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SubQuad introduces a novel machine learning pipeline that overcomes the near-quadratic computational costs of analyzing large-scale immune repertoires through GPU-accelerated affinity kernels and MinHash prefiltering. By integrating fairness-constrained clustering, this system effectively addresses dataset imbalances to ensure equitable representation of rare clonotypes in vaccine target prioritization and biomarker discovery. The approach represents a significant advancement in scalable, bias-aware computational methods for immunology research.
SubQuad: Near-Quadratic-Free Structure Inference with Distribution-Balanced Objectives in Adaptive Receptor framework
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. We introduce SubQuad, an end-to-end pipeline that addresses these challenges by combining antigen-aware, near-subquadratic retrieval with GPU-accelerated affinity kernels, learned multimodal fusion, and fairness-constrained clustering. The system employs compact MinHash prefiltering to sharply reduce candidate comparisons, a differentiable gating module that adaptively weights complementary alignment and embedding channels on a per-pair basis, and an automated calibration routine that enforces proportional representation of rare antigen-specific subgroups. On large viral and tumor repertoires SubQuad achieves measured gains in throughput and peak memory usage while preserving or improving recall@k, cluster purity, and subgroup equity. By co-designing indexing, similarity fusion, and equity-aware objectives, SubQuad offers a scalable, bias-aware platform for repertoire mining and downstream translational tasks such as vaccine target prioritization and biomarker discovery.
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. We introduce SubQuad, an end-to-end pipeline that addresses these challenges by combining antigen-aware, near-subquadratic retrieval with GPU-accelerated affinity kernels, learned multimodal fusion, and fairness-constrained clustering. The system employs compact MinHash prefiltering to sharply reduce candidate comparisons, a differentiable gating module that adaptively weights complementary alignment and embedding channels on a per-pair basis, and an automated calibration routine that enforces proportional representation of rare antigen-specific subgroups. On large viral and tumor repertoires SubQuad achieves measured gains in throughput and peak memory usage while preserving or improving recall@k, cluster purity, and subgroup equity. By co-designing indexing, similarity fusion, and equity-aware objectives, SubQuad offers a scalable, bias-aware platform for repertoire mining and downstream translational tasks such as vaccine target prioritization and biomarker discovery.
27 pages, 9 figures. In the previous version, Juntendo University was erroneously listed as the affiliation; we must clarify that this paper has absolutely no relation to Juntendo University. Therefore, we have replaced this affiliation in the new version
Machine Learning (cs.LG); Artificial Intelligence (cs.AI)
arXiv:2602.17330 [cs.LG]
(or arXiv:2602.17330v5 [cs.LG] for this version)
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