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Researcher profile

Gary P. T. Choi

Gary P. T. Choi contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
Computational GeometryComputer Visioncond-mat.softGraphicscond-mat.mtrl-sciQuantitative Methodsmath.DGmath.NAmath.CVcond-mat.dis-nncond-mat.stat-mechDistributed, Parallel, and Cluster ComputingMachine Learningmath.OCnlin.PSNumerical Analysisphysics.app-phphysics.flu-dynRobotics

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Published work

15 published item(s)

preprint2026arXiv

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

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.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

Planar morphometry via functional shape data analysis and quasi-conformal mappings

The study of shapes is one of the most fundamental problems in life sciences. Although numerous methods have been developed for the morphometry of planar biological shapes over the past several decades, most of them focus solely on either the outer silhouettes or the interior features of the shapes without capturing the coupling between them. Moreover, many existing shape mapping techniques are limited to establishing correspondence between planar structures without further allowing for the quantitative analysis or modelling of shape changes. In this work, we introduce FDA-QC, a novel planar morphometry method that combines functional shape data analysis (FDA) techniques and quasi-conformal (QC) mappings, taking both the boundary and interior of the planar shapes into consideration. Specifically, closed planar curves are represented by their square-root velocity functions and registered by elastic matching in the function space. The induced boundary correspondence is then extended to the entire planar domains by a quasi-conformal map, optionally with landmark constraints. Moreover, the proposed FDA-QC method can naturally lead to a unified framework for shape morphing and shape variation quantification. We apply the FDA-QC method to various leaf and insect wing datasets, and the experimental results show that the proposed combined approach captures morphological variation more effectively than purely boundary-based or interior-based descriptions. Altogether, our work paves a new way for understanding the growth and form of planar biological shapes.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

A unifying framework for $n$-dimensional quasi-conformal mappings

With the advancement of computer technology, there is a surge of interest in effective mapping methods for objects in higher-dimensional spaces. To establish a one-to-one correspondence between objects, higher-dimensional quasi-conformal theory can be utilized for ensuring the bijectivity of the mappings. In addition, it is often desirable for the mappings to satisfy certain prescribed geometric constraints and possess low distortion in conformality or volume. In this work, we develop a unifying framework for computing $n$-dimensional quasi-conformal mappings. More specifically, we propose a variational model that integrates quasi-conformal distortion, volumetric distortion, landmark correspondence, intensity mismatch and volume prior information to handle a large variety of deformation problems. We further prove the existence of a minimizer for the proposed model and devise efficient numerical methods to solve the optimization problem. We demonstrate the effectiveness of the proposed framework using various experiments in two- and three-dimensions, with applications to medical image registration, adaptive remeshing and shape modeling.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Automatic Landmark Detection and Registration of Brain Cortical Surfaces via Quasi-Conformal Geometry and Convolutional Neural Networks

In medical imaging, surface registration is extensively used for performing systematic comparisons between anatomical structures, with a prime example being the highly convoluted brain cortical surfaces. To obtain a meaningful registration, a common approach is to identify prominent features on the surfaces and establish a low-distortion mapping between them with the feature correspondence encoded as landmark constraints. Prior registration works have primarily focused on using manually labeled landmarks and solving highly nonlinear optimization problems, which are time-consuming and hence hinder practical applications. In this work, we propose a novel framework for the automatic landmark detection and registration of brain cortical surfaces using quasi-conformal geometry and convolutional neural networks. We first develop a landmark detection network (LD-Net) that allows for the automatic extraction of landmark curves given two prescribed starting and ending points based on the surface geometry. We then utilize the detected landmarks and quasi-conformal theory for achieving the surface registration. Specifically, we develop a coefficient prediction network (CP-Net) for predicting the Beltrami coefficients associated with the desired landmark-based registration and a mapping network called the disk Beltrami solver network (DBS-Net) for generating quasi-conformal mappings from the predicted Beltrami coefficients, with the bijectivity guaranteed by quasi-conformal theory. Experimental results are presented to demonstrate the effectiveness of our proposed framework. Altogether, our work paves a new way for surface-based morphometry and medical shape analysis.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Modular representation and control of floppy networks

Geometric graph models of systems as diverse as proteins, robots, and mechanical structures from DNA assemblies to architected materials point towards a unified way to represent and control them in space and time. While much work has been done in the context of characterizing the behavior of these networks close to critical points associated with bond and rigidity percolation, isostaticity, etc., much less is known about floppy, under-constrained networks that are far more common in nature and technology. Here we combine geometric rigidity and algebraic sparsity to provide a framework for identifying the zero-energy floppy modes via a representation that illuminates the underlying hierarchy and modularity of the network, and thence the control of its nestedness and locality. Our framework allows us to demonstrate a range of applications of this approach that include robotic reaching tasks with motion primitives, and predicting the linear and nonlinear response of elastic networks based solely on infinitesimal rigidity and sparsity, which we test using physical experiments. Our approach is thus likely to be of use broadly in dissecting the geometrical properties of floppy networks using algebraic sparsity to optimize their function and performance.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Quasicrystal kirigami

