Xiaohui Chen

Bingzhi Zhang, Peng Xu, Xiaohui Chen et al.

Deep generative models are key-enabling technology to computer vision, text generation, and large language models. Denoising diffusion probabilistic models (DDPMs) have recently gained much attention due to their ability to generate diverse and high-quality samples in many computer vision tasks, as well as to incorporate flexible model architectures and a relatively simple training scheme. Quantum generative models, empowered by entanglement and superposition, have brought new insight to learning classical and quantum data. Inspired by the classical counterpart, we propose the quantum denoising diffusion probabilistic model (QuDDPM) to enable efficiently trainable generative learning of quantum data. QuDDPM adopts sufficient layers of circuits to guarantee expressivity, while it introduces multiple intermediate training tasks as interpolation between the target distribution and noise to avoid barren plateau and guarantee efficient training. We provide bounds on the learning error and demonstrate QuDDPM's capability in learning correlated quantum noise model, quantum many-body phases, and topological structure of quantum data. The results provide a paradigm for versatile and efficient quantum generative learning.

Maria Luisa Taccari, Jonathan Nuttall, Xiaohui Chen et al.

Numerical simulations of groundwater flow are used to analyze and predict the response of an aquifer system to its change in state by approximating the solution of the fundamental groundwater physical equations. The most used and classical methodologies, such as Finite Difference (FD) and Finite Element (FE) Methods, use iterative solvers which are associated with high computational cost. This study proposes a physics-based convolutional encoder-decoder neural network as a surrogate model to quickly calculate the response of the groundwater system. Holding strong promise in cross-domain mappings, encoder-decoder networks are applicable for learning complex input-output mappings of physical systems. This manuscript presents an Attention U-Net model that attempts to capture the fundamental input-output relations of the groundwater system and generates solutions of hydraulic head in the whole domain given a set of physical parameters and boundary conditions. The model accurately predicts the steady state response of a highly heterogeneous groundwater system given the locations and piezometric head of up to 3 wells as input. The network learns to pay attention only in the relevant parts of the domain and the generated hydraulic head field corresponds to the target samples in great detail. Even relative to coarse finite difference approximations the proposed model is shown to be significantly faster than a comparative state-of-the-art numerical solver, thus providing a base for further development of the presented networks as surrogate models for groundwater prediction.

Yinkai Wang, Yan Zhou Chen, Xiaohui Chen et al.

Small-molecule identification from tandem mass spectrometry (MS/MS) remains a bottleneck in untargeted settings where spectral libraries are incomplete. While deep learning offers a solution, current approaches typically fall into two extremes: explicit generative models that construct molecular graphs atom-by-atom, or joint contrastive models that learn cross-modal subspaces from scratch. We introduce SpecBridge, a novel implicit alignment framework that treats structure identification as a geometric alignment problem. SpecBridge fine-tunes a self-supervised spectral encoder (DreaMS) to project directly into the latent space of a frozen molecular foundation model (ChemBERTa), and then performs retrieval by cosine similarity to a fixed bank of precomputed molecular embeddings. Across MassSpecGym, Spectraverse, and MSnLib benchmarks, SpecBridge improves top-1 retrieval accuracy by roughly 20-25% relative to strong neural baselines, while keeping the number of trainable parameters small. These results suggest that aligning to frozen foundation models is a practical, stable alternative to designing new architectures from scratch. The code for SpecBridge is released at https://github.com/HassounLab/SpecBridge.

Junfeng Nie, Alvin Jin, Xiaohui Chen

Existing approaches for synthetic tabular data generation are based on either purely generative models or LLMs, both of which struggle with data heterogeneity, logical consistency, rare-event coverage, and robustness in low-data regimes. In this paper, we propose a hierarchical hybrid top-down and bottom-up (H-TDBU) framework that decouples semantic structures from stochastic texture. In the top-down path, structure-driven logical constraints and cross-modal alignment rules are constructed, while in the bottom-up path, lightweight tabular generators are used to learn local statistical patterns from real data. The two paths are consolidated in a unified synthesis engine with an iterative feedback loop. We evaluate the framework on weak multimodal financial benchmarks combining tabular and sentiment-text data. Experimental results show that our H-TDBU approach improves train-synthetic-test-real performance over neural baseline methods while preserving semantic consistency. Our results suggest that hierarchical rule-guided synthesis provides an effective mechanism for combining controllability, semantic coherence, and statistical fidelity in synthetic data generation.

Yubo Zhuang, Xiaohui Chen, Yun Yang

Clustering is an important exploratory data analysis technique to group objects based on their similarity. The widely used $K$-means clustering method relies on some notion of distance to partition data into a fewer number of groups. In the Euclidean space, centroid-based and distance-based formulations of the $K$-means are equivalent. In modern machine learning applications, data often arise as probability distributions and a natural generalization to handle measure-valued data is to use the optimal transport metric. Due to non-negative Alexandrov curvature of the Wasserstein space, barycenters suffer from regularity and non-robustness issues. The peculiar behaviors of Wasserstein barycenters may make the centroid-based formulation fail to represent the within-cluster data points, while the more direct distance-based $K$-means approach and its semidefinite program (SDP) relaxation are capable of recovering the true cluster labels. In the special case of clustering Gaussian distributions, we show that the SDP relaxed Wasserstein $K$-means can achieve exact recovery given the clusters are well-separated under the $2$-Wasserstein metric. Our simulation and real data examples also demonstrate that distance-based $K$-means can achieve better classification performance over the standard centroid-based $K$-means for clustering probability distributions and images.

