Xinyu Lin

h-index2
2papers
35citations

2 Papers

3.9CVFeb 16, 2023Code
Fossil Image Identification using Deep Learning Ensembles of Data Augmented Multiviews

Chengbin Hou, Xinyu Lin, Hanhui Huang et al.

Identification of fossil species is crucial to evolutionary studies. Recent advances from deep learning have shown promising prospects in fossil image identification. However, the quantity and quality of labeled fossil images are often limited due to fossil preservation, conditioned sampling, and expensive and inconsistent label annotation by domain experts, which pose great challenges to training deep learning based image classification models. To address these challenges, we follow the idea of the wisdom of crowds and propose a multiview ensemble framework, which collects Original (O), Gray (G), and Skeleton (S) views of each fossil image reflecting its different characteristics to train multiple base models, and then makes the final decision via soft voting. Experiments on the largest fusulinid dataset with 2400 images show that the proposed OGS consistently outperforms baselines (using a single model for each view), and obtains superior or comparable performance compared to OOO (using three base models for three the same Original views). Besides, as the training data decreases, the proposed framework achieves more gains. While considering the identification consistency estimation with respect to human experts, OGS receives the highest agreement with the original labels of dataset and with the re-identifications of two human experts. The validation performance provides a quantitative estimation of consistency across different experts and genera. We conclude that the proposed framework can present state-of-the-art performance in the fusulinid fossil identification case study. This framework is designed for general fossil identification and it is expected to see applications to other fossil datasets in future work. The source code is publicly available at https://github.com/houchengbin/Fossil-Image-Identification to benefit future research in fossil image identification.

7.5AIMar 19
CAPSUL: A Comprehensive Human Protein Benchmark for Subcellular Localization

Yicheng Hu, Xinyu Lin, Shulin Li et al.

Subcellular localization is a crucial biological task for drug target identification and function annotation. Although it has been biologically realized that subcellular localization is closely associated with protein structure, no existing dataset offers comprehensive 3D structural information with detailed subcellular localization annotations, thus severely hindering the application of promising structure-based models on this task. To address this gap, we introduce a new benchmark called $\mathbf{CAPSUL}$, a $\mathbf{C}$omprehensive hum$\mathbf{A}$n $\mathbf{P}$rotein benchmark for $\mathbf{SU}$bcellular $\mathbf{L}$ocalization. It features a dataset that integrates diverse 3D structural representations with fine-grained subcellular localization annotations carefully curated by domain experts. We evaluate this benchmark using a variety of state-of-the-art sequence-based and structure-based models, showcasing the importance of involving structural features in this task. Furthermore, we explore reweighting and single-label classification strategies to facilitate future investigation on structure-based methods for this task. Lastly, we showcase the powerful interpretability of structure-based methods through a case study on the Golgi apparatus, where we discover a decisive localization pattern $α$-helix from attention mechanisms, demonstrating the potential for bridging the gap with intuitive biological interpretability and paving the way for data-driven discoveries in cell biology.