Huajun Chen

Zhuo Chen, Lingbing Guo, Yin Fang et al.

As a crucial extension of entity alignment (EA), multi-modal entity alignment (MMEA) aims to identify identical entities across disparate knowledge graphs (KGs) by exploiting associated visual information. However, existing MMEA approaches primarily concentrate on the fusion paradigm of multi-modal entity features, while neglecting the challenges presented by the pervasive phenomenon of missing and intrinsic ambiguity of visual images. In this paper, we present a further analysis of visual modality incompleteness, benchmarking latest MMEA models on our proposed dataset MMEA-UMVM, where the types of alignment KGs covering bilingual and monolingual, with standard (non-iterative) and iterative training paradigms to evaluate the model performance. Our research indicates that, in the face of modality incompleteness, models succumb to overfitting the modality noise, and exhibit performance oscillations or declines at high rates of missing modality. This proves that the inclusion of additional multi-modal data can sometimes adversely affect EA. To address these challenges, we introduce UMAEA , a robust multi-modal entity alignment approach designed to tackle uncertainly missing and ambiguous visual modalities. It consistently achieves SOTA performance across all 97 benchmark splits, significantly surpassing existing baselines with limited parameters and time consumption, while effectively alleviating the identified limitations of other models. Our code and benchmark data are available at https://github.com/zjukg/UMAEA.

Zhuo Chen, Jiaoyan Chen, Wen Zhang et al.

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 multi-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.

Wen Zhang, Yushan Zhu, Mingyang Chen et al.

Knowledge graphs (KG) are essential background knowledge providers in many tasks. When designing models for KG-related tasks, one of the key tasks is to devise the Knowledge Representation and Fusion (KRF) module that learns the representation of elements from KGs and fuses them with task representations. While due to the difference of KGs and perspectives to be considered during fusion across tasks, duplicate and ad hoc KRF modules design are conducted among tasks. In this paper, we propose a novel knowledge graph pretraining model KGTransformer that could serve as a uniform KRF module in diverse KG-related tasks. We pretrain KGTransformer with three self-supervised tasks with sampled sub-graphs as input. For utilization, we propose a general prompt-tuning mechanism regarding task data as a triple prompt to allow flexible interactions between task KGs and task data. We evaluate pretrained KGTransformer on three tasks, triple classification, zero-shot image classification, and question answering. KGTransformer consistently achieves better results than specifically designed task models. Through experiments, we justify that the pretrained KGTransformer could be used off the shelf as a general and effective KRF module across KG-related tasks. The code and datasets are available at https://github.com/zjukg/KGTransformer.

Xiang Zhuang, Qiang Zhang, Bin Wu et al.

Molecular property is usually observed with a limited number of samples, and researchers have considered property prediction as a few-shot problem. One important fact that has been ignored by prior works is that each molecule can be recorded with several different properties simultaneously. To effectively utilize many-to-many correlations of molecules and properties, we propose a Graph Sampling-based Meta-learning (GS-Meta) framework for few-shot molecular property prediction. First, we construct a Molecule-Property relation Graph (MPG): molecule and properties are nodes, while property labels decide edges. Then, to utilize the topological information of MPG, we reformulate an episode in meta-learning as a subgraph of the MPG, containing a target property node, molecule nodes, and auxiliary property nodes. Third, as episodes in the form of subgraphs are no longer independent of each other, we propose to schedule the subgraph sampling process with a contrastive loss function, which considers the consistency and discrimination of subgraphs. Extensive experiments on 5 commonly-used benchmarks show GS-Meta consistently outperforms state-of-the-art methods by 5.71%-6.93% in ROC-AUC and verify the effectiveness of each proposed module. Our code is available at https://github.com/HICAI-ZJU/GS-Meta.

Zhuo Chen, Wen Zhang, Yufeng Huang et al.

In this work, we share our experience on tele-knowledge pre-training for fault analysis, a crucial task in telecommunication applications that requires a wide range of knowledge normally found in both machine log data and product documents. To organize this knowledge from experts uniformly, we propose to create a Tele-KG (tele-knowledge graph). Using this valuable data, we further propose a tele-domain language pre-training model TeleBERT and its knowledge-enhanced version, a tele-knowledge re-training model KTeleBERT. which includes effective prompt hints, adaptive numerical data encoding, and two knowledge injection paradigms. Concretely, our proposal includes two stages: first, pre-training TeleBERT on 20 million tele-related corpora, and then re-training it on 1 million causal and machine-related corpora to obtain KTeleBERT. Our evaluation on multiple tasks related to fault analysis in tele-applications, including root-cause analysis, event association prediction, and fault chain tracing, shows that pre-training a language model with tele-domain data is beneficial for downstream tasks. Moreover, the KTeleBERT re-training further improves the performance of task models, highlighting the effectiveness of incorporating diverse tele-knowledge into the model.

