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Researcher profile

Huajun Chen

Huajun Chen contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
Artificial IntelligenceComputation and LanguageMachine LearningComputer VisionBiomoleculesInformation RetrievalLogic in Computer ScienceQuantitative Methods

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Published work

19 published item(s)

preprint2026arXiv

ChemVA: Advancing Large Language Models on Chemical Reaction Diagrams Understanding

While Large Language Models (LLMs) have revolutionized scientific text processing, they exhibit a significant capability gap when interpreting chemical reaction diagrams. We identify two fundamental bottlenecks restricting current systems: a Visual Deficit, where generic vision encoders struggle to resolve the strict topological connectivity of dense molecular graphs, and a Semantic Disconnect, where standard linear strings, such as SMILES, fail to effectively activate the model's latent chemical reasoning. To bridge these gaps, we propose the Chemical Visual Activation (ChemVA) framework, which employs a Visual Anchor mechanism to ground functional groups via hybrid-granularity detection, followed by a semantic alignment approach that translates visual features into entity names to maximize knowledge activation in LLMs. We evaluate our approach on OCRD-Bench, a newly constructed dataset featuring dense visual-semantic contexts and comprehensive reaction coverage to evaluate the full spectrum from recognition to reasoning. Extensive experiments on OCRD-Bench demonstrate that ChemVA achieves 92.0% structural recognition accuracy. By bridging visual and semantic bottlenecks, our framework delivers a consistent performance gain of approximately 20 percentage points across 9 diverse LLMs, enabling open-weight models to rival proprietary SOTA systems in complex chemical reasoning tasks.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

Learning an Efficient Multi-Turn Dialogue Evaluator from Multiple LLM Judges

Evaluating the conversational abilities of large language models (LLMs) remains a challenging task. Current mainstream approaches primarily rely on the "LLM-as-a-judge" paradigm, where an LLM is prompted to serve as an evaluator to assess dialogue quality. However, such methods often suffer from various biases, which undermine the reliability and consistency of the evaluation results. To mitigate these biases, recent methods employ multiple LLMs as judges and aggregate their judgments to select the optimal assessment. Although effective, this multi-judge approach incurs significant computational overhead during inference. In this paper, we propose an efficient dialogue evaluator that captures the collective wisdom of multiple LLM judges by aggregating their preference knowledge into a single model. Our approach preserves the advantages of diverse multi-judge feedback while drastically reducing the evaluation cost, enabling fast, flexible, and fine-grained dialogue quality assessment. Extensive experiments on seven single rating and pairwise comparison dialogue evaluation benchmarks demonstrate that our method outperforms existing baselines across diverse scenarios, showcasing its efficiency and robustness.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

StressEval: Failure-Driven Dynamic Benchmarking for Knowledge-Intensive Reasoning in Large Language Models

Static benchmarks for LLMs are increasingly compromised by contamination and overfitting especially on knowledge intensive reasoning tasks While recent dynamic benchmarks can alleviate staleness they often increase difficulty at the expense of answerability and controllability In this paper we propose StressEval a failure driven data synthesis framework that turns observed model failures into dynamic challenging and controllable test instances StressEval consists of three stages first it constructs a semi structured difficulty card that identifies the failed reasoning step and its root cause second it applies a dual perspective instance synthesis method that targets both knowledge gaps and reasoning breakdowns while preserving the underlying difficulty factors and third it applies a gating mechanism to retain only grounded unambiguous instances Seeding from multiple knowledge intensive reasoning datasets we employ StressEval to build Dynamic OneEval a focused suite of challenging dynamic benchmark Across several state of the art LLMs Dynamic OneEval yields substantially larger performance drops than the original benchmarks while retaining explicit difficulty factors enabling more actionable iteration

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

Transformer Interpretability from Perspective of Attention and Gradient

Although researchers' attention is more focused on the performance of Transformer models, the interpretation of Transformer can never be ignored. Gradient is widely utilized in Transformer interpretation. From the perspective of attention and gradient, we conduct an in-depth study of Transformer interpretation and propose a method to achieve it by guiding the gradient direction, or more precisely, the attention direction. The method enables more comprehensive interpretation of feature regions, offers detail interpretation, and helps to better understand Transformer mechanism. Leveraging the difference in how Vision Transformer (ViT) and humans perceive images, we alter the class of an image in a way that is almost imperceptible to the human eye. This class rewriting phenomenon may potentially pose security risks in certain scenarios.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Deep Reinforcement Learning for Entity Alignment

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.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Disentangled Ontology Embedding for Zero-shot Learning

