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.

GUME: Graphs and User Modalities Enhancement for Long-Tail Multimodal Recommendation

Multimodal recommendation systems (MMRS) have received considerable attention from the research community due to their ability to jointly utilize information from user behavior and product images and text. Previous research has two main issues. First, many long-tail items in recommendation systems have limited interaction data, making it difficult to learn comprehensive and informative representations. However, past MMRS studies have overlooked this issue. Secondly, users' modality preferences are crucial to their behavior. However, previous research has primarily focused on learning item modality representations, while user modality representations have remained relatively simplistic.To address these challenges, we propose a novel Graphs and User Modalities Enhancement (GUME) for long-tail multimodal recommendation. Specifically, we first enhance the user-item graph using multimodal similarity between items. This improves the connectivity of long-tail items and helps them learn high-quality representations through graph propagation. Then, we construct two types of user modalities: explicit interaction features and extended interest features. By using the user modality enhancement strategy to maximize mutual information between these two features, we improve the generalization ability of user modality representations. Additionally, we design an alignment strategy for modality data to remove noise from both internal and external perspectives. Extensive experiments on four publicly available datasets demonstrate the effectiveness of our approach.

Enhancing Tabular Data Optimization with a Flexible Graph-based Reinforced Exploration Strategy

Tabular data optimization methods aim to automatically find an optimal feature transformation process that generates high-value features and improves the performance of downstream machine learning tasks. Current frameworks for automated feature transformation rely on iterative sequence generation tasks, optimizing decision strategies through performance feedback from downstream tasks. However, these approaches fail to effectively utilize historical decision-making experiences and overlook potential relationships among generated features, thus limiting the depth of knowledge extraction. Moreover, the granularity of the decision-making process lacks dynamic backtracking capabilities for individual features, leading to insufficient adaptability when encountering inefficient pathways, adversely affecting overall robustness and exploration efficiency. To address the limitations observed in current automatic feature engineering frameworks, we introduce a novel method that utilizes a feature-state transformation graph to effectively preserve the entire feature transformation journey, where each node represents a specific transformation state. During exploration, three cascading agents iteratively select nodes and idea mathematical operations to generate new transformation states. This strategy leverages the inherent properties of the graph structure, allowing for the preservation and reuse of valuable transformations. It also enables backtracking capabilities through graph pruning techniques, which can rectify inefficient transformation paths. To validate the efficacy and flexibility of our approach, we conducted comprehensive experiments and detailed case studies, demonstrating superior performance in diverse scenarios.

Holistic Memory Diversification for Incremental Learning in Growing Graphs

This paper addresses the challenge of incremental learning in growing graphs with increasingly complex tasks. The goal is to continually train a graph model to handle new tasks while retaining its inference ability on previous tasks. Existing methods usually neglect the importance of memory diversity, limiting in effectively selecting high-quality memory from previous tasks and remembering broad previous knowledge within the scarce memory on graphs. To address that, we introduce a novel holistic Diversified Memory Selection and Generation (DMSG) framework for incremental learning in graphs, which first introduces a buffer selection strategy that considers both intra-class and inter-class diversities, employing an efficient greedy algorithm for sampling representative training nodes from graphs into memory buffers after learning each new task. Then, to adequately rememorize the knowledge preserved in the memory buffer when learning new tasks, we propose a diversified memory generation replay method. This method first utilizes a variational layer to generate the distribution of buffer node embeddings and sample synthesized ones for replaying. Furthermore, an adversarial variational embedding learning method and a reconstruction-based decoder are proposed to maintain the integrity and consolidate the generalization of the synthesized node embeddings, respectively. Finally, we evaluate our model on node classification tasks involving increasing class numbers. Extensive experimental results on publicly accessible datasets demonstrate the superiority of DMSG over state-of-the-art methods.

Enhanced Gene Selection in Single-Cell Genomics: Pre-Filtering Synergy and Reinforced Optimization

Recent advancements in single-cell genomics necessitate precision in gene panel selection to interpret complex biological data effectively. Those methods aim to streamline the analysis of scRNA-seq data by focusing on the most informative genes that contribute significantly to the specific analysis task. Traditional selection methods, which often rely on expert domain knowledge, embedded machine learning models, or heuristic-based iterative optimization, are prone to biases and inefficiencies that may obscure critical genomic signals. Recognizing the limitations of traditional methods, we aim to transcend these constraints with a refined strategy. In this study, we introduce an iterative gene panel selection strategy that is applicable to clustering tasks in single-cell genomics. Our method uniquely integrates results from other gene selection algorithms, providing valuable preliminary boundaries or prior knowledge as initial guides in the search space to enhance the efficiency of our framework. Furthermore, we incorporate the stochastic nature of the exploration process in reinforcement learning (RL) and its capability for continuous optimization through reward-based feedback. This combination mitigates the biases inherent in the initial boundaries and harnesses RL's adaptability to refine and target gene panel selection dynamically. To illustrate the effectiveness of our method, we conducted detailed comparative experiments, case studies, and visualization analysis.