Zhuo Chen, Yufeng Huang, Jiaoyan Chen et al.

Zero-shot learning (ZSL) aims to predict unseen classes whose samples have never appeared during training. One of the most effective and widely used semantic information for zero-shot image classification are attributes which are annotations for class-level visual characteristics. However, the current methods often fail to discriminate those subtle visual distinctions between images due to not only the shortage of fine-grained annotations, but also the attribute imbalance and co-occurrence. In this paper, we present a transformer-based end-to-end ZSL method named DUET, which integrates latent semantic knowledge from the pre-trained language models (PLMs) via a self-supervised multi-modal learning paradigm. Specifically, we (1) developed a cross-modal semantic grounding network to investigate the model's capability of disentangling semantic attributes from the images; (2) applied an attribute-level contrastive learning strategy to further enhance the model's discrimination on fine-grained visual characteristics against the attribute co-occurrence and imbalance; (3) proposed a multi-task learning policy for considering multi-model objectives. We find that our DUET can achieve state-of-the-art performance on three standard ZSL benchmarks and a knowledge graph equipped ZSL benchmark. Its components are effective and its predictions are interpretable.

Yin Fang, Xiaozhuan Liang, Ningyu Zhang et al.

Large Language Models (LLMs), with their remarkable task-handling capabilities and innovative outputs, have catalyzed significant advancements across a spectrum of fields. However, their proficiency within specialized domains such as biomolecular studies remains limited. To address this challenge, we introduce Mol-Instructions, a comprehensive instruction dataset designed for the biomolecular domain. Mol-Instructions encompasses three key components: molecule-oriented instructions, protein-oriented instructions, and biomolecular text instructions. Each component aims to improve the understanding and prediction capabilities of LLMs concerning biomolecular features and behaviors. Through extensive instruction tuning experiments on LLMs, we demonstrate the effectiveness of Mol-Instructions in enhancing large models' performance in the intricate realm of biomolecular studies, thus fostering progress in the biomolecular research community. Mol-Instructions is publicly available for ongoing research and will undergo regular updates to enhance its applicability.

Zezhong Xu, Wen Zhang, Peng Ye et al.

Answering complex queries over knowledge graphs (KG) is an important yet challenging task because of the KG incompleteness issue and cascading errors during reasoning. Recent query embedding (QE) approaches to embed the entities and relations in a KG and the first-order logic (FOL) queries into a low dimensional space, answering queries by dense similarity search. However, previous works mainly concentrate on the target answers, ignoring intermediate entities' usefulness, which is essential for relieving the cascading error problem in logical query answering. In addition, these methods are usually designed with their own geometric or distributional embeddings to handle logical operators like union, intersection, and negation, with the sacrifice of the accuracy of the basic operator - projection, and they could not absorb other embedding methods to their models. In this work, we propose a Neural and Symbolic Entangled framework (ENeSy) for complex query answering, which enables the neural and symbolic reasoning to enhance each other to alleviate the cascading error and KG incompleteness. The projection operator in ENeSy could be any embedding method with the capability of link prediction, and the other FOL operators are handled without parameters. With both neural and symbolic reasoning results contained, ENeSy answers queries in ensembles. ENeSy achieves the SOTA performance on several benchmarks, especially in the setting of the training model only with the link prediction task.

Wen Zhang, Zhen Yao, Mingyang Chen et al.

Since the dynamic characteristics of knowledge graphs, many inductive knowledge graph representation learning (KGRL) works have been proposed in recent years, focusing on enabling prediction over new entities. NeuralKG-ind is the first library of inductive KGRL as an important update of NeuralKG library. It includes standardized processes, rich existing methods, decoupled modules, and comprehensive evaluation metrics. With NeuralKG-ind, it is easy for researchers and engineers to reproduce, redevelop, and compare inductive KGRL methods. The library, experimental methodologies, and model re-implementing results of NeuralKG-ind are all publicly released at https://github.com/zjukg/NeuralKG/tree/ind .

Lingbing Guo, Yuqiang Han, Qiang Zhang et al.

Embedding-based methods have attracted increasing attention in recent entity alignment (EA) studies. Although great promise they can offer, there are still several limitations. The most notable is that they identify the aligned entities based on cosine similarity, ignoring the semantics underlying the embeddings themselves. Furthermore, these methods are shortsighted, heuristically selecting the closest entity as the target and allowing multiple entities to match the same candidate. To address these limitations, we model entity alignment as a sequential decision-making task, in which an agent sequentially decides whether two entities are matched or mismatched based on their representation vectors. The proposed reinforcement learning (RL)-based entity alignment framework can be flexibly adapted to most embedding-based EA methods. The experimental results demonstrate that it consistently advances the performance of several state-of-the-art methods, with a maximum improvement of 31.1% on Hits@1.

