Zhen Bi

Zhen Bi, Jing Chen, Yinuo Jiang et al.

Current generative knowledge graph construction approaches usually fail to capture structural knowledge by simply flattening natural language into serialized texts or a specification language. However, large generative language model trained on structured data such as code has demonstrated impressive capability in understanding natural language for structural prediction and reasoning tasks. Intuitively, we address the task of generative knowledge graph construction with code language model: given a code-format natural language input, the target is to generate triples which can be represented as code completion tasks. Specifically, we develop schema-aware prompts that effectively utilize the semantic structure within the knowledge graph. As code inherently possesses structure, such as class and function definitions, it serves as a useful model for prior semantic structural knowledge. Furthermore, we employ a rationale-enhanced generation method to boost the performance. Rationales provide intermediate steps, thereby improving knowledge extraction abilities. Experimental results indicate that the proposed approach can obtain better performance on benchmark datasets compared with baselines. Code and datasets are available in https://github.com/zjunlp/DeepKE/tree/main/example/llm.

Zhen Bi, Ningyu Zhang, Yinuo Jiang et al.

In the realm of embodied artificial intelligence, the reasoning capabilities of Large Language Models (LLMs) play a pivotal role. Although there are effective methods like program-of-thought prompting for LLMs which uses programming language to tackle complex reasoning tasks, the specific impact of code data on the improvement of reasoning capabilities remains under-explored. To address this gap, we propose complexity-impacted reasoning score (CIRS), which combines structural and logical attributes, to measure the correlation between code and reasoning abilities. Specifically, we use the abstract syntax tree to encode the structural information and calculate logical complexity by considering the difficulty and the cyclomatic complexity. Through an empirical analysis, we find not all code data of complexity can be learned or understood by LLMs. Optimal level of complexity is critical to the improvement of reasoning abilities by program-aided prompting. Then we design an auto-synthesizing and stratifying algorithm, and apply it to instruction generation for mathematical reasoning and code data filtering for code generation tasks. Extensive results demonstrates the effectiveness of our proposed approach. Code will be integrated into the EasyInstruct framework at https://github.com/zjunlp/EasyInstruct.

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.

Zhen Bi, Ningyu Zhang, Yida Xue et al.

Ocean science, which delves into the oceans that are reservoirs of life and biodiversity, is of great significance given that oceans cover over 70% of our planet's surface. Recently, advances in Large Language Models (LLMs) have transformed the paradigm in science. Despite the success in other domains, current LLMs often fall short in catering to the needs of domain experts like oceanographers, and the potential of LLMs for ocean science is under-explored. The intrinsic reasons are the immense and intricate nature of ocean data as well as the necessity for higher granularity and richness in knowledge. To alleviate these issues, we introduce OceanGPT, the first-ever large language model in the ocean domain, which is expert in various ocean science tasks. We also propose OceanGPT, a novel framework to automatically obtain a large volume of ocean domain instruction data, which generates instructions based on multi-agent collaboration. Additionally, we construct the first oceanography benchmark, OceanBench, to evaluate the capabilities of LLMs in the ocean domain. Though comprehensive experiments, OceanGPT not only shows a higher level of knowledge expertise for oceans science tasks but also gains preliminary embodied intelligence capabilities in ocean technology.

Yan Wang, Zhixuan Chu, Zihao Xue et al.

Reasoning-based LLM guardrails improve safety moderation by generating explicit rationales before issuing final decisions. However, their rationales do not always lead to faithful enforcement: a model may recognize a harmful intent in its reasoning but still predict a safe label, or issue an unsafe decision without policy-grounded justification. We identify this safety-critical failure mode as the deliberation-to-enforcement gap. Unlike general chain-of-thought faithfulness, guardrail reliability requires policy execution consistency: the generated reasoning should be grounded in the safety policy, and the final decision should be entailed by that reasoning. We propose ConsisGuard, a consistency-aware framework for reasoning-based LLM guardrails. ConsisGuard performs Policy-to-Decision Trajectory Distillation and Functional Coupling Alignment, aligning the internal coupling between safety deliberation and decision enforcement. Experiments on prompt and response harmfulness detection benchmarks show that ConsisGuard improves detection performance while reducing policy execution failures. These results suggest that reliable reasoning-based guardrails require accurate faithful execution of safety policies.

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.

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.

Yixin Ou, Ningyu Zhang, Honghao Gui et al.

In recent years, instruction tuning has gained increasing attention and emerged as a crucial technique to enhance the capabilities of Large Language Models (LLMs). To construct high-quality instruction datasets, many instruction processing approaches have been proposed, aiming to achieve a delicate balance between data quantity and data quality. Nevertheless, due to inconsistencies that persist among various instruction processing methods, there is no standard open-source instruction processing implementation framework available for the community, which hinders practitioners from further developing and advancing. To facilitate instruction processing research and development, we present EasyInstruct, an easy-to-use instruction processing framework for LLMs, which modularizes instruction generation, selection, and prompting, while also considering their combination and interaction. EasyInstruct is publicly released and actively maintained at https://github.com/zjunlp/EasyInstruct, along with an online demo app and a demo video for quick-start, calling for broader research centered on instruction data and synthetic data.

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.

Luoqiu Li, Xiang Chen, Zhen Bi et al.

Recent neural-based relation extraction approaches, though achieving promising improvement on benchmark datasets, have reported their vulnerability towards adversarial attacks. Thus far, efforts mostly focused on generating adversarial samples or defending adversarial attacks, but little is known about the difference between normal and adversarial samples. In this work, we take the first step to leverage the salience-based method to analyze those adversarial samples. We observe that salience tokens have a direct correlation with adversarial perturbations. We further find the adversarial perturbations are either those tokens not existing in the training set or superficial cues associated with relation labels. To some extent, our approach unveils the characters against adversarial samples. We release an open-source testbed, "DiagnoseAdv" in https://github.com/zjunlp/DiagnoseAdv.

Ningyu Zhang, Mosha Chen, Zhen Bi et al.

Artificial Intelligence (AI), along with the recent progress in biomedical language understanding, is gradually changing medical practice. With the development of biomedical language understanding benchmarks, AI applications are widely used in the medical field. However, most benchmarks are limited to English, which makes it challenging to replicate many of the successes in English for other languages. To facilitate research in this direction, we collect real-world biomedical data and present the first Chinese Biomedical Language Understanding Evaluation (CBLUE) benchmark: a collection of natural language understanding tasks including named entity recognition, information extraction, clinical diagnosis normalization, single-sentence/sentence-pair classification, and an associated online platform for model evaluation, comparison, and analysis. To establish evaluation on these tasks, we report empirical results with the current 11 pre-trained Chinese models, and experimental results show that state-of-the-art neural models perform by far worse than the human ceiling. Our benchmark is released at \url{https://tianchi.aliyun.com/dataset/dataDetail?dataId=95414&lang=en-us}.