Exploring Graph Tasks with Pure LLMs: A Comprehensive Benchmark and Investigation

Graph-structured data has become increasingly prevalent across various domains, raising the demand for effective models to handle graph tasks like node classification and link prediction. Traditional graph learning models like Graph Neural Networks (GNNs) have made significant strides, but their capabilities in handling graph data remain limited in certain contexts. In recent years, large language models (LLMs) have emerged as promising candidates for graph tasks, yet most studies focus primarily on performance benchmarks and fail to address their broader potential, including their ability to handle limited data, their transferability across tasks, and their robustness. In this work, we provide a comprehensive exploration of LLMs applied to graph tasks. We evaluate the performance of pure LLMs, including those without parameter optimization and those fine-tuned with instructions, across various scenarios. Our analysis goes beyond accuracy, assessing LLM ability to perform in few-shot/zero-shot settings, transfer across domains, understand graph structures, and demonstrate robustness in challenging scenarios. We conduct extensive experiments with 16 graph learning models alongside 6 LLMs (e.g., Llama3B, GPT-4o, Qwen-plus), comparing their performance on datasets like Cora, PubMed, ArXiv, and Products. Our findings show that LLMs, particularly those with instruction tuning, outperform traditional models in few-shot settings, exhibit strong domain transferability, and demonstrate excellent generalization and robustness. This work offers valuable insights into the capabilities of LLMs for graph learning, highlighting their advantages and potential for real-world applications, and paving the way for future research in this area. Codes and datasets are released in https://github.com/myflashbarry/LLM-benchmarking.

Uni-Retrieval: A Multi-Style Retrieval Framework for STEM's Education

In AI-facilitated teaching, leveraging various query styles to interpret abstract text descriptions is crucial for ensuring high-quality teaching. However, current retrieval models primarily focus on natural text-image retrieval, making them insufficiently tailored to educational scenarios due to the ambiguities in the retrieval process. In this paper, we propose a diverse expression retrieval task tailored to educational scenarios, supporting retrieval based on multiple query styles and expressions. We introduce the STEM Education Retrieval Dataset (SER), which contains over 24,000 query pairs of different styles, and the Uni-Retrieval, an efficient and style-diversified retrieval vision-language model based on prompt tuning. Uni-Retrieval extracts query style features as prototypes and builds a continuously updated Prompt Bank containing prompt tokens for diverse queries. This bank can updated during test time to represent domain-specific knowledge for different subject retrieval scenarios. Our framework demonstrates scalability and robustness by dynamically retrieving prompt tokens based on prototype similarity, effectively facilitating learning for unknown queries. Experimental results indicate that Uni-Retrieval outperforms existing retrieval models in most retrieval tasks. This advancement provides a scalable and precise solution for diverse educational needs.

Towards Trustworthy Retrieval Augmented Generation for Large Language Models: A Survey

Retrieval-Augmented Generation (RAG) is an advanced technique designed to address the challenges of Artificial Intelligence-Generated Content (AIGC). By integrating context retrieval into content generation, RAG provides reliable and up-to-date external knowledge, reduces hallucinations, and ensures relevant context across a wide range of tasks. However, despite RAG's success and potential, recent studies have shown that the RAG paradigm also introduces new risks, including robustness issues, privacy concerns, adversarial attacks, and accountability issues. Addressing these risks is critical for future applications of RAG systems, as they directly impact their trustworthiness. Although various methods have been developed to improve the trustworthiness of RAG methods, there is a lack of a unified perspective and framework for research in this topic. Thus, in this paper, we aim to address this gap by providing a comprehensive roadmap for developing trustworthy RAG systems. We place our discussion around five key perspectives: reliability, privacy, safety, fairness, explainability, and accountability. For each perspective, we present a general framework and taxonomy, offering a structured approach to understanding the current challenges, evaluating existing solutions, and identifying promising future research directions. To encourage broader adoption and innovation, we also highlight the downstream applications where trustworthy RAG systems have a significant impact.

