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Hanwen Xu

Hanwen Xu contributes to research discovery and scholarly infrastructure.

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Published work

5 published item(s)

preprint2026arXiv

LLM Agents Enable User-Governed Personalization Beyond Platform Boundaries

Personalization today is fundamentally platform-centric: services build user representations from the behavioral fragments they observe. Yet no platform can construct a complete picture of the user, as competitive incentives, legal constraints, user privacy concerns, and epistemic limits create persistent data barriers. This paper argues for a shift from platform-centric personalization to user-governed personalization, where only the user can integrate fragmented contexts across platforms and the offline world. The key asymmetry lies in data access: only users can aggregate their own cross-platform and offline information. Large language model (LLM) agents make such integration practically feasible for the first time by enabling reasoning over heterogeneous personal data and transforming users' cross-context information into actionable personalization capabilities. We provide proof-of-concept evidence that users equipped with cross-platform data exports and an off-the-shelf LLM agent can outperform single-platform personalization baselines. We conclude by outlining a research agenda for building scalable user-governed personalization systems.

preprint2026arXiv

MicroDiffuse3D: A Foundation Model for 3D Microscopy Imaging Restoration

Chemical imaging enables label-free visualization of cells, tissues and living systems while providing direct biochemical information that is difficult to obtain with conventional fluorescence microscopy. Despite its promise in applications ranging from intraoperative diagnosis to drug-response analysis, its broader use remains limited by slow data acquisition, particularly for three-dimensional imaging. Here we present MicroDiffuse3D, a pretrained foundation model for 3D microscopy image restoration that recovers high-quality volumetric structure from degraded low-resolution measurements acquired at substantially higher throughput. We evaluated MicroDiffuse3D across three challenging restoration settings, including 3D super-resolution under 16-fold volumetric sparsity, joint degradation in resolution and noise, and 3D denoising in the low signal-to-noise ratio (SNR) regime, where the model delivered clear gains over strong baselines. Under the sparse 3D super-resolution setting, MicroDiffuse3D produced clearer continuity across depth with fewer artifacts and improved segmentation quality by 10.58% and line-profile concordance by 15.59%. Together, our results establish pretrained 3D restoration as a broadly applicable strategy for overcoming the throughput and SNR limitations in volumetric chemical imaging, enabling high-resolution analysis at scales and speeds that were previously difficult to achieve.

preprint2024arXiv

A multi-objective optimization framework for terrain modification based on a combined hydrological and earthwork cost-benefit

The escalating risk of urban inundation has drawn increased attention to urban stormwater management. This study proposes a multi-objective optimization for terrain modification, combining the Non-dominated Sorting Genetic Algorithm II (NSGA-II) with digital elevation model (DEM)-based hydrological cost factor analysis. To reduce the precipitation erosive forces and runoff kinetic energy, the resulting framework offers the possibility of efficiently searching numerous solutions for trade-off sets that meet three conflicting objectives: minimizing maximum flow velocity, maximizing runoff path length and minimizing earthwork costs. Our application case study in Høje Taastrup, Denmark, demonstrates the ability of the optimization framework to iteratively generate diversified modification scenarios, which form the reference for topography planning. The three individual objective preferred solutions, a balanced solution, and twenty solutions under regular ordering are selected and visualized to determine the limits of the optimization and the cost-effectiveness tendency. Integrating genetic algorithms with DEM-based hydrological analysis demonstrates the potential to consider more complicated hydrological benefit objectives with open-ended characteristics. It provides a novel and efficient way to optimize topographic characteristics for improving holistic stormwater management strategies.

preprint2023arXiv

Large-scale Global Low-rank Optimization for Computational Compressed Imaging

Computational reconstruction plays a vital role in computer vision and computational photography. Most of the conventional optimization and deep learning techniques explore local information for reconstruction. Recently, nonlocal low-rank (NLR) reconstruction has achieved remarkable success in improving accuracy and generalization. However, the computational cost has inhibited NLR from seeking global structural similarity, which consequentially keeps it trapped in the tradeoff between accuracy and efficiency and prevents it from high-dimensional large-scale tasks. To address this challenge, we report here the global low-rank (GLR) optimization technique, realizing highly-efficient large-scale reconstruction with global self-similarity. Inspired by the self-attention mechanism in deep learning, GLR extracts exemplar image patches by feature detection instead of conventional uniform selection. This directly produces key patches using structural features to avoid burdensome computational redundancy. Further, it performs patch matching across the entire image via neural-based convolution, which produces the global similarity heat map in parallel, rather than conventional sequential block-wise matching. As such, GLR improves patch grouping efficiency by more than one order of magnitude. We experimentally demonstrate GLR's effectiveness on temporal, frequency, and spectral dimensions, including different computational imaging modalities of compressive temporal imaging, magnetic resonance imaging, and multispectral filter array demosaicing. This work presents the superiority of inherent fusion of deep learning strategies and iterative optimization, and breaks the persistent dilemma of the tradeoff between accuracy and efficiency for various large-scale reconstruction tasks.

preprint2022arXiv

ProTranslator: zero-shot protein function prediction using textual description

Accurately finding proteins and genes that have a certain function is the prerequisite for a broad range of biomedical applications. Despite the encouraging progress of existing computational approaches in protein function prediction, it remains challenging to annotate proteins to a novel function that is not collected in the Gene Ontology and does not have any annotated proteins. This limitation, a side effect from the widely-used multi-label classification problem setting of protein function prediction, hampers the progress of studying new pathways and biological processes, and further slows down research in various biomedical areas. Here, we tackle this problem by annotating proteins to a function only based on its textual description so that we do not need to know any associated proteins for this function. The key idea of our method ProTranslator is to redefine protein function prediction as a machine translation problem, which translates the description word sequence of a function to the amino acid sequence of a protein. We can then transfer annotations from functions that have similar textual description to annotate a novel function. We observed substantial improvement in annotating novel functions and sparsely annotated functions on CAFA3, SwissProt and GOA datasets. We further demonstrated how our method accurately predicted gene members for a given pathway in Reactome, KEGG and MSigDB only based on the pathway description. Finally, we showed how ProTranslator enabled us to generate the textual description instead of the function label for a set of proteins, providing a new scheme for protein function prediction. We envision ProTranslator will give rise to a protein function "search engine" that returns a list of proteins based on the free text queried by the user.