MolBind: Multimodal Alignment of Language, Molecules, and Proteins

Recent advancements in biology and chemistry have leveraged multi-modal learning, integrating molecules and their natural language descriptions to enhance drug discovery. However, current pre-training frameworks are limited to two modalities, and designing a unified network to process different modalities (e.g., natural language, 2D molecular graphs, 3D molecular conformations, and 3D proteins) remains challenging due to inherent gaps among them. In this work, we propose MolBind, a framework that trains encoders for multiple modalities through contrastive learning, mapping all modalities to a shared feature space for multi-modal semantic alignment. To facilitate effective pre-training of MolBind on multiple modalities, we also build and collect a high-quality dataset with four modalities, MolBind-M4, including graph-language, conformation-language, graph-conformation, and conformation-protein paired data. MolBind shows superior zero-shot learning performance across a wide range of tasks, demonstrating its strong capability of capturing the underlying semantics of multiple modalities.

3M-Diffusion: Latent Multi-Modal Diffusion for Text-Guided Generation of Molecular Graphs

Generating molecules with desired properties is a critical task with broad applications in drug discovery and materials design. Inspired by recent advances in large language models, there is a growing interest in using natural language descriptions of molecules to generate molecules with the desired properties. Most existing methods focus on generating molecules that precisely match the text description. However, practical applications call for methods that generate diverse, and ideally novel, molecules with the desired properties. We propose 3M-Diffusion, a novel multi-modal molecular graph generation method, to address this challenge. 3M-Diffusion first encodes molecular graphs into a graph latent space aligned with text descriptions. It then reconstructs the molecular structure and atomic attributes based on the given text descriptions using the molecule decoder. It then learns a probabilistic mapping from the text space to the latent molecular graph space using a diffusion model. The results of our extensive experiments on several datasets demonstrate that 3M-Diffusion can generate high-quality, novel and diverse molecular graphs that semantically match the textual description provided.

Simple and Asymmetric Graph Contrastive Learning without Augmentations

Graph Contrastive Learning (GCL) has shown superior performance in representation learning in graph-structured data. Despite their success, most existing GCL methods rely on prefabricated graph augmentation and homophily assumptions. Thus, they fail to generalize well to heterophilic graphs where connected nodes may have different class labels and dissimilar features. In this paper, we study the problem of conducting contrastive learning on homophilic and heterophilic graphs. We find that we can achieve promising performance simply by considering an asymmetric view of the neighboring nodes. The resulting simple algorithm, Asymmetric Contrastive Learning for Graphs (GraphACL), is easy to implement and does not rely on graph augmentations and homophily assumptions. We provide theoretical and empirical evidence that GraphACL can capture one-hop local neighborhood information and two-hop monophily similarity, which are both important for modeling heterophilic graphs. Experimental results show that the simple GraphACL significantly outperforms state-of-the-art graph contrastive learning and self-supervised learning methods on homophilic and heterophilic graphs. The code of GraphACL is available at https://github.com/tengxiao1/GraphACL.

On the Safety of Open-Sourced Large Language Models: Does Alignment Really Prevent Them From Being Misused?

Large Language Models (LLMs) have achieved unprecedented performance in Natural Language Generation (NLG) tasks. However, many existing studies have shown that they could be misused to generate undesired content. In response, before releasing LLMs for public access, model developers usually align those language models through Supervised Fine-Tuning (SFT) or Reinforcement Learning with Human Feedback (RLHF). Consequently, those aligned large language models refuse to generate undesired content when facing potentially harmful/unethical requests. A natural question is "could alignment really prevent those open-sourced large language models from being misused to generate undesired content?''. In this work, we provide a negative answer to this question. In particular, we show those open-sourced, aligned large language models could be easily misguided to generate undesired content without heavy computations or careful prompt designs. Our key idea is to directly manipulate the generation process of open-sourced LLMs to misguide it to generate undesired content including harmful or biased information and even private data. We evaluate our method on 4 open-sourced LLMs accessible publicly and our finding highlights the need for more advanced mitigation strategies for open-sourced LLMs.

Fairness-aware Message Passing for Graph Neural Networks

Graph Neural Networks (GNNs) have shown great power in various domains. However, their predictions may inherit societal biases on sensitive attributes, limiting their adoption in real-world applications. Although many efforts have been taken for fair GNNs, most existing works just adopt widely used fairness techniques in machine learning to graph domains and ignore or don't have a thorough understanding of the message passing mechanism with fairness constraints, which is a distinctive feature of GNNs. To fill the gap, we propose a novel fairness-aware message passing framework GMMD, which is derived from an optimization problem that considers both graph smoothness and representation fairness. GMMD can be intuitively interpreted as encouraging a node to aggregate representations of other nodes from different sensitive groups while subtracting representations of other nodes from the same sensitive group, resulting in fair representations. We also provide a theoretical analysis to justify that GMMD can guarantee fairness, which leads to a simpler and theory-guided variant GMMD-S. Extensive experiments on graph benchmarks show that our proposed framework can significantly improve the fairness of various backbone GNN models while maintaining high accuracy.

