Xiaozhuan Liang

Ningyu Zhang, Lei Li, Xiang Chen et al.

Analogical reasoning is fundamental to human cognition and holds an important place in various fields. However, previous studies mainly focus on single-modal analogical reasoning and ignore taking advantage of structure knowledge. Notably, the research in cognitive psychology has demonstrated that information from multimodal sources always brings more powerful cognitive transfer than single modality sources. To this end, we introduce the new task of multimodal analogical reasoning over knowledge graphs, which requires multimodal reasoning ability with the help of background knowledge. Specifically, we construct a Multimodal Analogical Reasoning dataSet (MARS) and a multimodal knowledge graph MarKG. We evaluate with multimodal knowledge graph embedding and pre-trained Transformer baselines, illustrating the potential challenges of the proposed task. We further propose a novel model-agnostic Multimodal analogical reasoning framework with Transformer (MarT) motivated by the structure mapping theory, which can obtain better performance. Code and datasets are available in https://github.com/zjunlp/MKG_Analogy.

Xiang Chen, Lei Li, Ningyu Zhang et al.

Prompt learning approaches have made waves in natural language processing by inducing better few-shot performance while they still follow a parametric-based learning paradigm; the oblivion and rote memorization problems in learning may encounter unstable generalization issues. Specifically, vanilla prompt learning may struggle to utilize atypical instances by rote during fully-supervised training or overfit shallow patterns with low-shot data. To alleviate such limitations, we develop RetroPrompt with the motivation of decoupling knowledge from memorization to help the model strike a balance between generalization and memorization. In contrast with vanilla prompt learning, RetroPrompt constructs an open-book knowledge-store from training instances and implements a retrieval mechanism during the process of input, training and inference, thus equipping the model with the ability to retrieve related contexts from the training corpus as cues for enhancement. Extensive experiments demonstrate that RetroPrompt can obtain better performance in both few-shot and zero-shot settings. Besides, we further illustrate that our proposed RetroPrompt can yield better generalization abilities with new datasets. Detailed analysis of memorization indeed reveals RetroPrompt can reduce the reliance of language models on memorization; thus, improving generalization for downstream tasks. Code is available in https://github.com/zjunlp/PromptKG/tree/main/research/RetroPrompt.

Zhen Bi, Siyuan Cheng, Jing Chen et al.

Transformers have achieved remarkable performance in widespread fields, including natural language processing, computer vision and graph mining. However, vanilla Transformer architectures have not yielded promising improvements in the Knowledge Graph (KG) representations, where the translational distance paradigm dominates this area. Note that vanilla Transformer architectures struggle to capture the intrinsically heterogeneous structural and semantic information of knowledge graphs. To this end, we propose a new variant of Transformer for knowledge graph representations dubbed Relphormer. Specifically, we introduce Triple2Seq which can dynamically sample contextualized sub-graph sequences as the input to alleviate the heterogeneity issue. We propose a novel structure-enhanced self-attention mechanism to encode the relational information and keep the semantic information within entities and relations. Moreover, we utilize masked knowledge modeling for general knowledge graph representation learning, which can be applied to various KG-based tasks including knowledge graph completion, question answering, and recommendation. Experimental results on six datasets show that Relphormer can obtain better performance compared with baselines. Code is available in https://github.com/zjunlp/Relphormer.

Xiaozhuan Liang, Ningyu Zhang, Siyuan Cheng et al.

Pretrained language models can be effectively stimulated by textual prompts or demonstrations, especially in low-data scenarios. Recent works have focused on automatically searching discrete or continuous prompts or optimized verbalizers, yet studies for the demonstration are still limited. Concretely, the demonstration examples are crucial for an excellent final performance of prompt-tuning. In this paper, we propose a novel pluggable, extensible, and efficient approach named contrastive demonstration tuning, which is free of demonstration sampling. Furthermore, the proposed approach can be: (i) Plugged into any previous prompt-tuning approaches; (ii) Extended to widespread classification tasks with a large number of categories. Experimental results on 16 datasets illustrate that our method integrated with previous approaches LM-BFF and P-tuning can yield better performance. Code is available in https://github.com/zjunlp/PromptKG/tree/main/research/Demo-Tuning.

Bozhong Tian, Xiaozhuan Liang, Siyuan Cheng et al.

Large Language Models (LLMs) trained on extensive corpora inevitably retain sensitive data, such as personal privacy information and copyrighted material. Recent advancements in knowledge unlearning involve updating LLM parameters to erase specific knowledge. However, current unlearning paradigms are mired in vague forgetting boundaries, often erasing knowledge indiscriminately. In this work, we introduce KnowUnDo, a benchmark containing copyrighted content and user privacy domains to evaluate if the unlearning process inadvertently erases essential knowledge. Our findings indicate that existing unlearning methods often suffer from excessive unlearning. To address this, we propose a simple yet effective method, MemFlex, which utilizes gradient information to precisely target and unlearn sensitive parameters. Experimental results show that MemFlex is superior to existing methods in both precise knowledge unlearning and general knowledge retaining of LLMs. Code and dataset are released at https://github.com/zjunlp/KnowUnDo.

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.

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.

Qizhi Pei, Lijun Wu, Kaiyuan Gao et al.

