Modeling Spectral–Temporal Information for Estimating Cotton Verticillium Wilt Severity Using a Transformer-TCN Deep Learning Framework

Hyperspectral remote sensing provides essential biochemical and structural information for crop disease monitoring, yet its application to cotton Verticillium wilt has largely focused on single-period evaluations or multi-temporal classifications. Such approaches overlook the progressive nature of this vascular disease, whose pigment, water, and mesophyll responses evolve over time, making temporal hyperspectral information critical for reliable severity estimation but still insufficiently utilized. To overcome this limitation, we conducted daily time-series observations on cotton leaves and collected 2895 hyperspectral reflectance measurements and 770 high-resolution RGB images together with disease severity records, generating a temporally dense spectral-severity dataset spanning symptom-free to severe stages. Five categories of disease-related vegetation indices were derived and organized into 5-day spectral–temporal slices. Based on these features, we introduce a dual-branch Transformer-TCN model that integrates global temporal dependencies captured by self-attention with local temporal variations resolved by dilated causal convolutions for severity inversion. The model delivers the strongest performance with an R2 of 0.8813, exceeding multiple single and hybrid time-series alternatives by 0.0446–0.1407 in R2, equivalent to a relative improvement of 5.33–19.00%. Temporal spectral features also outperform their non-temporal counterparts, highlighting that disease progression dynamics captured by time-series spectra are critical for reliable severity retrieval. Feature contribution analysis indicates that the blue red index BRI provides the highest contribution, consistent with the single-index time-series modelling results. Photosynthesis- and water-related indices provide secondary but complementary support. Collectively, our results demonstrate that the dual-branch Transformer-TCN model can capture complex spectral–temporal relationships between cotton Verticillium wilt and disease severity, providing methodological support for crop disease monitoring and evaluation.