Have We Designed Generalizable Structural Knowledge Promptings? Systematic Evaluation and Rethinking

Large language models (LLMs) have demonstrated exceptional performance in text generation within current NLP research. However, the lack of factual accuracy is still a dark cloud hanging over the LLM skyscraper. Structural knowledge prompting (SKP) is a prominent paradigm to integrate external knowledge into LLMs by incorporating structural representations, achieving state-of-the-art results in many knowledge-intensive tasks. However, existing methods often focus on specific problems, lacking a comprehensive exploration of the generalization and capability boundaries of SKP. This paper aims to evaluate and rethink the generalization capability of the SKP paradigm from four perspectives including Granularity, Transferability, Scalability, and Universality. To provide a thorough evaluation, we introduce a novel multi-granular, multi-level benchmark called SUBARU, consisting of 9 different tasks with varying levels of granularity and difficulty.

Is Large Language Model Good at Triple Set Prediction? An Empirical Study

The core of the Knowledge Graph Completion (KGC) task is to predict and complete the missing relations or nodes in a KG. Common KGC tasks are mostly about inferring unknown elements with one or two elements being known in a triple. In comparison, the Triple Set Prediction (TSP) task is a more realistic knowledge graph completion task. It aims to predict all elements of unknown triples based on the information from known triples. In recent years, large language models (LLMs) have exhibited significant advancements in language comprehension, demonstrating considerable potential for KGC tasks. However, the potential of LLM on the TSP task has not yet to be investigated. Thus in this paper we proposed a new framework to explore the strengths and limitations of LLM in the TSP task. Specifically, the framework consists of LLM-based rule mining and LLM-based triple set prediction. The relation list of KG embedded within rich semantic information is first leveraged to prompt LLM in the generation of rules. This process is both efficient and independent of statistical information, making it easier to mine effective and realistic rules. For each subgraph, the specified rule is applied in conjunction with the relevant triples within that subgraph to guide the LLM in predicting the missing triples. Subsequently, the predictions from all subgraphs are consolidated to derive the complete set of predicted triples on KG. Finally, the method is evaluated on the relatively complete CFamily dataset. The experimental results indicate that when LLMs are required to adhere to a large amount of factual knowledge to predict missing triples, significant hallucinations occurs, leading to a noticeable decline in performance. To further explore the causes of this phenomenon, this paper presents a comprehensive analysis supported by a detailed case study.

UniHR: Hierarchical Representation Learning for Unified Knowledge Graph Link Prediction

Beyond-triple fact representations including hyper-relational facts with auxiliary key-value pairs, temporal facts with additional timestamps, and nested facts implying relationships between facts, are gaining significant attention. However, existing link prediction models are usually designed for one specific type of facts, making it difficult to generalize to other fact representations. To overcome this limitation, we propose a Unified Hierarchical Representation learning framework (UniHR) for unified knowledge graph link prediction. It consists of a unified Hierarchical Data Representation (HiDR) module and a unified Hierarchical Structure Learning (HiSL) module as graph encoder. The HiDR module unifies hyper-relational KGs, temporal KGs, and nested factual KGs into triple-based representations. Then HiSL incorporates intra-fact and inter-fact message passing, focusing on enhancing the semantic information within individual facts and enriching the structural information between facts. Experimental results across 7 datasets from 3 types of KGs demonstrate that our UniHR outperforms baselines designed for one specific kind of KG, indicating strong generalization capability of HiDR form and the effectiveness of HiSL module. Code and data are available at https://github.com/Lza12a/UniHR.

MKGL: Mastery of a Three-Word Language

Large language models (LLMs) have significantly advanced performance across a spectrum of natural language processing (NLP) tasks. Yet, their application to knowledge graphs (KGs), which describe facts in the form of triplets and allow minimal hallucinations, remains an underexplored frontier. In this paper, we investigate the integration of LLMs with KGs by introducing a specialized KG Language (KGL), where a sentence precisely consists of an entity noun, a relation verb, and ends with another entity noun. Despite KGL's unfamiliar vocabulary to the LLM, we facilitate its learning through a tailored dictionary and illustrative sentences, and enhance context understanding via real-time KG context retrieval and KGL token embedding augmentation. Our results reveal that LLMs can achieve fluency in KGL, drastically reducing errors compared to conventional KG embedding methods on KG completion. Furthermore, our enhanced LLM shows exceptional competence in generating accurate three-word sentences from an initial entity and interpreting new unseen terms out of KGs.

Croppable Knowledge Graph Embedding

Knowledge Graph Embedding (KGE) is a common method for Knowledge Graphs (KGs) to serve various artificial intelligence tasks. The suitable dimensions of the embeddings depend on the storage and computing conditions of the specific application scenarios. Once a new dimension is required, a new KGE model needs to be trained from scratch, which greatly increases the training cost and limits the efficiency and flexibility of KGE in serving various scenarios. In this work, we propose a novel KGE training framework MED, through which we could train once to get a croppable KGE model applicable to multiple scenarios with different dimensional requirements, sub-models of the required dimensions can be cropped out of it and used directly without any additional training. In MED, we propose a mutual learning mechanism to improve the low-dimensional sub-models performance and make the high-dimensional sub-models retain the capacity that low-dimensional sub-models have, an evolutionary improvement mechanism to promote the high-dimensional sub-models to master the knowledge that the low-dimensional sub-models can not learn, and a dynamic loss weight to balance the multiple losses adaptively. Experiments on 3 KGE models over 4 standard KG completion datasets, 3 real application scenarios over a real-world large-scale KG, and the experiments of extending MED to the language model BERT show the effectiveness, high efficiency, and flexible extensibility of MED.

