arXiv subjects

Qihe Chen

Publications and source records attributed to Qihe Chen.

5 recordsLinked to original sources

arXiv2026

CryoACE: An Atom-centric Framework for Accurate and Automated Model Building in Cryo-EM

Protein automodeling from cryo-EM density maps faces unique challenges in enforcing physicochemical validity and managing conformational heterogeneity. Current solvers are often limited to static predictions or require computationally intensive heuristic searches. We present CryoACE, an end-to-end framework that reconstructs precise atomic graphs for both homogeneous and heterogeneous structures. Our method features two key innovations: an atom-centric reconstruction paradigm, where density features are sampled directly at atomic coordinates and iteratively recycled to refine structures, replacing expensive voxel convolutions for efficient multimodal fusion; and a training-free guidance mechanism that leverages predicted local resolution priors to resolve dynamic ambiguity. Validated on a newly constructed high-quality dataset, CryoACE significantly outperforms existing baselines on static benchmarks and, for the first time, unveils atomic-level dynamic conformations on complex real-world datasets like EMPIAR-10345 without relying on pre-built static structures.

cs.AI↗

arXiv2024

DRACO: A Denoising-Reconstruction Autoencoder for Cryo-EM

Foundation models in computer vision have demonstrated exceptional performance in zero-shot and few-shot tasks by extracting multi-purpose features from large-scale datasets through self-supervised pre-training methods. However, these models often overlook the severe corruption in cryogenic electron microscopy (cryo-EM) images by high-level noises. We introduce DRACO, a Denoising-Reconstruction Autoencoder for CryO-EM, inspired by the Noise2Noise (N2N) approach. By processing cryo-EM movies into odd and even images and treating them as independent noisy observations, we apply a denoising-reconstruction hybrid training scheme. We mask both images to create denoising and reconstruction tasks. For DRACO's pre-training, the quality of the dataset is essential, we hence build a high-quality, diverse dataset from an uncurated public database, including over 270,000 movies or micrographs. After pre-training, DRACO naturally serves as a generalizable cryo-EM image denoiser and a foundation model for various cryo-EM downstream tasks. DRACO demonstrates the best performance in denoising, micrograph curation, and particle picking tasks compared to state-of-the-art baselines.

cs.CV↗

arXiv2023

CryoGEM: Physics-Informed Generative Cryo-Electron Microscopy

In the past decade, deep conditional generative models have revolutionized the generation of realistic images, extending their application from entertainment to scientific domains. Single-particle cryo-electron microscopy (cryo-EM) is crucial in resolving near-atomic resolution 3D structures of proteins, such as the SARS- COV-2 spike protein. To achieve high-resolution reconstruction, a comprehensive data processing pipeline has been adopted. However, its performance is still limited as it lacks high-quality annotated datasets for training. To address this, we introduce physics-informed generative cryo-electron microscopy (CryoGEM), which for the first time integrates physics-based cryo-EM simulation with a generative unpaired noise translation to generate physically correct synthetic cryo-EM datasets with realistic noises. Initially, CryoGEM simulates the cryo-EM imaging process based on a virtual specimen. To generate realistic noises, we leverage an unpaired noise translation via contrastive learning with a novel mask-guided sampling scheme. Extensive experiments show that CryoGEM is capable of generating authentic cryo-EM images. The generated dataset can used as training data for particle picking and pose estimation models, eventually improving the reconstruction resolution.

cs.CV↗

arXiv2023

Can Quadruped Navigation Robots be Used as Guide Dogs?

Quadruped robots have the potential to guide blind and low vision (BLV) people due to their highly flexible locomotion and emotional value provided by their bionic forms. However, the development of quadruped guide robots rarely involves BLV users' participatory designs and evaluations. In this paper, we conducted two empirical experiments both in indoor controlled and outdoor field scenarios, exploring the benefits and drawbacks of quadruped guide robots. The results show that the nowadays commercial quadruped robots exposed significant disadvantages in usability and trust compared with wheeled robots. It is concluded that the moving gait and walking noise of quadruped robots would limit the guiding effectiveness to a certain extent, and the empathetic effect of its bionic form for BLV users could not be fully reflected. Based on the findings of wheeled robots and quadruped robots' advantages, we discuss the design implications for the future guide robot design for BLV users. This paper reports the first empirical experiment about quadruped guide robots with BLV users and preliminary explores their potential improvement space in substituting guide dogs, which can inspire the further specialized design of quadruped guide robots.

cs.HC↗

arXiv2023

"I am the follower, also the boss": Exploring Different Levels of Autonomy and Machine Forms of Guiding Robots for the Visually Impaired

Guiding robots, in the form of canes or cars, have recently been explored to assist blind and low vision (BLV) people. Such robots can provide full or partial autonomy when guiding. However, the pros and cons of different forms and autonomy for guiding robots remain unknown. We sought to fill this gap. We designed autonomy-switchable guiding robotic cane and car. We conducted a controlled lab-study (N=12) and a field study (N=9) on BLV. Results showed that full autonomy received better walking performance and subjective ratings in the controlled study, whereas participants used more partial autonomy in the natural environment as demanding more control. Besides, the car robot has demonstrated abilities to provide a higher sense of safety and navigation efficiency compared with the cane robot. Our findings offered empirical evidence about how the BLV community perceived different machine forms and autonomy, which can inform the design of assistive robots.

cs.HC↗