Browsing by Author "Han, Xusi"

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    Classification in Cryo-Electron Tomograms
    (The Eurographics Association, 2019) Gubins, Ilja; Schot, Gijs van der; Veltkamp, Remco C.; Förster, Friedrich; Du, Xuefeng; Zeng, Xiangrui; Zhu, Zhenxi; Chang, Lufan; Xu, Min; Moebel, Emmanuel; Martinez-Sanchez, Antonio; Kervrann, Charles; Lai, Tuan M.; Han, Xusi; Terashi, Genki; Kihara, Daisuke; Himes, Benjamin A.; Wan, Xiaohua; Zhang, Jingrong; Gao, Shan; Hao, Yu; Lv, Zhilong; Wan, Xiaohua; Yang, Zhidong; Ding, Zijun; Cui, Xuefeng; Zhang, Fa; Biasotti, Silvia and Lavoué, Guillaume and Veltkamp, Remco
    Different imaging techniques allow us to study the organization of life at different scales. Cryo-electron tomography (cryo-ET) has the ability to three-dimensionally visualize the cellular architecture as well as the structural details of macro-molecular assemblies under near-native conditions. Due to beam sensitivity of biological samples, an inidividual tomogram has a maximal resolution of 5 nanometers. By averaging volumes, each depicting copies of the same type of a molecule, resolutions beyond 4 Å have been achieved. Key in this process is the ability to localize and classify the components of interest, which is challenging due to the low signal-to-noise ratio. Innovation in computational methods remains key to mine biological information from the tomograms. To promote such innovation, we organize this SHREC track and provide a simulated dataset with the goal of establishing a benchmark in localization and classification of biological particles in cryo-electron tomograms. The publicly available dataset contains ten reconstructed tomograms obtained from a simulated cell-like volume. Each volume contains twelve different types of proteins, varying in size and structure. Participants had access to 9 out of 10 of the cell-like ground-truth volumes for learning-based methods, and had to predict protein class and location in the test tomogram. Five groups submitted eight sets of results, using seven different methods. While our sample size gives only an anecdotal overview of current approaches in cryo-ET classification, we believe it shows trends and highlights interesting future work areas. The results show that learning-based approaches is the current trend in cryo-ET classification research and specifically end-to-end 3D learning-based approaches achieve the best performance.
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    Protein Shape Retrieval Contest
    (The Eurographics Association, 2019) Langenfeld, Florent; Axenopoulos, Apostolos; Benhabiles, Halim; Daras, Petros; Giachetti, Andrea; Han, Xusi; Hammoudi, Karim; Kihara, Daisuke; Lai, Tuan M.; Liu, Haiguang; Melkemi, Mahmoud; Mylonas, Stelios K.; Terashi, Genki; Wang, Yufan; Windal, Feryal; Montes, Matthieu; Biasotti, Silvia and Lavoué, Guillaume and Veltkamp, Remco
    This track aimed at retrieving protein evolutionary classification based on their surfaces meshes only. Given that proteins are dynamic, non-rigid objects and that evolution tends to conserve patterns related to their activity and function, this track offers a challenging issue using biologically relevant molecules. We evaluated the performance of 5 different algorithms and analyzed their ability, over a dataset of 5,298 objects, to retrieve various conformations of identical proteins and various conformations of ortholog proteins (proteins from different organisms and showing the same activity). All methods were able to retrieve a member of the same class as the query in at least 94% of the cases when considering the first match, but show more divergent when more matches were considered. Last, similarity metrics trained on databases dedicated to proteins improved the results.