Hong Cheng

Xiangguo Sun, Jiawen Zhang, Xixi Wu et al.

Artificial General Intelligence (AGI) has revolutionized numerous fields, yet its integration with graph data, a cornerstone in our interconnected world, remains nascent. This paper presents a pioneering survey on the emerging domain of graph prompts in AGI, addressing key challenges and opportunities in harnessing graph data for AGI applications. Despite substantial advancements in AGI across natural language processing and computer vision, the application to graph data is relatively underexplored. This survey critically evaluates the current landscape of AGI in handling graph data, highlighting the distinct challenges in cross-modality, cross-domain, and cross-task applications specific to graphs. Our work is the first to propose a unified framework for understanding graph prompt learning, offering clarity on prompt tokens, token structures, and insertion patterns in the graph domain. We delve into the intrinsic properties of graph prompts, exploring their flexibility, expressiveness, and interplay with existing graph models. A comprehensive taxonomy categorizes over 100 works in this field, aligning them with pre-training tasks across node-level, edge-level, and graph-level objectives. Additionally, we present, ProG, a Python library, and an accompanying website, to support and advance research in graph prompting. The survey culminates in a discussion of current challenges and future directions, offering a roadmap for research in graph prompting within AGI. Through this comprehensive analysis, we aim to catalyze further exploration and practical applications of AGI in graph data, underlining its potential to reshape AGI fields and beyond. ProG and the website can be accessed by \url{https://github.com/WxxShirley/Awesome-Graph-Prompt}, and \url{https://github.com/sheldonresearch/ProG}, respectively.

Xiangguo Sun, Hong Cheng, Jia Li et al.

Recently, ''pre-training and fine-tuning'' has been adopted as a standard workflow for many graph tasks since it can take general graph knowledge to relieve the lack of graph annotations from each application. However, graph tasks with node level, edge level, and graph level are far diversified, making the pre-training pretext often incompatible with these multiple tasks. This gap may even cause a ''negative transfer'' to the specific application, leading to poor results. Inspired by the prompt learning in natural language processing (NLP), which has presented significant effectiveness in leveraging prior knowledge for various NLP tasks, we study the prompting topic for graphs with the motivation of filling the gap between pre-trained models and various graph tasks. In this paper, we propose a novel multi-task prompting method for graph models. Specifically, we first unify the format of graph prompts and language prompts with the prompt token, token structure, and inserting pattern. In this way, the prompting idea from NLP can be seamlessly introduced to the graph area. Then, to further narrow the gap between various graph tasks and state-of-the-art pre-training strategies, we further study the task space of various graph applications and reformulate downstream problems to the graph-level task. Afterward, we introduce meta-learning to efficiently learn a better initialization for the multi-task prompt of graphs so that our prompting framework can be more reliable and general for different tasks. We conduct extensive experiments, results from which demonstrate the superiority of our method.

Chaohao Yuan, Zhenjie Song, Ercan Engin Kuruoglu et al.

Graph Transformers (GTs) have emerged as a promising graph learning tool, leveraging their all-pair connected property to effectively capture global information. To address the over-smoothing problem in deep GNNs, global attention was initially introduced, eliminating the necessity for using deep GNNs. However, through empirical and theoretical analysis, we verify that the introduced global attention exhibits severe over-smoothing, causing node representations to become indistinguishable due to its inherent low-pass filtering. This effect is even stronger than that observed in GNNs. To mitigate this, we propose PageRank Transformer (ParaFormer), which features a PageRank-enhanced attention module designed to mimic the behavior of deep Transformers. We theoretically and empirically demonstrate that ParaFormer mitigates over-smoothing by functioning as an adaptive-pass filter. Experiments show that ParaFormer achieves consistent performance improvements across both node classification and graph classification tasks on 11 datasets ranging from thousands to millions of nodes, validating its efficacy. The supplementary material, including code and appendix, can be found in https://github.com/chaohaoyuan/ParaFormer.

Jie Tan, Yu Rong, Kangfei Zhao et al.

