Recently, multi-modal embedding methods have flourished in entity alignment. As state-of-the-art approaches evolve rapidly, visual modality (i.e., images) missing emerges as a critical challenge. While visual modality typically offers the most informative signals in multi-modal entity alignment (MMEA), it is frequently unavailable for many entities. The existing methods commonly use dummy vectors to represent visual-missing embeddings, which negatively impacts both model training and inference. In this paper, we propose robust multi-modal entity alignment (rMMEA), which leverages ranking-based knowledge distillation and mutual information (MI) estimation to address missing modalities while enhancing noise robustness. Unlike conventional teacher-student distillation that requires the student to replicate teacher outputs, our rMMEA learns soft rankings from pure and complete modality sides while capturing implicit key semantics of teacher embeddings through mutual information maximization, allowing rMMEA to avoid strict point-to-point alignment. The experimental results across multiple benchmarks and settings demonstrate that rMMEA significantly outperforms the state-of-the-art anti-modality-missing methods in terms of effectiveness and efficiency.

Yichi Zhang, Zhuo Chen, Lingbing Guo, Jun Xu, Mengshu Sun, Zhizhen Liu, Lei Liang, Wen Zhang, Huajun Chen. Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). 2026.

Large Language Models (LLMs) have recently emerged as a powerful paradigm for Knowledge Graph Completion (KGC), offering strong reasoning and generalization capabilities beyond traditional embedding-based approaches. However, existing LLM-based methods often struggle to fully exploit structured semantic representations, as the continuous embedding space of pretrained KG models is fundamentally misaligned with the discrete token space of LLMs. This discrepancy hinders effective semantic transfer and limits their performance. To address this challenge, we propose ReaLM, a novel and effective framework that bridges the gap between KG embeddings and LLM tokenization through the mechanism of residual vector quantization. ReaLM discretizes pretrained KG embeddings into compact code sequences and integrates them as learnable tokens within the LLM vocabulary, enabling seamless fusion of symbolic and contextual knowledge. Furthermore, we incorporate ontology-guided class constraints to enforce semantic consistency, refining entity predictions based on class-level compatibility. Extensive experiments on two widely used benchmark datasets demonstrate that ReaLM achieves state-of-the-art performance, confirming its effectiveness in aligning structured knowledge with large-scale language models. The implementation is publicly available at https://github.com/xiumu-gg/ReaLM.

Recent advancements in large language models (LLMs) have significantly improved various natural language processing (NLP) tasks. Typically, LLMs are trained to predict the next token, aligning well with many NLP tasks. However, in knowledge graph (KG) scenarios, entities are the fundamental units and identifying an entity requires at least several tokens. This leads to a granularity mismatch between KGs and natural languages. To address this issue, we propose K-ON, which integrates KG knowledge into the LLM by employing multiple head layers for next k-step prediction. K-ON can not only generate entity-level results in one step, but also enables contrastive loss against entities, which is the most powerful tool in KG representation learning. Experimental results show that K-ON outperforms state-of-the-art methods that incorporate text and even the other modalities.

Multi-modal knowledge graph completion (MMKGC) aims to discover unobserved knowledge from given multi-modal knowledge graphs (MMKG), collaboratively leveraging structural information from the triples and multi-modal information of the entities to overcome the inherent incompleteness. Existing MMKGC methods usually extract multi-modal features with pre-trained models and employ fusion modules to integrate multi-modal features for the entities. This often results in coarse handling of multi-modal entity information, overlooking the nuanced, fine-grained semantic details and their complex interactions. To tackle this shortfall, we introduce a novel framework MyGO to tokenize, fuse, and augment the fine-grained multi-modal representations of entities and enhance the MMKGC performance. Motivated by the tokenization technology, MyGO tokenizes multi-modal entity information as fine-grained discrete tokens and learns entity representations with a cross-modal entity encoder. To further augment the multi-modal representations, MyGO incorporates fine-grained contrastive learning to highlight the specificity of the entity representations. Experiments on standard MMKGC benchmarks reveal that our method surpasses 19 of the latest models, underlining its superior performance.

Yichi Zhang, Zhuo Chen, Lingbing Guo, Yajing Xu, Shaokai Chen, Mengshu Sun, Binbin Hu, Zhiqiang Zhang, Lei Liang, Wen Zhang, Huajun Chen. Proceedings of the 63rd Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). 2025.

