Towards Graph Prompt Learning: A Survey and Beyond

Large-scale "pre-train and prompt learning" paradigms have demonstrated remarkable adaptability, enabling broad applications across diverse domains such as question answering, image recognition, and multimodal retrieval. This approach fully leverages the potential of large-scale pre-trained models, reducing downstream data requirements and computational costs while enhancing model applicability across various tasks. Graphs, as versatile data structures that capture relationships between entities, play pivotal roles in fields such as social network analysis, recommender systems, and biological graphs. Despite the success of pre-train and prompt learning paradigms in Natural Language Processing (NLP) and Computer Vision (CV), their application in graph domains remains nascent. In graph-structured data, not only do the node and edge features often have disparate distributions, but the topological structures also differ significantly. This diversity in graph data can lead to incompatible patterns or gaps between pre-training and fine-tuning on downstream graphs. We aim to bridge this gap by summarizing methods for alleviating these disparities. This includes exploring prompt design methodologies, comparing related techniques, assessing application scenarios and datasets, and identifying unresolved problems and challenges. This survey categorizes over 100 relevant works in this field, summarizing general design principles and the latest applications, including text-attributed graphs, molecules, proteins, and recommendation systems. Through this extensive review, we provide a foundational understanding of graph prompt learning, aiming to impact not only the graph mining community but also the broader Artificial General Intelligence (AGI) community.

DisenSemi: Semi-supervised Graph Classification via Disentangled Representation Learning

Graph classification is a critical task in numerous multimedia applications, where graphs are employed to represent diverse types of multimedia data, including images, videos, and social networks. Nevertheless, in real-world scenarios, labeled graph data can be limited or scarce. To address this issue, we focus on the problem of semi-supervised graph classification, which involves both supervised and unsupervised models learning from labeled and unlabeled data. In contrast to recent approaches that transfer the entire knowledge from the unsupervised model to the supervised one, we argue that an effective transfer should only retain the relevant semantics that align well with the supervised task. In this paper, we propose a novel framework named DisenSemi, which learns disentangled representation for semi-supervised graph classification. Specifically, a disentangled graph encoder is proposed to generate factor-wise graph representations for both supervised and unsupervised models. Then we train two models via supervised objective and mutual information (MI)-based constraints respectively. To ensure the meaningful transfer of knowledge from the unsupervised encoder to the supervised one, we further define an MI-based disentangled consistency regularization between two models and identify the corresponding rationale that aligns well with the current graph classification task. Experimental results on a range of publicly accessible datasets reveal the effectiveness of our DisenSemi.

Anti-Collapse Loss for Deep Metric Learning Based on Coding Rate Metric

Deep metric learning (DML) aims to learn a discriminative high-dimensional embedding space for downstream tasks like classification, clustering, and retrieval. Prior literature predominantly focuses on pair-based and proxy-based methods to maximize inter-class discrepancy and minimize intra-class diversity. However, these methods tend to suffer from the collapse of the embedding space due to their over-reliance on label information. This leads to sub-optimal feature representation and inferior model performance. To maintain the structure of embedding space and avoid feature collapse, we propose a novel loss function called Anti-Collapse Loss. Specifically, our proposed loss primarily draws inspiration from the principle of Maximal Coding Rate Reduction. It promotes the sparseness of feature clusters in the embedding space to prevent collapse by maximizing the average coding rate of sample features or class proxies. Moreover, we integrate our proposed loss with pair-based and proxy-based methods, resulting in notable performance improvement. Comprehensive experiments on benchmark datasets demonstrate that our proposed method outperforms existing state-of-the-art methods. Extensive ablation studies verify the effectiveness of our method in preventing embedding space collapse and promoting generalization performance.

