The "arms race" of Large Language Models (LLMs) demands novel, challenging, and diverse benchmarks to faithfully examine their progresses. We introduce GraphArena, a benchmarking tool designed to evaluate LLMs on graph computational problems using million-scale real-world graphs from diverse scenarios such as knowledge graphs, social networks, and molecular structures. GraphArena offers a suite of 10 computational tasks, encompassing four polynomial-time (e.g., Shortest Distance) and six NP-complete challenges (e.g., Travelling Salesman Problem). It features a rigorous evaluation framework that classifies LLM outputs as correct, suboptimal (feasible but not optimal), or hallucinatory (properly formatted but infeasible). Evaluation of 10 leading LLMs, including GPT-4o and LLaMA3-70B-Instruct, reveals that even top-performing models struggle with larger, more complex graph problems and exhibit hallucination issues. Despite the application of strategies such as chain-of-thought prompting, these issues remain unresolved. GraphArena contributes a valuable supplement to the existing LLM benchmarks and is open-sourced at https://github.com/squareRoot3/GraphArena.
Ensemble models often improve generalization performances in challenging tasks. Yet, traditional techniques based on prediction averaging incur three well-known disadvantages: the computational overhead of training multiple models, increased latency, and memory requirements at test time. To address these issues, the Stochastic Weight Averaging (SWA) technique maintains a running average of model parameters from a specific epoch onward. Despite its potential benefits, maintaining a running average of parameters can hinder generalization, as an underlying running model begins to overfit. Conversely, an inadequately chosen starting point can render SWA more susceptible to underfitting compared to an underlying running model. In this work, we propose Adaptive Stochastic Weight Averaging (ASWA) technique that updates a running average of model parameters, only when generalization performance is improved on the validation dataset. Hence, ASWA can be seen as a combination of SWA with the early stopping technique, where the former accepts all updates on a parameter ensemble model and the latter rejects any update on an underlying running model. We conducted extensive experiments ranging from image classification to multi-hop reasoning over knowledge graphs. Our experiments over 11 benchmark datasets with 7 baseline models suggest that ASWA leads to a statistically better generalization across models and datasets
Natural language question answering (QA) over structured data sources such as tables and knowledge graphs have been widely investigated, especially with Large Language Models (LLMs) in recent years. The main solutions include question to formal query parsing and retrieval-based answer generation. However, current methods of the former often suffer from weak generalization, failing to dealing with multi-types of sources, while the later is limited in trustfulness. In this paper, we propose TrustUQA, a trustful QA framework that can simultaneously support multiple types of structured data in a unified way. To this end, it adopts an LLM-friendly and unified knowledge representation method called Condition Graph(CG), and uses an LLM and demonstration-based two-level method for CG querying. For enhancement, it is also equipped with dynamic demonstration retrieval. We have evaluated TrustUQA with 5 benchmarks covering 3 types of structured data. It outperforms 2 existing unified structured data QA methods. In comparison with the baselines that are specific to one data type, it achieves state-of-the-art on 2 of the datasets. Further more, we have demonstrated the potential of our method for more general QA tasks, QA over mixed structured data and QA across structured data. The code is available at https://github.com/zjukg/TrustUQA.
Multilingual Knowledge Graph Completion (mKGC) aim at solving queries like (h, r, ?) in different languages by reasoning a tail entity t thus improving multilingual knowledge graphs. Previous studies leverage multilingual pretrained language models (PLMs) and the generative paradigm to achieve mKGC. Although multilingual pretrained language models contain extensive knowledge of different languages, its pretraining tasks cannot be directly aligned with the mKGC tasks. Moreover, the majority of KGs and PLMs currently available exhibit a pronounced English-centric bias. This makes it difficult for mKGC to achieve good results, particularly in the context of low-resource languages. To overcome previous problems, this paper introduces global and local knowledge constraints for mKGC. The former is used to constrain the reasoning of answer entities, while the latter is used to enhance the representation of query contexts. The proposed method makes the pretrained model better adapt to the mKGC task. Experimental results on public datasets demonstrate that our method outperforms the previous SOTA on Hits@1 and Hits@10 by an average of 12.32% and 16.03%, which indicates that our proposed method has significant enhancement on mKGC.