Kirigami, the art of introducing cuts in thin sheets to enable articulation and deployment, has become an inspiration for a novel class of mechanical metamaterials with unusual properties. Here we complement the use of periodic tiling patterns for kirigami designs by showing that quasicrystals can also serve as the basis for designing deployable kirigami structures, and analyze the geometrical, topological and mechanical properties of these aperiodic kirigami structures.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

Adaptive area-preserving parameterization of open and closed anatomical surfaces

The parameterization of open and closed anatomical surfaces is of fundamental importance in many biomedical applications. Spherical harmonics, a set of basis functions defined on the unit sphere, are widely used for anatomical shape description. However, establishing a one-to-one correspondence between the object surface and the entire unit sphere may induce a large geometric distortion in case the shape of the surface is too different from a perfect sphere. In this work, we propose adaptive area-preserving parameterization methods for simply-connected open and closed surfaces with the target of the parameterization being a spherical cap. Our methods optimize the shape of the parameter domain along with the mapping from the object surface to the parameter domain. The object surface will be globally mapped to an optimal spherical cap region of the unit sphere in an area-preserving manner while also exhibiting low conformal distortion. We further develop a set of spherical harmonics-like basis functions defined over the adaptive spherical cap domain, which we call the adaptive harmonics. Experimental results show that the proposed parameterization methods outperform the existing methods for both open and closed anatomical surfaces in terms of area and angle distortion. Surface description of the object surfaces can be effectively achieved using a novel combination of the adaptive parameterization and the adaptive harmonics. Our work provides a novel way of mapping anatomical surfaces with improved accuracy and greater flexibility. More broadly, the idea of using an adaptive parameter domain allows easy handling of a wide range of biomedical shapes.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

Quasiconformal model with CNN features for large deformation image registration

Image registration has been widely studied over the past several decades, with numerous applications in science, engineering and medicine. Most of the conventional mathematical models for large deformation image registration rely on prescribed landmarks, which usually require tedious manual labeling and are prone to error. In recent years, there has been a surge of interest in the use of machine learning for image registration. In this paper, we develop a novel method for large deformation image registration by a fusion of quasiconformal theory and convolutional neural network (CNN). More specifically, we propose a quasiconformal energy model with a novel fidelity term that incorporates the features extracted using a pre-trained CNN, thereby allowing us to obtain meaningful registration results without any guidance of prescribed landmarks. Moreover, unlike many prior image registration methods, the bijectivity of our method is guaranteed by quasiconformal theory. Experimental results are presented to demonstrate the effectiveness of the proposed method. More broadly, our work sheds light on how rigorous mathematical theories and practical machine learning approaches can be integrated for developing computational methods with improved performance.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Deterministic and stochastic control of kirigami topology

Kirigami, the creative art of paper cutting, is a promising paradigm for mechanical metamaterials. However, to make kirigami-inspired structures a reality requires controlling the topology of kirigami to achieve connectivity and rigidity. We address this question by deriving the maximum number of cuts (minimum number of links) that still allow us to preserve global rigidity and connectivity of the kirigami. A deterministic hierarchical construction method yields an efficient topological way to control both the number of connected pieces and the total degrees of freedom. A statistical approach to the control of rigidity and connectivity in kirigami with random cuts complements the deterministic pathway, and shows that both the number of connected pieces and the degrees of freedom show percolation transitions as a function of the density of cuts (links). Together this provides a general framework for the control of rigidity and connectivity in planar kirigami.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Efficient Feature-based Image Registration by Mapping Sparsified Surfaces

With the advancement in the digital camera technology, the use of high resolution images and videos has been widespread in the modern society. In particular, image and video frame registration is frequently applied in computer graphics and film production. However, conventional registration approaches usually require long computational time for high resolution images and video frames. This hinders the application of the registration approaches in the modern industries. In this work, we first propose a new image representation method to accelerate the registration process by triangulating the images effectively. For each high resolution image or video frame, we compute an optimal coarse triangulation which captures the important features of the image. Then, we apply a surface registration algorithm to obtain a registration map which is used to compute the registration of the high resolution image. Experimental results suggest that our overall algorithm is efficient and capable to achieve a high compression rate while the accuracy of the registration is well retained when compared with the conventional grid-based approach. Also, the computational time of the registration is significantly reduced using our triangulation-based approach.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Parallelizable global conformal parameterization of simply-connected surfaces via partial welding