Yichi Zhang, Zhuo Chen, Yin Fang et al.

Deploying large language models (LLMs) to real scenarios for domain-specific question answering (QA) is a key thrust for LLM applications, which poses numerous challenges, especially in ensuring that responses are both accommodating to user requirements and appropriately leveraging domain-specific knowledge bases. They are the two major difficulties for LLM application as vanilla fine-tuning falls short of addressing. Combining these requirements, we conceive of them as the requirement for the model's preference to be harmoniously aligned with humans'. Thus, we introduce Knowledgeable Preference AlignmenT (KnowPAT), which constructs two kinds of preference sets to tackle the two issues. Besides, we design a new alignment objective to align the LLM preference with different human preferences uniformly, aiming to optimize LLM performance in real-world, domain-specific QA settings. Adequate experiments and comprehensive comparisons with 15 baseline methods illustrate that our KnowPAT is a superior pipeline for real-scenario domain-specific QA with LLMs.

Jintian Zhang, Cheng Peng, Mengshu Sun et al.

Despite the recent advancements in Large Language Models (LLMs), which have significantly enhanced the generative capabilities for various NLP tasks, LLMs still face limitations in directly handling retrieval tasks. However, many practical applications demand the seamless integration of both retrieval and generation. This paper introduces a novel and efficient One-pass Generation and retrieval framework (OneGen), designed to improve LLMs' performance on tasks that require both generation and retrieval. The proposed framework bridges the traditionally separate training approaches for generation and retrieval by incorporating retrieval tokens generated autoregressively. This enables a single LLM to handle both tasks simultaneously in a unified forward pass. We conduct experiments on two distinct types of composite tasks, RAG and Entity Linking, to validate the pluggability, effectiveness, and efficiency of OneGen in training and inference. Furthermore, our results show that integrating generation and retrieval within the same context preserves the generative capabilities of LLMs while improving retrieval performance. To the best of our knowledge, OneGen is the first to enable LLMs to conduct vector retrieval during the generation.

Lei Liang, Mengshu Sun, Zhengke Gui et al.

The recently developed retrieval-augmented generation (RAG) technology has enabled the efficient construction of domain-specific applications. However, it also has limitations, including the gap between vector similarity and the relevance of knowledge reasoning, as well as insensitivity to knowledge logic, such as numerical values, temporal relations, expert rules, and others, which hinder the effectiveness of professional knowledge services. In this work, we introduce a professional domain knowledge service framework called Knowledge Augmented Generation (KAG). KAG is designed to address the aforementioned challenges with the motivation of making full use of the advantages of knowledge graph(KG) and vector retrieval, and to improve generation and reasoning performance by bidirectionally enhancing large language models (LLMs) and KGs through five key aspects: (1) LLM-friendly knowledge representation, (2) mutual-indexing between knowledge graphs and original chunks, (3) logical-form-guided hybrid reasoning engine, (4) knowledge alignment with semantic reasoning, and (5) model capability enhancement for KAG. We compared KAG with existing RAG methods in multihop question answering and found that it significantly outperforms state-of-theart methods, achieving a relative improvement of 19.6% on 2wiki and 33.5% on hotpotQA in terms of F1 score. We have successfully applied KAG to two professional knowledge Q&A tasks of Ant Group, including E-Government Q&A and E-Health Q&A, achieving significant improvement in professionalism compared to RAG methods.

Siyuan Cheng, Xiaozhuan Liang, Zhen Bi et al.

Existing data-centric methods for protein science generally cannot sufficiently capture and leverage biology knowledge, which may be crucial for many protein tasks. To facilitate research in this field, we create ProteinKG65, a knowledge graph for protein science. Using gene ontology and Uniprot knowledge base as a basis, we transform and integrate various kinds of knowledge with aligned descriptions and protein sequences, respectively, to GO terms and protein entities. ProteinKG65 is mainly dedicated to providing a specialized protein knowledge graph, bringing the knowledge of Gene Ontology to protein function and structure prediction. We also illustrate the potential applications of ProteinKG65 with a prototype. Our dataset can be downloaded at https://w3id.org/proteinkg65.

Zeyuan Wang, Qiang Zhang, Keyan Ding et al.

