arXiv subjects

Xin Wang

Publications and source records attributed to Xin Wang.

At least 973 records · Page 54Linked to original sources

arXiv2024

iMD4GC: Incomplete Multimodal Data Integration to Advance Precise Treatment Response Prediction and Survival Analysis for Gastric Cancer

Gastric cancer (GC) is a prevalent malignancy worldwide, ranking as the fifth most common cancer with over 1 million new cases and 700 thousand deaths in 2020. Locally advanced gastric cancer (LAGC) accounts for approximately two-thirds of GC diagnoses, and neoadjuvant chemotherapy (NACT) has emerged as the standard treatment for LAGC. However, the effectiveness of NACT varies significantly among patients, with a considerable subset displaying treatment resistance. Ineffective NACT not only leads to adverse effects but also misses the optimal therapeutic window, resulting in lower survival rate. However, existing multimodal learning methods assume the availability of all modalities for each patient, which does not align with the reality of clinical practice. The limited availability of modalities for each patient would cause information loss, adversely affecting predictive accuracy. In this study, we propose an incomplete multimodal data integration framework for GC (iMD4GC) to address the challenges posed by incomplete multimodal data, enabling precise response prediction and survival analysis. Specifically, iMD4GC incorporates unimodal attention layers for each modality to capture intra-modal information. Subsequently, the cross-modal interaction layers explore potential inter-modal interactions and capture complementary information across modalities, thereby enabling information compensation for missing modalities. To evaluate iMD4GC, we collected three multimodal datasets for GC study: GastricRes (698 cases) for response prediction, GastricSur (801 cases) for survival analysis, and TCGA-STAD (400 cases) for survival analysis. The scale of our datasets is significantly larger than previous studies. The iMD4GC achieved impressive performance with an 80.2% AUC on GastricRes, 71.4% C-index on GastricSur, and 66.1% C-index on TCGA-STAD, significantly surpassing other compared methods.

eess.IV↗

arXiv2024

Exploring the Potential of Large Language Models in Graph Generation

Large language models (LLMs) have achieved great success in many fields, and recent works have studied exploring LLMs for graph discriminative tasks such as node classification. However, the abilities of LLMs for graph generation remain unexplored in the literature. Graph generation requires the LLM to generate graphs with given properties, which has valuable real-world applications such as drug discovery, while tends to be more challenging. In this paper, we propose LLM4GraphGen to explore the ability of LLMs for graph generation with systematical task designs and extensive experiments. Specifically, we propose several tasks tailored with comprehensive experiments to address key questions regarding LLMs' understanding of different graph structure rules, their ability to capture structural type distributions, and their utilization of domain knowledge for property-based graph generation. Our evaluations demonstrate that LLMs, particularly GPT-4, exhibit preliminary abilities in graph generation tasks, including rule-based and distribution-based generation. We also observe that popular prompting methods, such as few-shot and chain-of-thought prompting, do not consistently enhance performance. Besides, LLMs show potential in generating molecules with specific properties. These findings may serve as foundations for designing good LLMs based models for graph generation and provide valuable insights and further research.

cs.LG↗

arXiv2024

CSST large-scale structure analysis pipeline: I. constructing reference mock galaxy redshift surveys

In this paper, we set out to construct a set of reference mock galaxy redshift surveys (MGRSs) for the future Chinese Space-station Survey Telescope (CSST) observation, where subsequent survey selection effects can be added and evaluated. This set of MGRSs is generated using the dark matter subhalos extracted from a high-resolution Jiutian $N$-body simulation of the standard $Λ$CDM cosmogony with $Ω_m=0.3111$, $Ω_Λ=0.6889$, and $σ_8=0.8102$. The simulation has a boxsize of $1~h^{-1} {\rm Gpc}$, and consists of $6144^3$ particles with mass resolution $3.723 \times 10^{8} h^{-1} M_\odot $. In order to take into account the effect of redshift evolution, we first use all 128 snapshots in the Jiutian simulation to generate a light-cone halo/subhalo catalog. Next, galaxy luminosities are assigned to the main and subhalo populations using the subhalo abundance matching (SHAM) method with the DESI $z$-band luminosity functions at different redshifts. Multi-band photometries, as well as images, are then assigned to each mock galaxy using a 3-dimensional parameter space nearest neighbor sampling of the DESI LS observational galaxies and groups. Finally, the CSST and DESI LS survey geometry and magnitude limit cuts are applied to generate the required MGRSs. As we have checked, this set of MGRSs can generally reproduce the observed galaxy luminosity/mass functions within 0.1 dex for galaxies with $L > 10^8 L_\odot$ (or $M_* > 10^{8.5} M_\odot$) and within 1-$σ$ level for galaxies with $L < 10^8L_\odot$ (or $M_* < 10^{8.5} M_\odot$). Together with the CSST slitless spectra and redshifts for our DESI LS seed galaxies that are under construction, we will set out to test various slitless observational selection effects in subsequent probes.