When studying ecosystems, hierarchical trees are often used to organize entities based on proximity criteria, such as the taxonomy in microbiology, social classes in geography, or product types in retail businesses, offering valuable insights into entity relationships. Despite their significance, current count-data models do not leverage this structured information. In particular, the widely used Poisson log-normal (PLN) model, known for its ability to model interactions between entities from count data, lacks the possibility to incorporate such hierarchical tree structures, limiting its applicability in domains characterized by such complexities. To address this matter, we introduce the PLN-Tree model as an extension of the PLN model, specifically designed for modeling hierarchical count data. By integrating structured variational inference techniques, we propose an adapted training procedure and establish identifiability results, enhancing both theoretical foundations and practical interpretability. Experiments on synthetic datasets and human gut microbiome data highlight generative improvements when using PLN-Tree, demonstrating the practical interest of knowledge graphs like the taxonomy in microbiome modeling. Additionally, we present a proof-of-concept implication of the identifiability results by illustrating the practical benefits of using identifiable features for classification tasks, showcasing the versatility of the framework.
Large language models have become integral to question-answering applications despite their propensity for generating hallucinations and factually inaccurate content. Querying knowledge graphs to reduce hallucinations in LLM meets the challenge of incomplete knowledge coverage in knowledge graphs. On the other hand, updating knowledge graphs by information extraction and knowledge graph completion faces the knowledge update misalignment issue. In this work, we introduce a collaborative augmentation framework, CogMG, leveraging knowledge graphs to address the limitations of LLMs in QA scenarios, explicitly targeting the problems of incomplete knowledge coverage and knowledge update misalignment. The LLMs identify and decompose required knowledge triples that are not present in the KG, enriching them and aligning updates with real-world demands. We demonstrate the efficacy of this approach through a supervised fine-tuned LLM within an agent framework, showing significant improvements in reducing hallucinations and enhancing factual accuracy in QA responses. Our code and video are publicly available.
Few-shot Knowledge Graph (KG) Relational Reasoning aims to predict unseen triplets (i.e., query triplets) for rare relations in KGs, given only several triplets of these relations as references (i.e., support triplets). This task has gained significant traction due to the widespread use of knowledge graphs in various natural language processing applications. Previous approaches have utilized meta-training methods and manually constructed meta-relation sets to tackle this task. Recent efforts have focused on edge-mask-based methods, which exploit the structure of the contextualized graphs of target triplets (i.e., a subgraph containing relevant triplets in the KG). However, existing edge-mask-based methods have limitations in extracting insufficient information from KG and are highly influenced by spurious information in KG. To overcome these challenges, we propose SAFER (Subgraph Adaptation for Few-shot Relational Reasoning), a novel approach that effectively adapts the information in contextualized graphs to various subgraphs generated from support and query triplets to perform the prediction. Specifically, SAFER enables the extraction of more comprehensive information from support triplets while minimizing the impact of spurious information when predicting query triplets. Experimental results on three prevalent datasets demonstrate the superiority of our proposed framework SAFER.
Knowledge-enhanced pre-trained language models (KEPLMs) leverage relation triples from knowledge graphs (KGs) and integrate these external data sources into language models via self-supervised learning. Previous works treat knowledge enhancement as two independent operations, i.e., knowledge injection and knowledge integration. In this paper, we propose to learn Knowledge-Enhanced language representations with Hierarchical Reinforcement Learning (KEHRL), which jointly addresses the problems of detecting positions for knowledge injection and integrating external knowledge into the model in order to avoid injecting inaccurate or irrelevant knowledge. Specifically, a high-level reinforcement learning (RL) agent utilizes both internal and prior knowledge to iteratively detect essential positions in texts for knowledge injection, which filters out less meaningful entities to avoid diverting the knowledge learning direction. Once the entity positions are selected, a relevant triple filtration module is triggered to perform low-level RL to dynamically refine the triples associated with polysemic entities through binary-valued actions. Experiments validate KEHRL's effectiveness in probing factual knowledge and enhancing the model's performance on various natural language understanding tasks.
