Drug-target interaction prediction (DTI) is essential in various applications including drug discovery and clinical application. There are two perspectives of input data widely used in DTI prediction: Intrinsic data represents how drugs or targets are constructed, and extrinsic data represents how drugs or targets are related to other biological entities. However, any of the two perspectives of input data can be scarce for some drugs or targets, especially for those unpopular or newly discovered. Furthermore, ground-truth labels for specific interaction types can also be scarce. Therefore, we propose the first method to tackle DTI prediction under input data and/or label scarcity. To make our model functional when only one perspective of input data is available, we design two separate experts to process intrinsic and extrinsic data respectively and fuse them adaptively according to different samples. Furthermore, to make the two perspectives complement each other and remedy label scarcity, two experts synergize with each other in a mutually supervised way to exploit the enormous unlabeled data. Extensive experiments on 3 real-world datasets under different extents of input data scarcity and/or label scarcity demonstrate our model outperforms states of the art significantly and steadily, with a maximum improvement of 53.53%. We also test our model without any data scarcity and it still outperforms current methods.

Pretraining language models on formal languages can improve their acquisition of natural language, but it is unclear which features of the formal language impart an inductive bias that leads to effective transfer. Drawing on insights from linguistics and complexity theory, we hypothesize that effective transfer occurs when the formal language both captures dependency structures in natural language and remains within the computational limitations of the model architecture. Focusing on transformers, we find that formal languages with both these properties enable language models to achieve lower loss on natural language and better linguistic generalization compared to other languages. In fact, pre-pretraining, or training on formal-then-natural language, reduces loss more efficiently than the same amount of natural language. For a 1B-parameter language model trained on roughly 1.6B tokens of natural language, pre-pretraining achieves the same loss and better linguistic generalization with a 33% smaller token budget. We also give mechanistic evidence of cross-task transfer from formal to natural language: attention heads acquired during formal language pretraining remain crucial for the model's performance on syntactic evaluations.

Retrieval-augmented generation (RAG) improves the response quality of large language models (LLMs) by retrieving knowledge from external databases. Typical RAG approaches split the text database into chunks, organizing them in a flat structure for efficient searches. To better capture the inherent dependencies and structured relationships across the text database, researchers propose to organize textual information into an indexing graph, known asgraph-based RAG. However, we argue that the limitation of current graph-based RAG methods lies in the redundancy of the retrieved information, rather than its insufficiency. Moreover, previous methods use a flat structure to organize retrieved information within the prompts, leading to suboptimal performance. To overcome these limitations, we propose PathRAG, which retrieves key relational paths from the indexing graph, and converts these paths into textual form for prompting LLMs. Specifically, PathRAG effectively reduces redundant information with flow-based pruning, while guiding LLMs to generate more logical and coherent responses with path-based prompting. Experimental results show that PathRAG consistently outperforms state-of-the-art baselines across six datasets and five evaluation dimensions. The code is available at the following link: https://github.com/BUPT-GAMMA/PathRAG

Recommender systems (RS) serve as a fundamental tool for navigating the vast expanse of online information, with deep learning advancements playing an increasingly important role in improving ranking accuracy. Among these, graph neural networks (GNNs) excel at extracting higher-order structural information, while large language models (LLMs) are designed to process and comprehend natural language, making both approaches highly effective and widely adopted. Recent research has focused on graph foundation models (GFMs), which integrate the strengths of GNNs and LLMs to model complex RS problems more efficiently by leveraging the graph-based structure of user-item relationships alongside textual understanding. In this survey, we provide a comprehensive overview of GFM-based RS technologies by introducing a clear taxonomy of current approaches, diving into methodological details, and highlighting key challenges and future directions. By synthesizing recent advancements, we aim to offer valuable insights into the evolving landscape of GFM-based recommender systems.

To preserve user privacy in recommender systems, federated recommendation (FR) based on federated learning (FL) emerges, keeping the personal data on the local client and updating a model collaboratively. Unlike FL, FR has a unique sparse aggregation mechanism, where the embedding of each item is updated by only partial clients, instead of full clients in a dense aggregation of general FL. Recently, as an essential principle of FL, model security has received increasing attention, especially for Byzantine attacks, where malicious clients can send arbitrary updates. The problem of exploring the Byzantine robustness of FR is particularly critical since in the domains applying FR, e.g., e-commerce, malicious clients can be injected easily by registering new accounts. However, existing Byzantine works neglect the unique sparse aggregation of FR, making them unsuitable for our problem. Thus, we make the first effort to investigate Byzantine attacks on FR from the perspective of sparse aggregation, which is non-trivial: it is not clear how to define Byzantine robustness under sparse aggregations and design Byzantine attacks under limited knowledge/capability. In this paper, we reformulate the Byzantine robustness under sparse aggregation by defining the aggregation for a single item as the smallest execution unit. Then we propose a family of effective attack strategies, named Spattack, which exploit the vulnerability in sparse aggregation and are categorized along the adversary's knowledge and capability. Extensive experimental results demonstrate that Spattack can effectively prevent convergence and even break down defenses under a few malicious clients, raising alarms for securing FR systems.