Maria Luisa Taccari, Oded Ovadia, He Wang et al.

This paper presents a comprehensive comparison of various machine learning models, namely U-Net, U-Net integrated with Vision Transformers (ViT), and Fourier Neural Operator (FNO), for time-dependent forward modelling in groundwater systems. Through testing on synthetic datasets, it is demonstrated that U-Net and U-Net + ViT models outperform FNO in accuracy and efficiency, especially in sparse data scenarios. These findings underscore the potential of U-Net-based models for groundwater modelling in real-world applications where data scarcity is prevalent.

Xiaohui Chen, Yukun Li, Aonan Zhang et al.

Learning to generate graphs is challenging as a graph is a set of pairwise connected, unordered nodes encoding complex combinatorial structures. Recently, several works have proposed graph generative models based on normalizing flows or score-based diffusion models. However, these models need to generate nodes and edges in parallel from the same process, whose dimensionality is unnecessarily high. We propose NVDiff, which takes the VGAE structure and uses a score-based generative model (SGM) as a flexible prior to sample node vectors. By modeling only node vectors in the latent space, NVDiff significantly reduces the dimension of the diffusion process and thus improves sampling speed. Built on the NVDiff framework, we introduce an attention-based score network capable of capturing both local and global contexts of graphs. Experiments indicate that NVDiff significantly reduces computations and can model much larger graphs than competing methods. At the same time, it achieves superior or competitive performances over various datasets compared to previous methods.

Xiaohui Chen, Yinkai Wang, Yuanqi Du et al.

Self-supervised training methods for transformers have demonstrated remarkable performance across various domains. Previous transformer-based models, such as masked autoencoders (MAE), typically utilize a single normalization layer for both the [CLS] symbol and the tokens. We propose in this paper a simple modification that employs separate normalization layers for the tokens and the [CLS] symbol to better capture their distinct characteristics and enhance downstream task performance. Our method aims to alleviate the potential negative effects of using the same normalization statistics for both token types, which may not be optimally aligned with their individual roles. We empirically show that by utilizing a separate normalization layer, the [CLS] embeddings can better encode the global contextual information and are distributed more uniformly in its anisotropic space. When replacing the conventional normalization layer with the two separate layers, we observe an average 2.7% performance improvement over the image, natural language, and graph domains.

Xiaohui Chen, Yongfei Liu, Yingxiang Yang et al.

Recent advancements in text-to-image (T2I) generative models have shown remarkable capabilities in producing diverse and imaginative visuals based on text prompts. Despite the advancement, these diffusion models sometimes struggle to translate the semantic content from the text into images entirely. While conditioning on the layout has shown to be effective in improving the compositional ability of T2I diffusion models, they typically require manual layout input. In this work, we introduce a novel approach to improving T2I diffusion models using Large Language Models (LLMs) as layout generators. Our method leverages the Chain-of-Thought prompting of LLMs to interpret text and generate spatially reasonable object layouts. The generated layout is then used to enhance the generated images' composition and spatial accuracy. Moreover, we propose an efficient adapter based on a cross-attention mechanism, which explicitly integrates the layout information into the stable diffusion models. Our experiments demonstrate significant improvements in image quality and layout accuracy, showcasing the potential of LLMs in augmenting generative image models.

Yubo Zhuang, Xiaohui Chen, Yun Yang

Clustering is a widely deployed unsupervised learning tool. Model-based clustering is a flexible framework to tackle data heterogeneity when the clusters have different shapes. Likelihood-based inference for mixture distributions often involves non-convex and high-dimensional objective functions, imposing difficult computational and statistical challenges. The classic expectation-maximization (EM) algorithm is a computationally thrifty iterative method that maximizes a surrogate function minorizing the log-likelihood of observed data in each iteration, which however suffers from bad local maxima even in the special case of the standard Gaussian mixture model with common isotropic covariance matrices. On the other hand, recent studies reveal that the unique global solution of a semidefinite programming (SDP) relaxed $K$-means achieves the information-theoretically sharp threshold for perfectly recovering the cluster labels under the standard Gaussian mixture model. In this paper, we extend the SDP approach to a general setting by integrating cluster labels as model parameters and propose an iterative likelihood adjusted SDP (iLA-SDP) method that directly maximizes the exact observed likelihood in the presence of data heterogeneity. By lifting the cluster assignment to group-specific membership matrices, iLA-SDP avoids centroids estimation -- a key feature that allows exact recovery under well-separateness of centroids without being trapped by their adversarial configurations. Thus iLA-SDP is less sensitive than EM to initialization and more stable on high-dimensional data. Our numeric experiments demonstrate that iLA-SDP can achieve lower mis-clustering errors over several widely used clustering methods including $K$-means, SDP and EM algorithms.