Electronic Medical Records (EMRs), while integral to modern healthcare, present challenges for clinical reasoning and diagnosis due to their complexity and information redundancy. To address this, we proposed medIKAL (Integrating Knowledge Graphs as Assistants of LLMs), a framework that combines Large Language Models (LLMs) with knowledge graphs (KGs) to enhance diagnostic capabilities. medIKAL assigns weighted importance to entities in medical records based on their type, enabling precise localization of candidate diseases within KGs. It innovatively employs a residual network-like approach, allowing initial diagnosis by the LLM to be merged into KG search results. Through a path-based reranking algorithm and a fill-in-the-blank style prompt template, it further refined the diagnostic process. We validated medIKAL's effectiveness through extensive experiments on a newly introduced open-sourced Chinese EMR dataset, demonstrating its potential to improve clinical diagnosis in real-world settings.
Large Language Models (LLMs) have shown unprecedented performance in various real-world applications. However, they are known to generate factually inaccurate outputs, a.k.a. the hallucination problem. In recent years, incorporating external knowledge extracted from Knowledge Graphs (KGs) has become a promising strategy to improve the factual accuracy of LLM-generated outputs. Nevertheless, most existing explorations rely on LLMs themselves to perform KG knowledge extraction, which is highly inflexible as LLMs can only provide binary judgment on whether a certain knowledge (e.g., a knowledge path in KG) should be used. In addition, LLMs tend to pick only knowledge with direct semantic relationship with the input text, while potentially useful knowledge with indirect semantics can be ignored. In this work, we propose a principled framework KELP with three stages to handle the above problems. Specifically, KELP is able to achieve finer granularity of flexible knowledge extraction by generating scores for knowledge paths with input texts via latent semantic matching. Meanwhile, knowledge paths with indirect semantic relationships with the input text can also be considered via trained encoding between the selected paths in KG and the input text. Experiments on real-world datasets validate the effectiveness of KELP.
Improving the performance of large language models (LLMs) in complex question-answering (QA) scenarios has always been a research focal point. Recent studies have attempted to enhance LLMs' performance by combining step-wise planning with external retrieval. While effective for advanced models like GPT-3.5, smaller LLMs face challenges in decomposing complex questions, necessitating supervised fine-tuning. Previous work has relied on manual annotation and knowledge distillation from teacher LLMs, which are time-consuming and not accurate enough. In this paper, we introduce a novel framework for enhancing LLMs' planning capabilities by using planning data derived from knowledge graphs (KGs). LLMs fine-tuned with this data have improved planning capabilities, better equipping them to handle complex QA tasks that involve retrieval. Evaluations on multiple datasets, including our newly proposed benchmark, highlight the effectiveness of our framework and the benefits of KG-derived planning data.
Salient facts of sociopolitical events are distilled into quadruples following a format of subject, relation, object, and timestamp. Machine learning methods, such as graph neural networks (GNNs) and recurrent neural networks (RNNs), have been built to make predictions and infer relations on the quadruple-based knowledge graphs (KGs). In many applications, quadruples are extended to quintuples with auxiliary attributes such as text summaries that describe the quadruple events. In this paper, we comprehensively investigate how large language models (LLMs) streamline the design of event prediction frameworks using quadruple-based or quintuple-based data while maintaining competitive accuracy. We propose LEAP, a unified framework that leverages large language models as event predictors. Specifically, we develop multiple prompt templates to frame the object prediction (OP) task as a standard question-answering (QA) task, suitable for instruction fine-tuning with an encoder-decoder LLM. For multi-event forecasting (MEF) task, we design a simple yet effective prompt template for each event quintuple. This novel approach removes the need for GNNs and RNNs, instead utilizing an encoder-only LLM to generate fixed intermediate embeddings, which are processed by a customized downstream head with a self-attention mechanism to predict potential relation occurrences in the future. Extensive experiments on multiple real-world datasets using various evaluation metrics validate the effectiveness of our approach.
