FineMolTex: Towards Fine-grained Molecular Graph-Text Pre-training

Understanding molecular structure and related knowledge is crucial for scientific research. Recent studies integrate molecular graphs with their textual descriptions to enhance molecular representation learning. However, they focus on the whole molecular graph and neglect frequently occurring subgraphs, known as motifs,which are essential for determining molecular properties. Without such fine-grained knowledge, these models struggle to generalize to unseen molecules and tasks that require motif-level insights. To bridge this gap, we propose FineMolTex, a novel Fine-grained Molecular graph-Text pre-training framework to jointly learn coarse-grained molecule-level knowledge and fine-grained motif-level knowledge. Specifically, FineMolTex consists of two pre-training tasks: a contrastive alignment task for coarse-grained matching and a masked multi-modal modeling task for fine-grained matching. In particular, the latter predicts the labels of masked motifs and words, leveraging insights from each other, thereby enabling FineMolTex to understand the fine-grained matching between motifs and words. Finally, we conduct extensive experiments across three downstream tasks, achieving up to 230% improvement in the text-based molecule editing task. Additionally, our case studies reveal that FineMolTex successfully captures fine-grained knowledge, potentially offering valuable insights for drug discovery and catalyst design.

Can Large Language Models Improve the Adversarial Robustness of Graph Neural Networks?

Graph neural networks (GNNs) are vulnerable to adversarial perturbations, especially for topology attacks, and many methods that improve the robustness of GNNs have received considerable attention. Recently, we have witnessed the significant success of large language models (LLMs), leading many to explore the great potential of LLMs on GNNs. However, they mainly focus on improving the performance of GNNs by utilizing LLMs to enhance the node features. Therefore, we ask: Will the robustness of GNNs also be enhanced with the powerful understanding and inference capabilities of LLMs? By presenting the empirical results, we find that despite that LLMs can improve the robustness of GNNs, there is still an average decrease of 23.1% in accuracy, implying that the GNNs remain extremely vulnerable against topology attack. Therefore, another question is how to extend the capabilities of LLMs on graph adversarial robustness. In this paper, we propose an LLM-based robust graph structure inference framework, LLM4RGNN, which distills the inference capabilities of GPT-4 into a local LLM for identifying malicious edges and an LM-based edge predictor for finding missing important edges, so as to recover a robust graph structure. Extensive experiments demonstrate that LLM4RGNN consistently improves the robustness across various GNNs. Even in some cases where the perturbation ratio increases to 40%, the accuracy of GNNs is still better than that on the clean graph.

Minimum Topology Attacks for Graph Neural Networks

With the great popularity of Graph Neural Networks (GNNs), their robustness to adversarial topology attacks has received significant attention. Although many attack methods have been proposed, they mainly focus on fixed-budget attacks, aiming at finding the most adversarial perturbations within a fixed budget for target node. However, considering the varied robustness of each node, there is an inevitable dilemma caused by the fixed budget, i.e., no successful perturbation is found when the budget is relatively small, while if it is too large, the yielding redundant perturbations will hurt the invisibility. To break this dilemma, we propose a new type of topology attack, named minimum-budget topology attack, aiming to adaptively find the minimum perturbation sufficient for a successful attack on each node. To this end, we propose an attack model, named MiBTack, based on a dynamic projected gradient descent algorithm, which can effectively solve the involving non-convex constraint optimization on discrete topology. Extensive results on three GNNs and four real-world datasets show that MiBTack can successfully lead all target nodes misclassified with the minimum perturbation edges. Moreover, the obtained minimum budget can be used to measure node robustness, so we can explore the relationships of robustness, topology, and uncertainty for nodes, which is beyond what the current fixed-budget topology attacks can offer.

