Breaking Noise Shortcuts in Self-Supervised Learning via Noise-Aligned View Generation

Self-supervised learning (SSL) is increasingly applied to scientific imaging domains, such as microscopy, where labels are scarce but noisy data is abundant. These domains exhibit significant signal-dependent noise, which can create a representational shortcut: since both augmented views derive from the same noisy image, the encoder can boost view agreement by also encoding noise patterns rather than semantic content. To enable noise-robust representation learning without knowledge of underlying noise models, we introduce Self-Aligned Noise Augmentation (SEANA), a drop-in module that generates noise-aware SSL views. SEANA learns an invertible variance-stabilizing transform (VST) from noisy data, then estimates the clean signal and resamples independent noise in learned VST space, requiring no clean targets, no dataset-specific denoiser training or use at inference, and no changes to the SSL objective or encoder. On CIFAR-10 and ImageNet-100 under synthetic Gaussian, Poisson–Gaussian, and multiplicative noise, SEANA improves clean-test linear-probe accuracy across contrastive/non-contrastive SSL methods, indicating higher-quality representations. On real fluorescence microscopy, SEANA improves Jurkat cell-cycle stage classification by up to 28.6pp over standard SSL and 27.5pp over denoiser-preprocessed baselines. In both settings, SEANA outperforms the denoiser-preprocessed SSL pipeline, demonstrating that learned VST-space noise-aligned resampling yields more robust representations than denoising alone. Code will be made publicly available.