Physics-Aligned Self-Supervised Learning for Scientific Imaging
Authors: Bashir Kazimi, Stefan Sandfeld
Organizations: Institute for Materials Data Science and Informatics (IAS-9), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany · Chair of Materials Data Science and Materials Informatics, Faculty 5 – Georesources and Materials Engineering, RWTH Aachen University, 52056, Aachen, Germany
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.
Scientific observations generate large quantities of unlabeled data which is laborious to hand-label, making unsupervised learning techniques valuable for processing datasets. Among these approaches, contrastive learning provides a convenient mechanism for extracting structural representations from unannotated datasets. For natural imagery, the general approach is to use a variety of data-space augmentation methods in order to generate synthetic samples; however, for scientific observations data-space perturbations can fundamentally alter the underlying data. Our proposed method is to generate contrastive samples by perturbing the network weights rather than the underlying data, thus more closely preserving the structure of the data. We demonstrate this technique using a SimCLR-based pipeline applied over radar observations of meteors, and show performance gains under matched protocols.
Self-supervised learning (SSL) is a standard approach for representation learning in aerial imagery. Existing methods enforce invariance between augmented views, which works well when augmentations preserve semantic content. However, aerial images are frequently degraded by haze, motion blur, rain, and occlusion that remove critical evidence. Enforcing alignment between a clean and a severely degraded view can introduce spurious structure into the latent space. This study proposes a training strategy and architectural modification to enhance SSL robustness to such corruptions. It introduces a per-sample, per-factor trust weight into the alignment objective, combined with the base contrastive loss as an additive residual. A stop-gradient is applied to the trust weight instead of a multiplicative gate. While a multiplicative gate is a natural choice, experiments show it impairs the backbone, whereas our additive-residual approach improves it. Using a 200-epoch protocol on a 210,000-image corpus, the method achieves the highest mean linear-probe accuracy among six backbones on EuroSAT, AID, and NWPU-RESISC45 (90.20% compared to 88.46% for SimCLR and 89.82% for VICReg). It yields the largest improvements under severe information-erasing corruptions on EuroSAT (+19.9 points on haze at s=5 over SimCLR). The method also demonstrates consistent gains of +1 to +3 points in Mahalanobis AUROC on a zero-shot cross-domain stress test using BDD100K weather splits. Two ablations (scalar uncertainty and cosine gate) indicate the additive-residual formulation is the primary source of these improvements. An evidential variant using Dempster-Shafer fusion introduces interpretable signals of conflict and ignorance. These findings offer a concrete design principle for uncertainty-aware SSL. Code is publicly available at https://github.com/WadiiBoulila/trust-ssl.
Self-supervised learning (SSL) is increasingly used in medical image analysis to reduce dependence on costly expert annotations by learning transferable representations from unlabeled data. However, SSL performance depends not only on model architecture, but also on whether the pretext task preserves information required by the downstream clinical objective. This review presents a task-oriented synthesis of SSL methods for medical imaging, focusing on how pretext-task design interacts with imaging modality, label availability, and downstream performance. We analyze 75 studies published from 2017 to 2025 and organize them into four paradigms: contrastive learning, non-contrastive and predictive learning, generative and reconstruction-based learning, and hybrid learning. Rather than cataloging methods chronologically, we examine how these paradigms support classification, segmentation, detection, reconstruction, and regression. The evidence suggests that no SSL strategy is universally optimal. Contrastive objectives generally encourage global discriminative representations and are well aligned with classification, but may underrepresent subtle or localized pathology. Spatial prediction, masked modeling, and reconstruction-based objectives better preserve anatomical structure and are often more suitable for segmentation and dense prediction. Hybrid methods can provide balanced representations, although they increase training complexity. Across modalities, SSL is most beneficial in low-label and few-shot regimes, but its effectiveness depends on modality-aware augmentation, pathology-preserving corruption, and clinically meaningful evaluation. We conclude with practical design guidelines and identify open challenges, including pathology-aware pretext tasks, resource-efficient training for high-dimensional data, and standardized evaluation protocols.