Conformal surface parameterization is useful in graphics, imaging and visualization, with applications to texture mapping, atlas construction, registration, remeshing and so on. With the increasing capability in scanning and storing data, dense 3D surface meshes are common nowadays. While meshes with higher resolution better resemble smooth surfaces, they pose computational difficulties for the existing parameterization algorithms. In this work, we propose a novel parallelizable algorithm for computing the global conformal parameterization of simply-connected surfaces via partial welding maps. A given simply-connected surface is first partitioned into smaller subdomains. The local conformal parameterizations of all subdomains are then computed in parallel. The boundaries of the parameterized subdomains are subsequently integrated consistently using a novel technique called partial welding, which is developed based on conformal welding theory. Finally, by solving the Laplace equation for each subdomain using the updated boundary conditions, we obtain a global conformal parameterization of the given surface, with bijectivity guaranteed by quasi-conformal theory. By including additional shape constraints, our method can be easily extended to achieve disk conformal parameterization for simply-connected open surfaces and spherical conformal parameterization for genus-0 closed surfaces. Experimental results are presented to demonstrate the effectiveness of our proposed algorithm. When compared to the state-of-the-art conformal parameterization methods, our method achieves a significant improvement in both computational time and accuracy.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Self-excited motions of volatile drops on swellable sheets

When a volatile droplet is deposited on a floating swellable sheet, it becomes asymmetric, lobed and mobile. We describe and quantify this phenomena that involves nonequilibrium swelling, evaporation and motion, working together to realize a self-excitable spatially extended oscillator. Solvent penetration causes the film to swell locally and eventually buckle, changing its shape and the drop responds by moving. Simultaneously, solvent evaporation from the swollen film causes it to regain its shape once the droplet has moved away. The process repeats and leads to complex pulsatile spinning and/or sliding movements. We use a one-dimensional experiment to highlight the slow swelling of and evaporation from the film and the fast motion of the drop, a characteristic of excitable systems. Finally, we provide a phase diagram for droplet excitability as a function of drop size and film thickness and scaling laws for the motion of the droplet.

0 citations0 reviewsNo code linkedOpen access
preprint2019arXiv

Tooth morphometry using quasi-conformal theory

Shape analysis is important in anthropology, bioarchaeology and forensic science for interpreting useful information from human remains. In particular, teeth are morphologically stable and hence well-suited for shape analysis. In this work, we propose a framework for tooth morphometry using quasi-conformal theory. Landmark-matching Teichmüller maps are used for establishing a 1-1 correspondence between tooth surfaces with prescribed anatomical landmarks. Then, a quasi-conformal statistical shape analysis model based on the Teichmüller mapping results is proposed for building a tooth classification scheme. We deploy our framework on a dataset of human premolars to analyze the tooth shape variation among genders and ancestries. Experimental results show that our method achieves much higher classification accuracy with respect to both gender and ancestry when compared to the existing methods. Furthermore, our model reveals the underlying tooth shape difference between different genders and ancestries in terms of the local geometric distortion and curvatures.

0 citations0 reviewsNo code linkedOpen access
preprint2018arXiv

Programming shape using kirigami tessellations

Kirigami tessellations, regular planar patterns formed by cutting flat, thin sheets, have attracted recent scientific interest for their rich geometries, surprising material properties and promise for technologies. Here we pose and solve the inverse problem of designing the number, size, and orientation of cuts that allows us to convert a closed, compact regular kirigami tessellation of the plane into a deployment that conforms approximately to any prescribed target shape in two and three dimensions. We do this by first identifying the constraints on the lengths and angles of generalized kirigami tessellations which guarantee that their reconfigured face geometries can be contracted from a non-trivial deployed shape to a novel planar cut pattern. We encode these conditions in a flexible constrained optimization framework which allows us to deform the geometry of periodic kirigami tesselations with three, four, and sixfold symmetry, among others, into generalized kirigami patterns that deploy to a wide variety of prescribed boundary target shapes. Physically fabricated models verify our inverse design approach and allow us to determine the tunable material response of the resulting structures. We then extend our framework to create generalized kirigami patterns that deploy to approximate curved surfaces in $\mathbb{R}^3$. Altogether, this work illustrates a novel framework for designing complex, shape-changing sheets from simple cuts showing the power of kirigami tessellations as flexible mechanical metamaterials.

0 citations0 reviewsNo code linkedOpen access
preprint2017arXiv

Density-equalizing maps for simply-connected open surfaces

In this paper, we are concerned with the problem of creating flattening maps of simply-connected open surfaces in $\mathbb{R}^3$. Using a natural principle of density diffusion in physics, we propose an effective algorithm for computing density-equalizing flattening maps with any prescribed density distribution. By varying the initial density distribution, a large variety of mappings with different properties can be achieved. For instance, area-preserving parameterizations of simply-connected open surfaces can be easily computed. Experimental results are presented to demonstrate the effectiveness of our proposed method. Applications to data visualization and surface remeshing are explored.

0 citations0 reviewsNo code linkedOpen access