Life sciences · Preprint
arXiv · September 14, 2026
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Multimodal embedding models encode heterogeneous inputs into a shared embedding space, enabling efficient similarity computation across modalities and tasks. Most existing methods optimize cosine-based contrastive objectives, which promote stable training but restrict semantic compatibility to angular geometry, precluding embedding norms from serving as an additional semantic signal. However, directly optimizing the more expressive dot-product similarity, which leverages both angular and norm information, underperforms cosine-based training and exhibits unstable training dynamics. We attribute this discrepancy to premature optimization-space expansion, manifested as angular--norm entanglement and directional anisotropy in the representation space and further compounded by full-parameter fine-tuning. In this paper, we propose PACE, a two-stage framework that progressively expands both the representation and trainable parameter spaces. Stage I combines cosine-based objective with low-rank adaptation to establish a reliable angular geometry within constrained optimization spaces. Stage II switches to dot-product similarity and full-parameter fine-tuning, enabling embedding directions and norms to jointly encode semantic information. We further introduce Focal Embedding Loss, a confidence-adaptive objective that downweights queries with high positive retrieval confidence while emphasizing ambiguous queries with competitive negatives. Experiments across multiple backbone scales and diverse multimodal embedding tasks consistently validate the effectiveness of PACE.