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Shu Wu

Shu Wu appears in the imported research catalog. Authorship, coauthor and topic links are available while profile ownership is still unclaimed.

ResearcherUnclaimed source record
Computation and LanguageArtificial IntelligenceBiomoleculesMachine Learningq-bio.MNQuantitative Methods

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Published work

3 published item(s)

preprint2026arXiv

KBQA-R1: Reinforcing Large Language Models for Knowledge Base Question Answering

Knowledge Base Question Answering (KBQA) challenges models to bridge the gap between natural language and strict knowledge graph schemas by generating executable logical forms. While Large Language Models (LLMs) have advanced this field, current approaches often struggle with a dichotomy of failure: they either generate hallucinated queries without verifying schema existence or exhibit rigid, template-based reasoning that mimics synthesized traces without true comprehension of the environment. To address these limitations, we present \textbf{KBQA-R1}, a framework that shifts the paradigm from text imitation to interaction optimization via Reinforcement Learning. Treating KBQA as a multi-turn decision process, our model learns to navigate the knowledge base using a list of actions, leveraging Group Relative Policy Optimization (GRPO) to refine its strategies based on concrete execution feedback rather than static supervision. Furthermore, we introduce \textbf{Referenced Rejection Sampling (RRS)}, a data synthesis method that resolves cold-start challenges by strictly aligning reasoning traces with ground-truth action sequences. Extensive experiments on WebQSP, GrailQA, and GraphQuestions demonstrate that KBQA-R1 achieves state-of-the-art performance, effectively grounding LLM reasoning in verifiable execution.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

Predict the Retrieval! Test time adaptation for Retrieval Augmented Generation

Retrieval-Augmented Generation (RAG) has emerged as a powerful approach for enhancing large language models' question-answering capabilities through the integration of external knowledge. However, when adapting RAG systems to specialized domains, challenges arise from distribution shifts, resulting in suboptimal generalization performance. In this work, we propose TTARAG, a test-time adaptation method that dynamically updates the language model's parameters during inference to improve RAG system performance in specialized domains. Our method introduces a simple yet effective approach where the model learns to predict retrieved content, enabling automatic parameter adjustment to the target domain. Through extensive experiments across six specialized domains, we demonstrate that TTARAG achieves substantial performance improvements over baseline RAG systems. Code available at https://github.com/sunxin000/TTARAG.

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preprint2026arXiv

Reading the Cell, Designing the Cure: Perturbation-Conditioned Molecular Diffusion for Function-Oriented Drug Design

When reliable target structures are unavailable at scale or phenotypes arise from dysregulated pathways, transcriptomic perturbations provide a system-level functional readout for drug action. In this work, we formalize \emph{Transcriptome-based Drug Design (TBDD)} as a generative inverse problem: designing drug molecules conditioned on desired transcriptomic state transitions. We analyze the inherently ill-posed nature of this task, which is further complicated by the profound domain gap between biology and chemistry and by the sparsity of transcriptomic signals. To address these challenges, we propose \textbf{\themodel{}} (A \textbf{C}ell\textbf{U}lar \textbf{R}esponse \textbf{E}ngine), a multi-resolution transcriptome-guided diffusion framework. \themodel{} features a specialized \textbf{Transcriptome Perturbation Functional Feature Extractor (TFE)} that (1) distills function-oriented perturbation embeddings from pre/post states, (2) aligns these signatures to dual chemical views to bridge the cross-modal gap, and (3) performs heterogeneity-aware aggregation to extract robust state-specific signals from noisy transcriptomic data. Extensive evaluations on both standard benchmarks and rigorous out-of-distribution protocols demonstrate that \themodel{} consistently outperforms strong baselines in structural quality and functional consistency. Furthermore, we validate its practical utility via a zero-shot gene-inhibitor design task, highlighting the potential of phenotype-driven generative discovery.

0 citations0 reviewsNo code linkedOpen access