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, which are selected based on their importance. By leveraging insights from both modalities, FineMolTex is able 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.

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

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.

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.

With the great popularity of Graph Neural Networks (GNNs), the robustness of GNNs to adversarial attacks has received increasing attention. However, existing works neglect adversarial label-flipping attacks, where the attacker can manipulate an unnoticeable fraction of training labels. Exploring the robustness of GNNs to label-flipping attacks is highly critical, especially when labels are collected from external sources and false labels are easy to inject (e.g., recommendation systems). In this work, we introduce the first study of adversarial label-flipping attacks on GNNs. We propose an effective attack model LafAK based on approximated closed form of GNNs and continuous surrogate of non-differentiable objective, efficiently generating attacks via gradient-based optimizers. Furthermore, we show that one key reason for the vulnerability of GNNs to label-flipping attack is overfitting to flipped nodes. Based on this observation, we propose a defense framework which introduces a community-preserving self-supervised task as regularization to avoid overfitting. We demonstrate the effectiveness of our proposed attack model to GNNs on four real-world datasets. The effectiveness of our defense framework is also well validated by the substantial improvements of defense based GNN and its variants under label-flipping attacks.