EpiFormer: Learning Antigen-Antibody Interactions for Epitope Prediction via Geometric Deep Learning
arXiv:2606. 04154v1 Announce Type: cross Abstract: Antibodies neutralize foreign antigens by binding to specific surface regions called epitopes.
arXiv:2608. 20104v1 Announce Type: cross Abstract: Artificial immune networks (AINs) are naturally memory-forming systems, but conventional visual AINs often rely on flattened vector affinity that ignores spatial structure.
arXiv:2606. 04154v1 Announce Type: cross Abstract: Antibodies neutralize foreign antigens by binding to specific surface regions called epitopes.
arXiv:2602. 17330v5 Announce Type: replace-cross Abstract: Comparative analysis of adaptive immune repertoires at population scale is hampered by two practical bottlenecks: the near-quadratic cost of pairwise affinity evaluations and dataset imbalances that obscure clinically important minority clonotypes.
arXiv:2605. 21610v2 Announce Type: replace Abstract: Antibody design methods condition on antigen structure to generate complementarity-determining regions (CDR), yet a systematic evaluation of baseline methods reveals that they largely ignore the antigen input.
arXiv:2605. 20282v3 Announce Type: replace-cross Abstract: Machine unlearning in Vertical Federated Learning (VFL) has attracted growing interest, yet existing methods certify forgetting solely using output-level metrics.
arXiv:2605. 10840v3 Announce Type: replace-cross Abstract: We present Clin-JEPA, a multi-phase co-training framework for joint-embedding predictive (JEPA) pretraining on EHR patient trajectories.
arXiv:2607. 25531v1 Announce Type: cross Abstract: Contemporary machine learning struggles to learn continually, reuse prior knowledge, and expose a comprehensible internal structure.
arXiv:2602. 01051v5 Announce Type: replace Abstract: Repertoire-level analysis of T cell receptors offers a biologically grounded signal for disease detection and immune monitoring, yet practical deployment is impeded by label sparsity, cohort heterogeneity, and the computational burden of adapting large encoders to new tasks.
arXiv:2605. 20282v2 Announce Type: replace-cross Abstract: Machine unlearning in Vertical Federated Learning (VFL) has attracted growing interest, yet existing methods certify forgetting solely using output-level metrics.
arXiv:2411. 16073v4 Announce Type: replace-cross Abstract: Inspired by the Well-initialized Lottery Ticket Hypothesis (WLTH), we introduce Soft-TransFormers (Soft-TF), a continual learning framework that adapts a frozen pre-trained Transformer through task-specific soft subnetworks: real-valued multiplicative masks over the query, key, value, and output projections of selected self-attention layers.
The paper introduces Activation Boundary Matching for Low‑Rank Adaptation (ABM‑LoRA), a task‑informed initialization strategy that uses the signs of layer‑wise pre‑activations from a brief probe adapter as targets for a fresh adapter. By training with a margin‑based hinge objective on these activation boundaries, ABM‑LoRA captures useful adaptation directions that standard LoRA initializers miss, while requiring only a few forward passes. Experiments show that ABM‑LoRA outperforms or matches existing LoRA, SVD, and gradient‑based initializers across multiple models and benchmarks, including T5‑base/GLUE, ConvNeXt‑T, Swin‑T, Qwen2.5‑1.5B, and LLaMA2‑7B.
arXiv:2603. 25157v3 Announce Type: replace-cross Abstract: Recent vision backbones, such as Transformer families and state-space models like Mamba, have achieved remarkable progress on image recognition.
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...