# PhyloSDF: Phylogenetically-Conditioned Neural Generation of 3D Skull Morphology via Residual Flow Matching

arXiv: https://arxiv.org/abs/2604.25371 · HTML: https://mlsanity.com/paper/2604.25371/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Medical imaging and segmentation, one of 14 directions in Diffusion models.
- Builds on 22 of its 52 references that are in the map.
- First posted on arXiv 28 Apr 2026.

## Placed in

- Diffusion models / [Medical imaging and segmentation](https://mlsanity.com/diffusion/medical-imaging-and-segmentation/)

## Builds on (most cited first, 22 of 22)

- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [Denoising Diffusion Implicit Models](https://mlsanity.com/paper/2010.02502/) (2020)
- [Flow Matching for Generative Modeling](https://mlsanity.com/paper/2210.02747/) (2022)
- [Generative Adversarial Networks](https://mlsanity.com/paper/2203.00667/) (2022)
- [Gaussian Error Linear Units (GELUs)](https://mlsanity.com/paper/1606.08415/) (2016)
- [DeepSDF: Learning Continuous Signed Distance Functions for Shape Representation](https://mlsanity.com/paper/1901.05103/) (2019)
- [Occupancy Networks: Learning 3D Reconstruction in Function Space](https://mlsanity.com/paper/1812.03828/) (2018)
- [Learning Implicit Fields for Generative Shape Modeling](https://mlsanity.com/paper/1812.02822/) (2018)
- [Building Normalizing Flows with Stochastic Interpolants](https://mlsanity.com/paper/2209.15571/) (2022)
- [Improving and generalizing flow-based generative models with minibatch optimal transport](https://mlsanity.com/paper/2302.00482/) (2023)
- [Implicit Geometric Regularization for Learning Shapes](https://mlsanity.com/paper/2002.10099/) (2020)
- [Differentiable Volumetric Rendering: Learning Implicit 3D Representations without 3D Supervision](https://mlsanity.com/paper/1912.07372/) (2019)
- [LION: Latent Point Diffusion Models for 3D Shape Generation](https://mlsanity.com/paper/2210.06978/) (2022)
- [PointFlow: 3D Point Cloud Generation with Continuous Normalizing Flows](https://mlsanity.com/paper/1906.12320/) (2019)
- [Rethinking Network Design and Local Geometry in Point Cloud: A Simple Residual MLP Framework](https://mlsanity.com/paper/2202.07123/) (2022)
- [PolyGen: An Autoregressive Generative Model of 3D Meshes](https://mlsanity.com/paper/2002.10880/) (2020)
- [Neural Unsigned Distance Fields for Implicit Function Learning](https://mlsanity.com/paper/2010.13938/) (2020)
- [Effectively Unbiased FID and Inception Score and where to find them](https://mlsanity.com/paper/1911.07023/) (2019)
- [DualSDF: Semantic Shape Manipulation using a Two-Level Representation](https://mlsanity.com/paper/2004.02869/) (2020)
- [On Memorization in Probabilistic Deep Generative Models](https://mlsanity.com/paper/2106.03216/) (2021)
- [Efficient Score Pre-computation for Diffusion Models via Cross-Matrix Krylov Projection](https://mlsanity.com/paper/2511.17634/) (2025)

## Abstract (arXiv)

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 Fr'echet 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.