The paper introduces CARNIVAL, a model for protein annotation in cryo-electron tomography (cryo-ET) volumes that leverages simulated data and a forward model to generate domain‑specific augmented paired views for self‑supervised training. By incorporating simulation‑derived protein positions and identities into the architecture and loss function, the model localises semantic information at protein locations. CARNIVAL is evaluated on real tomograms without finetuning and outperforms a state‑of‑the‑art contrastive model that lacks forward‑model paired views or privileged information.
By Bogdan Toader, Kiarash Jamali, Tanmay A. M. Bharat, Sjors H. W. Scheres
arXiv:2606. 00955v1 Announce Type: new Abstract: Despite the growing availability of cryo-electron microscopy (cryo-EM) density maps, effectively leveraging them for protein representation remains challenging.
By Dan Luo, Xuan Lin, Peng Zhou, Junwen Zhu, Tengfei Ma, Xiangxiang Zeng, Yiping Liu
arXiv:2606. 10255v1 Announce Type: cross Abstract: Cryo-electron tomography (cryoET) has emerged as a powerful tool in structural and cellular biology by enabling direct visualization of macromolecular structures within intact cells, thereby linking molecular architecture to cellular organization in a native context.
By Jonathan Schwartz, Utz Heinrich Ermel, C. Braxton Owens, Zhuowen Zhao, Ariana Peck, Gus L. W. Hart, Grant J. Jensen, Bridget Carragher, Dari Kimanius
arXiv:2604.10766v5 Announce Type: replace
Abstract: Open-set 3D macromolecule detection in cryogenic electron tomography eliminates the need for target-specific model retraining. However, strict VRAM...
By Ming-Yang Ho, Alberto Bartesaghi
arXiv:2608.21427v1 Announce Type: new
Abstract: Tuberculosis (TB) is one of the most common and dangerous bacterial ailments. Every year, it causes a large number of deaths worldwide. Although many d...
By Bidhan Biswas, Shahadat Hossain Sohag, Nabil Ashab, Soumit Kumar Kundu, Saif Mahmud Parvez
arXiv:2608.28838v1 Announce Type: cross
Abstract: Cryo-electron microscopy (cryo-EM) determines the structures of proteins and macromolecular assemblies at near-atomic resolution, and the final 3D re...
By Riku Itsuji, Yuanhao Wang, Xingjian Li, Seonghui Min, Hideo Saito, Min Xu
arXiv:2609.08463v1 Announce Type: cross
Abstract: We apply transfer learning (TL) to construct data-driven models of inclusive electron-nucleus cross sections. Starting from an ensemble of deep neura...
By Krzysztof M. Graczyk, Beata E. Kowal, Rwik Dharmapal Banerjee, Jose Luis Bonilla, Hemant Prasad, Jan T. Sobczyk
arXiv:2507. 06764v5 Announce Type: replace-cross Abstract: In this work, we propose Fast Equivariant Imaging (FEI), a novel unsupervised learning framework to rapidly and efficiently train deep imaging networks without ground-truth data.
By Guixian Xu, Jinglai Li, Junqi Tang
arXiv:2609.37605v1 Announce Type: cross
Abstract: Supervised deep learning has advanced sparse-view tomographic reconstruction. However, conventional models, which typically map filtered back-project...
By AmirEhsan Khorashadizadeh, Benjam\'in B\'ejar
arXiv:2606. 31332v1 Announce Type: new Abstract: Protein automodeling from cryo-EM density maps faces unique challenges in enforcing physicochemical validity and managing conformational heterogeneity.
By Minzhang Li, Mingrui Li, Weichen Qin, Qihe Chen, Sixian Shen, Yuan Pei, Jiakai Zhang, Jingyi Yu
The article presents a systematic meta-algorithm for spawning and aggregating multi-class cryo-EM reconstruction jobs, formalizing iterative classification and filtering strategies used by practitioners. It claims to be the first method capable of ab initio reconstruction on datasets with dozens of distinct species, achieving 97% accuracy on a 45-class subset of Tomotwin-100 and 75% on the full dataset, and successfully recovering ribosomal assembly states from an unfiltered experimental cryo-EM dataset. The approach scales with compute resources and aims to underpin automated cryo-EM workflows in contemporary experimental settings.
By Alkin Kaz, Arda Kaz, Ellen D. Zhong
arXiv:2610.01358v1 Announce Type: cross
Abstract: Single-particle cryo-electron microscopy (cryo-EM) has become a widely adopted technique for biomolecular structure determination. The conventional c...
By Advaith Maddipatla, M\"art-Erik M\"aeots, Marco Pegoraro, Nikolaus Dr\"ager, Roberto Covino, Sanketh Vedula, Martin Pacesa, Alex M. Bronstein