Combinatorial medication recommendation(CMR) is a fundamental task of healthcare, which offers opportunities for clinical physicians to provide more precise prescriptions for patients with intricate health conditions, particularly in the scenarios of long-term medical care. Previous research efforts have sought to extract meaningful information from electronic health records (EHRs) to facilitate combinatorial medication recommendations. Existing learning-based approaches further consider the chemical structures of medications, but ignore the textual medication descriptions in which the functionalities are clearly described. Furthermore, the textual knowledge derived from the EHRs of patients remains largely underutilized. To address these issues, we introduce the Natural Language-Assisted Multi-modal Medication Recommendation(NLA-MMR), a multi-modal alignment framework designed to learn knowledge from the patient view and medication view jointly. Specifically, NLA-MMR formulates CMR as an alignment problem from patient and medication modalities. In this vein, we employ pretrained language models(PLMs) to extract in-domain knowledge regarding patients and medications, serving as the foundational representation for both modalities. In the medication modality, we exploit both chemical structures and textual descriptions to create medication representations. In the patient modality, we generate the patient representations based on textual descriptions of diagnosis, procedure, and symptom. Extensive experiments conducted on three publicly accessible datasets demonstrate that NLA-MMR achieves new state-of-the-art performance, with a notable average improvement of 4.72% in Jaccard score. Our source code is publicly available on https://github.com/jtan1102/NLA-MMR_CIKM_2024.

Haihong Zhao, Aochuan Chen, Xiangguo Sun et al.

Large Language Models (LLMs) have revolutionized the fields of computer vision (CV) and natural language processing (NLP). One of the most notable advancements of LLMs is that a single model is trained on vast and diverse datasets spanning multiple domains -- a paradigm we term `All in One'. This methodology empowers LLMs with super generalization capabilities, facilitating an encompassing comprehension of varied data distributions. Leveraging these capabilities, a single LLM demonstrates remarkable versatility across a variety of domains -- a paradigm we term `One for All'. However, applying this idea to the graph field remains a formidable challenge, with cross-domain pretraining often resulting in negative transfer. This issue is particularly important in few-shot learning scenarios, where the paucity of training data necessitates the incorporation of external knowledge sources. In response to this challenge, we propose a novel approach called Graph COordinators for PrEtraining (GCOPE), that harnesses the underlying commonalities across diverse graph datasets to enhance few-shot learning. Our novel methodology involves a unification framework that amalgamates disparate graph datasets during the pretraining phase to distill and transfer meaningful knowledge to target tasks. Extensive experiments across multiple graph datasets demonstrate the superior efficacy of our approach. By successfully leveraging the synergistic potential of multiple graph datasets for pretraining, our work stands as a pioneering contribution to the realm of graph foundational model.

Jialin Wu, Kecen Li, Zhicong Huang et al.

Many machine learning models are fine-tuned from large language models (LLMs) to achieve high performance in specialized domains like code generation, biomedical analysis, and mathematical problem solving. However, this fine-tuning process often introduces a critical vulnerability: the systematic degradation of safety alignment, undermining ethical guidelines and increasing the risk of harmful outputs. Addressing this challenge, we introduce EnchTable, a novel framework designed to transfer and maintain safety alignment in downstream LLMs without requiring extensive retraining. EnchTable leverages a Neural Tangent Kernel (NTK)-based safety vector distillation method to decouple safety constraints from task-specific reasoning, ensuring compatibility across diverse model architectures and sizes. Additionally, our interference-aware merging technique effectively balances safety and utility, minimizing performance compromises across various task domains. We implemented a fully functional prototype of EnchTable on three different task domains and three distinct LLM architectures, and evaluated its performance through extensive experiments on eleven diverse datasets, assessing both utility and model safety. Our evaluations include LLMs from different vendors, demonstrating EnchTable's generalization capability. Furthermore, EnchTable exhibits robust resistance to static and dynamic jailbreaking attacks, outperforming vendor-released safety models in mitigating adversarial prompts. Comparative analyses with six parameter modification methods and two inference-time alignment baselines reveal that EnchTable achieves a significantly lower unsafe rate, higher utility score, and universal applicability across different task domains. Additionally, we validate EnchTable can be seamlessly integrated into various deployment pipelines without significant overhead.

Chaohao Yuan, Kangfei Zhao, Ercan Engin Kuruoglu et al.

Graph Transformers (GTs) have demonstrated a strong capability in modeling graph structures by addressing the intrinsic limitations of graph neural networks (GNNs), such as over-smoothing and over-squashing. Recent studies have proposed diverse architectures, enhanced explainability, and practical applications for Graph Transformers. In light of these rapid developments, we conduct a comprehensive review of Graph Transformers, covering aspects such as their architectures, theoretical foundations, and applications within this survey. We categorize the architecture of Graph Transformers according to their strategies for processing structural information, including graph tokenization, positional encoding, structure-aware attention and model ensemble. Furthermore, from the theoretical perspective, we examine the expressivity of Graph Transformers in various discussed architectures and contrast them with other advanced graph learning algorithms to discover the connections. Furthermore, we provide a summary of the practical applications where Graph Transformers have been utilized, such as molecule, protein, language, vision, traffic, brain and material data. At the end of this survey, we will discuss the current challenges and prospective directions in Graph Transformers for potential future research.