The rise of Multi-modal Pre-training highlights the necessity for a unified Multi-Modal Knowledge Graph (MMKG) representation learning framework. Such a framework is essential for embedding structured knowledge into multi-modal Large Language Models effectively, alleviating issues like knowledge misconceptions and multi-modal hallucinations. In this work, we explore the efficacy of models in accurately embedding entities within MMKGs through two pivotal tasks: Multi-modal Knowledge Graph Completion (MKGC) and Multi-modal Entity Alignment (MMEA). Building on this foundation, we propose a novel SNAG method that utilizes a Transformer-based architecture equipped with modality-level noise masking to robustly integrate multi-modal entity features in KGs. By incorporating specific training objectives for both MKGC and MMEA, our approach achieves SOTA performance across a total of ten datasets, demonstrating its versatility. Moreover, SNAG can not only function as a standalone model but also enhance other existing methods, providing stable performance improvements. Code and data are available at https://github.com/zjukg/SNAG.

Learning high-quality multi-modal entity representations is an important goal of multi-modal knowledge graph (MMKG) representation learning, which can en- hance reasoning tasks within the MMKGs, such as MMKG completion (MMKGC). The main challenge is to collaboratively model the structural information concealed in massive triples and the multi-modal features of the entities. Existing methods focus on crafting elegant entity-wise multi-modal fusion strategies, yet they over- look the utilization of multi-perspective features concealed within the modalities under diverse relational contexts. To address this issue, we introduce a novel framework with Mixture of Modality Knowledge experts (MOMOK for short) to learn adaptive multi-modal entity representations for better MMKGC. We design relation-guided modality knowledge experts to acquire relation-aware modality embeddings and integrate the predictions from multi-modalities to achieve joint decisions. Additionally, we disentangle the experts by minimizing their mutual information. Experiments on four public MMKG benchmarks demonstrate the outstanding performance of MOMOK under complex scenarios. Our code and data are available at https://github.com/zjukg/MoMoK.

Knowledge graphs (KGs) are widely used to store multi-source and heterogeneous structural knowledge, making federated knowledge graph completion (FedKGC) a crucial research topic. FedKGC aims to complete distributed KGs while maintaining privacy and security. Existing FedKGC methods primarily rely on uni-modal structural embedding aggregation for global knowledge sharing, which suffers from the demanding assumption that intersecting entities exist across different clients and are known by the omniscient server. Meanwhile, these uni-modal structure-only methods neglect the exploitation of client-side multi-modal information. In this paper, we propose a new framework MuCo2 to kill two birds with one stone and facilitate client-server co-design through multi-modal codebooks (MuCo). Moving beyond the traditional structure-only paradigm, we introduce multi-modal information of entities as the foundation for KGC modeling and communication. We design a MuCo-based fine-grained KGC model on the client and a MuCo-based communication mechanism on the server, which does not require entity mapping in global aggregation anymore. Comprehensive experiments demonstrate the effectiveness, generalization, reasonability, efficiency, and explainability of MuCo2.

Multi-modal large language models (MLLMs) incorporate heterogeneous modalities into LLMs, enabling a comprehensive understanding of diverse scenarios and objects. Despite the proliferation of evaluation benchmarks and leaderboards for MLLMs, they predominantly overlook the critical capacity of MLLMs to comprehend world knowledge with structured abstractions that appear in visual form. To address this gap, we propose a novel evaluation paradigm and devise M3STR, an innovative benchmark grounded in the Multi-Modal Map for STRuctured understanding. This benchmark leverages multi-modal knowledge graphs to synthesize images encapsulating subgraph architectures enriched with multi-modal entities. M3STR necessitates that MLLMs not only recognize the multi-modal entities within the visual inputs but also decipher intricate relational topologies among them. We delineate the benchmark's statistical profiles and automated construction pipeline, accompanied by an extensive empirical analysis of 26 state-of-the-art MLLMs. Our findings reveal persistent deficiencies in processing abstractive visual information with structured knowledge, thereby charting a pivotal trajectory for advancing MLLMs' holistic reasoning capacities. Code and data are released at https://github.com/zjukg/M3STR

Despite recent successes in natural language processing and computer vision, Transformer faces scalability issues when processing graphs, e.g., computing the full node-to-node attention on knowledge graphs (KGs) with million of entities is still infeasible. The existing methods mitigate this problem by considering only the local neighbors, sacrificing the Transformer’s ability to attend to elements at any distance. This paper proposes a new Transformer architecture called Dual-Encoding Transformer (DET). DET comprises a structural encoder to aggregate information from nearby neighbors, and a semantic encoder to seek for semantically relevant nodes. We adopt a semantic neighbor search approach inspired by multiple sequence alignment (MSA) algorithms used in biological sciences. By stacking the two encoders alternately, similar to the MSA Transformer for protein representation, our method achieves superior performance compared to state-of-the-art attention-based methods on complex relational graphs like KGs and citation networks. Additionally, DET remains competitive for smaller graphs such as molecules.