SF-GNN: Self Filter for Message Lossless Propagation in Deep Graph Neural Network

Graph Neural Network (GNN), with the main idea of encoding graph structure information of graphs by propagation and aggregation, has developed rapidly. It achieved excellent performance in representation learning of multiple types of graphs such as homogeneous graphs, heterogeneous graphs, and more complex graphs like knowledge graphs. However, merely stacking GNN layers may not improve the model's performance and can even be detrimental. For the phenomenon of performance degradation in deep GNNs, we propose a new perspective. Unlike the popular explanations of over-smoothing or over-squashing, we think the issue arises from the interference of low-quality node representations during message propagation. We introduce a simple and general method, SF-GNN, to address this problem. In SF-GNN, we define two representations for each node, one is the node representation that represents the feature of the node itself, and the other is the message representation specifically for propagating messages to neighbor nodes. A self-filter module evaluates the quality of the node representation and decides whether to integrate it into the message propagation based on this quality assessment. Experiments on node classification tasks for both homogeneous and heterogeneous graphs, as well as link prediction tasks on knowledge graphs, demonstrate that our method can be applied to various GNN models and outperforms state-of-the-art baseline methods in addressing deep GNN degradation.

ZeroDDI: A Zero-Shot Drug-Drug Interaction Event Prediction Method with Semantic Enhanced Learning and Dual-Modal Uniform Alignment

Drug-drug interactions (DDIs) can result in various pharmacological changes, which can be categorized into different classes known as DDI events (DDIEs). In recent years, previously unobserved/unseen DDIEs have been emerging, posing a new classification task when unseen classes have no labelled instances in the training stage, which is formulated as a zero-shot DDIE prediction (ZS-DDIE) task. However, existing computational methods are not directly applicable to ZS-DDIE, which has two primary challenges: obtaining suitable DDIE representations and handling the class imbalance issue. To overcome these challenges, we propose a novel method named ZeroDDI for the ZS-DDIE task. Specifically, we design a biological semantic enhanced DDIE representation learning module, which emphasizes the key biological semantics and distills discriminative molecular substructure-related semantics for DDIE representation learning. Furthermore, we propose a dual-modal uniform alignment strategy to distribute drug pair representations and DDIE semantic representations uniformly in a unit sphere and align the matched ones, which can mitigate the issue of class imbalance. Extensive experiments showed that ZeroDDI surpasses the baselines and indicate that it is a promising tool for detecting unseen DDIEs. Our code has been released in https://github.com/wzy-Sarah/ZeroDDI.

Heterogeneous Causal Metapath Graph Neural Network for Gene-Microbe-Disease Association Prediction

The recent focus on microbes in human medicine highlights their potential role in the genetic framework of diseases. To decode the complex interactions among genes, microbes, and diseases, computational predictions of gene-microbe-disease (GMD) associations are crucial. Existing methods primarily address gene-disease and microbe-disease associations, but the more intricate triple-wise GMD associations remain less explored. In this paper, we propose a Heterogeneous Causal Metapath Graph Neural Network (HCMGNN) to predict GMD associations. HCMGNN constructs a heterogeneous graph linking genes, microbes, and diseases through their pairwise associations, and utilizes six predefined causal metapaths to extract directed causal subgraphs, which facilitate the multi-view analysis of causal relations among three entity types. Within each subgraph, we employ a causal semantic sharing message passing network for node representation learning, coupled with an attentive fusion method to integrate these representations for predicting GMD associations. Our extensive experiments show that HCMGNN effectively predicts GMD associations and addresses association sparsity issue by enhancing the graph's semantics and structure.

TrustUQA: A Trustful Framework for Unified Structured Data Question Answering

Natural language question answering (QA) over structured data sources such as tables and knowledge graphs (KGs) have been widely investigated, for example with Large Language Models (LLMs). 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 multiple sources simultaneously, while the later is limited in trustfulness. In this paper, we propose UnifiedTQA, 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 UnifiedTQA with 5 benchmarks covering 3 types of structured data. It outperforms 2 existing unified structured data QA methods and in comparison with the baselines that are specific to a data type, it achieves state-of-the-art on 2 of them. Further more, we demonstrates potential of our method for more general QA tasks, QA over mixed structured data and QA across structured data.

Start from Zero: Triple Set Prediction for Automatic Knowledge Graph Completion

Knowledge graph (KG) completion aims to find out missing triples in a KG. Some tasks, such as link prediction and instance completion, have been proposed for KG completion. They are triple-level tasks with some elements in a missing triple given to predict the missing element of the triple. However, knowing some elements of the missing triple in advance is not always a realistic setting. In this paper, we propose a novel graph-level automatic KG completion task called Triple Set Prediction (TSP) which assumes none of the elements in the missing triples is given. TSP is to predict a set of missing triples given a set of known triples. To properly and accurately evaluate this new task, we propose 4 evaluation metrics including 3 classification metrics and 1 ranking metric, considering both the partial-open-world and the closed-world assumptions. Furthermore, to tackle the huge candidate triples for prediction, we propose a novel and efficient subgraph-based method GPHT that can predict the triple set fast. To fairly compare the TSP results, we also propose two types of methods RuleTensor-TSP and KGE-TSP applying the existing rule- and embedding-based methods for TSP as baselines. During experiments, we evaluate the proposed methods on two datasets extracted from Wikidata following the relation-similarity partial-open-world assumption proposed by us, and also create a complete family data set to evaluate TSP results following the closed-world assumption. Results prove that the methods can successfully generate a set of missing triples and achieve reasonable scores on the new task, and GPHT performs better than the baselines with significantly shorter prediction time. The datasets and code for experiments are available at https://github.com/zjukg/GPHT-for-TSP.