GraphTranslator: Aligning Graph Model to Large Language Model for Open-ended Tasks

Large language models (LLMs) like ChatGPT, exhibit powerful zero-shot and instruction-following capabilities, have catalyzed a revolutionary transformation across diverse fields, especially for open-ended tasks. While the idea is less explored in the graph domain, despite the availability of numerous powerful graph models (GMs), they are restricted to tasks in a pre-defined form. Although several methods applying LLMs to graphs have been proposed, they fail to simultaneously handle the pre-defined and open-ended tasks, with LLM as a node feature enhancer or as a standalone predictor. To break this dilemma, we propose to bridge the pretrained GM and LLM by a Translator, named GraphTranslator, aiming to leverage GM to handle the pre-defined tasks effectively and utilize the extended interface of LLMs to offer various open-ended tasks for GM. To train such Translator, we propose a Producer capable of constructing the graph-text alignment data along node information, neighbor information and model information. By translating node representation into tokens, GraphTranslator empowers an LLM to make predictions based on language instructions, providing a unified perspective for both pre-defined and open-ended tasks. Extensive results demonstrate the effectiveness of our proposed GraphTranslator on zero-shot node classification. The graph question answering experiments reveal our GraphTranslator potential across a broad spectrum of open-ended tasks through language instructions. Our code is available at: https://github.com/alibaba/GraphTranslator.

Endowing Pre-trained Graph Models with Provable Fairness

Pre-trained graph models (PGMs) aim to capture transferable inherent structural properties and apply them to different downstream tasks. Similar to pre-trained language models, PGMs also inherit biases from human society, resulting in discriminatory behavior in downstream applications. The debiasing process of existing fair methods is generally coupled with parameter optimization of GNNs. However, different downstream tasks may be associated with different sensitive attributes in reality, directly employing existing methods to improve the fairness of PGMs is inflexible and inefficient. Moreover, most of them lack a theoretical guarantee, i.e., provable lower bounds on the fairness of model predictions, which directly provides assurance in a practical scenario. To overcome these limitations, we propose a novel adapter-tuning framework that endows pre-trained graph models with provable fairness (called GraphPAR). GraphPAR freezes the parameters of PGMs and trains a parameter-efficient adapter to flexibly improve the fairness of PGMs in downstream tasks. Specifically, we design a sensitive semantic augmenter on node representations, to extend the node representations with different sensitive attribute semantics for each node. The extended representations will be used to further train an adapter, to prevent the propagation of sensitive attribute semantics from PGMs to task predictions. Furthermore, with GraphPAR, we quantify whether the fairness of each node is provable, i.e., predictions are always fair within a certain range of sensitive attribute semantics. Experimental evaluations on real-world datasets demonstrate that GraphPAR achieves state-of-the-art prediction performance and fairness on node classification task. Furthermore, based on our GraphPAR, around 90\% nodes have provable fairness.

Towards Graph Foundation Models: A Survey and Beyond

Emerging as fundamental building blocks for diverse artificial intelligence applications, foundation models have achieved notable success across natural language processing and many other domains. Parallelly, graph machine learning has witnessed a transformative shift, with shallow methods giving way to deep learning approaches. The emergence and homogenization capabilities of foundation models have piqued the interest of graph machine learning researchers, sparking discussions about developing the next graph learning paradigm that is pre-trained on broad graph data and can be adapted to a wide range of downstream graph tasks. However, there is currently no clear definition and systematic analysis for this type of work. In this article, we propose the concept of graph foundation models (GFMs), and provide the first comprehensive elucidation on their key characteristics and technologies. Following that, we categorize existing works towards GFMs into three categories based on their reliance on graph neural networks and large language models. Beyond providing a comprehensive overview of the current landscape of graph foundation models, this article also discusses potential research directions for this evolving field.

Provable Training for Graph Contrastive Learning

Graph Contrastive Learning (GCL) has emerged as a popular training approach for learning node embeddings from augmented graphs without labels. Despite the key principle that maximizing the similarity between positive node pairs while minimizing it between negative node pairs is well established, some fundamental problems are still unclear. Considering the complex graph structure, are some nodes consistently well-trained and following this principle even with different graph augmentations? Or are there some nodes more likely to be untrained across graph augmentations and violate the principle? How to distinguish these nodes and further guide the training of GCL? To answer these questions, we first present experimental evidence showing that the training of GCL is indeed imbalanced across all nodes. To address this problem, we propose the metric "node compactness", which is the lower bound of how a node follows the GCL principle related to the range of augmentations. We further derive the form of node compactness theoretically through bound propagation, which can be integrated into binary cross-entropy as a regularization. To this end, we propose the PrOvable Training (POT) for GCL, which regularizes the training of GCL to encode node embeddings that follows the GCL principle better. Through extensive experiments on various benchmarks, POT consistently improves the existing GCL approaches, serving as a friendly plugin.