Recent research trends in computational biology have increasingly focused on integrating text and bio-entity modeling, especially in the context of molecules and proteins. However, previous efforts like BioT5 faced challenges in generalizing across diverse tasks and lacked a nuanced understanding of molecular structures, particularly in their textual representations (e.g., IUPAC). This paper introduces BioT5+, an extension of the BioT5 framework, tailored to enhance biological research and drug discovery. BioT5+ incorporates several novel features: integration of IUPAC names for molecular understanding, inclusion of extensive bio-text and molecule data from sources like bioRxiv and PubChem, the multi-task instruction tuning for generality across tasks, and a numerical tokenization technique for improved processing of numerical data. These enhancements allow BioT5+ to bridge the gap between molecular representations and their textual descriptions, providing a more holistic understanding of biological entities, and largely improving the grounded reasoning of bio-text and bio-sequences. The model is pre-trained and fine-tuned with a large number of experiments, including \emph{3 types of problems (classification, regression, generation), 15 kinds of tasks, and 21 total benchmark datasets}, demonstrating the remarkable performance and state-of-the-art results in most cases. BioT5+ stands out for its ability to capture intricate relationships in biological data, thereby contributing significantly to bioinformatics and computational biology. Our code is available at \url{https://github.com/QizhiPei/BioT5}.

Ningyu Zhang, Bozhong Tian, Siyuan Cheng et al.

Knowledge editing for large language models can offer an efficient solution to alter a model's behavior without negatively impacting the overall performance. However, the current approaches encounter issues with limited generalizability across tasks, necessitating one distinct editor for each task, significantly hindering the broader applications. To address this, we take the first step to analyze the multi-task generalization issue in knowledge editing. Specifically, we develop an instruction-based editing technique, termed InstructEdit, which facilitates the editor's adaptation to various task performances simultaneously using simple instructions. With only one unified editor for each LLM, we empirically demonstrate that InstructEdit can improve the editor's control, leading to an average 14.86% increase in Reliability in multi-task editing setting. Furthermore, experiments involving holdout unseen task illustrate that InstructEdit consistently surpass previous strong baselines. To further investigate the underlying mechanisms of instruction-based knowledge editing, we analyze the principal components of the editing gradient directions, which unveils that instructions can help control optimization direction with stronger OOD generalization. Code and datasets are available in https://github.com/zjunlp/EasyEdit.

Kangwei Liu, Siyuan Cheng, Bozhong Tian et al.

Large language models (LLMs) have been increasingly applied to automated harmful content detection tasks, assisting moderators in identifying policy violations and improving the overall efficiency and accuracy of content review. However, existing resources for harmful content detection are predominantly focused on English, with Chinese datasets remaining scarce and often limited in scope. We present a comprehensive, professionally annotated benchmark for Chinese content harm detection, which covers six representative categories and is constructed entirely from real-world data. Our annotation process further yields a knowledge rule base that provides explicit expert knowledge to assist LLMs in Chinese harmful content detection. In addition, we propose a knowledge-augmented baseline that integrates both human-annotated knowledge rules and implicit knowledge from large language models, enabling smaller models to achieve performance comparable to state-of-the-art LLMs. Code and data are available at https://github.com/zjunlp/ChineseHarm-bench.

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.

Ningyu Zhang, Xin Xu, Liankuan Tao et al.

We present an open-source and extensible knowledge extraction toolkit DeepKE, supporting complicated low-resource, document-level and multimodal scenarios in the knowledge base population. DeepKE implements various information extraction tasks, including named entity recognition, relation extraction and attribute extraction. With a unified framework, DeepKE allows developers and researchers to customize datasets and models to extract information from unstructured data according to their requirements. Specifically, DeepKE not only provides various functional modules and model implementation for different tasks and scenarios but also organizes all components by consistent frameworks to maintain sufficient modularity and extensibility. We release the source code at GitHub in https://github.com/zjunlp/DeepKE with Google Colab tutorials and comprehensive documents for beginners. Besides, we present an online system in http://deepke.openkg.cn/EN/re_doc_show.html for real-time extraction of various tasks, and a demo video.

Liang He, Peiran Jin, Yaosen Min et al.

Proteins, essential to biological systems, perform functions intricately linked to their three-dimensional structures. Understanding the relationship between protein structures and their amino acid sequences remains a core challenge in protein modeling. While traditional protein foundation models benefit from pre-training on vast unlabeled datasets, they often struggle to capture critical co-evolutionary information, which evolutionary-based methods excel at. In this study, we introduce a novel pre-training strategy for protein foundation models that emphasizes the interactions among amino acid residues to enhance the extraction of both short-range and long-range co-evolutionary features from sequence data. Trained on a large-scale protein sequence dataset, our model demonstrates superior generalization ability, outperforming established baselines of similar size, including the ESM model, across diverse downstream tasks. Experimental results confirm the model's effectiveness in integrating co-evolutionary information, marking a significant step forward in protein sequence-based modeling.

Yuxuan Cai, Xiaozhuan Liang, Xinghua Wang et al.

As large language models (LLMs) become increasingly powerful, the sequential nature of autoregressive generation creates a fundamental throughput bottleneck that limits the practical deployment. While Multi-Token Prediction (MTP) has demonstrated remarkable benefits for model training efficiency and performance, its inherent potential for inference acceleration remains largely unexplored. This paper introduces FastMTP, a simple yet effective method that improves multi-step draft quality by aligning MTP training with its inference pattern, significantly enhancing speculative decoding performance. Our approach fine-tunes a single MTP head with position-shared weights on self-distilled data, enabling it to capture dependencies among consecutive future tokens and maintain high acceptance rates across multiple recursive draft steps. By integrating language-aware dynamic vocabulary compression into the MTP head, we further reduce computational overhead in the drafting process. Experimental results across seven diverse benchmarks demonstrate that FastMTP achieves an average of 2.03x speedup compared to standard next token prediction with lossless output quality, outperforming vanilla MTP by 82%. FastMTP requires only lightweight training and seamlessly integrates with existing inference frameworks, offering a practical and rapidly deployable solution for accelerating LLM inference.

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}.