Large Language Models (LLMs) have revolutionized the field of natural language processing, but they fall short in comprehending biological sequences such as proteins. To address this challenge, we propose InstructProtein, an innovative LLM that possesses bidirectional generation capabilities in both human and protein languages: (i) taking a protein sequence as input to predict its textual function description and (ii) using natural language to prompt protein sequence generation. To achieve this, we first pre-train an LLM on both protein and natural language corpora, enabling it to comprehend individual languages. Then supervised instruction tuning is employed to facilitate the alignment of these two distinct languages. Herein, we introduce a knowledge graph-based instruction generation framework to construct a high-quality instruction dataset, addressing annotation imbalance and instruction deficits in existing protein-text corpus. In particular, the instructions inherit the structural relations between proteins and function annotations in knowledge graphs, which empowers our model to engage in the causal modeling of protein functions, akin to the chain-of-thought processes in natural languages. Extensive experiments on bidirectional protein-text generation tasks show that InstructProtein outperforms state-of-the-art LLMs by large margins. Moreover, InstructProtein serves as a pioneering step towards text-based protein function prediction and sequence design, effectively bridging the gap between protein and human language understanding.

Yichi Zhang, Zhuo Chen, Lingbing Guo et al.

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

Yichi Zhang, Zhuo Chen, Lei Liang et al.

Multi-modal knowledge graph completion (MMKGC) aims to predict the missing triples in the multi-modal knowledge graphs by incorporating structural, visual, and textual information of entities into the discriminant models. The information from different modalities will work together to measure the triple plausibility. Existing MMKGC methods overlook the imbalance problem of modality information among entities, resulting in inadequate modal fusion and inefficient utilization of the raw modality information. To address the mentioned problems, we propose Adaptive Multi-modal Fusion and Modality Adversarial Training (AdaMF-MAT) to unleash the power of imbalanced modality information for MMKGC. AdaMF-MAT achieves multi-modal fusion with adaptive modality weights and further generates adversarial samples by modality-adversarial training to enhance the imbalanced modality information. Our approach is a co-design of the MMKGC model and training strategy which can outperform 19 recent MMKGC methods and achieve new state-of-the-art results on three public MMKGC benchmarks. Our code and data have been released at https://github.com/zjukg/AdaMF-MAT.

Yichi Zhang, Zhuo Chen, Lingbing Guo et al.

Multi-modal knowledge graph completion (MMKGC) aims to discover unobserved knowledge from given knowledge graphs, 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, resulting 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. Code and data can be found in https://github.com/zjukg/MyGO

Kehua Feng, Keyan Ding, Hongzhi Tan et al.

Reliable evaluation of large language models (LLMs) is impeded by two key challenges: objective metrics often fail to reflect human perception of natural language, and exhaustive human labeling is prohibitively expensive. Here, we propose a sample-efficient human evaluation method for LLMs based on the principle of MAximum Discrepancy (MAD) Competition. Our method automatically and adaptively selects a compact set of input instructions that maximize semantic discrepancy between pairs of LLM responses. Human evaluators then perform three-alternative forced choices on these paired responses, which are aggregated into a global ranking using Elo rating. We apply our approach to compare eight widely used LLMs across four tasks: scientific knowledge understanding, mathematical reasoning, creative and functional writing, and code generation and explanation. Experimental results show that our sample-efficient evaluation method recovers "gold-standard" model rankings with a handful of MAD-selected instructions, reveals respective strengths and weaknesses of each LLM, and offers nuanced insights to guide future LLM development. Code is available at https://github.com/weiji-Feng/MAD-Eval .

Runnan Fang, Xiaobin Wang, Yuan Liang et al.

In the interaction between agents and their environments, agents expand their capabilities by planning and executing actions. However, LLM-based agents face substantial challenges when deployed in novel environments or required to navigate unconventional action spaces. To empower agents to autonomously explore environments, optimize workflows, and enhance their understanding of actions, we propose SynWorld, a framework that allows agents to synthesize possible scenarios with multi-step action invocation within the action space and perform Monte Carlo Tree Search (MCTS) exploration to effectively refine their action knowledge in the current environment. Our experiments demonstrate that SynWorld is an effective and general approach to learning action knowledge in new environments. Code is available at https://github.com/zjunlp/SynWorld.

Yichi Zhang, Binbin Hu, Zhuo Chen et al.

Knowledge graphs (KGs) provide reliable external knowledge for a wide variety of AI tasks in the form of structured triples. Knowledge graph pre-training (KGP) aims to pre-train neural networks on large-scale KGs and provide unified interfaces to enhance different downstream tasks, which is a key direction for KG management, maintenance, and applications. Existing works often focus on purely research questions in open domains, or they are not open source due to data security and privacy in real scenarios. Meanwhile, existing studies have not explored the training efficiency and transferability of KGP models in depth. To address these problems, We propose a framework MuDoK to achieve multi-domain collaborative pre-training and efficient prefix prompt tuning to serve diverse downstream tasks like recommendation and text understanding. Our design is a plug-and-play prompt learning approach that can be flexibly adapted to different downstream task backbones. In response to the lack of open-source benchmarks, we constructed a new multi-domain KGP benchmark called KPI with two large-scale KGs and six different sub-domain tasks to evaluate our method and open-sourced it for subsequent research. We evaluated our approach based on constructed KPI benchmarks using diverse backbone models in heterogeneous downstream tasks. The experimental results show that our framework brings significant performance gains, along with its generality, efficiency, and transferability.