astro-ph.GA↗

arXiv2024

EHA: Entanglement-variational Hardware-efficient Ansatz for Eigensolvers

Variational quantum eigensolvers (VQEs) are one of the most important and effective applications of quantum computing, especially in the current noisy intermediate-scale quantum (NISQ) era. There are mainly two ways for VQEs: problem-agnostic and problem-specific. For problem-agnostic methods, they often suffer from trainability issues. For problem-specific methods, their performance usually relies upon choices of initial reference states which are often hard to determine. In this paper, we propose an Entanglement-variational Hardware-efficient Ansatz (EHA), and numerically compare it with some widely used ansatzes by solving benchmark problems in quantum many-body systems and quantum chemistry. Our EHA is problem-agnostic and hardware-efficient, especially suitable for NISQ devices and having potential for wide applications. EHA can achieve a higher level of accuracy in finding ground states and their energies in most cases even compared with problem-specific methods. The performance of EHA is robust to choices of initial states and parameters initialization and it has the ability to quickly adjust the entanglement to the required amount, which is also the fundamental reason for its superiority.

quant-ph↗

arXiv2024

Reconstructing the Baryonic Acoustic Oscillations in the presence of photo-$z$ uncertainties

The reconstruction method has been widely employed to improve the Baryon Acoustic Oscillations (BAO) measurement in spectroscopic survey data analysis. In this study, we explore the reconstruction of the BAO signals in the realm of photometric data. By adapting the Zel'dovich reconstruction technique, we develop a formalism to reconstruct the transverse BAO in the presence of photo-$z$ uncertainties \change{under the plane-parallel approximation}. We access the performance of the BAO reconstruction through comoving $N$-body simulations. The transverse reconstruction potential can be derived by solving a 2D potential equation, with the surface density and the radial potential contribution acting as the source terms. The solution is predominantly determined by the surface density. As is evident in dense samples, such as the matter field, the transverse BAO reconstruction can enhance both the strength of the BAO signals and their cross correlation with the initial conditions. At $z=0$, the cross correlation is increased by a factor of 1.2 at $ k_\perp = 0.2 \, \mathrm{Mpc}^{-1}h $ and 1.4 at $ k_\perp = 0.3 \, \mathrm{Mpc}^{-1}h $, respectively. We contrast the 2D potential results with the 3D Poisson equation solution, wherein we directly solve the potential equation using the position in photo-$z$ space, and find good agreement. Additionally, we examine the impact of various conditions, such as the smoothing scales and the level of photo-$z$ uncertainties, on the reconstruction results. We envision the straightforward application of this method to survey data.

astro-ph.CO↗

arXiv2024

A forward-modelling approach to overcome PSF smearing and fit flexible models to the chemical structure of galaxies

Historically, metallicity profiles of galaxies have been modelled using a radially symmetric, two-parameter linear model, which reveals that most galaxies are more metal-rich in their central regions than their outskirts. However, this model is known to yield inaccurate results when the point-spread function (PSF) of a telescope is large. Furthermore, a radially symmetric model cannot capture asymmetric structures within a galaxy. In this work, we present an extension of the popular forward-modelling python package LENSTRONOMY, which allows the user to overcome both of these obstacles. We demonstrate the new features of this code base through two illustrative examples on simulated data. First, we show that through forward modelling, LENSTRONOMY is able to recover accurately the metallicity gradients of galaxies, even when the PSF is comparable to the size of a galaxy, as long as the data is observed with a sufficient number of pixels. Additionally, we demonstrate how LENSTRONOMY is able to fit irregular metallicity profiles to galaxies that are not well-described by a simple surface brightness profile. This opens up pathways for detailed investigations into the connections between morphology and chemical structure for galaxies at cosmological distances using the transformative capabilities of JWST. Our code is publicly available and open source, and can also be used to model spatial distributions of other galaxy properties that are traced by its surface brightness profile.

