arXiv subjects

Haoyang Li

Publications and source records attributed to Haoyang Li.

At least 199 records · Page 11Linked to original sources

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

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

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

Intent-aware Recommendation via Disentangled Graph Contrastive Learning

Graph neural network (GNN) based recommender systems have become one of the mainstream trends due to the powerful learning ability from user behavior data. Understanding the user intents from behavior data is the key to recommender systems, which poses two basic requirements for GNN-based recommender systems. One is how to learn complex and diverse intents especially when the user behavior is usually inadequate in reality. The other is different behaviors have different intent distributions, so how to establish their relations for a more explainable recommender system. In this paper, we present the Intent-aware Recommendation via Disentangled Graph Contrastive Learning (IDCL), which simultaneously learns interpretable intents and behavior distributions over those intents. Specifically, we first model the user behavior data as a user-item-concept graph, and design a GNN based behavior disentangling module to learn the different intents. Then we propose the intent-wise contrastive learning to enhance the intent disentangling and meanwhile infer the behavior distributions. Finally, the coding rate reduction regularization is introduced to make the behaviors of different intents orthogonal. Extensive experiments demonstrate the effectiveness of IDCL in terms of substantial improvement and the interpretability.

cs.IR↗

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

CodeS: Towards Building Open-source Language Models for Text-to-SQL

Language models have shown promising performance on the task of translating natural language questions into SQL queries (Text-to-SQL). However, most of the state-of-the-art (SOTA) approaches rely on powerful yet closed-source large language models (LLMs), such as ChatGPT and GPT-4, which may have the limitations of unclear model architectures, data privacy risks, and expensive inference overheads. To address the limitations, we introduce CodeS, a series of pre-trained language models with parameters ranging from 1B to 15B, specifically designed for the text-to-SQL task. CodeS is a fully open-source language model, which achieves superior accuracy with much smaller parameter sizes. This paper studies the research challenges in building CodeS. To enhance the SQL generation abilities of CodeS, we adopt an incremental pre-training approach using a specifically curated SQL-centric corpus. Based on this, we address the challenges of schema linking and rapid domain adaptation through strategic prompt construction and a bi-directional data augmentation technique. We conduct comprehensive evaluations on multiple datasets, including the widely used Spider benchmark, the newly released BIRD benchmark, robustness-diagnostic benchmarks such as Spider-DK, Spider-Syn, Spider-Realistic, and Dr.Spider, as well as two real-world datasets created for financial and academic applications. The experimental results show that our CodeS achieves new SOTA accuracy and robustness on nearly all challenging text-to-SQL benchmarks.

cs.CL↗

arXiv2024

Cross-Space Adaptive Filter: Integrating Graph Topology and Node Attributes for Alleviating the Over-smoothing Problem

The vanilla Graph Convolutional Network (GCN) uses a low-pass filter to extract low-frequency signals from graph topology, which may lead to the over-smoothing problem when GCN goes deep. To this end, various methods have been proposed to create an adaptive filter by incorporating an extra filter (e.g., a high-pass filter) extracted from the graph topology. However, these methods heavily rely on topological information and ignore the node attribute space, which severely sacrifices the expressive power of the deep GCNs, especially when dealing with disassortative graphs. In this paper, we propose a cross-space adaptive filter, called CSF, to produce the adaptive-frequency information extracted from both the topology and attribute spaces. Specifically, we first derive a tailored attribute-based high-pass filter that can be interpreted theoretically as a minimizer for semi-supervised kernel ridge regression. Then, we cast the topology-based low-pass filter as a Mercer's kernel within the context of GCNs. This serves as a foundation for combining it with the attribute-based filter to capture the adaptive-frequency information. Finally, we derive the cross-space filter via an effective multiple-kernel learning strategy, which unifies the attribute-based high-pass filter and the topology-based low-pass filter. This helps to address the over-smoothing problem while maintaining effectiveness. Extensive experiments demonstrate that CSF not only successfully alleviates the over-smoothing problem but also promotes the effectiveness of the node classification task.