Hongyuan Lu, Wai Lam, Hong Cheng et al.

Incorporating personas information allows diverse and engaging responses in dialogue response generation. Unfortunately, prior works have primarily focused on self personas and have overlooked the value of partner personas. Moreover, in practical applications, the availability of ground truth partner personas is often not the case. This paper attempts to tackle these issues by offering a novel framework that leverages automatic partner personas generation to enhance the succeeding dialogue generation. We incorporate reinforcement learning with a dedicatedly designed critic network for reward judgement. Experimental results from both automatic and human evaluation demonstrate a) Our framework is capable of generating relevant, informative and coherent partner personas, even compared to the ground truth partner personas. b) Generated partner personas enhance the succeeding response generation, thus surpassing our baselines and comparison model when partner personas are missing during the inference stage. c) Our framework generates responses that are more informative and engaging than our baseline conditioned on the ground truth partner personas during inference. d) Our dedicatedly designed critic network reinforces our framework effectively. Finally, our framework gives better explainability and reduces the demands for external databases for partner personas.

Jia Li, Jiajin Li, Yang Liu et al.

In this paper, we consider an inverse problem in graph learning domain -- ``given the graph representations smoothed by Graph Convolutional Network (GCN), how can we reconstruct the input graph signal?" We propose Graph Deconvolutional Network (GDN) and motivate the design of GDN via a combination of inverse filters in spectral domain and de-noising layers in wavelet domain, as the inverse operation results in a high frequency amplifier and may amplify the noise. We demonstrate the effectiveness of the proposed method on several tasks including graph feature imputation and graph structure generation.

Jia Li, Mengzhou Liu, Honglei Zhang et al.

We present Mask-GVAE, a variational generative model for blind denoising large discrete graphs, in which "blind denoising" means we don't require any supervision from clean graphs. We focus on recovering graph structures via deleting irrelevant edges and adding missing edges, which has many applications in real-world scenarios, for example, enhancing the quality of connections in a co-authorship network. Mask-GVAE makes use of the robustness in low eigenvectors of graph Laplacian against random noise and decomposes the input graph into several stable clusters. It then harnesses the huge computations by decoding probabilistic smoothed subgraphs in a variational manner. On a wide variety of benchmarks, Mask-GVAE outperforms competing approaches by a significant margin on PSNR and WL similarity.

Mudit Chaudhary, Borislav Dzodzo, Sida Huang et al.

Dialog systems enriched with external knowledge can handle user queries that are outside the scope of the supporting databases/APIs. In this paper, we follow the baseline provided in DSTC9 Track 1 and propose three subsystems, KDEAK, KnowleDgEFactor, and Ens-GPT, which form the pipeline for a task-oriented dialog system capable of accessing unstructured knowledge. Specifically, KDEAK performs knowledge-seeking turn detection by formulating the problem as natural language inference using knowledge from dialogs, databases and FAQs. KnowleDgEFactor accomplishes the knowledge selection task by formulating a factorized knowledge/document retrieval problem with three modules performing domain, entity and knowledge level analyses. Ens-GPT generates a response by first processing multiple knowledge snippets, followed by an ensemble algorithm that decides if the response should be solely derived from a GPT2-XL model, or regenerated in combination with the top-ranking knowledge snippet. Experimental results demonstrate that the proposed pipeline system outperforms the baseline and generates high-quality responses, achieving at least 58.77% improvement on BLEU-4 score.

Jia Li, Tomas Yu, Da-Cheng Juan et al.

Recent studies have indicated that Graph Convolutional Networks (GCNs) act as a \emph{low pass} filter in spectral domain and encode smoothed node representations. In this paper, we consider their opposite, namely Graph Deconvolutional Networks (GDNs) that reconstruct graph signals from smoothed node representations. We motivate the design of Graph Deconvolutional Networks via a combination of inverse filters in spectral domain and de-noising layers in wavelet domain, as the inverse operation results in a \emph{high pass} filter and may amplify the noise. Based on the proposed GDN, we further propose a graph autoencoder framework that first encodes smoothed graph representations with GCN and then decodes accurate graph signals with GDN. We demonstrate the effectiveness of the proposed method on several tasks including unsupervised graph-level representation , social recommendation and graph generation

Jia Li, Tomasyu Yu, Jiajin Li et al.