DEMO: A Statistical Perspective for Efficient Image-Text Matching

Image-text matching has been a long-standing problem, which seeks to connect vision and language through semantic understanding. Due to the capability to manage large-scale raw data, unsupervised hashing-based approaches have gained prominence recently. They typically construct a semantic similarity structure using the natural distance, which subsequently provides guidance to the model optimization process. However, the similarity structure could be biased at the boundaries of semantic distributions, causing error accumulation during sequential optimization. To tackle this, we introduce a novel hashing approach termed Distribution-based Structure Mining with Consistency Learning (DEMO) for efficient image-text matching. From a statistical view, DEMO characterizes each image using multiple augmented views, which are considered as samples drawn from its intrinsic semantic distribution. Then, we employ a non-parametric distribution divergence to ensure a robust and precise similarity structure. In addition, we introduce collaborative consistency learning which not only preserves the similarity structure in the Hamming space but also encourages consistency between retrieval distribution from different directions in a self-supervised manner. Through extensive experiments on three benchmark image-text matching datasets, we demonstrate that DEMO achieves superior performance compared with many state-of-the-art methods.

An Evaluation of Large Language Models in Bioinformatics Research

Large language models (LLMs) such as ChatGPT have gained considerable interest across diverse research communities. Their notable ability for text completion and generation has inaugurated a novel paradigm for language-interfaced problem solving. However, the potential and efficacy of these models in bioinformatics remain incompletely explored. In this work, we study the performance LLMs on a wide spectrum of crucial bioinformatics tasks. These tasks include the identification of potential coding regions, extraction of named entities for genes and proteins, detection of antimicrobial and anti-cancer peptides, molecular optimization, and resolution of educational bioinformatics problems. Our findings indicate that, given appropriate prompts, LLMs like GPT variants can successfully handle most of these tasks. In addition, we provide a thorough analysis of their limitations in the context of complicated bioinformatics tasks. In conclusion, we believe that this work can provide new perspectives and motivate future research in the field of LLMs applications, AI for Science and bioinformatics.

Learning with Imbalanced Noisy Data by Preventing Bias in Sample Selection

Learning with noisy labels has gained increasing attention because the inevitable imperfect labels in real-world scenarios can substantially hurt the deep model performance. Recent studies tend to regard low-loss samples as clean ones and discard high-loss ones to alleviate the negative impact of noisy labels. However, real-world datasets contain not only noisy labels but also class imbalance. The imbalance issue is prone to causing failure in the loss-based sample selection since the under-learning of tail classes also leans to produce high losses. To this end, we propose a simple yet effective method to address noisy labels in imbalanced datasets. Specifically, we propose Class-Balance-based sample Selection (CBS) to prevent the tail class samples from being neglected during training. We propose Confidence-based Sample Augmentation (CSA) for the chosen clean samples to enhance their reliability in the training process. To exploit selected noisy samples, we resort to prediction history to rectify labels of noisy samples. Moreover, we introduce the Average Confidence Margin (ACM) metric to measure the quality of corrected labels by leveraging the model's evolving training dynamics, thereby ensuring that low-quality corrected noisy samples are appropriately masked out. Lastly, consistency regularization is imposed on filtered label-corrected noisy samples to boost model performance. Comprehensive experimental results on synthetic and real-world datasets demonstrate the effectiveness and superiority of our proposed method, especially in imbalanced scenarios. Comprehensive experimental results on synthetic and real-world datasets demonstrate the effectiveness and superiority of our proposed method, especially in imbalanced scenarios.

Hierarchical Graph Pattern Understanding for Zero-Shot VOS

The optical flow guidance strategy is ideal for obtaining motion information of objects in the video. It is widely utilized in video segmentation tasks. However, existing optical flow-based methods have a significant dependency on optical flow, which results in poor performance when the optical flow estimation fails for a particular scene. The temporal consistency provided by the optical flow could be effectively supplemented by modeling in a structural form. This paper proposes a new hierarchical graph neural network (GNN) architecture, dubbed hierarchical graph pattern understanding (HGPU), for zero-shot video object segmentation (ZS-VOS). Inspired by the strong ability of GNNs in capturing structural relations, HGPU innovatively leverages motion cues (\ie, optical flow) to enhance the high-order representations from the neighbors of target frames. Specifically, a hierarchical graph pattern encoder with message aggregation is introduced to acquire different levels of motion and appearance features in a sequential manner. Furthermore, a decoder is designed for hierarchically parsing and understanding the transformed multi-modal contexts to achieve more accurate and robust results. HGPU achieves state-of-the-art performance on four publicly available benchmarks (DAVIS-16, YouTube-Objects, Long-Videos and DAVIS-17). Code and pre-trained model can be found at \url{https://github.com/NUST-Machine-Intelligence-Laboratory/HGPU}.

