Shiyu Wang

Shiyu Wang, Xiaojie Guo, Xuanyang Lin et al.

Developing deep generative models has been an emerging field due to the ability to model and generate complex data for various purposes, such as image synthesis and molecular design. However, the advancement of deep generative models is limited by challenges to generate objects that possess multiple desired properties: 1) the existence of complex correlation among real-world properties is common but hard to identify; 2) controlling individual property enforces an implicit partially control of its correlated properties, which is difficult to model; 3) controlling multiple properties under various manners simultaneously is hard and under-explored. We address these challenges by proposing a novel deep generative framework that recovers semantics and the correlation of properties through disentangled latent vectors. The correlation is handled via an explainable mask pooling layer, and properties are precisely retained by generated objects via the mutual dependence between latent vectors and properties. Our generative model preserves properties of interest while handling correlation and conflicts of properties under a multi-objective optimization framework. The experiments demonstrate our model's superior performance in generating data with desired properties.

Jingkai Yan, Shiyu Wang, Xinyu Rain Wei et al.

In scientific and engineering scenarios, a recurring task is the detection of low-dimensional families of signals or patterns. A classic family of approaches, exemplified by template matching, aims to cover the search space with a dense template bank. While simple and highly interpretable, it suffers from poor computational efficiency due to unfavorable scaling in the signal space dimensionality. In this work, we study TpopT (TemPlate OPTimization) as an alternative scalable framework for detecting low-dimensional families of signals which maintains high interpretability. We provide a theoretical analysis of the convergence of Riemannian gradient descent for TpopT, and prove that it has a superior dimension scaling to covering. We also propose a practical TpopT framework for nonparametric signal sets, which incorporates techniques of embedding and kernel interpolation, and is further configurable into a trainable network architecture by unrolled optimization. The proposed trainable TpopT exhibits significantly improved efficiency-accuracy tradeoffs for gravitational wave detection, where matched filtering is currently a method of choice. We further illustrate the general applicability of this approach with experiments on handwritten digit data.

Zhiwei Liu, Jielin Qiu, Shiyu Wang et al.

The rapid rise of Large Language Models (LLMs)-based intelligent agents underscores the need for robust, scalable evaluation frameworks. Existing methods rely on static benchmarks and labor-intensive data collection, limiting practical assessment. We introduce MCPEval, an open-source Model Context Protocol (MCP)-based framework that automates end-to-end task generation and deep evaluation of LLM agents across diverse domains. MCPEval standardizes metrics, seamlessly integrates with native agent tools, and eliminates manual effort in building evaluation pipelines. Empirical results across five real-world domains show its effectiveness in revealing nuanced, domain-specific performance. We publicly release MCPEval https://github.com/SalesforceAIResearch/MCPEval to promote reproducible and standardized LLM agent evaluation.

Liangwei Yang, Jing Ma, Jianguo Zhang et al.

Graph neural networks (GNNs) on text--attributed graphs (TAGs) typically encode node texts using pretrained language models (PLMs) and propagate these embeddings through linear neighborhood aggregation. However, the representation spaces of modern PLMs are highly non--linear and geometrically structured, where textual embeddings reside on curved semantic manifolds rather than flat Euclidean spaces. Linear aggregation on such manifolds inevitably distorts geometry and causes semantic drift--a phenomenon where aggregated representations deviate from the intrinsic manifold, losing semantic fidelity and expressive power. To quantitatively investigate this problem, this work introduces a local PCA--based metric that measures the degree of semantic drift and provides the first quantitative framework to analyze how different aggregation mechanisms affect manifold structure. Building upon these insights, we propose Geodesic Aggregation, a manifold--aware mechanism that aggregates neighbor information along geodesics via log--exp mappings on the unit sphere, ensuring that representations remain faithful to the semantic manifold during message passing. We further develop GeoGNN, a practical instantiation that integrates spherical attention with manifold interpolation. Extensive experiments across four benchmark datasets and multiple text encoders show that GeoGNN substantially mitigates semantic drift and consistently outperforms strong baselines, establishing the importance of manifold--aware aggregation in text--attributed graph learning.

Bo Pan, Muran Qin, Shiyu Wang et al.