FedGCS: A Generative Framework for Efficient Client Selection in Federated Learning via Gradient-based Optimization

Federated Learning faces significant challenges in statistical and system heterogeneity, along with high energy consumption, necessitating efficient client selection strategies. Traditional approaches, including heuristic and learning-based methods, fall short of addressing these complexities holistically. In response, we propose FedGCS, a novel generative client selection framework that innovatively recasts the client selection process as a generative task. Drawing inspiration from the methodologies used in large language models, FedGCS efficiently encodes abundant decision-making knowledge within a continuous representation space, enabling efficient gradient-based optimization to search for optimal client selection that will be finally output via generation. The framework comprises four steps: (1) automatic collection of diverse "selection-score" pair data using classical client selection methods; (2) training an encoder-evaluator-decoder framework on this data to construct a continuous representation space; (3) employing gradient-based optimization in this space for optimal client selection; (4) generating the final optimal client selection via using beam search for the well-trained decoder. FedGCS outperforms traditional methods by being more comprehensive, generalizable, and efficient, simultaneously optimizing for model performance, latency, and energy consumption. The effectiveness of FedGCS is proven through extensive experimental analyses.

scCDCG: Efficient Deep Structural Clustering for single-cell RNA-seq via Deep Cut-informed Graph Embedding

Single-cell RNA sequencing (scRNA-seq) is essential for unraveling cellular heterogeneity and diversity, offering invaluable insights for bioinformatics advancements. Despite its potential, traditional clustering methods in scRNA-seq data analysis often neglect the structural information embedded in gene expression profiles, crucial for understanding cellular correlations and dependencies. Existing strategies, including graph neural networks, face challenges in handling the inefficiency due to scRNA-seq data's intrinsic high-dimension and high-sparsity. Addressing these limitations, we introduce scCDCG (single-cell RNA-seq Clustering via Deep Cut-informed Graph), a novel framework designed for efficient and accurate clustering of scRNA-seq data that simultaneously utilizes intercellular high-order structural information. scCDCG comprises three main components: (i) A graph embedding module utilizing deep cut-informed techniques, which effectively captures intercellular high-order structural information, overcoming the over-smoothing and inefficiency issues prevalent in prior graph neural network methods. (ii) A self-supervised learning module guided by optimal transport, tailored to accommodate the unique complexities of scRNA-seq data, specifically its high-dimension and high-sparsity. (iii) An autoencoder-based feature learning module that simplifies model complexity through effective dimension reduction and feature extraction. Our extensive experiments on 6 datasets demonstrate scCDCG's superior performance and efficiency compared to 7 established models, underscoring scCDCG's potential as a transformative tool in scRNA-seq data analysis. Our code is available at: https://github.com/XPgogogo/scCDCG.

DP-CRE: Continual Relation Extraction via Decoupled Contrastive Learning and Memory Structure Preservation

Continuous Relation Extraction (CRE) aims to incrementally learn relation knowledge from a non-stationary stream of data. Since the introduction of new relational tasks can overshadow previously learned information, catastrophic forgetting becomes a significant challenge in this domain. Current replay-based training paradigms prioritize all data uniformly and train memory samples through multiple rounds, which would result in overfitting old tasks and pronounced bias towards new tasks because of the imbalances of the replay set. To handle the problem, we introduce the DecouPled CRE (DP-CRE) framework that decouples the process of prior information preservation and new knowledge acquisition. This framework examines alterations in the embedding space as new relation classes emerge, distinctly managing the preservation and acquisition of knowledge. Extensive experiments show that DP-CRE significantly outperforms other CRE baselines across two datasets.

scInterpreter: Training Large Language Models to Interpret scRNA-seq Data for Cell Type Annotation

Despite the inherent limitations of existing Large Language Models in directly reading and interpreting single-cell omics data, they demonstrate significant potential and flexibility as the Foundation Model. This research focuses on how to train and adapt the Large Language Model with the capability to interpret and distinguish cell types in single-cell RNA sequencing data. Our preliminary research results indicate that these foundational models excel in accurately categorizing known cell types, demonstrating the potential of the Large Language Models as effective tools for uncovering new biological insights.

Resolving the Imbalance Issue in Hierarchical Disciplinary Topic Inference via LLM-based Data Augmentation

In addressing the imbalanced issue of data within the realm of Natural Language Processing, text data augmentation methods have emerged as pivotal solutions. This data imbalance is prevalent in the research proposals submitted during the funding application process. Such imbalances, resulting from the varying popularity of disciplines or the emergence of interdisciplinary studies, significantly impede the precision of downstream topic models that deduce the affiliated disciplines of these proposals. At the data level, proposals penned by experts and scientists are inherently complex technological texts, replete with intricate terminologies, which augmenting such specialized text data poses unique challenges. At the system level, this, in turn, compromises the fairness of AI-assisted reviewer assignment systems, which raises a spotlight on solving this issue. This study leverages large language models (Llama V1) as data generators to augment research proposals categorized within intricate disciplinary hierarchies, aiming to rectify data imbalances and enhance the equity of expert assignments. We first sample within the hierarchical structure to find the under-represented class. Then we designed a prompt for keyword-based research proposal generation. Our experiments attests to the efficacy of the generated data, demonstrating that research proposals produced using the prompts can effectively address the aforementioned issues and generate high quality scientific text data, thus help the model overcome the imbalanced issue.