Knowledge Graph (KG) and its variant of ontology have been widely used for knowledge representation, and have shown to be quite effective in augmenting Zero-shot Learning (ZSL). However, existing ZSL methods that utilize KGs all neglect the intrinsic complexity of inter-class relationships represented in KGs. One typical feature is that a class is often related to other classes in different semantic aspects. In this paper, we focus on ontologies for augmenting ZSL, and propose to learn disentangled ontology embeddings guided by ontology properties to capture and utilize more fine-grained class relationships in different aspects. We also contribute a new ZSL framework named DOZSL, which contains two new ZSL solutions based on generative models and graph propagation models, respectively, for effectively utilizing the disentangled ontology embeddings. Extensive evaluations have been conducted on five benchmarks across zero-shot image classification (ZS-IMGC) and zero-shot KG completion (ZS-KGC). DOZSL often achieves better performance than the state-of-the-art, and its components have been verified by ablation studies and case studies. Our codes and datasets are available at https://github.com/zjukg/DOZSL.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Knowledge Graph Reasoning with Logics and Embeddings: Survey and Perspective

Knowledge graph (KG) reasoning is becoming increasingly popular in both academia and industry. Conventional KG reasoning based on symbolic logic is deterministic, with reasoning results being explainable, while modern embedding-based reasoning can deal with uncertainty and predict plausible knowledge, often with high efficiency via vector computation. A promising direction is to integrate both logic-based and embedding-based methods, with the vision to have advantages of both. It has attracted wide research attention with more and more works published in recent years. In this paper, we comprehensively survey these works, focusing on how logics and embeddings are integrated. We first briefly introduce preliminaries, then systematically categorize and discuss works of logic and embedding-aware KG reasoning from different perspectives, and finally conclude and discuss the challenges and further directions.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Meta-Knowledge Transfer for Inductive Knowledge Graph Embedding

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.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Meta-Learning Based Knowledge Extrapolation for Knowledge Graphs in the Federated Setting

We study the knowledge extrapolation problem to embed new components (i.e., entities and relations) that come with emerging knowledge graphs (KGs) in the federated setting. In this problem, a model trained on an existing KG needs to embed an emerging KG with unseen entities and relations. To solve this problem, we introduce the meta-learning setting, where a set of tasks are sampled on the existing KG to mimic the link prediction task on the emerging KG. Based on sampled tasks, we meta-train a graph neural network framework that can construct features for unseen components based on structural information and output embeddings for them. Experimental results show that our proposed method can effectively embed unseen components and outperforms models that consider inductive settings for KGs and baselines that directly use conventional KG embedding methods.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Molecular Contrastive Learning with Chemical Element Knowledge Graph

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.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

NeuralKG: An Open Source Library for Diverse Representation Learning of Knowledge Graphs

NeuralKG is an open-source Python-based library for diverse representation learning of knowledge graphs. It implements three different series of Knowledge Graph Embedding (KGE) methods, including conventional KGEs, GNN-based KGEs, and Rule-based KGEs. With a unified framework, NeuralKG successfully reproduces link prediction results of these methods on benchmarks, freeing users from the laborious task of reimplementing them, especially for some methods originally written in non-python programming languages. Besides, NeuralKG is highly configurable and extensible. It provides various decoupled modules that can be mixed and adapted to each other. Thus with NeuralKG, developers and researchers can quickly implement their own designed models and obtain the optimal training methods to achieve the best performance efficiently. We built an website in http://neuralkg.zjukg.cn to organize an open and shared KG representation learning community. The source code is all publicly released at https://github.com/zjukg/NeuralKG.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

PKGM: A Pre-trained Knowledge Graph Model for E-commerce Application

In recent years, knowledge graphs have been widely applied as a uniform way to organize data and have enhanced many tasks requiring knowledge. In online shopping platform Taobao, we built a billion-scale e-commerce product knowledge graph. It organizes data uniformly and provides item knowledge services for various tasks such as item recommendation. Usually, such knowledge services are provided through triple data, while this implementation includes (1) tedious data selection works on product knowledge graph and (2) task model designing works to infuse those triples knowledge. More importantly, product knowledge graph is far from complete, resulting error propagation to knowledge enhanced tasks. To avoid these problems, we propose a Pre-trained Knowledge Graph Model (PKGM) for the billion-scale product knowledge graph. On the one hand, it could provide item knowledge services in a uniform way with service vectors for embedding-based and item-knowledge-related task models without accessing triple data. On the other hand, it's service is provided based on implicitly completed product knowledge graph, overcoming the common the incomplete issue. We also propose two general ways to integrate the service vectors from PKGM into downstream task models. We test PKGM in five knowledge-related tasks, item classification, item resolution, item recommendation, scene detection and sequential recommendation. Experimental results show that PKGM introduces significant performance gains on these tasks, illustrating the useful of service vectors from PKGM.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Prompt-Guided Injection of Conformation to Pre-trained Protein Model