Deep generative models have been widely used for their ability to generate realistic data samples in various areas, such as images, molecules, text, and speech. One major goal of data generation is controllability, namely to generate new data with desired properties. Despite growing interest in the area of controllable generation, significant challenges still remain, including 1) disentangling desired properties with unrelated latent variables, 2) out-of-distribution property control, and 3) objective optimization for out-of-distribution property control. To address these challenges, in this paper, we propose a general framework to enhance VAE-based data generators with property controllability and ensure disentanglement. Our proposed objective can be optimized on both data seen and unseen in the training set. We propose a training procedure to train the objective in a semi-supervised manner by iteratively conducting mutual mappings between the data and properties. The proposed framework is implemented on four VAE-based controllable generators to evaluate its performance on property error, disentanglement, generation quality, and training time. The results indicate that our proposed framework enables more precise control over the properties of generated samples in a short training time, ensuring the disentanglement and keeping the validity of the generated samples.

Shiyu Wang, Xiaojie Guo, Liang Zhao

Periodic graphs are graphs consisting of repetitive local structures, such as crystal nets and polygon mesh. Their generative modeling has great potential in real-world applications such as material design and graphics synthesis. Classical models either rely on domain-specific predefined generation principles (e.g., in crystal net design), or follow geometry-based prescribed rules. Recently, deep generative models has shown great promise in automatically generating general graphs. However, their advancement into periodic graphs have not been well explored due to several key challenges in 1) maintaining graph periodicity; 2) disentangling local and global patterns; and 3) efficiency in learning repetitive patterns. To address them, this paper proposes Periodical-Graph Disentangled Variational Auto-encoder (PGD-VAE), a new deep generative models for periodic graphs that can automatically learn, disentangle, and generate local and global graph patterns. Specifically, we develop a new periodic graph encoder consisting of global-pattern encoder and local-pattern encoder that ensures to disentangle the representation into global and local semantics. We then propose a new periodic graph decoder consisting of local structure decoder, neighborhood decoder, and global structure decoder, as well as the assembler of their outputs that guarantees periodicity. Moreover, we design a new model learning objective that helps ensure the invariance of local-semantic representations for the graphs with the same local structure. Comprehensive experimental evaluations have been conducted to demonstrate the effectiveness of the proposed method. The code of proposed PGD-VAE is availabe at https://github.com/shi-yu-wang/PGD-VAE.

Shiyu Wang

Writer identification has practical applications for forgery detection and forensic science. Most models based on deep neural networks extract features from character image or sub-regions in character image, which ignoring features contained in page-region image. Our proposed global regular network (GRN) pays attention to these features. GRN network consists of two branches: one branch takes page handwriting as input to extract global features, and the other takes word handwriting as input to extract local features. Global features and local features merge in a global residual way to form overall features of the handwriting. The proposed GRN has two attributions: one is adding a branch to extract features contained in page; the other is using residual attention network to extract local feature. Experiments demonstrate the effectiveness of both strategies. On CVL dataset, our models achieve impressive 99.98% top-1 accuracy and 100% top-5 accuracy with shorter training time and fewer network parameters, which exceeded the state-of-the-art structure. The experiment shows the powerful ability of the network in the field of writer identification. The source code is available at https://github.com/wangshiyu001/GRN.

Shiyu Wang, Mariam Avagyan, Yihan Shen et al.

Learned denoisers play a fundamental role in various signal generation (e.g., diffusion models) and reconstruction (e.g., compressed sensing) architectures, whose success derives from their ability to leverage low-dimensional structure in data. Existing denoising methods, however, either rely on local approximations that require a linear scan of the entire dataset or treat denoising as generic function approximation problems, often sacrificing efficiency and interpretability. We consider the problem of efficiently denoising a new noisy data point sampled from an unknown $d$-dimensional manifold $M \in \mathbb{R}^D$, using only noisy samples. This work proposes a framework for test-time efficient manifold denoising, by framing the concept of "learning-to-denoise" as "learning-to-optimize". We have two technical innovations: (i) online learning methods which learn to optimize over the manifold of clean signals using only noisy data, effectively "growing" an optimizer one sample at a time. (ii) mixed-order methods which guarantee that the learned optimizers achieve global optimality, ensuring both efficiency and near-optimal denoising performance. We corroborate these claims with theoretical analyses of both the complexity and denoising performance of mixed-order traversal. Our experiments on scientific manifolds demonstrate significantly improved complexity-performance tradeoffs compared to nearest neighbor search, which underpins existing provable denoising approaches based on exhaustive search.