astro-ph.IM↗

arXiv2024

Curriculum Graph Machine Learning: A Survey

Graph machine learning has been extensively studied in both academia and industry. However, in the literature, most existing graph machine learning models are designed to conduct training with data samples in a random order, which may suffer from suboptimal performance due to ignoring the importance of different graph data samples and their training orders for the model optimization status. To tackle this critical problem, curriculum graph machine learning (Graph CL), which integrates the strength of graph machine learning and curriculum learning, arises and attracts an increasing amount of attention from the research community. Therefore, in this paper, we comprehensively overview approaches on Graph CL and present a detailed survey of recent advances in this direction. Specifically, we first discuss the key challenges of Graph CL and provide its formal problem definition. Then, we categorize and summarize existing methods into three classes based on three kinds of graph machine learning tasks, i.e., node-level, link-level, and graph-level tasks. Finally, we share our thoughts on future research directions. To the best of our knowledge, this paper is the first survey for curriculum graph machine learning.

cs.LG↗

arXiv2024

UAV-Enabled Asynchronous Federated Learning

To exploit unprecedented data generation in mobile edge networks, federated learning (FL) has emerged as a promising alternative to the conventional centralized machine learning (ML). However, there are some critical challenges for FL deployment. One major challenge called straggler issue severely limits FL's coverage where the device with the weakest channel condition becomes the bottleneck of the model aggregation performance. Besides, the huge uplink communication overhead compromises the effectiveness of FL, which is particularly pronounced in large-scale systems. To address the straggler issue, we propose the integration of an unmanned aerial vehicle (UAV) as the parameter server (UAV-PS) to coordinate the FL implementation. We further employ over-the-air computation technique that leverages the superposition property of wireless channels for efficient uplink communication. Specifically, in this paper, we develop a novel UAV-enabled over-the-air asynchronous FL (UAV-AFL) framework which supports the UAV-PS in updating the model continuously to enhance the learning performance. Moreover, we conduct a convergence analysis to quantitatively capture the impact of model asynchrony, device selection and communication errors on the UAV-AFL learning performance. Based on this, a unified communication-learning problem is formulated to maximize asymptotical learning performance by optimizing the UAV-PS trajectory, device selection and over-the-air transceiver design. Simulation results demonstrate that the proposed scheme achieves substantially learning efficiency improvement compared with the state-of-the-art approaches.

eess.SP↗

arXiv2024

Optimizing Latent Graph Representations of Surgical Scenes for Zero-Shot Domain Transfer

Purpose: Advances in deep learning have resulted in effective models for surgical video analysis; however, these models often fail to generalize across medical centers due to domain shift caused by variations in surgical workflow, camera setups, and patient demographics. Recently, object-centric learning has emerged as a promising approach for improved surgical scene understanding, capturing and disentangling visual and semantic properties of surgical tools and anatomy to improve downstream task performance. In this work, we conduct a multi-centric performance benchmark of object-centric approaches, focusing on Critical View of Safety assessment in laparoscopic cholecystectomy, then propose an improved approach for unseen domain generalization. Methods: We evaluate four object-centric approaches for domain generalization, establishing baseline performance. Next, leveraging the disentangled nature of object-centric representations, we dissect one of these methods through a series of ablations (e.g. ignoring either visual or semantic features for downstream classification). Finally, based on the results of these ablations, we develop an optimized method specifically tailored for domain generalization, LG-DG, that includes a novel disentanglement loss function. Results: Our optimized approach, LG-DG, achieves an improvement of 9.28% over the best baseline approach. More broadly, we show that object-centric approaches are highly effective for domain generalization thanks to their modular approach to representation learning. Conclusion: We investigate the use of object-centric methods for unseen domain generalization, identify method-agnostic factors critical for performance, and present an optimized approach that substantially outperforms existing methods.