Xiaohui Chen, Xi Chen, Liping Liu

Variational Graph Autoencoders (VGAEs) are powerful models for unsupervised learning of node representations from graph data. In this work, we systematically analyze modeling node attributes in VGAEs and show that attribute decoding is important for node representation learning. We further propose a new learning model, interpretable NOde Representation with Attribute Decoding (NORAD). The model encodes node representations in an interpretable approach: node representations capture community structures in the graph and the relationship between communities and node attributes. We further propose a rectifying procedure to refine node representations of isolated notes, improving the quality of these nodes' representations. Our empirical results demonstrate the advantage of the proposed model when learning graph data in an interpretable approach.

Xiaohui Chen, Yinkai Wang, Jiaxing He et al.

Graph generation is a critical task in numerous domains, including molecular design and social network analysis, due to its ability to model complex relationships and structured data. While most modern graph generative models utilize adjacency matrix representations, this work revisits an alternative approach that represents graphs as sequences of node set and edge set. We advocate for this approach due to its efficient encoding of graphs and propose a novel representation. Based on this representation, we introduce the Graph Generative Pre-trained Transformer (G2PT), an auto-regressive model that learns graph structures via next-token prediction. To further exploit G2PT's capabilities as a general-purpose foundation model, we explore fine-tuning strategies for two downstream applications: goal-oriented generation and graph property prediction. We conduct extensive experiments across multiple datasets. Results indicate that G2PT achieves superior generative performance on both generic graph and molecule datasets. Furthermore, G2PT exhibits strong adaptability and versatility in downstream tasks from molecular design to property prediction. Code available at https://github.com/tufts-ml/G2PT,

Mingchen Jiang, Peng Xu, Xichen Ye et al.

Distributional data have become increasingly prominent in modern signal processing, highlighting the necessity of computing optimal transport (OT) maps across multiple probability distributions. Nevertheless, recent studies on neural OT methods predominantly focused on the efficient computation of a single map between two distributions. To address this challenge, we introduce a novel approach to learning transport maps for new empirical distributions. Specifically, we employ the transformer architecture to produce embeddings from distributional data of varying length; these embeddings are then fed into a hypernetwork to generate neural OT maps. Various numerical experiments were conducted to validate the embeddings and the generated OT maps. The model implementation and the code are provided on https://github.com/jiangmingchen/HOTET.

Xiaohui Chen, Xu Han, Jiajing Hu et al.

A graph generative model defines a distribution over graphs. One type of generative model is constructed by autoregressive neural networks, which sequentially add nodes and edges to generate a graph. However, the likelihood of a graph under the autoregressive model is intractable, as there are numerous sequences leading to the given graph; this makes maximum likelihood estimation challenging. Instead, in this work we derive the exact joint probability over the graph and the node ordering of the sequential process. From the joint, we approximately marginalize out the node orderings and compute a lower bound on the log-likelihood using variational inference. We train graph generative models by maximizing this bound, without using the ad-hoc node orderings of previous methods. Our experiments show that the log-likelihood bound is significantly tighter than the bound of previous schemes. Moreover, the models fitted with the proposed algorithm can generate high-quality graphs that match the structures of target graphs not seen during training. We have made our code publicly available at \hyperref[https://github.com/tufts-ml/graph-generation-vi]{https://github.com/tufts-ml/graph-generation-vi}.

Yanxu Mao, Xiaohui Chen, Peipei Liu et al.

Document-level relation extraction (DocRE) aims to extract relations between entities from unstructured document text. Compared to sentence-level relation extraction, it requires more complex semantic understanding from a broader text context. Currently, some studies are utilizing logical rules within evidence sentences to enhance the performance of DocRE. However, in the data without provided evidence sentences, researchers often obtain a list of evidence sentences for the entire document through evidence retrieval (ER). Therefore, DocRE suffers from two challenges: firstly, the relevance between evidence and entity pairs is weak; secondly, there is insufficient extraction of complex cross-relations between long-distance multi-entities. To overcome these challenges, we propose GEGA, a novel model for DocRE. The model leverages graph neural networks to construct multiple weight matrices, guiding attention allocation to evidence sentences. It also employs multi-scale representation aggregation to enhance ER. Subsequently, we integrate the most efficient evidence information to implement both fully supervised and weakly supervised training processes for the model. We evaluate the GEGA model on three widely used benchmark datasets: DocRED, Re-DocRED, and Revisit-DocRED. The experimental results indicate that our model has achieved comprehensive improvements compared to the existing SOTA model.

Mingyang Wu, Xiaohui Chen, Li-Ping Liu

Recently developed deep neural models like NetGAN, CELL, and Variational Graph Autoencoders have made progress but face limitations in replicating key graph statistics on generating large graphs. Diffusion-based methods have emerged as promising alternatives, however, most of them present challenges in computational efficiency and generative performance. EDGE is effective at modeling large networks, but its current denoising approach can be inefficient, often leading to wasted computational resources and potential mismatches in its generation process. In this paper, we propose enhancements to the EDGE model to address these issues. Specifically, we introduce a degree-specific noise schedule that optimizes the number of active nodes at each timestep, significantly reducing memory consumption. Additionally, we present an improved sampling scheme that fine-tunes the generative process, allowing for better control over the similarity between the synthesized and the true network. Our experimental results demonstrate that the proposed modifications not only improve the efficiency but also enhance the accuracy of the generated graphs, offering a robust and scalable solution for graph generation tasks.

