Hua‐Jun Chen

Xiang Chen, Lei Li, Ningyu Zhang et al.

Pre-trained language models have contributed significantly to relation extraction by demonstrating remarkable few-shot learning abilities. However, prompt tuning methods for relation extraction may still fail to generalize to those rare or hard patterns. Note that the previous parametric learning paradigm can be viewed as memorization regarding training data as a book and inference as the close-book test. Those long-tailed or hard patterns can hardly be memorized in parameters given few-shot instances. To this end, we regard RE as an open-book examination and propose a new semiparametric paradigm of retrieval-enhanced prompt tuning for relation extraction. We construct an open-book datastore for retrieval regarding prompt-based instance representations and corresponding relation labels as memorized key-value pairs. During inference, the model can infer relations by linearly interpolating the base output of PLM with the non-parametric nearest neighbor distribution over the datastore. In this way, our model not only infers relation through knowledge stored in the weights during training but also assists decision-making by unwinding and querying examples in the open-book datastore. Extensive experiments on benchmark datasets show that our method can achieve state-of-the-art in both standard supervised and few-shot settings. Code are available in https://github.com/zjunlp/PromptKG/tree/main/research/RetrievalRE.

Zhen Yao, Wen Zhang, Mingyang Chen et al.

Knowledge graph embedding (KGE), which maps entities and relations in a knowledge graph into continuous vector spaces, has achieved great success in predicting missing links in knowledge graphs. However, knowledge graphs often contain incomplete triples that are difficult to inductively infer by KGEs. To address this challenge, we resort to analogical inference and propose a novel and general self-supervised framework AnKGE to enhance KGE models with analogical inference capability. We propose an analogical object retriever that retrieves appropriate analogical objects from entity-level, relation-level, and triple-level. And in AnKGE, we train an analogy function for each level of analogical inference with the original element embedding from a well-trained KGE model as input, which outputs the analogical object embedding. In order to combine inductive inference capability from the original KGE model and analogical inference capability enhanced by AnKGE, we interpolate the analogy score with the base model score and introduce the adaptive weights in the score function for prediction. Through extensive experiments on FB15k-237 and WN18RR datasets, we show that AnKGE achieves competitive results on link prediction task and well performs analogical inference.

Zekun Xi, Wenbiao Yin, Jizhan Fang et al.

Machine writing with large language models often relies on retrieval-augmented generation. However, these approaches remain confined within the boundaries of the model's predefined scope, limiting the generation of content with rich information. Specifically, vanilla-retrieved information tends to lack depth, novelty, and suffers from redundancy, which negatively impacts the quality of generated articles, leading to shallow, unoriginal, and repetitive outputs. To address these issues, we propose OmniThink, a slow-thinking machine writing framework that emulates the human-like process of iterative expansion and reflection. The core idea behind OmniThink is to simulate the cognitive behavior of learners as they slowly deepen their knowledge of the topics. Experimental results demonstrate that OmniThink improves the knowledge density of generated articles without compromising metrics such as coherence and depth. Human evaluations and expert feedback further highlight the potential of OmniThink to address real-world challenges in the generation of long-form articles. Code is available at https://github.com/zjunlp/OmniThink.

Songze Li, Zhiqiang Liu, Zhengke Gui et al.

Large Language Models (LLMs) exhibit strong reasoning capabilities in complex tasks. However, they still struggle with hallucinations and factual errors in knowledge-intensive scenarios like knowledge graph question answering (KGQA). We attribute this to the semantic gap between structured knowledge graphs (KGs) and unstructured queries, caused by inherent differences in their focuses and structures. Existing methods usually employ resource-intensive, non-scalable workflows reasoning on vanilla KGs, but overlook this gap. To address this challenge, we propose a flexible framework, Enrich-on-Graph (EoG), which leverages LLMs' prior knowledge to enrich KGs, bridge the semantic gap between graphs and queries. EoG enables efficient evidence extraction from KGs for precise and robust reasoning, while ensuring low computational costs, scalability, and adaptability across different methods. Furthermore, we propose three graph quality evaluation metrics to analyze query-graph alignment in KGQA task, supported by theoretical validation of our optimization objectives. Extensive experiments on two KGQA benchmark datasets indicate that EoG can effectively generate high-quality KGs and achieve the state-of-the-art performance. Our code and data are available at https://github.com/zjukg/Enrich-on-Graph.

Yujie Luo, Zhuoyun Yu, Xuehai Wang et al.

Replicating AI research is a crucial yet challenging task for large language model (LLM) agents. Existing approaches often struggle to generate executable code, primarily due to insufficient background knowledge and the limitations of retrieval-augmented generation (RAG) methods, which fail to capture latent technical details hidden in referenced papers. Furthermore, previous approaches tend to overlook valuable implementation-level code signals and lack structured knowledge representations that support multi-granular retrieval and reuse. To overcome these challenges, we propose Executable Knowledge Graphs (xKG), a modular and pluggable knowledge base that automatically integrates technical insights, code snippets, and domain-specific knowledge extracted from scientific literature. When integrated into three agent frameworks with two different LLMs, xKG shows substantial performance gains (10.9% with o3-mini) on PaperBench, demonstrating its effectiveness as a general and extensible solution for automated AI research replication. Code will released at https://github.com/zjunlp/xKG.

Haiyang Yu, Ningyu Zhang, Shumin Deng et al.

