Yuxin Yang

Yuqi Zhang, Bo Fang, Yuxin Yang et al.

Predicting the structure of short peptides in protein binding pockets remains difficult because this regime requires physics-based conformational search, yet existing methods do not provide a practical way to carry out that search on current hardware. We present QSAD, a quantum-classical framework that reformulates peptide structure prediction as amino-acid-level Hamiltonian sampling and replaces iterative optimization with non-iterative Hamiltonian evolution. Executed entirely on IBM Heron R2 across 101 binding-pocket peptides (5-18 residues), QSAD improves prediction accuracy by 27-71% over all evaluated AI and quantum baselines while maintaining the lowest variance across tested lengths. QSAD also tolerates noise levels 3-5x beyond typical hardware error rates, where iterative methods fail, and reduces mean quantum execution time by 27x relative to VQE. The sampled ensemble further supports approximate reconstruction of protein energy landscapes. These results establish coarse-grained quantum sampling as a practical computational path for structure prediction in regimes where data-driven methods lack sufficient signal.

Aoxiong Zeng, Yuxin Yang, Xiangquan Yang

Supervised fine-tuning (SFT) is often treated as a capability-adaptation step, while alignment is attributed to later preference optimization or reinforcement learning. This separation is incomplete: when examples are scored and kept online during fine-tuning, the choice of which data to train on already changes the model's behavioral preferences. We study online data selection as an implicit alignment mechanism. Given the same base model, optimizer, and selected-token budget, we compare random, loss-based, quality-based, and diversity-based online selectors and measure the behavioral drift they induce without any preference optimization. The proposed evaluation tracks helpfulness, refusal rate, verbosity, truthfulness, sycophancy, calibration, and jailbreak robustness, together with diagnostics for which behavioral modes are over-represented in the selected data. We formalize online selection as a reweighted SFT objective whose weights define an implicit preference over response styles and safety postures, so that an online scorer plays the role usually assigned to a reward model. This view predicts that high-scoring data can systematically favor longer, more assertive, more compliant, or more refusal-prone behaviors depending on how the online score is defined. Empirically, selectors that are statistically indistinguishable in task accuracy diverge sharply in refusal rate, verbosity, and sycophancy, and we show that the direction of the shift is predictable from the attribute mixture of the selected data. We introduce Alignment Drift Auditing (ADA), a controlled protocol for quantifying selection-induced behavioral movement, and Alignment-Aware Selection (AAS), a diagnostic online selector that retains data efficiency while constraining drift along safety and style axes.

Tao Zhang, Ziqi Zhang, Zongyang Ma et al.

Knowledge-based Visual Question Answering (KB-VQA) requires models to retrieve visual entities matching the query image from large-scale encyclopedic knowledge bases and answer related questions. Existing multimodal Retrieval Augmented Generation (mRAG) methods rely on global visual features to match candidate entities, yet when the knowledge base contains numerous visually similar entities, the retriever struggles to distinguish them, populating the candidate set with visually similar but factually mismatched distractors. Since subsequent processing steps such as noise filtering are also confined to this fixed candidate set, errors from failed retrieval inevitably propagate to the final answer. To address these challenges, we propose MMAgent-R$^2$, an agentic mRAG framework that integrates visual reranking and active rejection as its internal verification mechanism. Visual reranking directly compares query and candidate images, capturing discriminative details beyond textual descriptions to precisely identify the target entity among similar candidates; active rejection discards unreliable results and retrieves additional candidates when no confident match is found, moving beyond the fixed candidate pool. We design a composite reward function with step-level verification rewards and achieve joint optimization of external retrieval, internal verification, and answer generation via GRPO training. Experiments on InfoSeek, E-VQA, and MMhops demonstrate that \ours{} achieves state-of-the-art performance, with particularly notable advantages in challenging retrieval scenarios and complex multi-image multi-hop reasoning tasks.