Shuofei Qiao, Zhisong Qiu, Baochang Ren et al.

Large Language Models (LLMs) have achieved considerable performance across various agentic planning tasks. However, traditional agent planning approaches adopt a "flood irrigation" methodology that indiscriminately injects gold trajectories, external feedback, and domain knowledge into agent models. This practice overlooks the fundamental human cognitive principle of situational self-awareness during decision-making-the ability to dynamically assess situational demands and strategically employ resources during decision-making. We propose agentic knowledgeable self-awareness to address this gap, a novel paradigm enabling LLM-based agents to autonomously regulate knowledge utilization. Specifically, we propose KnowSelf, a data-centric approach that applies agents with knowledgeable self-awareness like humans. Concretely, we devise a heuristic situation judgement criterion to mark special tokens on the agent's self-explored trajectories for collecting training data. Through a two-stage training process, the agent model can switch between different situations by generating specific special tokens, achieving optimal planning effects with minimal costs. Our experiments demonstrate that KnowSelf can outperform various strong baselines on different tasks and models with minimal use of external knowledge. Code is available at https://github.com/zjunlp/KnowSelf.

Yiwen Zhang, Keyan Ding, Yihang Wu et al.

Retrieving molecular structures from tandem mass spectra is a crucial step in rapid compound identification. Existing retrieval methods, such as traditional mass spectral library matching, suffer from limited spectral library coverage, while recent cross-modal representation learning frameworks often encounter modality misalignment, resulting in suboptimal retrieval accuracy and generalization. To address these limitations, we propose GLMR, a Generative Language Model-based Retrieval framework that mitigates the cross-modal misalignment through a two-stage process. In the pre-retrieval stage, a contrastive learning-based model identifies top candidate molecules as contextual priors for the input mass spectrum. In the generative retrieval stage, these candidate molecules are integrated with the input mass spectrum to guide a generative model in producing refined molecular structures, which are then used to re-rank the candidates based on molecular similarity. Experiments on both MassSpecGym and the proposed MassRET-20k dataset demonstrate that GLMR significantly outperforms existing methods, achieving over 40% improvement in top-1 accuracy and exhibiting strong generalizability.

Ningyu Zhang, Yunzhi Yao, Bozhong Tian et al.

Large Language Models (LLMs) have shown extraordinary capabilities in understanding and generating text that closely mirrors human communication. However, a primary limitation lies in the significant computational demands during training, arising from their extensive parameterization. This challenge is further intensified by the dynamic nature of the world, necessitating frequent updates to LLMs to correct outdated information or integrate new knowledge, thereby ensuring their continued relevance. Note that many applications demand continual model adjustments post-training to address deficiencies or undesirable behaviors. There is an increasing interest in efficient, lightweight methods for on-the-fly model modifications. To this end, recent years have seen a burgeoning in the techniques of knowledge editing for LLMs, which aim to efficiently modify LLMs' behaviors within specific domains while preserving overall performance across various inputs. In this paper, we first define the knowledge editing problem and then provide a comprehensive review of cutting-edge approaches. Drawing inspiration from educational and cognitive research theories, we propose a unified categorization criterion that classifies knowledge editing methods into three groups: resorting to external knowledge, merging knowledge into the model, and editing intrinsic knowledge. Furthermore, we introduce a new benchmark, KnowEdit, for a comprehensive empirical evaluation of representative knowledge editing approaches. Additionally, we provide an in-depth analysis of knowledge location, which can give a deeper understanding of the knowledge structures inherent within LLMs. Finally, we discuss several potential applications of knowledge editing, outlining its broad and impactful implications.

Yida Xue, Zhen Bi, Jinnan Yang et al.

Recent advances in Multimodal Large Language Models (MLLMs) have significantly enhanced their capabilities; however, their spatial perception abilities remain a notable limitation. To address this challenge, multimodal data synthesis offers a promising solution. Yet, ensuring that synthesized data adhere to spatial common sense is a non-trivial task. Our approach addresses this critical gap by providing a systematic framework for generating spatially coherent data. In this work, we introduce SKG2DATA, a novel multimodal synthesis approach guided by spatial knowledge graphs, grounded in the concept of knowledge-to-data generation. SKG2DATA employs an automated pipeline for constructing Spatial Knowledge Graph (SKG) that effectively captures human-like spatial cognition, including directional and distance relationships. These structured representations then serve as precise guidance for our integrated synthesis pipeline, where a diffusion model generates spatially-consistent images while a MLLM produces corresponding textual descriptions. The automated construction of SKG enables scalable generation of diverse yet realistic spatial configurations, overcoming the limitations of manual data collection and annotation. Extensive experiments demonstrate that data synthesized from diverse types of spatial knowledge, including direction and distance, enhance the spatial perception and reasoning abilities of MLLMs markedly, albeit with a slight cost to their general capabilities. We hope that the idea of knowledge-based data synthesis can advance the development of spatial intelligence. Code is available at https://github.com/zjunlp/Knowledge2Data.

