Bongjin Koo

Postdoctoral Scholar
University of California, Santa Barbara
bongjinkoo (at) ucsb.edu

About me

I am a Postdoctoral Scholar, working with Dr Nina Miolane at Geometric Intelligence Lab, University of California, Santa Barbara, USA. Previously, I worked with Prof Matthew J. Clarkson at WEISS (Wellcome / EPSRC Centre for Interventional and Surgical Sciences), University College London (UCL), UK. Before that, I worked with Prof Adrien Bartoli at EnCoV, Université Clermont Auvergne, France. I obtained a PhD in Computer Science supervised by Prof Niloy J. Mitra at Smart Geometry Processing Group, UCL.

Research interests

I utilise geometric/deep learning to discover the dynamics of protein shape changes (conformational changes) from cryo-EM images. In this context, I also develop models that are biophysically grounded and more interpretable while not sacrificing their accuracy.

Selected Publications

CryoChains: Heterogeneous Reconstruction of Molecular Assembly of Semi-flexible Chains from Cryo-EM Images

Bongjin Koo, Julien Martel, Ariana Peck, Axel Levy, Frédéric Poitevin, Nina Miolane
ICML Workshop on Computational Biology 2023 (accepted)

Heterogeneous Reconstruction of Deformable Atomic Models in Cryo-EM

Youssef Nashed, Ariana Peck, Julien Martel, Axel Levy, Bongjin Koo, Gordon Wetzstein, Nina Miolane, Daniel Ratner, Frédéric Poitevin
NeurIPS Machine Learning in Structural Biology Workshop 2022

3D Shape Variational Autoencoder Latent Disentanglement via Mini-Batch Feature Swapping for Bodies and Faces

Simone Foti, Bongjin Koo, Danail Stoyanov, Matthew J. Clarkson
CVPR 2022
[paper] [code] [video] [supplementary]

Automatic, Global Registration in Laparoscopic Liver Surgery

Bongjin Koo, Maria R. Robu, Moustafa Allam, Micha Pfeiffer, Stephen Thompson, Kurinchi Gurusamy, Brian Davidson, Stefanie Speidel, David Hawkes, Danail Stoyanov, Matthew J. Clarkson

Deformable Registration of a Preoperative 3D Liver Volume to a Laparoscopy Image using Contour and Shading Cues

Bongjin Koo, Erol Özgür, Bertrand Le Roy, Emmanuel Buc, Adrien Bartoli

Towards Zero-Waste Furniture Design

Bongjin Koo *, Jean Hergel*, Sylvain Lefebvre, Niloy J. Mitra
TVCG 2016
[paper] [project page]

Computational Fabrication Guided by Function and Material Usage

Bongjin Koo
PhD Thesis 2016

Imagining the Unseen: Stability-based Cuboid Arrangements for Scene Understanding

Tianjia Shao *, Aron Monszpart *, Youyi Zheng, Bongjin Koo, Weiwei Xu, Kun Zhou, Niloy J. Mitra
SIGGRAPH Asia 2014
[paper] [project page]

Creating Works-Like Prototypes of Mechanical Objects

Bongjin Koo, Wilmot Li, JiaXian Yao, Maneesh Agrawala, Niloy J. Mitra
SIGGRAPH Asia 2014
[paper] [project page]

(*Joint first authors)

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