cs.CV↗

arXiv2024

NAS-Bench-Graph: Benchmarking Graph Neural Architecture Search

Graph neural architecture search (GraphNAS) has recently aroused considerable attention in both academia and industry. However, two key challenges seriously hinder the further research of GraphNAS. First, since there is no consensus for the experimental setting, the empirical results in different research papers are often not comparable and even not reproducible, leading to unfair comparisons. Secondly, GraphNAS often needs extensive computations, which makes it highly inefficient and inaccessible to researchers without access to large-scale computation. To solve these challenges, we propose NAS-Bench-Graph, a tailored benchmark that supports unified, reproducible, and efficient evaluations for GraphNAS. Specifically, we construct a unified, expressive yet compact search space, covering 26,206 unique graph neural network (GNN) architectures and propose a principled evaluation protocol. To avoid unnecessary repetitive training, we have trained and evaluated all of these architectures on nine representative graph datasets, recording detailed metrics including train, validation, and test performance in each epoch, the latency, the number of parameters, etc. Based on our proposed benchmark, the performance of GNN architectures can be directly obtained by a look-up table without any further computation, which enables fair, fully reproducible, and efficient comparisons. To demonstrate its usage, we make in-depth analyses of our proposed NAS-Bench-Graph, revealing several interesting findings for GraphNAS. We also showcase how the benchmark can be easily compatible with GraphNAS open libraries such as AutoGL and NNI. To the best of our knowledge, our work is the first benchmark for graph neural architecture search.

cs.LG↗

arXiv2024

Disentangled Representation Learning with Large Language Models for Text-Attributed Graphs

Text-attributed graphs (TAGs) are prevalent on the web and research over TAGs such as citation networks, e-commerce networks and social networks has attracted considerable attention in the web community. Recently, large language models (LLMs) have demonstrated exceptional capabilities across a wide range of tasks. However, the existing works focus on harnessing the potential of LLMs solely relying on prompts to convey graph structure information to LLMs, thus suffering from insufficient understanding of the complex structural relationships within TAGs. To address this problem, in this paper we present the Disentangled Graph-Text Learner (DGTL) model, which is able to enhance the reasoning and predicting capabilities of LLMs for TAGs. Our proposed DGTL model incorporates graph structure information through tailored disentangled graph neural network (GNN) layers, enabling LLMs to capture the intricate relationships hidden in text-attributed graphs from multiple structural factors. Furthermore, DGTL operates with frozen pre-trained LLMs, reducing computational costs and allowing much more flexibility in combining with different LLM models. Experimental evaluations demonstrate the effectiveness of the proposed DGTL model on achieving superior or comparable performance over state-of-the-art baselines. Additionally, we also demonstrate that our DGTL model can offer natural language explanations for predictions, thereby significantly enhancing model interpretability.

cs.CL↗

arXiv2024

Out-of-Distribution Generalized Dynamic Graph Neural Network with Disentangled Intervention and Invariance Promotion

Dynamic graph neural networks (DyGNNs) have demonstrated powerful predictive abilities by exploiting graph structural and temporal dynamics. However, the existing DyGNNs fail to handle distribution shifts, which naturally exist in dynamic graphs, mainly because the patterns exploited by DyGNNs may be variant with respect to labels under distribution shifts. In this paper, we propose Disentangled Intervention-based Dynamic graph Attention networks with Invariance Promotion (I-DIDA) to handle spatio-temporal distribution shifts in dynamic graphs by discovering and utilizing invariant patterns, i.e., structures and features whose predictive abilities are stable across distribution shifts. Specifically, we first propose a disentangled spatio-temporal attention network to capture the variant and invariant patterns. By utilizing the disentangled patterns, we design a spatio-temporal intervention mechanism to create multiple interventional distributions and an environment inference module to infer the latent spatio-temporal environments, and minimize the variance of predictions among these intervened distributions and environments, so that our model can make predictions based on invariant patterns with stable predictive abilities under distribution shifts. Extensive experiments demonstrate the superiority of our method over state-of-the-art baselines under distribution shifts. Our work is the first study of spatio-temporal distribution shifts in dynamic graphs, to the best of our knowledge.