Andrew Gracyk, Xiaohui Chen

Optimal transport (OT) offers a versatile framework to compare complex data distributions in a geometrically meaningful way. Traditional methods for computing the Wasserstein distance and geodesic between probability measures require mesh-specific domain discretization and suffer from the curse-of-dimensionality. We present GeONet, a mesh-invariant deep neural operator network that learns the non-linear mapping from the input pair of initial and terminal distributions to the Wasserstein geodesic connecting the two endpoint distributions. In the offline training stage, GeONet learns the saddle point optimality conditions for the dynamic formulation of the OT problem in the primal and dual spaces that are characterized by a coupled PDE system. The subsequent inference stage is instantaneous and can be deployed for real-time predictions in the online learning setting. We demonstrate that GeONet achieves comparable testing accuracy to the standard OT solvers on simulation examples and the MNIST dataset with considerably reduced inference-stage computational cost by orders of magnitude.

Qi Liu, Xiaohui Chen, Zhihui Zhao et al.

Collusion among autonomous agents poses a critical security threat in embodied multi-agent systems (MAS), where coordinated behaviors can deviate from global objectives and lead to real-world consequences. Existing defenses, primarily based on identity control or post-hoc behavior analysis, are insufficient to address such threats in embodied settings due to delayed feedback and noisy observations in physical environments, which make behavioral deviations difficult to detect accurately and in a timely manner. To address this challenge, we propose a mutagenic incentive intervention approach that mitigates collusion by reshaping agents' payoff structures. By rewarding agents who report collusive behavior and penalizing identified participants, the mechanism induces strategic defection and renders collusion unstable. We further design supporting mechanisms, including reporting deposits, smart contract-based reward enforcement, and encrypted communication, to ensure robustness against misuse of the incentive mechanism and retaliation from penalized agents. We implement the proposed approach in both simulated and real-world embodied environments. Experimental results show that our method effectively suppresses collusion by inducing defection, while preserving system efficiency. It achieves performance comparable to the non-collusion baseline and outperforms representative reactive defenses, thereby fulfilling the desired security objectives. These results demonstrate the effectiveness of proactive incentive design as a practical paradigm for securing embodied multi-agent systems.

Yinkai Wang, Xiaohui Chen, Liping Liu et al.

The annotation (assigning structural chemical identities) of MS/MS spectra remains a significant challenge due to the enormous molecular diversity in biological samples and the limited scope of reference databases. Currently, the vast majority of spectral measurements remain in the "dark chemical space" without structural annotations. To improve annotation, we propose MADGEN (Mass-spec Attends to De Novo Molecular GENeration), a scaffold-based method for de novo molecular structure generation guided by mass spectrometry data. MADGEN operates in two stages: scaffold retrieval and spectra-conditioned molecular generation starting with the scaffold. In the first stage, given an MS/MS spectrum, we formulate scaffold retrieval as a ranking problem and employ contrastive learning to align mass spectra with candidate molecular scaffolds. In the second stage, starting from the retrieved scaffold, we employ the MS/MS spectrum to guide an attention-based generative model to generate the final molecule. Our approach constrains the molecular generation search space, reducing its complexity and improving generation accuracy. We evaluate MADGEN on three datasets (NIST23, CANOPUS, and MassSpecGym) and evaluate MADGEN's performance with a predictive scaffold retriever and with an oracle retriever. We demonstrate the effectiveness of using attention to integrate spectral information throughout the generation process to achieve strong results with the oracle retriever.

Xiaohui Chen, Satya Narayan Shukla, Mahmoud Azab et al.

How well can Multimodal Large Language Models (MLLMs) understand composite images? Composite images (CIs) are synthetic visuals created by merging multiple visual elements, such as charts, posters, or screenshots, rather than being captured directly by a camera. While CIs are prevalent in real-world applications, recent MLLM developments have primarily focused on interpreting natural images (NIs). Our research reveals that current MLLMs face significant challenges in accurately understanding CIs, often struggling to extract information or perform complex reasoning based on these images. We find that existing training data for CIs are mostly formatted for question-answer tasks (e.g., in datasets like ChartQA and ScienceQA), while high-quality image-caption datasets, critical for robust vision-language alignment, are only available for NIs. To bridge this gap, we introduce Composite Captions (CompCap), a flexible framework that leverages Large Language Models (LLMs) and automation tools to synthesize CIs with accurate and detailed captions. Using CompCap, we curate CompCap-118K, a dataset containing 118K image-caption pairs across six CI types. We validate the effectiveness of CompCap-118K by supervised fine-tuning MLLMs of three sizes: xGen-MM-inst.-4B and LLaVA-NeXT-Vicuna-7B/13B. Empirical results show that CompCap-118K significantly enhances MLLMs' understanding of CIs, yielding average gains of 1.7%, 2.0%, and 2.9% across eleven benchmarks, respectively.

Biao Yuan, Ana Heitor, He Wang et al.

