用深度学习从甲虫图像中自动提取演化特征,掩码效果最佳。
The Phantom of the Elytra -- Phylogenetic Trait Extraction from Images of Rove Beetles Using Deep Learning -- Is the Mask Enough?
- 用掩码、分割图和傅里叶描述符三种形态表示训练模型
- 掩码模型测试集对齐得分0.33±0.02,优于其他两种方法
- 适合需要自动化形态分析的生物分类研究者
传统系统发育分析依赖人工手动提取形态特征,难以扩展至大规模数据。深度学习虽有望实现自动化,但不同形态表示在特征提取中的有效性仍不明确。本研究对比了三种表示方式:完整分割图、二值掩码和甲虫轮廓的傅里叶描述符,在包含215种隐翅虫的Rove-Tree-11数据集上测试。结果表明,基于掩码的模型表现最优,测试集归一化对齐得分为0.33±0.02,优于傅里叶模型的0.45±0.01和分割模型的0.39±0.07。掩码模型可能因能有效捕捉形状特征并利用ResNet50的深层结构优势而表现更佳。相反,傅里叶模型因容量受限且轮廓拟合常出现误差,尤其在腿部等细部结构上表现不佳。结果提示,至少在该类甲虫中,背侧纹理特征的系统发育意义可能较低,需进一步验证。研究强调了选择合适形态表示对自动化系统发育研究的重要性,并呼吁加强自动形态特征提取的可解释性研究。
原文摘要 · Abstract (English)
Phylogenetic analysis traditionally relies on labor-intensive manual extraction of morphological traits, limiting its scalability for large datasets. Recent advances in deep learning offer the potential to automate this process, but the effectiveness of different morphological representations for phylogenetic trait extraction remains poorly understood. In this study, we compare the performance of deep learning models using three distinct morphological representations - full segmentations, binary masks, and Fourier descriptors of beetle outlines. We test this on the Rove-Tree-11 dataset, a curated collection of images from 215 rove beetle species. Our results demonstrate that the mask-based model outperformed the others, achieving a normalized Align Score of 0.33 plus/minus 0.02 on the test set, compared to 0.45 plus/minus 0.01 for the Fourier-based model and 0.39 plus/minus 0.07 for the segmentation-based model. The performance of the mask-based model likely reflects its ability to capture shape features while taking advantage of the depth and capacity of the ResNet50 architecture. These results also indicate that dorsal textural features, at least in this group of beetles, may be of lowered phylogenetic relevance, though further investigation is necessary to confirm this. In contrast, the Fourier-based model suffered from reduced capacity and occasional inaccuracies in outline approximations, particularly in fine structures like legs. These findings highlight the importance of selecting appropriate morphological representations for automated phylogenetic studies and the need for further research into explainability in automatic morphological trait extraction.
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