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Xiaohan Qin

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3 papers

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AAAI Conference 2026 Conference Paper

MSAnchor: De Novo Molecular Generation from Mass Spectrometry Data with Anchor-Extended Molecular Scaffolds

Xiaohan Qin
Chao Wang
Zhengyang Zhou
Linjiang Chen
Wenjie Du
Yang Wang

Tandem mass spectrometry (MS/MS) is a critical tool for identifying molecular structures. By efficiently separating molecular fragments based on their mass-to-charge (m/z) ratios, it facilitates molecular generation and subsequent scientific discoveries. However, de novo molecular generation from MS/MS spectra remains fundamentally constrained by two paramount challenges: the vast chemical space requires effective structural constraints, and the absence of fine-grained substructural generation weakens the correspondences between spectral features and molecular structures. In this work, we propose MSAnchor, a novel two-stage framework for MS/MS-based molecular structure generation. We mitigate the search space challenge through the introduction of Anchor-Extended Molecular Scaffold (AEMS) representation that explicitly encodes side-chain anchoring points, thereby dramatically reducing combinatorial complexity. Leveraging the explicit attachment sites provided by AEMS, we develop anchor-specific priors that establish effective alignments between spectral features and molecular substructures. This fine-grained substructural correspondence is further enhanced by a modified Conditional Information Bottleneck (CIB) module that extracts the most informative spectral components in a structure-aware manner. These innovations enable MSAnchor to generate molecular structures that closely reflect spectral characteristics while constraining combinatorial complexity. Extensive experiments on the CANOPUS and MassSpecGym datasets demonstrate that MSAnchor achieves state-of-the-art performance in molecular structure prediction from MS/MS spectra, with performance improvements that are particularly more pronounced for molecules with higher complexity.

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NeurIPS Conference 2025 Conference Paper

NTKMTL: Mitigating Task Imbalance in Multi-Task Learning from Neural Tangent Kernel Perspective

Xiaohan Qin
Xiaoxing Wang
Ning Liao
Junchi Yan

Multi-Task Learning (MTL) enables a single model to learn multiple tasks simultaneously, leveraging knowledge transfer among tasks for enhanced generalization, and has been widely applied across various domains. However, task imbalance remains a major challenge in MTL. Although balancing the convergence speeds of different tasks is an effective approach to address this issue, it is highly challenging to accurately characterize the training dynamics and convergence speeds of multiple tasks within the complex MTL system. To this end, we attempt to analyze the training dynamics in MTL by leveraging Neural Tangent Kernel (NTK) theory and propose a new MTL method, NTKMTL. Specifically, we introduce an extended NTK matrix for MTL and adopt spectral analysis to balance the convergence speeds of multiple tasks, thereby mitigating task imbalance. Based on the approximation via shared representation, we further propose NTKMTL-SR, achieving training efficiency while maintaining competitive performance. Extensive experiments demonstrate that our methods achieve state-of-the-art performance across a wide range of benchmarks, including both multi-task supervised learning and multi-task reinforcement learning. Source code is available at https: //github. com/jianke0604/NTKMTL.

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NeurIPS Conference 2024 Conference Paper

ReLIZO: Sample Reusable Linear Interpolation-based Zeroth-order Optimization

Xiaoxing Wang
Xiaohan Qin
Xiaokang Yang
Junchi Yan

Gradient estimation is critical in zeroth-order optimization methods, which aims to obtain the descent direction by sampling update directions and querying function evaluations. Extensive research has been conducted including smoothing and linear interpolation. The former methods smooth the objective function, causing a biased gradient estimation, while the latter often enjoys more accurate estimates, at the cost of large amounts of samples and queries at each iteration to update variables. This paper resorts to the linear interpolation strategy and proposes to reduce the complexity of gradient estimation by reusing queries in the prior iterations while maintaining the sample size unchanged. Specifically, we model the gradient estimation as a quadratically constrained linear program problem and manage to derive the analytical solution. It innovatively decouples the required sample size from the variable dimension without extra conditions required, making it able to leverage the queries in the prior iterations. Moreover, part of the intermediate variables that contribute to the gradient estimation can be directly indexed, significantly reducing the computation complexity. Experiments on both simulation functions and real scenarios (black-box adversarial attacks neural architecture search, and parameter-efficient fine-tuning for large language models), show its efficacy and efficiency. Our code is available at https: //github. com/Thinklab-SJTU/ReLIZO. git.

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