The emergence of neural networks constrained by physical governing equations has sparked a new trend in deep learning research, which is known as Physics-Informed Neural Networks (PINNs). However, solving high-dimensional problems with PINNs is still a substantial challenge, the space complexity brings difficulty to solving large multidirectional problems. In this paper, a novel PINN framework to quickly predict several three-dimensional Terzaghi consolidation cases under different conditions is proposed. Meanwhile, the loss functions for different cases are introduced, and their differences in three-dimensional consolidation problems are highlighted. The tuning strategies for the PINNs framework for three-dimensional consolidation problems are introduced. Then, the performance of PINNs is tested and compared with traditional numerical methods adopted in forward problems, and the coefficients of consolidation and the impact of noisy data in inverse problems are identified. Finally, the results are summarized and presented from three-dimensional simulations of PINNs, which show an accuracy rate of over 99% compared with ground truth for both forward and inverse problems. These results are desirable with good accuracy and can be used for soil settlement prediction, which demonstrates that the proposed PINNs framework can learn the three-dimensional consolidation PDE well. Keywords: Three-dimensional Terzaghi consolidation; Physics-informed neural networks (PINNs); Forward problems; Inverse problems; soil settlement

Biao Yuan, He Wang, Yanjie Song et al.

Modelling complex multiphysics systems governed by nonlinear and strongly coupled partial differential equations (PDEs) is a cornerstone in computational science and engineering. However, it remains a formidable challenge for traditional numerical solvers due to high computational cost, making them impractical for large-scale applications. Neural operators' reliance on data-driven training limits their applicability in real-world scenarios, as data is often scarce or expensive to obtain. Here, we propose a novel paradigm, physics-informed parallel neural operator (PIPNO), a scalable and unsupervised learning framework that enables data-free PDE modelling by leveraging only governing physical laws. The parallel kernel integration design, incorporating ensemble learning, significantly enhances both compatibility and computational efficiency, enabling scalable operator learning for nonlinear and strongly coupled PDEs. PIPNO efficiently captures nonlinear operator mappings across diverse physics, including geotechnical engineering, material science, electromagnetism, quantum mechanics, and fluid dynamics. The proposed method achieves high-fidelity and rapid predictions, outperforming existing operator learning approaches in modelling nonlinear and strongly coupled multiphysics systems. Therefore, PIPNO offers a powerful alternative to conventional solvers, broadening the applicability of neural operators for multiphysics modelling while ensuring efficiency, robustness, and scalability.

Xiaohui Chen, Tie Luo

In the field of Medical Imaging, extensive research has been dedicated to leveraging its potential in uncovering critical diagnostic features in patients. Artificial Intelligence (AI)-driven medical diagnosis relies on sophisticated machine learning and deep learning models to analyze, detect, and identify diseases from medical images. Despite the remarkable performance of these models, characterized by high accuracy, they grapple with trustworthiness issues. The introduction of a subtle perturbation to the original image empowers adversaries to manipulate the prediction output, redirecting it to other targeted or untargeted classes. Furthermore, the scarcity of publicly available medical images, constituting a bottleneck for reliable training, has led contemporary algorithms to depend on pretrained models grounded on a large set of natural images -- a practice referred to as transfer learning. However, a significant {\em domain discrepancy} exists between natural and medical images, which causes AI models resulting from transfer learning to exhibit heightened {\em vulnerability} to adversarial attacks. This paper proposes a {\em domain assimilation} approach that introduces texture and color adaptation into transfer learning, followed by a texture preservation component to suppress undesired distortion. We systematically analyze the performance of transfer learning in the face of various adversarial attacks under different data modalities, with the overarching goal of fortifying the model's robustness and security in medical imaging tasks. The results demonstrate high effectiveness in reducing attack efficacy, contributing toward more trustworthy transfer learning in biomedical applications.

Dong Li, Guihong Wan, Xintao Wu et al.

Foundation models have emerged as a powerful paradigm in computational pathology (CPath), enabling scalable and generalizable analysis of histopathological images. While early developments centered on uni-modal models trained solely on visual data, recent advances have highlighted the promise of multi-modal foundation models that integrate heterogeneous data sources such as textual reports, structured domain knowledge, and molecular profiles. In this survey, we provide a comprehensive and up-to-date review of multi-modal foundation models in CPath, with a particular focus on models built upon hematoxylin and eosin (H&E) stained whole slide images (WSIs) and tile-level representations. We categorize 32 state-of-the-art multi-modal foundation models into three major paradigms: vision-language, vision-knowledge graph, and vision-gene expression. We further divide vision-language models into non-LLM-based and LLM-based approaches. Additionally, we analyze 28 available multi-modal datasets tailored for pathology, grouped into image-text pairs, instruction datasets, and image-other modality pairs. Our survey also presents a taxonomy of downstream tasks, highlights training and evaluation strategies, and identifies key challenges and future directions. We aim for this survey to serve as a valuable resource for researchers and practitioners working at the intersection of pathology and AI.

Kaheon Kim, Rentian Yao, Changbo Zhu et al.

