Jie Wu
Publications
SubQuad: Near-Quadratic-Free Structure Inference with Distribution-Balanced Objectives in Adaptive Receptor framework
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.
NeuroSymActive: Differentiable Neural-Symbolic Reasoning with Active Exploration for Knowledge Graph Question Answering
Large pretrained language models and neural reasoning systems have advanced many natural language tasks, yet they remain challenged by knowledge-intensive queries that require precise, structured multi-hop inference. Knowledge graphs provide a compact symbolic substrate for factual grounding, but integrating graph structure with neural models is nontrivial: naively embedding graph facts into prompts leads to inefficiency and fragility, while purely symbolic or search-heavy approaches can be costly in retrievals and lack gradient-based refinement. We introduce NeuroSymActive, a modular framework that combines a differentiable neural-symbolic reasoning layer with an active, value-guided exploration controller for Knowledge Graph Question Answering. The method couples soft-unification style symbolic modules with a neural path evaluator and a Monte-Carlo style exploration policy that prioritizes high-value path expansions. Empirical results on standard KGQA benchmarks show that NeuroSymActive attains strong answer accuracy while reducing the number of expensive graph lookups and model calls compared to common retrieval-augmented baselines.