Scientific compound figures combine multiple labeled panels into a single image, and downstream pretraining and retrieval require panel-aligned visual-text pairs. However, in a PubMed Central (PMC)-scale crawl of 346,567 compound figures, 16.3% have no caption and are discarded by existing caption-decomposition pipelines. We propose FigEx2, a visual-conditioned framework that takes only a compound figure as input and jointly produces labeled panel boxes and panel-wise captions. FigEx2 introduces an Entity-Attention Kullback-Leibler (KL) regularizer that aligns the detector’s cross-attention with scientific entities annotated for each panel, providing a stable conditioning signal that also improves localization, and applies Group Relative Policy Optimization (GRPO) with a panel-level Entity-F1 reward to optimize scientific faithfulness. We curate BioSci-Fig-Cap for in-domain supervision and contribute physics and chemistry test suites for cross-disciplinary evaluation. FigEx2 achieves 0.751 mAP@0.5:0.95 on BioSci-Fig-Cap, and outperforms Qwen3-VL-8B by 6.80 Entity-F1 on MedICaT for captioning. It also transfers zero-shot to out-of-distribution domains.

Automatic understanding of figures in scientific papers is challenging since they often contain subfigures and subcaptions in complex layouts. In this paper, we propose FigEx, a vision-language model to extract aligned pairs of subfigures and subcaptions from scientific papers. We also release BioSci-Fig, a curated dataset of 7,174 compound figures with annotated subfigure bounding boxes and aligned subcaptions. On BioSci-Fig, FigEx improves subfigure detection AP^b over Grounding DINO by 0.023 and boosts caption separation BLEU over Llama-2-13B by 0.465. The source code is available at: https://github.com/Huang-AI4Medicine-Lab/FigEx.