Kaikwan Lau

Kaikwan Lau, Gary P. T. Choi

Generating novel, biologically plausible three-dimensional morphological structures is a fundamental challenge in computational evolutionary biology, hampered by extreme data scarcity and the requirement that generated shapes respect phylogenetic relationships among species. In this work, we present PhyloSDF, a phylogenetically-conditioned neural generative model for 3D biological morphology that integrates two innovations: (1) a DeepSDF auto-decoder regularized by a novel Phylogenetic Consistency Loss that structures the latent space to correlate with evolutionary distances (Pearson $r=0.993$); (2) a Residual Conditional Flow Matching (Residual CFM) architecture that factorizes generation into analytic species-centroid lookup and learned residual prediction, enabling generation from as few as ~4 specimens per species. We evaluate PhyloSDF on 100 micro-CT-scanned skulls of Darwin's Finches and their relatives across 24 species. The model generates novel meshes achieving 88-129% of real intra-species variation at the code level, with all 180 generated meshes verified as non-memorized. Residual CFM surpasses denoising diffusion (which fails entirely at this scale), standard flow matching (which mode-collapses to 3-6% variation), and a Gaussian mixture baseline in both fidelity (Chamfer Distance 0.00181 vs. 0.00190) and morphometric Fréchet distance (10,641 vs. 13,322). Leave-one-species-out experiments across 18 species demonstrate phylogenetic extrapolation capability, and smooth latent interpolations produce biologically plausible ancestral skull reconstructions.

Kaikwan Lau, Andrew S. Na, Justin W. L. Wan

This paper presents a novel framework to accelerate score-based diffusion models. It first converts the standard stable diffusion model into the Fokker-Planck formulation which results in solving large linear systems for each image. For training involving many images, it can lead to a high computational cost. The core innovation is a cross-matrix Krylov projection method that exploits mathematical similarities between matrices, using a shared subspace built from ``seed" matrices to rapidly solve for subsequent ``target" matrices. Our experiments show that this technique achieves a 15.8\% to 43.7\% time reduction over standard sparse solvers. Additionally, we compare our method against DDPM baselines in denoising tasks, showing a speedup of up to 115$\times$. Furthermore, under a fixed computational budget, our model is able to produce high-quality images while DDPM fails to generate recognizable content, illustrating our approach is a practical method for efficient generation in resource-limited settings.