arXiv:2605. 29228v2 Announce Type: replace Abstract: Protein structure classification (PSC) uses supervised learning to predict a protein's CATH/SCOP(e) class from the protein's sequence or 3D structural feature(s).
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.
arXiv:2608.29207v1 Announce Type: new Abstract: Protein structure modeling rests on a single computational primitive: the interaction between what a residue is (sequence content) and where it sits (t...
The paper introduces a scalable method to interpret sparse autoencoder (SAE) features in the ESM-2 protein language model by leveraging geometrically inspired features of the protein α‑carbon backbone. Across 8M layers of ESM-2, a false discovery rate–controlled analysis shows that local geometry is significantly associated with many SAE features, revealing substructure within known biological labels and enabling annotation of unannotated metagenomic proteins. Ablation experiments demonstrate that removing these geometric features shifts ESM-2’s predicted contact maps toward the descriptor, linking mechanistic interpretability with structural biology.
This paper introduces a new method for predicting transmembrane protein topology by employing the graph neural network SchNet. The model is trained on the same dataset used for DeepTMHMM, using 5‑fold cross‑validation, and incorporates all atom‑level embeddings rather than just sequence or alpha‑carbon features. Results indicate that GNNs hold significant promise for topological predictions without relying on pre‑trained weights.
arXiv:2607.01630v2 Announce Type: replace Abstract: Dynamic expansion methods for class-incremental learning (CIL) protect task-specific knowledge by growing dedicated tokens or subnetworks, yet our...
Dynamic expansion methods for class-incremental learning (CIL) protect task-specific knowledge by growing dedicated tokens or subnetworks, yet our analyses suggest that classification supervision alone does not sufficiently preserve task-agnostic shared backbone representations over long incremental sequences. We identify two intertwined challenges: cross-task confusion from sequential training on predominantly current-task data, which biases decision boundaries toward recent tasks; and under-optimized shared representations in the backbone that cap long-term discriminability as tasks accumulate.
Over the past decade, deep neural networks (DNNs) have achieved remarkable success on complex machine-learning tasks, yet the theoretical foundations of their performance remain incomplete. From a statistical viewpoint, a natural question is: can DNNs attain feature-learning and prediction consistency comparable to that of classical models?
arXiv:2510. 14217v2 Announce Type: replace Abstract: The spectral properties of feature embeddings offer critical insights into model generalization and representation quality.
arXiv:2608. 12906v1 Announce Type: cross Abstract: RNA-Protein Interactions (RPIs) are critical for regulating cellular functions.
arXiv:2504. 02839v2 Announce Type: replace-cross Abstract: Proteins move and deform to ensure their biological functions.
arXiv:2506. 13196v5 Announce Type: replace Abstract: Accurate prediction of protein-ligand binding affinity is critical for drug discovery.
The study evaluates self‑supervised learning (SSL) models pretrained on ImageNet‑1k and the Human Protein Atlas (HPA) Field‑of‑View (FOV) for protein localization in microscopy images. DINO‑based Vision Transformer backbones pretrained on either dataset transfer well to the OpenCell dataset, achieving strong performance even without fine‑tuning and improving further when fine‑tuned (0.704 ± 0.027 macro F1 on 17 classes). At the single‑cell level, the HPA‑pretrained model outperforms others in k‑nearest‑neighbor classification across all neighborhood sizes (macro F1 ≥ 0.515).