Low-Rank Adaptation (LoRA) is a parameter-efficient fine-tuning method that has been widely adopted in various downstream applications of LLMs. Together with the Mixture-of-Expert (MoE) technique, fine-tuning approaches have shown remarkable improvements in model capability. However, the coordination of multiple experts in existing studies solely relies on the weights assigned by the simple router function. Lack of communication and collaboration among experts exacerbate the instability of LLMs due to the imbalance load problem of MoE. To address this issue, we propose a novel MoE graph-based LLM fine-tuning framework GraphLoRA, in which a graph router function is designed to capture the collaboration signals among experts by graph neural networks (GNNs). GraphLoRA enables all experts to understand input knowledge and share information from neighbor experts by aggregating operations. Besides, to enhance each expert's capability and their collaborations, we design two novel coordination strategies: the Poisson distribution-based distinction strategy and the Normal distribution-based load balance strategy. Extensive experiments on four real-world datasets demonstrate the effectiveness of our GraphLoRA in parameter-efficient fine-tuning of LLMs, showing the benefits of facilitating collaborations of multiple experts in the graph router of GraphLoRA.

Large language models with retrieval-augmented generation encounter a pivotal challenge in intricate retrieval tasks, e.g., multi-hop question answering, which requires the model to navigate across multiple documents and generate comprehensive responses based on fragmented information. To tackle this challenge, we introduce a novel Knowledge Graph-based RAG framework with a hierarchical knowledge retriever, termed KG-Retriever. The retrieval indexing in KG-Retriever is constructed on a hierarchical index graph that consists of a knowledge graph layer and a collaborative document layer. The associative nature of graph structures is fully utilized to strengthen intra-document and inter-document connectivity, thereby fundamentally alleviating the information fragmentation problem and meanwhile improving the retrieval efficiency in cross-document retrieval of LLMs. With the coarse-grained collaborative information from neighboring documents and concise information from the knowledge graph, KG-Retriever achieves marked improvements on five public QA datasets, showing the effectiveness and efficiency of our proposed RAG framework.

Graphs are widely used for modeling relational data in real-world scenarios, such as social networks and urban computing. Existing LLM-based graph analysis approaches either integrate graph neural networks (GNNs) for specific machine learning tasks, limiting their transferability, or rely solely on LLMs' internal reasoning ability, resulting in suboptimal performance. To address these limitations, we take advantage of recent advances in LLM-based agents, which have shown capabilities of utilizing external knowledge or tools for problem solving. By simulating human problem-solving strategies such as analogy and collaboration, we propose a multi-agent system based on LLMs named GraphTeam, for graph analysis. GraphTeam consists of five LLM-based agents from three modules, and the agents with different specialities can collaborate with each other to address complex problems. Specifically, (1) input-output normalization module: the question agent extracts and refines four key arguments from the original question, facilitating the problem understanding, and the answer agent organizes the results to meet the output requirement; (2) external knowledge retrieval module: we first build a knowledge base consisting of relevant documentation and experience information, and then the search agent retrieves the most relevant entries for each question. (3) problem-solving module: given the retrieved information from search agent, the coding agent uses established algorithms via programming to generate solutions, and in case the coding agent does not work, the reasoning agent will directly compute the results without programming. Extensive experiments on six graph analysis benchmarks demonstrate that GraphTeam achieves state-of-the-art performance with an average 25.85% improvement over the best baseline in terms of accuracy. The code and data are available at https://github.com/BUPT-GAMMA/GraphTeam.

As LLMs exhibit a high degree of human-like capability, increasing attention has been paid to role-playing research areas in which responses generated by LLMs are expected to mimic human replies. This has promoted the exploration of role-playing agents in various applications, such as chatbots that can engage in natural conversations with users and virtual assistants that can provide personalized support and guidance. The crucial factor in the role-playing task is the effective utilization of character memory, which stores characters' profiles, experiences, and historical dialogues. Retrieval Augmented Generation (RAG) technology is used to access the related memory to enhance the response generation of role-playing agents. Most existing studies retrieve related information based on the semantic similarity of memory to maintain characters' personalized traits, and few attempts have been made to incorporate the emotional factor in the retrieval argument generation (RAG) of LLMs. Inspired by the Mood-Dependent Memory theory, which indicates that people recall an event better if they somehow reinstate during recall the original emotion they experienced during learning, we propose a novel emotion-aware memory retrieval framework, termed Emotional RAG, which recalls the related memory with consideration of emotional state in role-playing agents. Specifically, we design two kinds of retrieval strategies, i.e., combination strategy and sequential strategy, to incorporate both memory semantic and emotional states during the retrieval process. Extensive experiments on three representative role-playing datasets demonstrate that our Emotional RAG framework outperforms the method without considering the emotional factor in maintaining the personalities of role-playing agents. This provides evidence to further reinforce the Mood-Dependent Memory theory in psychology.

The need to analyze graphs is ubiquitous across various fields, from social networks to biological research and recommendation systems. Therefore, enabling the ability of large language models (LLMs) to process graphs is an important step toward more advanced general intelligence. However, current LLM benchmarks on graph analysis require models to directly reason over the prompts describing graph topology, and are thus limited to small graphs with only a few dozens of nodes. In contrast, human experts typically write programs based on popular libraries for task solving, and can thus handle graphs with different scales. To this end, a question naturally arises: can LLMs analyze graphs like professionals? In this paper, we introduce ProGraph, a manually crafted benchmark containing 3 categories of graph tasks. The benchmark expects solutions based on programming instead of directly reasoning over raw inputs. Our findings reveal that the performance of current LLMs is unsatisfactory, with the best model achieving only 36% accuracy. To bridge this gap, we propose LLM4Graph datasets, which include crawled documents and auto-generated codes based on 6 widely used graph libraries. By augmenting closed-source LLMs with document retrieval and fine-tuning open-source ones on the codes, we show 11-32% absolute improvements in their accuracies. Our results underscore that the capabilities of LLMs in handling structured data are still under-explored, and show the effectiveness of LLM4Graph in enhancing LLMs' proficiency of graph analysis. The benchmark, datasets and enhanced open-source models are available at https://github.com/BUPT-GAMMA/ProGraph.