Wen Zhang, Long Jin, Yushan Zhu et al.

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.

Ningyu Zhang, Zhen Bi, Xiaozhuan Liang et al.

Self-supervised protein language models have proved their effectiveness in learning the proteins representations. With the increasing computational power, current protein language models pre-trained with millions of diverse sequences can advance the parameter scale from million-level to billion-level and achieve remarkable improvement. However, those prevailing approaches rarely consider incorporating knowledge graphs (KGs), which can provide rich structured knowledge facts for better protein representations. We argue that informative biology knowledge in KGs can enhance protein representation with external knowledge. In this work, we propose OntoProtein, the first general framework that makes use of structure in GO (Gene Ontology) into protein pre-training models. We construct a novel large-scale knowledge graph that consists of GO and its related proteins, and gene annotation texts or protein sequences describe all nodes in the graph. We propose novel contrastive learning with knowledge-aware negative sampling to jointly optimize the knowledge graph and protein embedding during pre-training. Experimental results show that OntoProtein can surpass state-of-the-art methods with pre-trained protein language models in TAPE benchmark and yield better performance compared with baselines in protein-protein interaction and protein function prediction. Code and datasets are available in https://github.com/zjunlp/OntoProtein.

Yin Fang, Qiang Zhang, Haihong Yang et al.

Molecular representation learning contributes to multiple downstream tasks such as molecular property prediction and drug design. To properly represent molecules, graph contrastive learning is a promising paradigm as it utilizes self-supervision signals and has no requirements for human annotations. However, prior works fail to incorporate fundamental domain knowledge into graph semantics and thus ignore the correlations between atoms that have common attributes but are not directly connected by bonds. To address these issues, we construct a Chemical Element Knowledge Graph (KG) to summarize microscopic associations between elements and propose a novel Knowledge-enhanced Contrastive Learning (KCL) framework for molecular representation learning. KCL framework consists of three modules. The first module, knowledge-guided graph augmentation, augments the original molecular graph based on the Chemical Element KG. The second module, knowledge-aware graph representation, extracts molecular representations with a common graph encoder for the original molecular graph and a Knowledge-aware Message Passing Neural Network (KMPNN) to encode complex information in the augmented molecular graph. The final module is a contrastive objective, where we maximize agreement between these two views of molecular graphs. Extensive experiments demonstrated that KCL obtained superior performances against state-of-the-art baselines on eight molecular datasets. Visualization experiments properly interpret what KCL has learned from atoms and attributes in the augmented molecular graphs. Our codes and data are available at https://github.com/ZJU-Fangyin/KCL.

Songze Li, Zhiqiang Liu, Zhaoyan Gong et al.

Large Language Models (LLMs) achieve excellent performance in natural language reasoning tasks through pre-training on vast unstructured text, enabling them to understand the logic in natural language and generate logic-consistent responses. However, the representational differences between unstructured and structured knowledge make LLMs inherently struggle to maintain logic consistency, leading to \textit{Logic Drift} challenges in structured knowledge reasoning tasks such as Knowledge Graph Question Answering (KGQA). Existing methods address this limitation by designing complex workflows embedded in prompts to guide LLM reasoning. Nevertheless, these approaches only provide input-level guidance and fail to fundamentally address the \textit{Logic Drift} in LLM outputs. Additionally, their inflexible reasoning workflows cannot adapt to different tasks and knowledge graphs. To enhance LLMs' logic consistency in structured knowledge reasoning, we specifically target the logits output from the autoregressive generation process. We propose the \textit{Logits-to-Logic} framework, which incorporates logits strengthening and logits filtering as core modules to correct logical defects in LLM outputs. Extensive experiments show that our approach significantly improves LLMs' logic consistency in structured knowledge reasoning and achieves state-of-the-art performance on multiple KGQA benchmarks.

Zhiyu Li, Shichao Song, Chenyang Xi et al.