Multi-Modal Knowledge Graphs (MMKGs) have proven valuable for various downstream tasks. However, scaling them up is challenging because building large-scale MMKGs often introduces mismatched images (i.e., noise). Most entities in KGs belong to the long tail, meaning there are few images of them available online. This scarcity makes it difficult to determine whether a found image matches the entity. To address this, we draw on the Triangle of Reference Theory and suggest enhancing vision-language models with concept guidance. Specifically, we introduce COG, a two-stage framework with COncept-Guided vision-language models. The framework comprises a Concept Integration module, which effectively identifies image-text pairs of long-tailed entities, and an Evidence Fusion module, which offers explainability and enables human verification. To demonstrate the effectiveness of COG, we create a dataset of 25k image-text pairs of long-tailed entities. Our comprehensive experiments show that COG not only improves the accuracy of recognizing long-tailed image-text pairs compared to baselines but also offers flexibility and explainability.
Existing frameworks for assessing robustness of large language models (LLMs) overly depend on specific benchmarks, increasing costs and failing to evaluate performance of LLMs in professional domains due to dataset limitations. This paper proposes a framework that systematically evaluates the robustness of LLMs under adversarial attack scenarios by leveraging knowledge graphs (KGs). Our framework generates original prompts from the triplets of knowledge graphs and creates adversarial prompts by poisoning, assessing the robustness of LLMs through the results of these adversarial attacks. We systematically evaluate the effectiveness of this framework and its modules. Experiments show that adversarial robustness of the ChatGPT family ranks as GPT-4-turbo > GPT-4o > GPT-3.5-turbo, and the robustness of large language models is influenced by the professional domains in which they operate.
Large language models (LLMs) demonstrate an impressive ability to internalize knowledge and answer natural language questions. Although previous studies validate that LLMs perform well on general knowledge while presenting poor performance on long-tail nuanced knowledge, the community is still doubtful about whether the traditional knowledge graphs should be replaced by LLMs. In this paper, we ask if the schema of knowledge graph (i.e., taxonomy) is made obsolete by LLMs. Intuitively, LLMs should perform well on common taxonomies and at taxonomy levels that are common to people. Unfortunately, there lacks a comprehensive benchmark that evaluates the LLMs over a wide range of taxonomies from common to specialized domains and at levels from root to leaf so that we can draw a confident conclusion. To narrow the research gap, we constructed a novel taxonomy hierarchical structure discovery benchmark named TaxoGlimpse to evaluate the performance of LLMs over taxonomies. TaxoGlimpse covers ten representative taxonomies from common to specialized domains with in-depth experiments of different levels of entities in this taxonomy from root to leaf. Our comprehensive experiments of eighteen state-of-the-art LLMs under three prompting settings validate that LLMs can still not well capture the knowledge of specialized taxonomies and leaf-level entities.
Multi-relational temporal graphs are powerful tools for modeling real-world data, capturing the evolving and interconnected nature of entities over time. Recently, many novel models are proposed for ML on such graphs intensifying the need for robust evaluation and standardized benchmark datasets. However, the availability of such resources remains scarce and evaluation faces added complexity due to reproducibility issues in experimental protocols. To address these challenges, we introduce Temporal Graph Benchmark 2.0 (TGB 2.0), a novel benchmarking framework tailored for evaluating methods for predicting future links on Temporal Knowledge Graphs and Temporal Heterogeneous Graphs with a focus on large-scale datasets, extending the Temporal Graph Benchmark. TGB 2.0 facilitates comprehensive evaluations by presenting eight novel datasets spanning five domains with up to 53 million edges. TGB 2.0 datasets are significantly larger than existing datasets in terms of number of nodes, edges, or timestamps. In addition, TGB 2.0 provides a reproducible and realistic evaluation pipeline for multi-relational temporal graphs. Through extensive experimentation, we observe that 1) leveraging edge-type information is crucial to obtain high performance, 2) simple heuristic baselines are often competitive with more complex methods, 3) most methods fail to run on our largest datasets, highlighting the need for research on more scalable methods.