cs.LG↗

arXiv2024

Out-of-Distribution Generalized Dynamic Graph Neural Network for Human Albumin Prediction

Human albumin is essential for indicating the body's overall health. Accurately predicting plasma albumin levels and determining appropriate doses are urgent clinical challenges, particularly in critically ill patients, to maintain optimal blood levels. However, human albumin prediction is non-trivial that has to leverage the dynamics of biochemical markers as well as the experience of treating patients. Moreover, the problem of distribution shift is often encountered in real clinical data, which may lead to a decline in the model prediction performance and reduce the reliability of the model's application. In this paper, we propose a framework named Out-of-Distribution Generalized Dynamic Graph Neural Network for Human Albumin Prediction (DyG-HAP), which is able to provide accurate albumin predictions for Intensity Care Unit (ICU) patients during hospitalization. We first model human albumin prediction as a dynamic graph regression problem to model the dynamics and patient relationship. Then, we propose a disentangled dynamic graph attention mechanism to capture and disentangle the patterns whose relationship to labels under distribution shifts is invariant and variant respectively. Last, we propose an invariant dynamic graph regression method to encourage the model to rely on invariant patterns to make predictions. Moreover, we propose a dataset named Albumin level testing and nutritional dosing data for Intensive Care (ANIC) for evaluation. Extensive experiments demonstrate the superiority of our method compared to several baseline methods in human albumin prediction.

cs.LG↗

arXiv2024

Spectral Invariant Learning for Dynamic Graphs under Distribution Shifts

Dynamic graph neural networks (DyGNNs) currently struggle with handling distribution shifts that are inherent in dynamic graphs. Existing work on DyGNNs with out-of-distribution settings only focuses on the time domain, failing to handle cases involving distribution shifts in the spectral domain. In this paper, we discover that there exist cases with distribution shifts unobservable in the time domain while observable in the spectral domain, and propose to study distribution shifts on dynamic graphs in the spectral domain for the first time. However, this investigation poses two key challenges: i) it is non-trivial to capture different graph patterns that are driven by various frequency components entangled in the spectral domain; and ii) it remains unclear how to handle distribution shifts with the discovered spectral patterns. To address these challenges, we propose Spectral Invariant Learning for Dynamic Graphs under Distribution Shifts (SILD), which can handle distribution shifts on dynamic graphs by capturing and utilizing invariant and variant spectral patterns. Specifically, we first design a DyGNN with Fourier transform to obtain the ego-graph trajectory spectrums, allowing the mixed dynamic graph patterns to be transformed into separate frequency components. We then develop a disentangled spectrum mask to filter graph dynamics from various frequency components and discover the invariant and variant spectral patterns. Finally, we propose invariant spectral filtering, which encourages the model to rely on invariant patterns for generalization under distribution shifts. Experimental results on synthetic and real-world dynamic graph datasets demonstrate the superiority of our method for both node classification and link prediction tasks under distribution shifts.

cs.LG↗

arXiv2024

Unsupervised Graph Neural Architecture Search with Disentangled Self-supervision

The existing graph neural architecture search (GNAS) methods heavily rely on supervised labels during the search process, failing to handle ubiquitous scenarios where supervisions are not available. In this paper, we study the problem of unsupervised graph neural architecture search, which remains unexplored in the literature. The key problem is to discover the latent graph factors that drive the formation of graph data as well as the underlying relations between the factors and the optimal neural architectures. Handling this problem is challenging given that the latent graph factors together with architectures are highly entangled due to the nature of the graph and the complexity of the neural architecture search process. To address the challenge, we propose a novel Disentangled Self-supervised Graph Neural Architecture Search (DSGAS) model, which is able to discover the optimal architectures capturing various latent graph factors in a self-supervised fashion based on unlabeled graph data. Specifically, we first design a disentangled graph super-network capable of incorporating multiple architectures with factor-wise disentanglement, which are optimized simultaneously. Then, we estimate the performance of architectures under different factors by our proposed self-supervised training with joint architecture-graph disentanglement. Finally, we propose a contrastive search with architecture augmentations to discover architectures with factor-specific expertise. Extensive experiments on 11 real-world datasets demonstrate that the proposed model is able to achieve state-of-the-art performance against several baseline methods in an unsupervised manner.

