publications

2025

1. 

   DiffeoMorph: Learning to Morph 3D Shapes Using Differentiable Agent-Based Simulations

   Seong Ho Pahng, Guoye Guan, Benjamin Fefferman, and Sahand Hormoz

   arXiv preprint arXiv:2512.17129, 2025

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   We introduce DiffeoMorph, an end-to-end differentiable framework for learning a morphogenesis protocol that guides a population of agents to morph into a target 3D shape. Each agent updates its position and internal state using an attention-based SE(3)-equivariant graph neural network, based on its own internal state and signals received from other agents.

2024

1. 

   LABS: linear amplification-based bisulfite sequencing for ultrasensitive cancer detection from cell-free DNA

   Xiao-Long Cui, Ji Nie, Houxiang Zhu, Krissana Kowitwanich, Alana V. Beadell, Diana C. West-Szymanski, Zhou Zhang, Urszula Dougherty, Akushika Kwesi, Zifeng Deng, Yan Li, Danqing Meng, Kevin Roggin, Teresa Barry, Ryan Owyang, Ben Fefferman, Chang Zeng, Lu Gao, Carolyn W. T. Zhao, Yuri Malina, Jiangbo Wei, Melanie Weigert, Wenjun Kang, Ajay Goel, Brian C.-H. Chiu, Marc Bissonnette, Wei Zhang, Mengjie Chen, and Chuan He

   Genome Biology, 2024

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   We report LABS, which enables linear amplification of bisulfite-treated DNA fragments in a genome-wide, unbiased fashion, detecting cancer abnormalities with sub-nanogram inputs. Applying LABS to 100 patient samples revealed cancer-specific patterns, copy number alterations, and enhanced cancer detection accuracy.