The optimal transport barycenter (a.k.a. Wasserstein barycenter) is a fundamental notion of averaging that extends from the Euclidean space to the Wasserstein space of probability distributions. Computation of the unregularized barycenter for discretized probability distributions on point clouds is a challenging task when the domain dimension $d > 1$. Most practical algorithms for approximating the barycenter problem are based on entropic regularization. In this paper, we introduce a nearly linear time $O(m \log{m})$ and linear space complexity $O(m)$ primal-dual algorithm, the Wasserstein-Descent $\dot{\mathbb{H}}^1$-Ascent (WDHA) algorithm, for computing the exact barycenter when the input probability density functions are discretized on an $m$-point grid. The key success of the WDHA algorithm hinges on alternating between two different yet closely related Wasserstein and Sobolev optimization geometries for the primal barycenter and dual Kantorovich potential subproblems. Under reasonable assumptions, we establish the convergence rate and iteration complexity of WDHA to its stationary point when the step size is appropriately chosen. Superior computational efficacy, scalability, and accuracy over the existing Sinkhorn-type algorithms are demonstrated on high-resolution (e.g., $1024 \times 1024$ images) 2D synthetic and real data.

Yinkai Wang, Jiaxing He, Yuanqi Du et al.

We consider the protein sequence engineering problem, which aims to find protein sequences with high fitness levels, starting from a given wild-type sequence. Directed evolution has been a dominating paradigm in this field which has an iterative process to generate variants and select via experimental feedback. We demonstrate large language models (LLMs), despite being trained on massive texts, are secretly protein sequence optimizers. With a directed evolutionary method, LLM can perform protein engineering through Pareto and experiment-budget constrained optimization, demonstrating success on both synthetic and experimental fitness landscapes.

Mu Tian, Xiaohui Chen, Yi Gao

Many deep learning based automated medical image segmentation systems, in reality, face difficulties in deployment due to the cost of massive data annotation and high latency in model iteration. We propose a dynamic interactive learning framework that addresses these challenges by integrating interactive segmentation into end-to-end weak supervised learning with streaming tasks. We develop novel replay and label smoothing schemes that overcome catastrophic forgetting and improve online learning robustness. For each image, our multi-round interactive segmentation module simultaneously optimizes both front-end predictions and deep learning segmenter. In each round, a 3D "proxy mask" is propagated from sparse user inputs based on image registration, serving as weak supervision that enable knowledge distillation from the unknown ground truth. In return, the trained segmenter explicitly guides next step's user interventions according to a spatial residual map from consecutive front or back-end predictions. Evaluation on 3D segmentation tasks (NCI-ISBI2013 and BraTS2015) shows that our framework generates online learning performances that match offline training benchmark. In addition, with a 62% reduction in total annotation efforts, our framework produces competitive dice scores comparing to online and offline learning which equipped with full ground truth. Furthermore, such a framework, with its flexibility and responsiveness, could be deployed behind hospital firewall that guarantees data security and easy maintenance.

Inga Girshfeld, Xiaohui Chen

We study the estimation problem of distribution-on-distribution regression, where both predictors and responses are probability measures. Existing approaches typically rely on a global optimal transport map or tangent-space linearization, which can be restrictive in approximation capacity and distort geometry in multivariate underlying domains. In this paper, we propose the \emph{Neural Local Wasserstein Regression}, a flexible nonparametric framework that models regression through locally defined transport maps in Wasserstein space. Our method builds on the analogy with classical kernel regression: kernel weights based on the 2-Wasserstein distance localize estimators around reference measures, while neural networks parameterize transport operators that adapt flexibly to complex data geometries. This localized perspective broadens the class of admissible transformations and avoids the limitations of global map assumptions and linearization structures. We develop a practical training procedure using DeepSets-style architectures and Sinkhorn-approximated losses, combined with a greedy reference selection strategy for scalability. Through synthetic experiments on Gaussian and mixture models, as well as distributional prediction tasks on MNIST, we demonstrate that our approach effectively captures nonlinear and high-dimensional distributional relationships that elude existing methods.

He Yang, Fei Ren, Francesco Calabro et al.

We are delighted to see the recent development of physics-informed extreme learning machine (PIELM) for its higher computational efficiency and accuracy compared to other physics-informed machine learning (PIML) paradigms. Since a comprehensive summary or review of PIELM is currently unavailable, we would like to take this opportunity to share our perspectives and experiences on this promising research direction. We can see that many efforts have been made to solve ordinary/partial differential equations (ODEs/PDEs) characterized by sharp gradients, nonlinearities, high-frequency behavior, hard constraints, uncertainty, multiphysics coupling, and interpretability. Despite these encouraging successes, many pressing challenges remain to be tackled, which also provides opportunities to develop more robust, interpretable, and generalizable PIELM frameworks for scientific and engineering applications.

Peng Xu, Chun-Ying Hou, Xiaohui Chen et al.

Clustering is a hard discrete optimization problem. Nonconvex approaches such as low-rank semidefinite programming (SDP) have recently demonstrated promising statistical and local algorithmic guarantees for cluster recovery. Due to the combinatorial structure of the $K$-means clustering problem, current relaxation algorithms struggle to balance their constraint feasibility and objective optimality, presenting tremendous challenges in computing the second-order critical points with rigorous guarantees. In this paper, we provide a new formulation of the $K$-means problem as a smooth unconstrained optimization over a submanifold and characterize its Riemannian structures to allow it to be solved using a second-order cubic-regularized Riemannian Newton algorithm. By factorizing the $K$-means manifold into a product manifold, we show how each Newton subproblem can be solved in linear time. Our numerical experiments show that the proposed method converges significantly faster than the state-of-the-art first-order nonnegative low-rank factorization method, while achieving similarly optimal statistical accuracy.