cs.LG↗

arXiv2024

AutoGL: A Library for Automated Graph Learning

Recent years have witnessed an upsurge in research interests and applications of machine learning on graphs. However, manually designing the optimal machine learning algorithms for different graph datasets and tasks is inflexible, labor-intensive, and requires expert knowledge, limiting its adaptivity and applicability. Automated machine learning (AutoML) on graphs, aiming to automatically design the optimal machine learning algorithm for a given graph dataset and task, has received considerable attention. However, none of the existing libraries can fully support AutoML on graphs. To fill this gap, we present Automated Graph Learning (AutoGL), the first dedicated library for automated machine learning on graphs. AutoGL is open-source, easy to use, and flexible to be extended. Specifically, we propose a three-layer architecture, consisting of backends to interface with devices, a complete automated graph learning pipeline, and supported graph applications. The automated machine learning pipeline further contains five functional modules: auto feature engineering, neural architecture search, hyper-parameter optimization, model training, and auto ensemble, covering the majority of existing AutoML methods on graphs. For each module, we provide numerous state-of-the-art methods and flexible base classes and APIs, which allow easy usage and customization. We further provide experimental results to showcase the usage of our AutoGL library. We also present AutoGL-light, a lightweight version of AutoGL to facilitate customizing pipelines and enriching applications, as well as benchmarks for graph neural architecture search. The codes of AutoGL are publicly available at https://github.com/THUMNLab/AutoGL.

cs.LG↗

arXiv2024

Simple Full-Spectrum Correlated k-Distribution Model based on Multilayer Perceptron

While neural networks have been successfully applied to the full-spectrum k-distribution (FSCK) method at a large range of thermodynamics with k-values predicted by a trained multilayer perceptron (MLP) model, the required a-values still need to be calculated on-the-fly, which theoretically degrades the FSCK method and may lead to errors. On the other hand, too complicated structure of the current MLP model inevitably slows down the calculation efficiency. Therefore, to compensate among accuracy, efficiency and storage, the simple MLP designed based on the nature of FSCK method are developed, i.e., the simple FSCK MLP (SFM) model, from which those correlated k-values and corresponding ka-values can be efficiently obtained. Several test cases have been carried out to compare the developed SFM model and other FSCK tools including look-up tables and traditional FSCK MLP (TFM) model. Results show that the SFM model can achieve excellent accuracy that is even better than look-up tables at a tiny computational cost that is far less than that of TFM model. Considering accuracy, efficiency and portability, the SFM model is not only an excellent tool for the prediction of spectral properties, but also provides a method to reduce the errors due to nonlinear effects.

cs.LG↗

arXiv2024

Lightweight Neural Network with Knowledge Distillation for CSI Feedback

Deep learning has shown promise in enhancing channel state information (CSI) feedback. However, many studies indicate that better feedback performance often accompanies higher computational complexity. Pursuing better performance-complexity tradeoffs is crucial to facilitate practical deployment, especially on computation-limited devices, which may have to use lightweight autoencoder with unfavorable performance. To achieve this goal, this paper introduces knowledge distillation (KD) to achieve better tradeoffs, where knowledge from a complicated teacher autoencoder is transferred to a lightweight student autoencoder for performance improvement. Specifically, two methods are proposed for implementation. Firstly, an autoencoder KD-based method is introduced by training a student autoencoder to mimic the reconstructed CSI of a pretrained teacher autoencoder. Secondly, an encoder KD-based method is proposed to reduce training overhead by performing KD only on the student encoder. Additionally, a variant of encoder KD is introduced to protect user equipment and base station vendor intellectual property. Numerical simulations demonstrate that the proposed methods can significantly improve the student autoencoder's performance, while reducing the number of floating point operations and inference time to 3.05%-5.28% and 13.80%-14.76% of the teacher network, respectively. Furthermore, the variant encoder KD method effectively enhances the student autoencoder's generalization capability across different scenarios, environments, and bandwidths.

eess.SP↗