Large Language Models (LLMs) have become an essential infrastructure for Artificial General Intelligence (AGI), yet their lack of well-defined memory management systems hinders the development of long-context reasoning, continual personalization, and knowledge consistency.Existing models mainly rely on static parameters and short-lived contextual states, limiting their ability to track user preferences or update knowledge over extended periods.While Retrieval-Augmented Generation (RAG) introduces external knowledge in plain text, it remains a stateless workaround without lifecycle control or integration with persistent representations.Recent work has modeled the training and inference cost of LLMs from a memory hierarchy perspective, showing that introducing an explicit memory layer between parameter memory and external retrieval can substantially reduce these costs by externalizing specific knowledge. Beyond computational efficiency, LLMs face broader challenges arising from how information is distributed over time and context, requiring systems capable of managing heterogeneous knowledge spanning different temporal scales and sources. To address this challenge, we propose MemOS, a memory operating system that treats memory as a manageable system resource. It unifies the representation, scheduling, and evolution of plaintext, activation-based, and parameter-level memories, enabling cost-efficient storage and retrieval. As the basic unit, a MemCube encapsulates both memory content and metadata such as provenance and versioning. MemCubes can be composed, migrated, and fused over time, enabling flexible transitions between memory types and bridging retrieval with parameter-based learning. MemOS establishes a memory-centric system framework that brings controllability, plasticity, and evolvability to LLMs, laying the foundation for continual learning and personalized modeling.

Yin Fang, Kangwei Liu, Ningyu Zhang et al.

As Large Language Models (LLMs) rapidly evolve, their influence in science is becoming increasingly prominent. The emerging capabilities of LLMs in task generalization and free-form dialogue can significantly advance fields like chemistry and biology. However, the field of single-cell biology, which forms the foundational building blocks of living organisms, still faces several challenges. High knowledge barriers and limited scalability in current methods restrict the full exploitation of LLMs in mastering single-cell data, impeding direct accessibility and rapid iteration. To this end, we introduce ChatCell, which signifies a paradigm shift by facilitating single-cell analysis with natural language. Leveraging vocabulary adaptation and unified sequence generation, ChatCell has acquired profound expertise in single-cell biology and the capability to accommodate a diverse range of analysis tasks. Extensive experiments further demonstrate ChatCell's robust performance and potential to deepen single-cell insights, paving the way for more accessible and intuitive exploration in this pivotal field. Our project homepage is available at https://zjunlp.github.io/project/ChatCell.

Junjie Wang, Mingyang Chen, Binbin Hu et al.

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.

Qiang Zhang, Keyang Ding, Tianwen Lyv et al.

Large Language Models (LLMs) have emerged as a transformative power in enhancing natural language comprehension, representing a significant stride toward artificial general intelligence. The application of LLMs extends beyond conventional linguistic boundaries, encompassing specialized linguistic systems developed within various scientific disciplines. This growing interest has led to the advent of scientific LLMs, a novel subclass specifically engineered for facilitating scientific discovery. As a burgeoning area in the community of AI for Science, scientific LLMs warrant comprehensive exploration. However, a systematic and up-to-date survey introducing them is currently lacking. In this paper, we endeavor to methodically delineate the concept of "scientific language", whilst providing a thorough review of the latest advancements in scientific LLMs. Given the expansive realm of scientific disciplines, our analysis adopts a focused lens, concentrating on the biological and chemical domains. This includes an in-depth examination of LLMs for textual knowledge, small molecules, macromolecular proteins, genomic sequences, and their combinations, analyzing them in terms of model architectures, capabilities, datasets, and evaluation. Finally, we critically examine the prevailing challenges and point out promising research directions along with the advances of LLMs. By offering a comprehensive overview of technical developments in this field, this survey aspires to be an invaluable resource for researchers navigating the intricate landscape of scientific LLMs.

Lingbing Guo, Qiang Zhang, Huajun Chen

Despite recent successes in natural language processing and computer vision, Transformer suffers from the scalability problem when dealing with graphs. The computational complexity is unacceptable for large-scale graphs, e.g., knowledge graphs. One solution is to consider only the near neighbors, which, however, will lose the key merit of Transformer to attend to the elements at any distance. In this paper, we propose a new Transformer architecture, named dual-encoding Transformer (DET). DET has a structural encoder to aggregate information from connected neighbors and a semantic encoder to focus on semantically useful distant nodes. In comparison with resorting to multi-hop neighbors, DET seeks the desired distant neighbors via self-supervised training. We further find these two encoders can be incorporated to boost each others' performance. Our experiments demonstrate DET has achieved superior performance compared to the respective state-of-the-art methods in dealing with molecules, networks and knowledge graphs with various sizes.

Qiang Zhang, Zeyuan Wang, Yuqiang Han et al.

