in which each transformer layer is locally optimized against intermediate representations of the trained model. By constructing lightweight, layer-specific reference solutions and projecting layers onto multiple intermediate outputs via different permutations, we obtain achievable baselines that enable fine-grained diagnosis of under-optimized layers. Experiments on decoder-only transformer models show that these layer-wise reference bounds can match or even surpass the trained model at various stages of training, exposing inefficiencies that remain hidden in aggregate loss curves. We further demonstrate that this analysis remains effective under binarization and quantized settings, where training dynamics are particularly fragile. Across all numerical results, the proposed bounds consistently separate apparent convergence from effective optimality, highlighting optimization opportunities that are invisible when relying on training loss alone.