Context-Aware Deep Learning for Defect Classification in Atomic-Resolution STEM

Artificial intelligence is rapidly advancing materials characterization, yet most applications in electron microscopy rely solely on image contrast, overlooking the chemical and experimental context that shapes image formation. This limitation makes defect classification inherently ambiguous, as similar contrasts can arise from different materials or imaging conditions. Here we develop a context-aware learning framework that integrates image-derived contrast with metadata describing composition, beam energy, and detector geometry. Using a systematically constructed dataset of ~55 million simulated patches spanning 576 cases across 96 doped monolayer transition-metal dichalcogenides, we show that conditioning on contextual variables transforms defect classification from an ill-posed image-only task into a well-posed, physically grounded problem. The framework achieves over 98% accuracy on simulations and near-human agreement on experimental data, with a 94% reduction in posterior entropy. By emphasizing contextual grounding over architectural complexity, this approach links experimental image contrast to the underlying chemical and imaging conditions, supporting physically grounded defect assignments and a general pathway toward multimodal AI models for autonomous materials characterization.