The paper introduces ImmuneAgent, a closed‑loop AI system that combines multimodal reasoning, continual meta‑learning, and wet‑lab feedback to identify broadly neutralizing antibodies (bnAbs) from human B cell repertoires. Applied to vaccinated or infected cohorts, ImmuneAgent achieved a 55% neutralization discovery rate and an 11% bnAb yield, outperforming existing sequence‑based predictors and co‑folding models. Five discovered antibodies provided full in vivo protection against lethal influenza, and the system uncovered conserved bnAb reservoirs and structural signatures that enabled cross‑viral antibody discovery without antigen‑specific sorting.
arXiv:2603. 13431v3 Announce Type: replace-cross Abstract: Computational antibody design has seen rapid methodological progress, with dozens of deep generative methods proposed in the past three years, yet the field lacks a standardized benchmark for fair comparison and model development.
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:2606. 04154v1 Announce Type: cross Abstract: Antibodies neutralize foreign antigens by binding to specific surface regions called epitopes.
arXiv:2607. 05846v1 Announce Type: cross Abstract: Accurate ranking of antibody candidates according to their binding affinity is essential for therapeutic antibody discovery.
arXiv:2606. 28270v1 Announce Type: new Abstract: The transition from static chat bots to autonomous agents--equipped with persistent memory, tool-use protocols, and multi-agent collaboration--has fundamentally expanded the AI threat landscape.
Accurate ranking of antibody candidates according to their binding affinity is essential for therapeutic antibody discovery. However, existing methods treat affinity comparisons independently and ignore the contextual information encoded in other labeled comparisons, limiting their ability to capture antigen-specific binding landscapes.
arXiv:2607. 20057v1 Announce Type: cross Abstract: Antibodies are essential proteins that play a central role in immune recognition by binding specific antigen molecules.
The paper introduces Conserved Immune Topology (CIT), a lightweight spatial representation that enhances cross‑cancer MSI‑H prediction by augmenting pathology foundation‑model embeddings with immune‑related descriptors. CIT identifies immune‑associated tiles via unsupervised clustering and encodes features such as tertiary lymphoid structures, peritumoral immune reactions, tumor‑infiltrating lymphocyte density, and immune‑tumor mixing, all without requiring annotations or target‑domain data. In cross‑site and cross‑cancer experiments on CPTAC‑COAD and TCGA‑STAD cohorts, CIT improved zero‑shot TransMIL AUC from 0.6627 to 0.7161, demonstrating that spatial immune topology can provide an organ‑invariant representation for MSI‑H prediction.
arXiv:2609.00518v1 Announce Type: new Abstract: Antibody-specific language models pretrained via masked language modeling (MLM) learn representations that are critical for downstream sequence design...
Antibodies are essential proteins that play a central role in immune recognition by binding specific antigen molecules. Although recent protein language models have enabled progress in single-chain protein modeling and generation, they often fall short in antigen-specific antibody design, where effective modeling requires explicit pairing between antibody and antigen, particularly at the epitope level.
arXiv:2609.14709v1 Announce Type: new Abstract: Immune therapies act across cell-intrinsic programs, tissue ecosystems, and patient-specific immune states, yet most predictors address these scales se...
CaliPPer is a post‑hoc framework that calibrates and predicts the performance of binding‑prediction models by combining a multi‑chain Sample‑to‑Domain Distance (S2DD) metric with distance‑aware Bayesian recalibration. It operates at three resolutions—generalisability score, aggregate performance prediction, and per‑sample confidence—achieving strong distance‑performance correlations (|r| = 0.80–0.92) and low prediction errors for AUROC, AP, and F1. In retrospective analyses of five published studies, CaliPPer increased true discovery rates, improving AUROC by up to +0.20 on unseen epitopes and variants and raising confirmed neoantigen findings from 0/5 to 3/5.