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.

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