Huahua Lin

Huahua Lin, Xiaohao Cai, Mark Nixon et al.

Planktonic foraminifera, marine protists characterized by their intricate chambered shells, serve as valuable indicators of past and present environmental conditions. Understanding their chamber growth trajectory provides crucial insights into organismal development and ecological adaptation under changing environments. However, automated tracing of chamber growth from imaging data remains largely unexplored, with existing approaches relying heavily on manual segmentation of each chamber, which is time-consuming and subjective. In this study, we propose an end-to-end pipeline that integrates instance segmentation, a computer vision technique not extensively explored in foraminifera, with a dedicated chamber ordering algorithm to automatically reconstruct three-dimensional growth trajectories from high-resolution computed tomography scans. We quantitatively and qualitatively evaluate multiple instance segmentation methods, each optimized for distinct spatial features of the chambers, and examine their downstream influence on growth-order reconstruction accuracy. Experimental results on expert-annotated datasets demonstrate that the proposed pipeline substantially reduces manual effort while maintaining biologically meaningful accuracy. Although segmentation models exhibit under-segmentation in smaller chambers due to reduced voxel fidelity and subtle inter-chamber connectivity, the chamber-ordering algorithm remains robust, achieving consistent reconstruction of developmental trajectories even under partial segmentation. This work provides the first fully automated and reproducible pipeline for digital foraminiferal growth analysis, establishing a foundation for large-scale, data-driven ecological studies.

Huahua Lin, Katayoun Farrahi, Xiaohao Cai

Understanding how neural representations respond to geometric transformations is essential for evaluating whether learned features preserve meaningful spatial structure. Existing approaches primarily assess robustness by comparing model outputs under transformed inputs, offering limited insight into how geometric information is organized within internal representations and failing to distinguish between information loss and re-encoding. In this work, we introduce SEIS (Subspace-based Equivariance and Invariance Scores), a subspace metric for analyzing layer-wise feature representations under geometric transformations, disentangling equivariance from invariance without requiring labels or explicit knowledge of the transformation. Synthetic validation confirms that SEIS correctly recovers known transformations. Applied to trained classification networks, SEIS reveals a transition from equivariance in early layers to invariance in deeper layers, and that data augmentation increases invariance while preserving equivariance. We further show that multi-task learning induces synergistic gains in both properties at the shared encoder, and skip connections restore equivariance lost during decoding.