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
Atelier is a self‑supervised framework that uses a transformer‑based hypernetwork to generate implicit neural representations (INRs) for cryo‑EM maps, enabling efficient, scale‑agnostic, coordinate‑conditioned feature extraction. Trained on 5,439 maps from the Electron Microscopy Data Bank, the pretrained INR provides continuous local feature fields that can be used as auxiliary channels for a 3D nested U‑Net, improving voxel‑level property prediction across eight tasks compared to a volume‑only baseline. The approach demonstrates that amortized INRs can serve as a geometry‑aware primitive for large‑scale cryo‑EM analysis.
By Phillip Lo, Sudarshan Babu, Dari Kimanius, Aly A. Khan
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: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
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