cs.LG↗

arXiv2024

Accelerating Text-to-Image Editing via Cache-Enabled Sparse Diffusion Inference

Due to the recent success of diffusion models, text-to-image generation is becoming increasingly popular and achieves a wide range of applications. Among them, text-to-image editing, or continuous text-to-image generation, attracts lots of attention and can potentially improve the quality of generated images. It's common to see that users may want to slightly edit the generated image by making minor modifications to their input textual descriptions for several rounds of diffusion inference. However, such an image editing process suffers from the low inference efficiency of many existing diffusion models even using GPU accelerators. To solve this problem, we introduce Fast Image Semantically Edit (FISEdit), a cached-enabled sparse diffusion model inference engine for efficient text-to-image editing. The key intuition behind our approach is to utilize the semantic mapping between the minor modifications on the input text and the affected regions on the output image. For each text editing step, FISEdit can automatically identify the affected image regions and utilize the cached unchanged regions' feature map to accelerate the inference process. Extensive empirical results show that FISEdit can be $3.4\times$ and $4.4\times$ faster than existing methods on NVIDIA TITAN RTX and A100 GPUs respectively, and even generates more satisfactory images.

cs.CV↗

arXiv2023

FAIR AI Models in High Energy Physics

The findable, accessible, interoperable, and reusable (FAIR) data principles provide a framework for examining, evaluating, and improving how data is shared to facilitate scientific discovery. Generalizing these principles to research software and other digital products is an active area of research. Machine learning (ML) models -- algorithms that have been trained on data without being explicitly programmed -- and more generally, artificial intelligence (AI) models, are an important target for this because of the ever-increasing pace with which AI is transforming scientific domains, such as experimental high energy physics (HEP). In this paper, we propose a practical definition of FAIR principles for AI models in HEP and describe a template for the application of these principles. We demonstrate the template's use with an example AI model applied to HEP, in which a graph neural network is used to identify Higgs bosons decaying to two bottom quarks. We report on the robustness of this FAIR AI model, its portability across hardware architectures and software frameworks, and its interpretability.

hep-ex↗

arXiv2023

Graph Invariant Learning with Subgraph Co-mixup for Out-Of-Distribution Generalization

Graph neural networks (GNNs) have been demonstrated to perform well in graph representation learning, but always lacking in generalization capability when tackling out-of-distribution (OOD) data. Graph invariant learning methods, backed by the invariance principle among defined multiple environments, have shown effectiveness in dealing with this issue. However, existing methods heavily rely on well-predefined or accurately generated environment partitions, which are hard to be obtained in practice, leading to sub-optimal OOD generalization performances. In this paper, we propose a novel graph invariant learning method based on invariant and variant patterns co-mixup strategy, which is capable of jointly generating mixed multiple environments and capturing invariant patterns from the mixed graph data. Specifically, we first adopt a subgraph extractor to identify invariant subgraphs. Subsequently, we design one novel co-mixup strategy, i.e., jointly conducting environment Mixup and invariant Mixup. For the environment Mixup, we mix the variant environment-related subgraphs so as to generate sufficiently diverse multiple environments, which is important to guarantee the quality of the graph invariant learning. For the invariant Mixup, we mix the invariant subgraphs, further encouraging to capture invariant patterns behind graphs while getting rid of spurious correlations for OOD generalization. We demonstrate that the proposed environment Mixup and invariant Mixup can mutually promote each other. Extensive experiments on both synthetic and real-world datasets demonstrate that our method significantly outperforms state-of-the-art under various distribution shifts.

cs.LG↗

arXiv2023

Graph Meets LLMs: Towards Large Graph Models

Large models have emerged as the most recent groundbreaking achievements in artificial intelligence, and particularly machine learning. However, when it comes to graphs, large models have not achieved the same level of success as in other fields, such as natural language processing and computer vision. In order to promote applying large models for graphs forward, we present a perspective paper to discuss the challenges and opportunities associated with developing large graph models. First, we discuss the desired characteristics of large graph models. Then, we present detailed discussions from three key perspectives: representation basis, graph data, and graph models. In each category, we provide a brief overview of recent advances and highlight the remaining challenges together with our visions. Finally, we discuss valuable applications of large graph models. We believe this perspective can encourage further investigations into large graph models, ultimately pushing us one step closer towards artificial general intelligence (AGI). We are the first to comprehensively study large graph models, to the best of our knowledge.

