Integrating Graphs with Large Language Models: Methods and Prospects

Large language models (LLMs) such as GPT-4 have emerged as frontrunners, showcasing unparalleled prowess in diverse applications, including answering queries, code generation, and more. Parallelly, graph-structured data, an intrinsic data type, is pervasive in real-world scenarios. Merging the capabilities of LLMs with graph-structured data has been a topic of keen interest. This paper bifurcates such integrations into two predominant categories. The first leverages LLMs for graph learning, where LLMs can not only augment existing graph algorithms but also stand as prediction models for various graph tasks. Conversely, the second category underscores the pivotal role of graphs in advancing LLMs. Mirroring human cognition, we solve complex tasks by adopting graphs in either reasoning or collaboration. Integrating with such structures can significantly boost the performance of LLMs in various complicated tasks. We also discuss and propose open questions for integrating LLMs with graph-structured data for the future direction of the field

PREM: A Simple Yet Effective Approach for Node-Level Graph Anomaly Detection

Node-level graph anomaly detection (GAD) plays a critical role in identifying anomalous nodes from graph-structured data in various domains such as medicine, social networks, and e-commerce. However, challenges have arisen due to the diversity of anomalies and the dearth of labeled data. Existing methodologies - reconstruction-based and contrastive learning - while effective, often suffer from efficiency issues, stemming from their complex objectives and elaborate modules. To improve the efficiency of GAD, we introduce a simple method termed PREprocessing and Matching (PREM for short). Our approach streamlines GAD, reducing time and memory consumption while maintaining powerful anomaly detection capabilities. Comprising two modules - a pre-processing module and an ego-neighbor matching module - PREM eliminates the necessity for message-passing propagation during training, and employs a simple contrastive loss, leading to considerable reductions in training time and memory usage. Moreover, through rigorous evaluations of five real-world datasets, our method demonstrated robustness and effectiveness. Notably, when validated on the ACM dataset, PREM achieved a 5% improvement in AUC, a 9-fold increase in training speed, and sharply reduce memory usage compared to the most efficient baseline.Comment: Accepted by IEEE International Conference of Data Mining 2023 (ICDM 2023

SIDE: Self-supervised Intermediate Domain Exploration for Source-free Domain Adaptation

Domain adaptation aims to alleviate the domain shift when transferring the knowledge learned from the source domain to the target domain. Due to privacy issues, source-free domain adaptation (SFDA), where source data is unavailable during adaptation, has recently become very demanding yet challenging. Existing SFDA methods focus on either self-supervised learning of target samples or reconstruction of virtual source data. The former overlooks the transferable knowledge in the source model, whilst the latter introduces even more uncertainty. To address the above issues, this paper proposes self-supervised intermediate domain exploration (SIDE) that effectively bridges the domain gap with an intermediate domain, where samples are cyclically filtered out in a self-supervised fashion. First, we propose cycle intermediate domain filtering (CIDF) to cyclically select intermediate samples with similar distributions over source and target domains. Second, with the aid of those intermediate samples, an inter-domain gap transition (IDGT) module is developed to mitigate possible distribution mismatches between the source and target data. Finally, we introduce cross-view consistency learning (CVCL) to maintain the intrinsic class discriminability whilst adapting the model to the target domain. Extensive experiments on three popular benchmarks, i.e. Office-31, Office-Home and VisDA-C, show that our proposed SIDE achieves competitive performance against state-of-the-art methods.Comment: code at https://github.com/se111/SID

A Dual-Stream Neural Network Explains the Functional Segregation of Dorsal and Ventral Visual Pathways in Human Brains

The human visual system uses two parallel pathways for spatial processing and object recognition. In contrast, computer vision systems tend to use a single feedforward pathway, rendering them less robust, adaptive, or efficient than human vision. To bridge this gap, we developed a dual-stream vision model inspired by the human eyes and brain. At the input level, the model samples two complementary visual patterns to mimic how the human eyes use magnocellular and parvocellular retinal ganglion cells to separate retinal inputs to the brain. At the backend, the model processes the separate input patterns through two branches of convolutional neural networks (CNN) to mimic how the human brain uses the dorsal and ventral cortical pathways for parallel visual processing. The first branch (WhereCNN) samples a global view to learn spatial attention and control eye movements. The second branch (WhatCNN) samples a local view to represent the object around the fixation. Over time, the two branches interact recurrently to build a scene representation from moving fixations. We compared this model with the human brains processing the same movie and evaluated their functional alignment by linear transformation. The WhereCNN and WhatCNN branches were found to differentially match the dorsal and ventral pathways of the visual cortex, respectively, primarily due to their different learning objectives. These model-based results lead us to speculate that the distinct responses and representations of the ventral and dorsal streams are more influenced by their distinct goals in visual attention and object recognition than by their specific bias or selectivity in retinal inputs. This dual-stream model takes a further step in brain-inspired computer vision, enabling parallel neural networks to actively explore and understand the visual surroundings

Beyond Smoothing: Unsupervised Graph Representation Learning with Edge Heterophily Discriminating

Unsupervised graph representation learning (UGRL) has drawn increasing research attention and achieved promising results in several graph analytic tasks. Relying on the homophily assumption, existing UGRL methods tend to smooth the learned node representations along all edges, ignoring the existence of heterophilic edges that connect nodes with distinct attributes. As a result, current methods are hard to generalize to heterophilic graphs where dissimilar nodes are widely connected, and also vulnerable to adversarial attacks. To address this issue, we propose a novel unsupervised Graph Representation learning method with Edge hEterophily discriminaTing (GREET) which learns representations by discriminating and leveraging homophilic edges and heterophilic edges. To distinguish two types of edges, we build an edge discriminator that infers edge homophily/heterophily from feature and structure information. We train the edge discriminator in an unsupervised way through minimizing the crafted pivot-anchored ranking loss, with randomly sampled node pairs acting as pivots. Node representations are learned through contrasting the dual-channel encodings obtained from the discriminated homophilic and heterophilic edges. With an effective interplaying scheme, edge discriminating and representation learning can mutually boost each other during the training phase. We conducted extensive experiments on 14 benchmark datasets and multiple learning scenarios to demonstrate the superiority of GREET.Comment: 14 pages, 7 tables, 6 figures, accepted by AAAI 202

MolFM: A Multimodal Molecular Foundation Model

Molecular knowledge resides within three different modalities of information sources: molecular structures, biomedical documents, and knowledge bases. Effective incorporation of molecular knowledge from these modalities holds paramount significance in facilitating biomedical research. However, existing multimodal molecular foundation models exhibit limitations in capturing intricate connections between molecular structures and texts, and more importantly, none of them attempt to leverage a wealth of molecular expertise derived from knowledge graphs. In this study, we introduce MolFM, a multimodal molecular foundation model designed to facilitate joint representation learning from molecular structures, biomedical texts, and knowledge graphs. We propose cross-modal attention between atoms of molecular structures, neighbors of molecule entities and semantically related texts to facilitate cross-modal comprehension. We provide theoretical analysis that our cross-modal pre-training captures local and global molecular knowledge by minimizing the distance in the feature space between different modalities of the same molecule, as well as molecules sharing similar structures or functions. MolFM achieves state-of-the-art performance on various downstream tasks. On cross-modal retrieval, MolFM outperforms existing models with 12.13% and 5.04% absolute gains under the zero-shot and fine-tuning settings, respectively. Furthermore, qualitative analysis showcases MolFM's implicit ability to provide grounding from molecular substructures and knowledge graphs. Code and models are available on https://github.com/BioFM/OpenBioMed.Comment: 31 pages, 15 figures, and 15 table