The generation of molecules with desired properties has become increasingly popular, revolutionizing the way scientists design molecular structures and providing valuable support for chemical and drug design. However, despite the potential of language models in molecule generation, they face challenges such as generating syntactically or chemically flawed molecules, having narrow domain focus, and struggling to create diverse and feasible molecules due to limited annotated data or external molecular databases. To tackle these challenges, we introduce MolGen, a pre-trained molecular language model tailored specifically for molecule generation. Through the reconstruction of over 100 million molecular SELFIES, MolGen internalizes structural and grammatical insights. This is further enhanced by domain-agnostic molecular prefix tuning, fostering robust knowledge transfer across diverse domains. Importantly, our chemical feedback paradigm steers the model away from "molecular hallucinations", ensuring alignment between the model's estimated probabilities and real-world chemical preferences. Extensive experiments on well-known benchmarks underscore MolGen's optimization capabilities in properties such as penalized logP, QED, and molecular docking. Additional analyses confirm its proficiency in accurately capturing molecule distributions, discerning intricate structural patterns, and efficiently exploring the chemical space (https://github.com/zjunlp/MolGen).

Recent embedding-based methods have achieved great successes in exploiting entity alignment from knowledge graph (KG) embeddings of multiple modalities. In this paper, we study embedding-based entity alignment (EEA) from a perspective of generative models. We show that EEA shares similarities with typical generative models and prove the effectiveness of the recently developed generative adversarial network (GAN)-based EEA methods theoretically. We then reveal that their incomplete objective limits the capacity on both entity alignment and entity synthesis (i.e., generating new entities). We mitigate this problem by introducing a generative EEA (GEEA) framework with the proposed mutual variational autoencoder (M-VAE) as the generative model. M-VAE enables entity conversion between KGs and generation of new entities from random noise vectors. We demonstrate the power of GEEA with theoretical analysis and empirical experiments on both entity alignment and entity synthesis tasks. The source code and datasets are available at github.com/zjukg/GEEA.

Large language model (LLM) based knowledge graph completion (KGC) aims to predict the missing triples in the KGs with LLMs. However, research about LLM-based KGC fails to sufficiently harness LLMs' inference proficiencies, overlooking critical structural information integral to KGs. In this paper, we explore methods to incorporate structural information into the LLMs, with the overarching goal of facilitating structure-aware reasoning. We first discuss on the existing LLM paradigms like in-context learning and instruction tuning, proposing basic structural information injection approaches. Then we propose a Knowledge Prefix Adapter (KoPA) to fulfill this stated goal. KoPA uses a structural pre-training phase to comprehend the intricate entities and relations within KGs, representing them as structural embeddings. Then KoPA communicates such cross-modal structural information understanding to the LLMs through a knowledge prefix adapter which projects the structural embeddings into the textual space and obtains virtual knowledge tokens positioned as a prefix of the input prompt. We conduct comprehensive experiments and provide incisive analysis. Our code and data are available at https://github.com/zjukg/KoPA.

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.

Multi-modal knowledge graph completion (MMKGC) aims to automatically discover the unobserved factual knowledge from a given multi-modal knowledge graph by collaboratively modeling the triple structure and multi-modal information from entities. However, real-world MMKGs present challenges due to their diverse and imbalanced nature, which means that the modality information can span various types (e.g., image, text, numeric, audio, video) but its distribution among entities is uneven, leading to missing modalities for certain entities. Existing works usually focus on common modalities like image and text while neglecting the imbalanced distribution phenomenon of modal information. To address these issues, we propose a comprehensive framework NativE to achieve MMKGC in the wild. NativE proposes a relation-guided dual adaptive fusion module that enables adaptive fusion for any modalities and employs a collaborative modality adversarial training framework to augment the imbalanced modality information. We construct a new benchmark called WildKGC with five datasets to evaluate our method. The empirical results compared with 21 recent baselines confirm the superiority of our method, consistently achieving state-of-the-art performance across different datasets and various scenarios while keeping efficient and generalizable. Our code and data are released at https://github.com/zjukg/NATIVE.

Multi-modal entity alignment (MMEA) aims to discover identical entities across different knowledge graphs (KGs) whose entities are associated with relevant images. However, current MMEA algorithms rely on KG-level modality fusion strategies for multi-modal entity representation, which ignores the variations of modality preferences of different entities, thus compromising robustness against noise in modalities such as blurry images and relations. This paper introduces MEAformer, a mlti-modal entity alignment transformer approach for meta modality hybrid, which dynamically predicts the mutual correlation coefficients among modalities for more fine-grained entity-level modality fusion and alignment. Experimental results demonstrate that our model not only achieves SOTA performance in multiple training scenarios, including supervised, unsupervised, iterative, and low-resource settings, but also has a limited number of parameters, efficient runtime, and interpretability. Our code is available at https://github.com/zjukg/MEAformer.