Pre-trained protein models (PTPMs) represent a protein with one fixed embedding and thus are not capable for diverse tasks. For example, protein structures can shift, namely protein folding, between several conformations in various biological processes. To enable PTPMs to produce task-aware representations, we propose to learn interpretable, pluggable and extensible protein prompts as a way of injecting task-related knowledge into PTPMs. In this regard, prior PTPM optimization with the masked language modeling task can be interpreted as learning a sequence prompt (Seq prompt) that enables PTPMs to capture the sequential dependency between amino acids. To incorporate conformational knowledge to PTPMs, we propose an interaction-conformation prompt (IC prompt) that is learned through back-propagation with the protein-protein interaction task. As an instantiation, we present a conformation-aware pre-trained protein model that learns both sequence and interaction-conformation prompts in a multi-task setting. We conduct comprehensive experiments on nine protein datasets. Results confirm our expectation that using the sequence prompt does not hurt PTPMs' performance on sequence-related tasks while incorporating the interaction-conformation prompt significantly improves PTPMs' performance on tasks where conformational knowledge counts. We also show the learned prompts can be combined and extended to deal with new complex tasks.

Mingyang Chen, Wen Zhang, Yushan Zhu et al.

Knowledge graphs (KGs) consisting of a large number of triples have become widespread recently, and many knowledge graph embedding (KGE) methods are proposed to embed entities and relations of a KG into continuous vector spaces. Such embedding methods simplify the operations of conducting various in-KG tasks (e.g., link prediction) and out-of-KG tasks (e.g., question answering). They can be viewed as general solutions for representing KGs. However, existing KGE methods are not applicable to inductive settings, where a model trained on source KGs will be tested on target KGs with entities unseen during model training. Existing works focusing on KGs in inductive settings can only solve the inductive relation prediction task. They can not handle other out-of-KG tasks as general as KGE methods since they don't produce embeddings for entities. In this paper, to achieve inductive knowledge graph embedding, we propose a model MorsE, which does not learn embeddings for entities but learns transferable meta-knowledge that can be used to produce entity embeddings. Such meta-knowledge is modeled by entity-independent modules and learned by meta-learning. Experimental results show that our model significantly outperforms corresponding baselines for in-KG and out-of-KG tasks in inductive settings.

Chi-Man Wong, Fan Feng, Wen Zhang et al.

Conversational Recommender Systems (CRSs) in E-commerce platforms aim to recommend items to users via multiple conversational interactions. Click-through rate (CTR) prediction models are commonly used for ranking candidate items. However, most CRSs are suffer from the problem of data scarcity and sparseness. To address this issue, we propose a novel knowledge-enhanced deep cross network (K-DCN), a two-step (pretrain and fine-tune) CTR prediction model to recommend items. We first construct a billion-scale conversation knowledge graph (CKG) from information about users, items and conversations, and then pretrain CKG by introducing knowledge graph embedding method and graph convolution network to encode semantic and structural information respectively.To make the CTR prediction model sensible of current state of users and the relationship between dialogues and items, we introduce user-state and dialogue-interaction representations based on pre-trained CKG and propose K-DCN.In K-DCN, we fuse the user-state representation, dialogue-interaction representation and other normal feature representations via deep cross network, which will give the rank of candidate items to be recommended.We experimentally prove that our proposal significantly outperforms baselines and show it's real application in Alime.

Yushan Zhu, Wen Zhang, Mingyang Chen et al.

Knowledge Graph Embedding (KGE) is a popular method for KG reasoning and training KGEs with higher dimension are usually preferred since they have better reasoning capability. However, high-dimensional KGEs pose huge challenges to storage and computing resources and are not suitable for resource-limited or time-constrained applications, for which faster and cheaper reasoning is necessary. To address this problem, we propose DualDE, a knowledge distillation method to build low-dimensional student KGE from pre-trained high-dimensional teacher KGE. DualDE considers the dual-influence between the teacher and the student. In DualDE, we propose a soft label evaluation mechanism to adaptively assign different soft label and hard label weights to different triples, and a two-stage distillation approach to improve the student's acceptance of the teacher. Our DualDE is general enough to be applied to various KGEs. Experimental results show that our method can successfully reduce the embedding parameters of a high-dimensional KGE by 7 times - 15 times and increase the inference speed by 2 times - 6 times while retaining a high performance. We also experimentally prove the effectiveness of our soft label evaluation mechanism and two-stage distillation approach via ablation study.

Jiaoyan Chen, Freddy Lecue, Jeff Z. Pan et al.

Machine learning explanation can significantly boost machine learning's application in decision making, but the usability of current methods is limited in human-centric explanation, especially for transfer learning, an important machine learning branch that aims at utilizing knowledge from one learning domain (i.e., a pair of dataset and prediction task) to enhance prediction model training in another learning domain. In this paper, we propose an ontology-based approach for human-centric explanation of transfer learning. Three kinds of knowledge-based explanatory evidence, with different granularities, including general factors, particular narrators and core contexts are first proposed and then inferred with both local ontologies and external knowledge bases. The evaluation with US flight data and DBpedia has presented their confidence and availability in explaining the transferability of feature representation in flight departure delay forecasting.