Kaheon Kim, Bohan Zhou, Changbo Zhu et al.

This paper introduces a new constraint-free concave dual formulation for the Wasserstein barycenter. Tailoring the vanilla dual gradient ascent algorithm to the Sobolev geometry, we derive a scalable Sobolev gradient ascent (SGA) algorithm to compute the barycenter for input distributions supported on a regular grid. Despite the algorithmic simplicity, we provide a global convergence analysis that achieves the same rate as the classical subgradient descent methods for minimizing nonsmooth convex functions in the Euclidean space. A central feature of our SGA algorithm is that the computationally expensive $c$-concavity projection operator enforced on the Kantorovich dual potentials is unnecessary to guarantee convergence, leading to significant algorithmic and theoretical simplifications over all existing primal and dual methods for computing the exact barycenter. Our numerical experiments demonstrate the superior empirical performance of SGA over the existing optimal transport barycenter solvers.

Hao-Ran Yang, Xiaohui Chen, Chuan-Xian Ren

Aiming to generalize the well-trained gaze estimation model to new target domains, Cross-domain Gaze Estimation (CDGE) is developed for real-world application scenarios. Existing CDGE methods typically extract the domain-invariant features to mitigate domain shift in feature space, which is proved insufficient by Generalized Label Shift (GLS) theory. In this paper, we introduce a novel GLS perspective to CDGE and modelize the cross-domain problem by label and conditional shift problem. A GLS correction framework is presented and a feasible realization is proposed, in which a importance reweighting strategy based on truncated Gaussian distribution is introduced to overcome the continuity challenges in label shift correction. To embed the reweighted source distribution to conditional invariant learning, we further derive a probability-aware estimation of conditional operator discrepancy. Extensive experiments on standard CDGE tasks with different backbone models validate the superior generalization capability across domain and applicability on various models of proposed method.

Xiaohui Chen, Tie Luo

Depression is a common mental health disorder that can cause consequential symptoms with continuously depressed mood that leads to emotional distress. One category of depression is Concealed Depression, where patients intentionally or unintentionally hide their genuine emotions through exterior optimism, thereby complicating and delaying diagnosis and treatment and leading to unexpected suicides. In this paper, we propose to diagnose concealed depression by using facial micro-expressions (FMEs) to detect and recognize underlying true emotions. However, the extremely low intensity and subtle nature of FMEs make their recognition a tough task. We propose a facial landmark-based Region-of-Interest (ROI) approach to address the challenge, and describe a low-cost and privacy-preserving solution that enables self-diagnosis using portable mobile devices in a personal setting (e.g., at home). We present results and findings that validate our method, and discuss other technical challenges and future directions in applying such techniques to real clinical settings.

Yubo Zhuang, Xiaohui Chen, Yun Yang et al.

$K$-means clustering is a widely used machine learning method for identifying patterns in large datasets. Recently, semidefinite programming (SDP) relaxations have been proposed for solving the $K$-means optimization problem, which enjoy strong statistical optimality guarantees. However, the prohibitive cost of implementing an SDP solver renders these guarantees inaccessible to practical datasets. In contrast, nonnegative matrix factorization (NMF) is a simple clustering algorithm widely used by machine learning practitioners, but it lacks a solid statistical underpinning and theoretical guarantees. In this paper, we consider an NMF-like algorithm that solves a nonnegative low-rank restriction of the SDP-relaxed $K$-means formulation using a nonconvex Burer--Monteiro factorization approach. The resulting algorithm is as simple and scalable as state-of-the-art NMF algorithms while also enjoying the same strong statistical optimality guarantees as the SDP. In our experiments, we observe that our algorithm achieves significantly smaller mis-clustering errors compared to the existing state-of-the-art while maintaining scalability.

Xiaohui Chen, Jiankai Sun, Taiqing Wang et al.

Data subsampling is widely used to speed up the training of large-scale recommendation systems. Most subsampling methods are model-based and often require a pre-trained pilot model to measure data importance via e.g. sample hardness. However, when the pilot model is misspecified, model-based subsampling methods deteriorate. Since model misspecification is persistent in real recommendation systems, we instead propose model-agnostic data subsampling methods by only exploring input data structure represented by graphs. Specifically, we study the topology of the user-item graph to estimate the importance of each user-item interaction (an edge in the user-item graph) via graph conductance, followed by a propagation step on the network to smooth out the estimated importance value. Since our proposed method is model-agnostic, we can marry the merits of both model-agnostic and model-based subsampling methods. Empirically, we show that combing the two consistently improves over any single method on the used datasets. Experimental results on KuaiRec and MIND datasets demonstrate that our proposed methods achieve superior results compared to baseline approaches.

Xiaohui Chen, Jiaxing He, Xu Han et al.