Mamba-Based Graph Convolutional Networks: Tackling Over-smoothing with Selective State Space

Graph Neural Networks (GNNs) have shown great success in various graph-based learning tasks. However, it often faces the issue of over-smoothing as the model depth increases, which causes all node representations to converge to a single value and become indistinguishable. This issue stems from the inherent limitations of GNNs, which struggle to distinguish the importance of information from different neighborhoods. In this paper, we introduce MbaGCN, a novel graph convolutional architecture that draws inspiration from the Mamba paradigm-originally designed for sequence modeling. MbaGCN presents a new backbone for GNNs, consisting of three key components: the Message Aggregation Layer, the Selective State Space Transition Layer, and the Node State Prediction Layer. These components work in tandem to adaptively aggregate neighborhood information, providing greater flexibility and scalability for deep GNN models. While MbaGCN may not consistently outperform all existing methods on each dataset, it provides a foundational framework that demonstrates the effective integration of the Mamba paradigm into graph representation learning. Through extensive experiments on benchmark datasets, we demonstrate that MbaGCN paves the way for future advancements in graph neural network research.

Graph Defense Diffusion Model

Graph Neural Networks (GNNs) demonstrate significant potential in various applications but remain highly vulnerable to adversarial attacks, which can greatly degrade their performance. Existing graph purification methods attempt to address this issue by filtering attacked graphs; however, they struggle to effectively defend against multiple types of adversarial attacks simultaneously due to their limited flexibility, and they lack comprehensive modeling of graph data due to their heavy reliance on heuristic prior knowledge. To overcome these challenges, we propose a more versatile approach for defending against adversarial attacks on graphs. In this work, we introduce the Graph Defense Diffusion Model (GDDM), a flexible purification method that leverages the denoising and modeling capabilities of diffusion models. The iterative nature of diffusion models aligns well with the stepwise process of adversarial attacks, making them particularly suitable for defense. By iteratively adding and removing noise, GDDM effectively purifies attacked graphs, restoring their original structure and features. Our GDDM consists of two key components: (1) Graph Structure-Driven Refiner, which preserves the basic fidelity of the graph during the denoising process, and ensures that the generated graph remains consistent with the original scope; and (2) Node Feature-Constrained Regularizer, which removes residual impurities from the denoised graph, further enhances the purification effect. Additionally, we design tailored denoising strategies to handle different types of adversarial attacks, improving the model's adaptability to various attack scenarios. Extensive experiments conducted on three real-world datasets demonstrate that GDDM outperforms state-of-the-art methods in defending against a wide range of adversarial attacks, showcasing its robustness and effectiveness.

Computational Protein Science in the Era of Large Language Models (LLMs)

Considering the significance of proteins, computational protein science has always been a critical scientific field, dedicated to revealing knowledge and developing applications within the protein sequence-structure-function paradigm. In the last few decades, Artificial Intelligence (AI) has made significant impacts in computational protein science, leading to notable successes in specific protein modeling tasks. However, those previous AI models still meet limitations, such as the difficulty in comprehending the semantics of protein sequences, and the inability to generalize across a wide range of protein modeling tasks. Recently, LLMs have emerged as a milestone in AI due to their unprecedented language processing & generalization capability. They can promote comprehensive progress in fields rather than solving individual tasks. As a result, researchers have actively introduced LLM techniques in computational protein science, developing protein Language Models (pLMs) that skillfully grasp the foundational knowledge of proteins and can be effectively generalized to solve a diversity of sequence-structure-function reasoning problems. While witnessing prosperous developments, it's necessary to present a systematic overview of computational protein science empowered by LLM techniques. First, we summarize existing pLMs into categories based on their mastered protein knowledge, i.e., underlying sequence patterns, explicit structural and functional information, and external scientific languages. Second, we introduce the utilization and adaptation of pLMs, highlighting their remarkable achievements in promoting protein structure prediction, protein function prediction, and protein design studies. Then, we describe the practical application of pLMs in antibody design, enzyme design, and drug discovery. Finally, we specifically discuss the promising future directions in this fast-growing field.

Knowledge Graph Retrieval-Augmented Generation for LLM-based Recommendation

Recommender systems have become increasingly vital in our daily lives, helping to alleviate the problem of information overload across various user-oriented online services. The emergence of Large Language Models (LLMs) has yielded remarkable achievements, demonstrating their potential for the development of next-generation recommender systems. Despite these advancements, LLM-based recommender systems face inherent limitations stemming from their LLM backbones, particularly issues of hallucinations and the lack of up-to-date and domain-specific knowledge. Recently, Retrieval-Augmented Generation (RAG) has garnered significant attention for addressing these limitations by leveraging external knowledge sources to enhance the understanding and generation of LLMs. However, vanilla RAG methods often introduce noise and neglect structural relationships in knowledge, limiting their effectiveness in LLM-based recommendations. To address these limitations, we propose to retrieve high-quality and up-to-date structure information from the knowledge graph (KG) to augment recommendations. Specifically, our approach develops a retrieval-augmented framework, termed K-RagRec, that facilitates the recommendation generation process by incorporating structure information from the external KG. Extensive experiments have been conducted to demonstrate the effectiveness of our proposed method.