Self-Explainable Graph Neural Networks for Link Prediction

Graph Neural Networks (GNNs) have achieved state-of-the-art performance for link prediction. However, GNNs suffer from poor interpretability, which limits their adoptions in critical scenarios that require knowing why certain links are predicted. Despite various methods proposed for the explainability of GNNs, most of them are post-hoc explainers developed for explaining node classification. Directly adopting existing post-hoc explainers for explaining link prediction is sub-optimal because: (i) post-hoc explainers usually adopt another strategy or model to explain a target model, which could misinterpret the target model; and (ii) GNN explainers for node classification identify crucial subgraphs around each node for the explanation; while for link prediction, one needs to explain the prediction for each pair of nodes based on graph structure and node attributes. Therefore, in this paper, we study a novel problem of self-explainable GNNs for link prediction, which can simultaneously give accurate predictions and explanations. Concretely, we propose a new framework and it can find various $K$ important neighbors of one node to learn pair-specific representations for links from this node to other nodes. These $K$ different neighbors represent important characteristics of the node and model various factors for links from it. Thus, $K$ neighbors can provide explanations for the existence of links. Experiments on both synthetic and real-world datasets verify the effectiveness of the proposed framework for link prediction and explanation.

A Comprehensive Survey on Trustworthy Graph Neural Networks: Privacy, Robustness, Fairness, and Explainability

Graph Neural Networks (GNNs) have made rapid developments in the recent years. Due to their great ability in modeling graph-structured data, GNNs are vastly used in various applications, including high-stakes scenarios such as financial analysis, traffic predictions, and drug discovery. Despite their great potential in benefiting humans in the real world, recent study shows that GNNs can leak private information, are vulnerable to adversarial attacks, can inherit and magnify societal bias from training data and lack interpretability, which have risk of causing unintentional harm to the users and society. For example, existing works demonstrate that attackers can fool the GNNs to give the outcome they desire with unnoticeable perturbation on training graph. GNNs trained on social networks may embed the discrimination in their decision process, strengthening the undesirable societal bias. Consequently, trustworthy GNNs in various aspects are emerging to prevent the harm from GNN models and increase the users' trust in GNNs. In this paper, we give a comprehensive survey of GNNs in the computational aspects of privacy, robustness, fairness, and explainability. For each aspect, we give the taxonomy of the related methods and formulate the general frameworks for the multiple categories of trustworthy GNNs. We also discuss the future research directions of each aspect and connections between these aspects to help achieve trustworthiness.

Learning Fair Models without Sensitive Attributes: A Generative Approach

Most existing fair classifiers rely on sensitive attributes to achieve fairness. However, for many scenarios, we cannot obtain sensitive attributes due to privacy and legal issues. The lack of sensitive attributes challenges many existing works. Though we lack sensitive attributes, for many applications, there usually exists features or information of various formats that are relevant to sensitive attributes. For example, a personal purchase history can reflect his or her race, which would be helpful for learning fair classifiers on race. However, the work on exploring relevant features for learning fair models without sensitive attributes is rather limited. Therefore, in this paper, we study a novel problem of learning fair models without sensitive attributes by exploring relevant features. We propose a probabilistic generative framework to effectively estimate the sensitive attribute from the training data with relevant features in various formats and utilize the estimated sensitive attribute information to learn fair models. Experimental results on real-world datasets show the effectiveness of our framework in terms of both accuracy and fairness.

ImGAGN:Imbalanced Network Embedding via Generative Adversarial Graph Networks

Imbalanced classification on graphs is ubiquitous yet challenging in many real-world applications, such as fraudulent node detection. Recently, graph neural networks (GNNs) have shown promising performance on many network analysis tasks. However, most existing GNNs have almost exclusively focused on the balanced networks, and would get unappealing performance on the imbalanced networks. To bridge this gap, in this paper, we present a generative adversarial graph network model, called ImGAGN to address the imbalanced classification problem on graphs. It introduces a novel generator for graph structure data, named GraphGenerator, which can simulate both the minority class nodes' attribute distribution and network topological structure distribution by generating a set of synthetic minority nodes such that the number of nodes in different classes can be balanced. Then a graph convolutional network (GCN) discriminator is trained to discriminate between real nodes and fake (i.e., generated) nodes, and also between minority nodes and majority nodes on the synthetic balanced network. To validate the effectiveness of the proposed method, extensive experiments are conducted on four real-world imbalanced network datasets. Experimental results demonstrate that the proposed method ImGAGN outperforms state-of-the-art algorithms for semi-supervised imbalanced node classification task.