Diffusion-based generative graph models have been proven effective in generating high-quality small graphs. However, they need to be more scalable for generating large graphs containing thousands of nodes desiring graph statistics. In this work, we propose EDGE, a new diffusion-based generative graph model that addresses generative tasks with large graphs. To improve computation efficiency, we encourage graph sparsity by using a discrete diffusion process that randomly removes edges at each time step and finally obtains an empty graph. EDGE only focuses on a portion of nodes in the graph at each denoising step. It makes much fewer edge predictions than previous diffusion-based models. Moreover, EDGE admits explicitly modeling the node degrees of the graphs, further improving the model performance. The empirical study shows that EDGE is much more efficient than competing methods and can generate large graphs with thousands of nodes. It also outperforms baseline models in generation quality: graphs generated by our approach have more similar graph statistics to those of the training graphs.

Yubo Zhuang, Xiaohui Chen, Yun Yang

Semidefinite programming (SDP) is a powerful tool for tackling a wide range of computationally hard problems such as clustering. Despite the high accuracy, semidefinite programs are often too slow in practice with poor scalability on large (or even moderate) datasets. In this paper, we introduce a linear time complexity algorithm for approximating an SDP relaxed $K$-means clustering. The proposed sketch-and-lift (SL) approach solves an SDP on a subsampled dataset and then propagates the solution to all data points by a nearest-centroid rounding procedure. It is shown that the SL approach enjoys a similar exact recovery threshold as the $K$-means SDP on the full dataset, which is known to be information-theoretically tight under the Gaussian mixture model. The SL method can be made adaptive with enhanced theoretic properties when the cluster sizes are unbalanced. Our simulation experiments demonstrate that the statistical accuracy of the proposed method outperforms state-of-the-art fast clustering algorithms without sacrificing too much computational efficiency, and is comparable to the original $K$-means SDP with substantially reduced runtime.

Xiaohui Chen, Ramtin Hosseini, Karen Panetta et al.

Predicting future sensory states is crucial for learning agents such as robots, drones, and autonomous vehicles. In this paper, we couple multiple sensory modalities with exploratory actions and propose a predictive neural network architecture to address this problem. Most existing approaches rely on large, manually annotated datasets, or only use visual data as a single modality. In contrast, the unsupervised method presented here uses multi-modal perceptions for predicting future visual frames. As a result, the proposed model is more comprehensive and can better capture the spatio-temporal dynamics of the environment, leading to more accurate visual frame prediction. The other novelty of our framework is the use of sub-networks dedicated to anticipating future haptic, audio, and tactile signals. The framework was tested and validated with a dataset containing 4 sensory modalities (vision, haptic, audio, and tactile) on a humanoid robot performing 9 behaviors multiple times on a large set of objects. While the visual information is the dominant modality, utilizing the additional non-visual modalities improves the accuracy of predictions.

Xu Han, Xiaohui Chen, Li-Ping Liu

When formulated as an unsupervised learning problem, anomaly detection often requires a model to learn the distribution of normal data. Previous works apply Generative Adversarial Networks (GANs) to anomaly detection tasks and show good performances from these models. Motivated by the observation that GAN ensembles often outperform single GANs in generation tasks, we propose to construct GAN ensembles for anomaly detection. In the proposed method, a group of generators and a group of discriminators are trained together, so every generator gets feedback from multiple discriminators, and vice versa. Compared to a single GAN, a GAN ensemble can better model the distribution of normal data and thus better detect anomalies. Our theoretical analysis of GANs and GAN ensembles explains the role of a GAN discriminator in anomaly detection. In the empirical study, we evaluate ensembles constructed from four types of base models, and the results show that these ensembles clearly outperform single models in a series of tasks of anomaly detection.

Xiaohui Chen, Yun Yang

We determine the information-theoretic cutoff value on separation of cluster centers for exact recovery of cluster labels in a $K$-component Gaussian mixture model with equal cluster sizes. Moreover, we show that a semidefinite programming (SDP) relaxation of the $K$-means clustering method achieves such sharp threshold for exact recovery without assuming the symmetry of cluster centers.

Xiaohui Chen, Yun Yang

We introduce the {\it diffusion $K$-means} clustering method on Riemannian submanifolds, which maximizes the within-cluster connectedness based on the diffusion distance. The diffusion $K$-means constructs a random walk on the similarity graph with vertices as data points randomly sampled on the manifolds and edges as similarities given by a kernel that captures the local geometry of manifolds. The diffusion $K$-means is a multi-scale clustering tool that is suitable for data with non-linear and non-Euclidean geometric features in mixed dimensions. Given the number of clusters, we propose a polynomial-time convex relaxation algorithm via the semidefinite programming (SDP) to solve the diffusion $K$-means. In addition, we also propose a nuclear norm regularized SDP that is adaptive to the number of clusters. In both cases, we show that exact recovery of the SDPs for diffusion $K$-means can be achieved under suitable between-cluster separability and within-cluster connectedness of the submanifolds, which together quantify the hardness of the manifold clustering problem. We further propose the {\it localized diffusion $K$-means} by using the local adaptive bandwidth estimated from the nearest neighbors. We show that exact recovery of the localized diffusion $K$-means is fully adaptive to the local probability density and geometric structures of the underlying submanifolds.