Reasoning system dynamics is one of the most important analytical approaches for many scientific studies. With the initial state of a system as input, the recent graph neural networks (GNNs)-based methods are capable of predicting the future state distant in time with high accuracy. Although these methods have diverse designs in modeling the coordinates and interacting forces of the system, we show that they actually share a common paradigm that learns the integration of the velocity over the interval between the initial and terminal coordinates. However, their integrand is constant w.r.t. time. Inspired by this observation, we propose a new approach to predict the integration based on several velocity estimations with Newton–Cotes formulas and prove its effectiveness theoretically. Extensive experiments on several benchmarks empirically demonstrate consistent and significant improvement compared with the state-of-the-art methods.

Embedding-based entity alignment (EEA) has recently received great attention. Despite significant performance improvement, few efforts have been paid to facilitate understanding of EEA methods. Most existing studies rest on the assumption that a small number of pre-aligned entities can serve as anchors connecting the embedding spaces of two KGs. Nevertheless, no one has investigated the rationality of such an assumption. To fill the research gap, we define a typical paradigm abstracted from existing EEA methods and analyze how the embedding discrepancy between two potentially aligned entities is implicitly bounded by a predefined margin in the score function. Further, we find that such a bound cannot guarantee to be tight enough for alignment learning. We mitigate this problem by proposing a new approach, named NeoEA, to explicitly learn KG-invariant and principled entity embeddings. In this sense, an EEA model not only pursues the closeness of aligned entities based on geometric distance, but also aligns the neural ontologies of two KGs by eliminating the discrepancy in embedding distribution and underlying ontology knowledge. Our experiments demonstrate consistent and significant performance improvement against the best-performing EEA methods.

We study the problem of knowledge graph (KG) embedding. A widely-established assumption to this problem is that similar entities are likely to have similar relational roles. However, existing related methods derive KG embeddings mainly based on triple-level learning, which lack the capability of capturing long-term relational dependencies of entities. Moreover, triple-level learning is insufficient for the propagation of semantic information among entities, especially for the case of cross-KG embedding. In this paper, we propose recurrent skipping networks (RSNs), which employ a skipping mechanism to bridge the gaps between entities. RSNs integrate recurrent neural networks (RNNs) with residual learning to efficiently capture the long-term relational dependencies within and between KGs. We design an end-to-end framework to support RSNs on different tasks. Our experimental results showed that RSNs outperformed state-of-the-art embedding-based methods for entity alignment and achieved competitive performance for KG completion.

We study the problem of embedding-based entity alignment between knowledge graphs (KGs). Previous works mainly focus on the relational structure of entities. Some further incorporate another type of features, such as attributes, for refinement. However, a vast of entity features are still unexplored or not equally treated together, which impairs the accuracy and robustness of embedding-based entity alignment. In this paper, we propose a novel framework that unifies multiple views of entities to learn embeddings for entity alignment. Specifically, we embed entities based on the views of entity names, relations and attributes, with several combination strategies. Furthermore, we design some cross-KG inference methods to enhance the alignment between two KGs. Our experiments on real-world datasets show that the proposed framework significantly outperforms the state-of-the-art embedding-based entity alignment methods. The selected views, cross-KG inference and combination strategies all contribute to the performance improvement.

Incompleteness of large knowledge graphs (KG) has motivated many researchers to propose methods to automatically find missing edges in KGs. A promising approach for KG completion (link prediction) is embedding a KG into a continuous vector space. There are different methods in the literature that learn a continuous representation of KG (latent features of KG). The benchmark dataset FB15k has been widely employed to evaluate these methods. However, It has been noted that FB15k contains many pairs of edges in which a pair represents the same relationship in reverse directions. Therefore, the inverse of numerous test triples occurs in the training set. To address this problem, FB15k-237, a subset of FB15k, was created by removing those inverse-duplicate relations to form a more challenging, realistic dataset. There is not any study that investigates how the aforementioned bias in this widely used benchmark dataset affects the results of embedding-based knowledge graph completion methods and whether their promising results are largely due to the bias. Motivated by this question, we conducted extensive experiments and report the link prediction results on FB15K and FB15k-237 using several embedding-based methods. We compare the results of different methods to see how their performances change in absence of inverse relations. Our experiment results demonstrate that the performance of embedding models in link prediction task diminishes tremendously when the inverse relationships do not exist anymore.