Proposal-Level Unsupervised Domain Adaptation for Open World Unbiased Detector

Open World Object Detection (OWOD) combines open-set object detection with incremental learning capabilities to handle the challenge of the open and dynamic visual world. Existing works assume that a foreground predictor trained on the seen categories can be directly transferred to identify the unseen categories' locations by selecting the top-k most confident foreground predictions. However, the assumption is hardly valid in practice. This is because the predictor is inevitably biased to the known categories, and fails under the shift in the appearance of the unseen categories. In this work, we aim to build an unbiased foreground predictor by re-formulating the task under Unsupervised Domain Adaptation, where the current biased predictor helps form the domains: the seen object locations and confident background locations as the source domain, and the rest ambiguous ones as the target domain. Then, we adopt the simple and effective self-training method to learn a predictor based on the domain-invariant foreground features, hence achieving unbiased prediction robust to the shift in appearance between the seen and unseen categories. Our approach's pipeline can adapt to various detection frameworks and UDA methods, empirically validated by OWOD evaluation, where we achieve state-of-the-art performance.

Dynamic Hypergraph Structure Learning for Traffic Flow Forecasting

This paper studies the problem of traffic flow forecasting, which aims to predict future traffic conditions on the basis of road networks and traffic conditions in the past. The problem is typically solved by modeling complex spatio-temporal correlations in traffic data using spatio-temporal graph neural networks (GNNs). However, the performance of these methods is still far from satisfactory since GNNs usually have limited representation capacity when it comes to complex traffic networks. Graphs, by nature, fall short in capturing non-pairwise relations. Even worse, existing methods follow the paradigm of message passing that aggregates neighborhood information linearly, which fails to capture complicated spatio-temporal high-order interactions. To tackle these issues, in this paper, we propose a novel model named Dynamic Hypergraph Structure Learning (DyHSL) for traffic flow prediction. To learn non-pairwise relationships, our DyHSL extracts hypergraph structural information to model dynamics in the traffic networks, and updates each node representation by aggregating messages from its associated hyperedges. Additionally, to capture high-order spatio-temporal relations in the road network, we introduce an interactive graph convolution block, which further models the neighborhood interaction for each node. Finally, we integrate these two views into a holistic multi-scale correlation extraction module, which conducts temporal pooling with different scales to model different temporal patterns. Extensive experiments on four popular traffic benchmark datasets demonstrate the effectiveness of our proposed DyHSL compared with a broad range of competing baselines.

Invariant Training 2D-3D Joint Hard Samples for Few-Shot Point Cloud Recognition

We tackle the data scarcity challenge in few-shot point cloud recognition of 3D objects by using a joint prediction from a conventional 3D model and a well-trained 2D model. Surprisingly, such an ensemble, though seems trivial, has hardly been shown effective in recent 2D-3D models. We find out the crux is the less effective training for the ''joint hard samples'', which have high confidence prediction on different wrong labels, implying that the 2D and 3D models do not collaborate well. To this end, our proposed invariant training strategy, called InvJoint, does not only emphasize the training more on the hard samples, but also seeks the invariance between the conflicting 2D and 3D ambiguous predictions. InvJoint can learn more collaborative 2D and 3D representations for better ensemble. Extensive experiments on 3D shape classification with widely adopted ModelNet10/40, ScanObjectNN and Toys4K, and shape retrieval with ShapeNet-Core validate the superiority of our InvJoint.