Graph Neural Networks (GNNs) and Variational Autoencoders (VAEs) have been widely used in modeling and generating graphs with latent factors. However, there is no clear explanation of what these latent factors are and why they perform well. In this work, we present Dirichlet Graph Variational Autoencoder (DGVAE) with graph cluster memberships as latent factors. Our study connects VAEs based graph generation and balanced graph cut, and provides a new way to understand and improve the internal mechanism of VAEs based graph generation. Specifically, we first interpret the reconstruction term of DGVAE as balanced graph cut in a principled way. Furthermore, motivated by the low pass characteristics in balanced graph cut, we propose a new variant of GNN named Heatts to encode the input graph into cluster memberships. Heatts utilizes the Taylor series for fast computation of heat kernels and has better low pass characteristics than Graph Convolutional Networks (GCN). Through experiments on graph generation and graph clustering, we demonstrate the effectiveness of our proposed framework.

Wei Shi, Siyuan Zhang, Zhiwei Zhang et al.

Named entity linking is to map an ambiguous mention in documents to an entity in a knowledge base. The named entity linking is challenging, given the fact that there are multiple candidate entities for a mention in a document. It is difficult to link a mention when it appears multiple times in a document, since there are conflicts by the contexts around the appearances of the mention. In addition, it is difficult since the given training dataset is small due to the reason that it is done manually to link a mention to its mapping entity. In the literature, there are many reported studies among which the recent embedding methods learn vectors of entities from the training dataset at document level. To address these issues, we focus on how to link entity for mentions at a sentence level, which reduces the noises introduced by different appearances of the same mention in a document at the expense of insufficient information to be used. We propose a new unified embedding method by maximizing the relationships learned from knowledge graphs. We confirm the effectiveness of our method in our experimental studies.

Jia Li, Yu Rong, Hong Cheng et al.

Node classification and graph classification are two graph learning problems that predict the class label of a node and the class label of a graph respectively. A node of a graph usually represents a real-world entity, e.g., a user in a social network, or a protein in a protein-protein interaction network. In this work, we consider a more challenging but practically useful setting, in which a node itself is a graph instance. This leads to a hierarchical graph perspective which arises in many domains such as social network, biological network and document collection. For example, in a social network, a group of people with shared interests forms a user group, whereas a number of user groups are interconnected via interactions or common members. We study the node classification problem in the hierarchical graph where a `node' is a graph instance, e.g., a user group in the above example. As labels are usually limited in real-world data, we design two novel semi-supervised solutions named \underline{SE}mi-supervised gr\underline{A}ph c\underline{L}assification via \underline{C}autious/\underline{A}ctive \underline{I}teration (or SEAL-C/AI in short). SEAL-C/AI adopt an iterative framework that takes turns to build or update two classifiers, one working at the graph instance level and the other at the hierarchical graph level. To simplify the representation of the hierarchical graph, we propose a novel supervised, self-attentive graph embedding method called SAGE, which embeds graph instances of arbitrary size into fixed-length vectors. Through experiments on synthetic data and Tencent QQ group data, we demonstrate that SEAL-C/AI not only outperform competing methods by a significant margin in terms of accuracy/Macro-F1, but also generate meaningful interpretations of the learned representations.

Fanhua Shang, James Cheng, Hong Cheng

Multi-relational learning has received lots of attention from researchers in various research communities. Most existing methods either suffer from superlinear per-iteration cost, or are sensitive to the given ranks. To address both issues, we propose a scalable core tensor trace norm Regularized Orthogonal Iteration Decomposition (ROID) method for full or incomplete tensor analytics, which can be generalized as a graph Laplacian regularized version by using auxiliary information or a sparse higher-order orthogonal iteration (SHOOI) version. We first induce the equivalence relation of the Schatten p-norm (0<p<\infty) of a low multi-linear rank tensor and its core tensor. Then we achieve a much smaller matrix trace norm minimization problem. Finally, we develop two efficient augmented Lagrange multiplier algorithms to solve our problems with convergence guarantees. Extensive experiments using both real and synthetic datasets, even though with only a few observations, verified both the efficiency and effectiveness of our methods.