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Xiaohui Chen

Publications and source records attributed to Xiaohui Chen.

At least 37 records · Page 2Linked to original sources
arXiv2026

Generative quantum machine learning via denoising diffusion probabilistic models

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.

quant-ph↗
arXiv2025

Neural Local Wasserstein Regression

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.

stat.ML↗
arXiv2025

Physics-Informed Extreme Learning Machine (PIELM): Opportunities and Challenges

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.

cs.LG↗
arXiv2025

A Generalized Label Shift Perspective for Cross-Domain Gaze Estimation

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.

cs.CV↗
arXiv2025

Holographic deep thermalization for secure and efficient quantum random state generation

Randomness is a cornerstone of science, underpinning fields such as statistics, information theory, dynamical systems, and thermodynamics. In quantum science, quantum randomness, especially random pure states, plays a pivotal role in fundamental questions like black hole physics and quantum complexity, as well as in practical applications such as quantum device benchmarking and quantum advantage certification. The conventional approach for generating genuine random states, called `deep thermalization', faces significant challenges, including scalability issues due to the need for a large ancilla system and susceptibility to attacks, as demonstrated in this work. We introduce holographic deep thermalization, a secure and hardware-efficient quantum random state generator. By adopting a sequential application of a scrambling-measure-reset process, it continuously trades space with time, and substantially reduces the required ancilla size to as small as a system-size independent constant; At the same time, it guarantees security by removing quantum correlation between the data system and attackers. Thanks to the resource reduction, our circuit-based implementation on IBM Quantum devices achieves genuine $5$-qubit random state generation utilizing only a total of $8$ qubits.

quant-ph↗
arXiv2025

Graph Generative Pre-trained Transformer

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,

cs.LG↗
arXiv2025

Optimal Transport Barycenter via Nonconvex-Concave Minimax Optimization

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.

stat.ML↗
arXiv2025

MADGEN: Mass-Spec attends to De Novo Molecular generation

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.

cs.LG↗
arXiv2025

Embedding Empirical Distributions for Computing Optimal Transport Maps

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.

cs.LG↗
arXiv2025

Multi-Modal Foundation Models for Computational Pathology: A Survey

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.

cs.CV↗
arXiv2025

High-fidelity Multiphysics Modelling for Rapid Predictions Using Physics-informed Parallel Neural Operator

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.

cs.LG↗
arXiv2025

Learning Density Evolution from Snapshot Data

Motivated by learning dynamical structures from static snapshot data, this paper presents a distribution-on-scalar regression approach for estimating the density evolution of a stochastic process from its noisy temporal point clouds. We propose an entropy-regularized nonparametric maximum likelihood estimator (E-NPMLE), which leverages the entropic optimal transport as a smoothing regularizer for the density flow. We show that the E-NPMLE has almost dimension-free statistical rates of convergence to the ground truth distributions, which exhibit a striking phase transition phenomenon in terms of the number of snapshots and per-snapshot sample size. To efficiently compute the E-NPMLE, we design a novel particle-based and grid-free coordinate KL divergence gradient descent (CKLGD) algorithm and prove its polynomial iteration complexity. Moreover, we provide numerical evidence on synthetic data to support our theoretical findings. This work contributes to the theoretical understanding and practical computation of estimating density evolution from noisy observations in arbitrary dimensions.

math.ST↗
arXiv2025

Cylindrical cavity expansion analysis under partially drained conditions for normalisation of excess water pressure in CPTU

Cone tip resistance and excess water pressure (EWP) measured by piezocone penetration tests (CPTU) may be significantly affected by the partially drained effect in soils with intermediate permeability. To capture this effect, the paper proposes a straightforward, hydro-mechanical coupling solution for cylindrical cavity expansion under partially drained conditions. The mechanical behaviour of soils is modelled using the elastoplastic Tresca model and water flow within porous soils is assumed to obey Darcys law. Two partial differential equations (PDEs) are established in the elastic and plastic zones, respectively, transforming the cavity expansion analysis into a typical Stefan problem with dynamic boundary conditions (i.e. a moving boundary at the elastoplastic interface). An approximate solution for the PDEs is derived by leveraging the variable transformation method. Based on the new solution, a novel normalised penetration rate is defined considering the rigidity index of soils, with which a unique backbone curve for CPTU is found. Finally, the backbone curve is compared with a database comprising 109 in-situ experimental tests, 101 centrifuge modelling tests, and numerical simulation results. The proposed solution may provide a useful theoretical tool for interpreting the consolidation coefficient of fine-grained soils from the penetration stage of multi-rate CPTU, which can enhance the interpretation reliability for CPTU dissipation tests.

physics.geo-ph↗
arXiv2025

Large Language Model is Secretly a Protein Sequence Optimizer

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.

cs.LG↗
arXiv2024

CompCap: Improving Multimodal Large Language Models with Composite Captions

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.

cs.CV↗
arXiv2024

Wasserstein Proximal Coordinate Gradient Algorithms

Motivated by approximation Bayesian computation using mean-field variational approximation and the computation of equilibrium in multi-species systems with cross-interaction, this paper investigates the composite geodesically convex optimization problem over multiple distributions. The objective functional under consideration is composed of a convex potential energy on a product of Wasserstein spaces and a sum of convex self-interaction and internal energies associated with each distribution. To efficiently solve this problem, we introduce the Wasserstein Proximal Coordinate Gradient (WPCG) algorithms with parallel, sequential, and random update schemes. Under a quadratic growth (QG) condition that is weaker than the usual strong convexity requirement on the objective functional, we show that WPCG converges exponentially fast to the unique global optimum. In the absence of the QG condition, WPCG is still demonstrated to converge to the global optimal solution, albeit at a slower polynomial rate. Numerical results for both motivating examples are consistent with our theoretical findings.

math.OC↗
arXiv2024

GEGA: Graph Convolutional Networks and Evidence Retrieval Guided Attention for Enhanced Document-level Relation Extraction

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.

cs.CL↗