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.
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.
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...
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.
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.
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.
arXiv:2605. 01625v3 Announce Type: replace Abstract: Proteins are inherently multiscale physical systems whose functional properties emerge from coordinated structural organization across multiple spatial resolutions, ranging from atomic interactions to global fold topology.
The paper introduces a multimodal framework that learns subcellularly resolved cell embeddings by integrating RNA expression profiles, protein sequence representations, and protein structural information. It uses a cross‑attention architecture to model interactions across distinct subcellular compartments, producing embeddings that capture both molecular expression patterns and functional protein properties. This approach is presented as the first to jointly incorporate transcriptomic data, protein sequences, and structural knowledge within a unified cross‑modal learning paradigm.
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...
The paper introduces a multimodal framework that learns subcellularly resolved cell embeddings by integrating RNA expression profiles, protein sequence representations, and protein structural information using a cross‑attention architecture. This approach models interactions within distinct subcellular compartments, producing fine‑grained embeddings that capture both molecular expression patterns and functional protein properties. It is presented as the first method to jointly incorporate transcriptomic data, sequence, and structural knowledge for subcellularly resolved cell representation.
arXiv:2606. 02629v1 Announce Type: cross Abstract: Protein-protein interactions (PPIs) are essential for many biological processes.
arXiv:2607. 19083v1 Announce Type: new Abstract: Equivariant graph neural networks provide a powerful modeling language for three-dimensional scientific data, but their reuse is often limited by implementations tied to specific tasks, outputs, and training regimes.
arXiv:2609.14097v1 Announce Type: cross Abstract: Subtomogram classification in cryo-electron tomography (cryo-ET) is a challenging problem due to the scarcity of labeled examples. While cryo-ET simu...