Implicit Data Synthesis for Contrastive Unsupervised Data Augmentation

Data augmentations define the invariances learned by self-supervised learning (SSL). Standard augmentation pipelines were designed for natural images, yet scientific imaging modalities are governed by physical measurement processes with distinct symmetry and acquisition constraints. Enforcing invariances that contradict these constraints can distort learned representations and limit downstream performance, but practitioners moving from machine learning into a new scientific modality currently have little guidance beyond transferring natural-image pipelines unexamined. We address this gap with a principled, reproducible procedure for augmentation design in scientific SSL: we formalise the physics-aligned augmentation set as a union of measurement-consistent symmetries and acquisition-driven perturbations, and we give a concrete, largely label-free workflow---enumerate candidates, label each by the measurement operator, validate with representation-geometry diagnostics, and confirm by single-factor ablation---for selecting them. We instantiate the procedure for real-space electron microscopy and reciprocal-space 4D-STEM diffraction, and evaluate it across five SSL paradigms (DINOv2, SimCLR, MAE, VICRegL, I-JEPA) on classification and crystal-orientation regression. Physics-aligned augmentations substantially improve downstream performance for objectives relying on cross-view consistency, reduce geodesic error and improve robustness under realistic acquisition variability (detector gain, resolution loss), and systematically reshape representation geometry. While our experiments use electron microscopy, the procedure is modality-agnostic and applies to other measurement-driven domains such as medical and remote-sensing imaging. These results position augmentation design as a primary, and controllable, source of inductive bias in scientific self-supervised learning.

Synthetic data is useful only when the added samples fill missing parts of the training distribution that matter for the downstream task. We introduce LiBaGS, a lightweight, generator-agnostic method for targeted synthetic training data selection. LiBaGS scores candidate synthetic samples by combining decision-boundary proximity, predictive uncertainty, real-data density, and support validity, so that selected samples are both informative and likely to remain on the real data manifold. We then use a boundary-gap allocation rule that targets sparse but realistic decision-boundary neighborhoods, rather than simply adding more data or selecting only the most uncertain candidates. LiBaGS also learns when enough synthetic samples have been added through a marginal-value stopping rule, assigns softer labels near ambiguous boundaries, and uses a diversity objective to avoid redundant near-duplicate selections. Experiments show that LiBaGS improves accuracy over classical oversampling, hard augmentation, uncertainty and density ablations, and targeted-generation selection criteria.

Semantic segmentation models struggle with data sparsity and rare or visually diverse regions, e.g., dense regions or small objects in aerial or autonomous mobility data. While synthetic augmentation is an appealing solution, directly generating new labeled data risks misalignment of labels and generated pixels. Existing solutions to this problem often rely on external models, or employ coarse heuristics such as indiscriminately augmenting all foreground objects or entire backgrounds, which wastes capacity on uninformative pixels. To address this, we propose an uncertainty-guided synthetic context augmentation strategy that strictly preserves label validity and efficiently maximizes pixel informativeness per synthetic sample - no external guardrails required. Using a baseline segmenter's predictive entropy, we identify uncertain semantic regions and inpaint only the complementary visual context. When fine-tuning the segmenter on this synthetic data, we compute the loss only over the original pixels, excluding inpainted regions. This focuses learning on the unmodified, uncertain regions while presenting them in novel contexts. We demonstrate substantial mIoU gains on Cityscapes, UAVID, and BDD100K with the largest gains on rare and difficult classes such as buses, trains, or (from the aerial perspective) cars. Our results demonstrate that uncertainty-guided context augmentation is a highly effective lever to improve segmentation performance on complex datasets, with code provided at https://github.com/XITASO/Preserve-the-Hard-Regenerate-the-Rest.