Capturing molecular knowledge with representation learning approaches holds significant potential in vast scientific fields such as chemistry and life science. An effective and generalizable molecular representation is expected to capture the consensus and complementary molecular expertise from diverse views and perspectives. However, existing works fall short in learning multi-view molecular representations, due to challenges in explicitly incorporating view information and handling molecular knowledge from heterogeneous sources. To address these issues, we present MV-Mol, a molecular representation learning model that harvests multi-view molecular expertise from chemical structures, unstructured knowledge from biomedical texts, and structured knowledge from knowledge graphs. We utilize text prompts to model view information and design a fusion architecture to extract view-based molecular representations. We develop a two-stage pre-training procedure, exploiting heterogeneous data of varying quality and quantity. Through extensive experiments, we show that MV-Mol provides improved representations that substantially benefit molecular property prediction. Additionally, MV-Mol exhibits state-of-the-art performance in multi-modal comprehension of molecular structures and texts. Code and data are available at https://github.com/PharMolix/OpenBioMed.
Rule mining on knowledge graphs allows for explainable link prediction. Contrarily, embedding-based methods for link prediction are well known for their generalization capabilities, but their predictions are not interpretable. Several approaches combining the two families have been proposed in recent years. The majority of the resulting hybrid approaches are usually trained within a unified learning framework, which often leads to convergence issues due to the complexity of the learning task. In this work, we propose a new way to combine the two families of approaches. Specifically, we enrich a given knowledge graph by means of its pre-trained entity and relation embeddings before applying rule mining systems on the enriched knowledge graph. To validate our approach, we conduct extensive experiments on seven benchmark datasets. An analysis of the results generated by our approach suggests that we discover new valuable rules on the enriched graphs. We provide an open source implementation of our approach as well as pretrained models and datasets at https://github.com/Jean-KOUAGOU/EnhancedRuleLearning
Entity summarization aims to compute concise summaries for entities in knowledge graphs. Existing datasets and benchmarks are often limited to a few hundred entities and discard graph structure in source knowledge graphs. This limitation is particularly pronounced when it comes to ground-truth summaries, where there exist only a few labeled summaries for evaluation and training. We propose WikES, a comprehensive benchmark comprising of entities, their summaries, and their connections. Additionally, WikES features a dataset generator to test entity summarization algorithms in different areas of the knowledge graph. Importantly, our approach combines graph algorithms and NLP models as well as different data sources such that WikES does not require human annotation, rendering the approach cost-effective and generalizable to multiple domains. Finally, WikES is scalable and capable of capturing the complexities of knowledge graphs in terms of topology and semantics. WikES features existing datasets for comparison. Empirical studies of entity summarization methods confirm the usefulness of our benchmark. Data, code, and models are available at: https://github.com/msorkhpar/wiki-entity-summarization.
Answering Questions over Knowledge Graphs (KGQA) is key to well-functioning autonomous language agents in various real-life applications. To improve the neural-symbolic reasoning capabilities of language agents powered by Large Language Models (LLMs) in KGQA, we propose the DecompositionAlignment-Reasoning Agent (DARA) framework. DARA effectively parses questions into formal queries through a dual mechanism: high-level iterative task decomposition and low-level task grounding. Importantly, DARA can be efficiently trained with a small number of high-quality reasoning trajectories. Our experimental results demonstrate that DARA fine-tuned on LLMs (e.g. Llama-2-7B, Mistral) outperforms both in-context learning-based agents with GPT-4 and alternative fine-tuned agents, across different benchmarks in zero-shot evaluation, making such models more accessible for real-life applications. We also show that DARA attains performance comparable to state-of-the-art enumerating-and-ranking-based methods for KGQA.