Self-Supervised Representation Learning: From Spectral Foundation Models to Auroral Emission Spectra

Foundation models are now increasingly being developed for Earth observation (EO), yet they often rely on stochastic masking that do not explicitly enforce physics constraints; a critical trustworthiness limitation, in particular for predictive models that guide public health decisions. In this work, we propose SpecTM (Spectral Targeted Masking), a physics-informed masking design that encourages the reconstruction of targeted bands from cross-spectral context during pretraining. To achieve this, we developed an adaptable multi-task (band reconstruction, bio-optical index inference, and 8-day-ahead temporal prediction) self-supervised learning (SSL) framework that encodes spectrally intrinsic representations via joint optimization, and evaluated it on a downstream microcystin concentration regression model using NASA PACE hyperspectral imagery over Lake Erie. SpecTM achieves R^2 = 0.695 (current week) and R^2 = 0.620 (8-day-ahead) predictions surpassing all baseline models by (+34% (0.51 Ridge) and +99% (SVR 0.31)) respectively. Our ablation experiments show targeted masking improves predictions by +0.037 R^2 over random masking. Furthermore, it outperforms strong baselines with 2.2x superior label efficiency under extreme scarcity. SpecTM enables physics-informed representation learning across EO domains and improves the interpretability of foundation models.

Astronomical spectra encode rich physical information, but drawing scientific conclusions from spectral features typically requires expert interpretation. This paper presents AstroSpecLM, a spectrum-language model that connects one-dimensional DESI spectra with Qwen3-4B to answer questions and provide explanations grounded in spectral evidence. Instead of generating question-answer pairs directly from templates or raw catalog fields, we first distill each spectrum into a compact set of catalog- and spectrum-derived facts, then use these facts as references to generate instruction-following conversations. The resulting model is competitive with specialist supervised baselines on classification and redshift estimation, while additionally producing natural-language explanations that reference specific spectral features. Our results indicate that grounding a language model in one-dimensional scientific spectra is feasible, and that fact-mediated instruction data yields a model capable of both prediction and explanation.

A spectral foundation model should remain useful when laboratories preprocess spectra differently. The standard test trains a classifier under one pipeline and evaluates under another, taking preserved accuracy as evidence of learned invariance. However, these models normalize each input before any learned parameter is applied. When normalization maps differently preprocessed spectra to the same vector, the encoder receives identical inputs and the measured invariance cannot be attributed to learning. We propose a normalization-only attribution control: compare the encoder against its normalization before interpreting transfer as learned invariance. On six Raman datasets the encoder does not measurably improve transfer over its normalization. A controlled experiment confirms invariance develops only when variation reaches the encoder past normalization. Across three systems, no encoder improves relative retention over its normalization. An audit of eighteen configurations across five modalities confirms the issue is widespread: the normalization-only control should be reported before crediting transfer to the encoder.