cs.LG↗

arXiv2023

Automated Bioinformatics Analysis via AutoBA

With the fast-growing and evolving omics data, the demand for streamlined and adaptable tools to handle the analysis continues to grow. In response to this need, we introduce Auto Bioinformatics Analysis (AutoBA), an autonomous AI agent based on a large language model designed explicitly for conventional omics data analysis. AutoBA simplifies the analytical process by requiring minimal user input while delivering detailed step-by-step plans for various bioinformatics tasks. Through rigorous validation by expert bioinformaticians, AutoBA's robustness and adaptability are affirmed across a diverse range of omics analysis cases, including whole genome sequencing (WGS), RNA sequencing (RNA-seq), single-cell RNA-seq, ChIP-seq, and spatial transcriptomics. AutoBA's unique capacity to self-design analysis processes based on input data variations further underscores its versatility. Compared with online bioinformatic services, AutoBA deploys the analysis locally, preserving data privacy. Moreover, different from the predefined pipeline, AutoBA has adaptability in sync with emerging bioinformatics tools. Overall, AutoBA represents a convenient tool, offering robustness and adaptability for complex omics data analysis.

q-bio.GN↗

arXiv2023

Urania: Visualizing Data Analysis Pipelines for Natural Language-Based Data Exploration

Exploratory Data Analysis (EDA) is an essential yet tedious process for examining a new dataset. To facilitate it, natural language interfaces (NLIs) can help people intuitively explore the dataset via data-oriented questions. However, existing NLIs primarily focus on providing accurate answers to questions, with few offering explanations or presentations of the data analysis pipeline used to uncover the answer. Such presentations are crucial for EDA as they enhance the interpretability and reliability of the answer, while also helping users understand the analysis process and derive insights. To fill this gap, we introduce Urania, a natural language interactive system that is able to visualize the data analysis pipelines used to resolve input questions. It integrates a natural language interface that allows users to explore data via questions, and a novel data-aware question decomposition algorithm that resolves each input question into a data analysis pipeline. This pipeline is visualized in the form of a datamation, with animated presentations of analysis operations and their corresponding data changes. Through two quantitative experiments and expert interviews, we demonstrated that our data-aware question decomposition algorithm outperforms the state-of-the-art technique in terms of execution accuracy, and that Urania can help people explore datasets better. In the end, we discuss the observations from the studies and the potential future works.

cs.HC↗

arXiv2023

Quantifying and mitigating optical surface loss in suspended GaAs photonic integrated circuits

Understanding and mitigating optical loss is critical to the development of high-performance photonic integrated circuits (PICs). Especially in high refractive index contrast compound semiconductor (III-V) PICs, surface absorption and scattering can be a significant loss mechanism, and needs to be suppressed. Here, we quantify the optical propagation loss due to surface state absorption in a suspended GaAs photonic integrated circuits (PIC) platform, probe its origins using X-ray photoemission spectroscopy (XPS) and spectroscopic ellipsometry (SE), and show that it can be mitigated by surface passivation using alumina ($Al_{2}O_{3}$). We also explore potential routes towards achieving passive device performance comparable to state-of-the-art silicon PICs

physics.optics↗

arXiv2023

RESDSQL: Decoupling Schema Linking and Skeleton Parsing for Text-to-SQL

One of the recent best attempts at Text-to-SQL is the pre-trained language model. Due to the structural property of the SQL queries, the seq2seq model takes the responsibility of parsing both the schema items (i.e., tables and columns) and the skeleton (i.e., SQL keywords). Such coupled targets increase the difficulty of parsing the correct SQL queries especially when they involve many schema items and logic operators. This paper proposes a ranking-enhanced encoding and skeleton-aware decoding framework to decouple the schema linking and the skeleton parsing. Specifically, for a seq2seq encoder-decode model, its encoder is injected by the most relevant schema items instead of the whole unordered ones, which could alleviate the schema linking effort during SQL parsing, and its decoder first generates the skeleton and then the actual SQL query, which could implicitly constrain the SQL parsing. We evaluate our proposed framework on Spider and its three robustness variants: Spider-DK, Spider-Syn, and Spider-Realistic. The experimental results show that our framework delivers promising performance and robustness. Our code is available at https://github.com/RUCKBReasoning/RESDSQL.

