Cross-modal translation requires models to capture shared semantics across modalities while preserving the fine-grained structure required by the target modality. Yet in real-world scientific domains, paired data are often imperfect, while obtaining clean pairs at scale is costly. Supervised fine-tuning (SFT) directly optimizes cross-modal translation through categorical token-level supervision, but this objective is sensitive to errors in the target sequences. JEPA offers a complementary representation-space objective, but most existing formulations focus on prediction within a modality rather than translation across modalities. We introduce Anchored Cross-Modal JEPA (AC-JEPA), an SFT-compatible plug-in that predicts masked intermediate states in both cross-modal directions using paired data. The joint-embedding objective targets cross-modal structure predictable from context, while the causal SFT path retains direct token-level supervision for the target sequence. During self-training, AC-JEPA learns from continuous latent targets derived from imperfect pseudo-labeled pairs, offering intrinsic tolerance to local data errors without promoting pseudo-tokens to hard categorical supervision. Using optical chemical structure recognition as a testbed, AC-JEPA trained on clean pairs achieves 76.07% accuracy on the Simple set of the WildMol benchmark, compared with 67.40% for SFT alone. Using the same pseudo-labeled data for both approaches, AC-JEPA-based self-training further raises accuracy to 80.23%, whereas accuracy under direct SFT drops from 67.40% to 63.47%. These results support SFT-anchored joint-embedding prediction as an effective strategy for cross-modal translation under both curated and imperfect supervision.

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