Long-tailed relation classification is a challenging problem as the head classes may dominate the training phase, thereby leading to the deterioration of the tail performance. Existing solutions usually address this issue via class-balancing strategies, e.g., data re-sampling and loss re-weighting, but all these methods adhere to the schema of entangling learning of the representation and classifier. In this study, we conduct an in-depth empirical investigation into the long-tailed problem and found that pre-trained models with instance-balanced sampling already capture the well-learned representations for all classes; moreover, it is possible to achieve better long-tailed classification ability at low cost by only adjusting the classifier. Inspired by this observation, we propose a robust classifier with attentive relation routing, which assigns soft weights by automatically aggregating the relations. Extensive experiments on two datasets demonstrate the effectiveness of our proposed approach. Code and datasets are available in https://github.com/zjunlp/deepke.

Mengru Wang, Ziwen Xu, Shengyu Mao et al.

Precise control over language model generation is vital for ensuring both safety and reliability. Although prompt engineering and steering are commonly used to intervene in model behaviors, the vast number of parameters in models often results in highly intertwined internal representations. This interdependency can limit control precision and sometimes lead to unintended side effects. Recent research has explored the use of sparse autoencoders (SAE) to disentangle knowledge in high-dimensional spaces for steering. However, these applications have been limited to toy tasks owing to the nontrivial issue of locating atomic knowledge components. In this paper, we propose Steering Target Atoms (STA), a novel method that isolates and manipulates disentangled knowledge components to enhance safety. Comprehensive experiments demonstrate the effectiveness of our approach. Further analysis reveals that steering exhibits superior robustness and flexibility, particularly in adversarial scenarios. We also apply the steering strategy to the large reasoning model, confirming its effectiveness in precise reasoning control.

Yin Fang, Xinle Deng, Kangwei Liu et al.

Large language models excel at interpreting complex natural language instructions, enabling them to perform a wide range of tasks. In the life sciences, single-cell RNA sequencing (scRNA-seq) data serves as the "language of cellular biology", capturing intricate gene expression patterns at the single-cell level. However, interacting with this "language" through conventional tools is often inefficient and unintuitive, posing challenges for researchers. To address these limitations, we present InstructCell, a multi-modal AI copilot that leverages natural language as a medium for more direct and flexible single-cell analysis. We construct a comprehensive multi-modal instruction dataset that pairs text-based instructions with scRNA-seq profiles from diverse tissues and species. Building on this, we develop a multi-modal cell language architecture capable of simultaneously interpreting and processing both modalities. InstructCell empowers researchers to accomplish critical tasks-such as cell type annotation, conditional pseudo-cell generation, and drug sensitivity prediction-using straightforward natural language commands. Extensive evaluations demonstrate that InstructCell consistently meets or exceeds the performance of existing single-cell foundation models, while adapting to diverse experimental conditions. More importantly, InstructCell provides an accessible and intuitive tool for exploring complex single-cell data, lowering technical barriers and enabling deeper biological insights.

Yin Hua, Zhiqiang Liu, Mingyang Chen et al.

In natural language processing (NLP) and computer vision (CV), the successful application of foundation models across diverse tasks has demonstrated their remarkable potential. However, despite the rich structural and textual information embedded in knowledge graphs (KGs), existing research of foundation model for KG has primarily focused on their structural aspects, with most efforts restricted to in-KG tasks (e.g., knowledge graph completion, KGC). This limitation has hindered progress in addressing more challenging out-of-KG tasks. In this paper, we introduce MERRY, a foundation model for general knowledge graph reasoning, and investigate its performance across two task categories: in-KG reasoning tasks (e.g., KGC) and out-of-KG tasks (e.g., KG question answering, KGQA). We not only utilize the structural information, but also the textual information in KGs. Specifically, we propose a multi-perspective Conditional Message Passing (CMP) encoding architecture to bridge the gap between textual and structural modalities, enabling their seamless integration. Additionally, we introduce a dynamic residual fusion module to selectively retain relevant textual information and a flexible edge scoring mechanism to adapt to diverse downstream tasks. Comprehensive evaluations on 28 datasets demonstrate that MERRY outperforms existing baselines in most scenarios, showcasing strong reasoning capabilities within KGs and excellent generalization to out-of-KG tasks such as KGQA.

Lingbing Guo, Yichi Zhang, Zhongpu Bo et al.

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.

Jing Yu, Yuqi Tang, Kehua Feng et al.

Large Language Models (LLMs) have shown impressive capabilities in contextual understanding and reasoning. However, evaluating their performance across diverse scientific domains remains underexplored, as existing benchmarks primarily focus on general domains and fail to capture the intricate complexity of scientific data. To bridge this gap, we construct SciCUEval, a comprehensive benchmark dataset tailored to assess the scientific context understanding capability of LLMs. It comprises ten domain-specific sub-datasets spanning biology, chemistry, physics, biomedicine, and materials science, integrating diverse data modalities including structured tables, knowledge graphs, and unstructured texts. SciCUEval systematically evaluates four core competencies: Relevant information identification, Information-absence detection, Multi-source information integration, and Context-aware inference, through a variety of question formats. We conduct extensive evaluations of state-of-the-art LLMs on SciCUEval, providing a fine-grained analysis of their strengths and limitations in scientific context understanding, and offering valuable insights for the future development of scientific-domain LLMs.

Hongbin Ye, Ningyu Zhang, Shumin Deng et al.

Triple extraction is an essential task in information extraction for natural language processing and knowledge graph construction. In this paper, we revisit the end-to-end triple extraction task for sequence generation. Since generative triple extraction may struggle to capture long-term dependencies and generate unfaithful triples, we introduce a novel model, contrastive triple extraction with a generative transformer. Specifically, we introduce a single shared transformer module for encoder-decoder-based generation. To generate faithful results, we propose a novel triplet contrastive training object. Moreover, we introduce two mechanisms to further improve model performance (i.e., batch-wise dynamic attention-masking and triple-wise calibration). Experimental results on three datasets (i.e., NYT, WebNLG, and MIE) show that our approach achieves better performance than that of baselines.