cs.CL↗

arXiv2023

Personalized and privacy-preserving federated heterogeneous medical image analysis with PPPML-HMI

Heterogeneous data is endemic due to the use of diverse models and settings of devices by hospitals in the field of medical imaging. However, there are few open-source frameworks for federated heterogeneous medical image analysis with personalization and privacy protection simultaneously without the demand to modify the existing model structures or to share any private data. In this paper, we proposed PPPML-HMI, an open-source learning paradigm for personalized and privacy-preserving federated heterogeneous medical image analysis. To our best knowledge, personalization and privacy protection were achieved simultaneously for the first time under the federated scenario by integrating the PerFedAvg algorithm and designing our novel cyclic secure aggregation with the homomorphic encryption algorithm. To show the utility of PPPML-HMI, we applied it to a simulated classification task namely the classification of healthy people and patients from the RAD-ChestCT Dataset, and one real-world segmentation task namely the segmentation of lung infections from COVID-19 CT scans. For the real-world task, PPPML-HMI achieved $\sim$5\% higher Dice score on average compared to conventional FL under the heterogeneous scenario. Meanwhile, we applied the improved deep leakage from gradients to simulate adversarial attacks and showed the solid privacy-preserving capability of PPPML-HMI. By applying PPPML-HMI to both tasks with different neural networks, a varied number of users, and sample sizes, we further demonstrated the strong robustness of PPPML-HMI.

eess.IV↗

arXiv2023

Audit to Forget: A Unified Method to Revoke Patients' Private Data in Intelligent Healthcare

Revoking personal private data is one of the basic human rights, which has already been sheltered by several privacy-preserving laws in many countries. However, with the development of data science, machine learning and deep learning techniques, this right is usually neglected or violated as more and more patients' data are being collected and used for model training, especially in intelligent healthcare, thus making intelligent healthcare a sector where technology must meet the law, regulations, and privacy principles to ensure that the innovation is for the common good. In order to secure patients' right to be forgotten, we proposed a novel solution by using auditing to guide the forgetting process, where auditing means determining whether a dataset has been used to train the model and forgetting requires the information of a query dataset to be forgotten from the target model. We unified these two tasks by introducing a new approach called knowledge purification. To implement our solution, we developed AFS, a unified open-source software, which is able to evaluate and revoke patients' private data from pre-trained deep learning models. We demonstrated the generality of AFS by applying it to four tasks on different datasets with various data sizes and architectures of deep learning networks. The software is publicly available at \url{https://github.com/JoshuaChou2018/AFS}.

cs.LG↗

arXiv2022

Out-Of-Distribution Generalization on Graphs: A Survey

Graph machine learning has been extensively studied in both academia and industry. Although booming with a vast number of emerging methods and techniques, most of the literature is built on the in-distribution hypothesis, i.e., testing and training graph data are identically distributed. However, this in-distribution hypothesis can hardly be satisfied in many real-world graph scenarios where the model performance substantially degrades when there exist distribution shifts between testing and training graph data. To solve this critical problem, out-of-distribution (OOD) generalization on graphs, which goes beyond the in-distribution hypothesis, has made great progress and attracted ever-increasing attention from the research community. In this paper, we comprehensively survey OOD generalization on graphs and present a detailed review of recent advances in this area. First, we provide a formal problem definition of OOD generalization on graphs. Second, we categorize existing methods into three classes from conceptually different perspectives, i.e., data, model, and learning strategy, based on their positions in the graph machine learning pipeline, followed by detailed discussions for each category. We also review the theories related to OOD generalization on graphs and introduce the commonly used graph datasets for thorough evaluations. Finally, we share our insights on future research directions. This paper is the first systematic and comprehensive review of OOD generalization on graphs, to the best of our knowledge.

cs.LG↗