ChartAdapter: Large Vision-Language Model for Chart Summarization

Chart summarization, which focuses on extracting key information from charts and interpreting it in natural language, is crucial for generating and delivering insights through effective and accessible data analysis. Traditional methods for chart understanding and summarization often rely on multi-stage pipelines, which may produce suboptimal semantic alignment between visual and textual information. In comparison, recently developed LLM-based methods are more dependent on the capability of foundation images or languages, while ignoring the characteristics of chart data and its relevant challenges. To address these limitations, we propose ChartAdapter, a novel lightweight transformer module designed to bridge the gap between charts and textual summaries. ChartAdapter employs learnable query vectors to extract implicit semantics from chart data and incorporates a cross-modal alignment projector to enhance vision-to-language generative learning. By integrating ChartAdapter with an LLM, we enable end-to-end training and efficient chart summarization. To further enhance the training, we introduce a three-stage hierarchical training procedure and develop a large-scale dataset specifically curated for chart summarization, comprising 190,618 samples. Experimental results on the standard Chart-to-Text testing set demonstrate that our approach significantly outperforms existing methods, including state-of-the-art models, in generating high-quality chart summaries. Ablation studies further validate the effectiveness of key components in ChartAdapter. This work highlights the potential of tailored LLM-based approaches to advance chart understanding and sets a strong foundation for future research in this area.

Adaptive Self-supervised Learning for Social Recommendations

In recent years, researchers have attempted to exploit social relations to improve the performance in recommendation systems. Generally, most existing social recommendation methods heavily depends on substantial domain knowledge and expertise in primary recommendation tasks for designing useful auxiliary tasks. Meanwhile, Self-Supervised Learning (SSL) recently has received considerable attention in the field of recommendation, since it can provide self-supervision signals in assisting the improvement of target recommendation systems by constructing self-supervised auxiliary tasks from raw data without human-annotated labels. Despite the great success, these SSL-based social recommendations are insufficient to adaptively balance various self-supervised auxiliary tasks, since assigning equal weights on various auxiliary tasks can result in sub-optimal recommendation performance, where different self-supervised auxiliary tasks may contribute differently to improving the primary social recommendation across different datasets. To address this issue, in this work, we propose Adaptive Self-supervised Learning for Social Recommendations (AdasRec) by taking advantage of various self-supervised auxiliary tasks. More specifically, an adaptive weighting mechanism is proposed to learn adaptive weights for various self-supervised auxiliary tasks, so as to balance the contribution of such self-supervised auxiliary tasks for enhancing representation learning in social recommendations. The adaptive weighting mechanism is used to assign different weights on auxiliary tasks to achieve an overall weighting of the entire auxiliary tasks and ultimately assist the primary recommendation task, achieved by a meta learning optimization problem with an adaptive weighting network. Comprehensive experiments on various real-world datasets are constructed to verify the effectiveness of our proposed method.

Score-based Generative Diffusion Models for Social Recommendations

With the prevalence of social networks on online platforms, social recommendation has become a vital technique for enhancing personalized recommendations. The effectiveness of social recommendations largely relies on the social homophily assumption, which presumes that individuals with social connections often share similar preferences. However, this foundational premise has been recently challenged due to the inherent complexity and noise present in real-world social networks. In this paper, we tackle the low social homophily challenge from an innovative generative perspective, directly generating optimal user social representations that maximize consistency with collaborative signals. Specifically, we propose the Score-based Generative Model for Social Recommendation (SGSR), which effectively adapts the Stochastic Differential Equation (SDE)-based diffusion models for social recommendations. To better fit the recommendation context, SGSR employs a joint curriculum training strategy to mitigate challenges related to missing supervision signals and leverages self-supervised learning techniques to align knowledge across social and collaborative domains. Extensive experiments on real-world datasets demonstrate the effectiveness of our approach in filtering redundant social information and improving recommendation performance.