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.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Relational Message Passing for Fully Inductive Knowledge Graph Completion

In knowledge graph completion (KGC), predicting triples involving emerging entities and/or relations, which are unseen when the KG embeddings are learned, has become a critical challenge. Subgraph reasoning with message passing is a promising and popular solution. Some recent methods have achieved good performance, but they (i) usually can only predict triples involving unseen entities alone, failing to address more realistic fully inductive situations with both unseen entities and unseen relations, and (ii) often conduct message passing over the entities with the relation patterns not fully utilized. In this study, we propose a new method named RMPI which uses a novel Relational Message Passing network for fully Inductive KGC. It passes messages directly between relations to make full use of the relation patterns for subgraph reasoning with new techniques on graph transformation, graph pruning, relation-aware neighborhood attention, addressing empty subgraphs, etc., and can utilize the relation semantics defined in the ontological schema of KG. Extensive evaluation on multiple benchmarks has shown the effectiveness of techniques involved in RMPI and its better performance compared with the existing methods that support fully inductive KGC. RMPI is also comparable to the state-of-the-art partially inductive KGC methods with very promising results achieved. Our codes and data are available at https://github.com/zjukg/RMPI.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Ruleformer: Context-aware Differentiable Rule Mining over Knowledge Graph

Rule mining is an effective approach for reasoning over knowledge graph (KG). Existing works mainly concentrate on mining rules. However, there might be several rules that could be applied for reasoning for one relation, and how to select appropriate rules for completion of different triples has not been discussed. In this paper, we propose to take the context information into consideration, which helps select suitable rules for the inference tasks. Based on this idea, we propose a transformer-based rule mining approach, Ruleformer. It consists of two blocks: 1) an encoder extracting the context information from subgraph of head entities with modified attention mechanism, and 2) a decoder which aggregates the subgraph information from the encoder output and generates the probability of relations for each step of reasoning. The basic idea behind Ruleformer is regarding rule mining process as a sequence to sequence task. To make the subgraph a sequence input to the encoder and retain the graph structure, we devise a relational attention mechanism in Transformer. The experiment results show the necessity of considering these information in rule mining task and the effectiveness of our model.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

OntoZSL: Ontology-enhanced Zero-shot Learning

Zero-shot Learning (ZSL), which aims to predict for those classes that have never appeared in the training data, has arisen hot research interests. The key of implementing ZSL is to leverage the prior knowledge of classes which builds the semantic relationship between classes and enables the transfer of the learned models (e.g., features) from training classes (i.e., seen classes) to unseen classes. However, the priors adopted by the existing methods are relatively limited with incomplete semantics. In this paper, we explore richer and more competitive prior knowledge to model the inter-class relationship for ZSL via ontology-based knowledge representation and semantic embedding. Meanwhile, to address the data imbalance between seen classes and unseen classes, we developed a generative ZSL framework with Generative Adversarial Networks (GANs). Our main findings include: (i) an ontology-enhanced ZSL framework that can be applied to different domains, such as image classification (IMGC) and knowledge graph completion (KGC); (ii) a comprehensive evaluation with multiple zero-shot datasets from different domains, where our method often achieves better performance than the state-of-the-art models. In particular, on four representative ZSL baselines of IMGC, the ontology-based class semantics outperform the previous priors e.g., the word embeddings of classes by an average of 12.4 accuracy points in the standard ZSL across two example datasets (see Figure 4).

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Generative Adversarial Zero-shot Learning via Knowledge Graphs

Zero-shot learning (ZSL) is to handle the prediction of those unseen classes that have no labeled training data. Recently, generative methods like Generative Adversarial Networks (GANs) are being widely investigated for ZSL due to their high accuracy, generalization capability and so on. However, the side information of classes used now is limited to text descriptions and attribute annotations, which are in short of semantics of the classes. In this paper, we introduce a new generative ZSL method named KG-GAN by incorporating rich semantics in a knowledge graph (KG) into GANs. Specifically, we build upon Graph Neural Networks and encode KG from two views: class view and attribute view considering the different semantics of KG. With well-learned semantic embeddings for each node (representing a visual category), we leverage GANs to synthesize compelling visual features for unseen classes. According to our evaluation with multiple image classification datasets, KG-GAN can achieve better performance than the state-of-the-art baselines.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Neural Entity Summarization with Joint Encoding and Weak Supervision

In a large-scale knowledge graph (KG), an entity is often described by a large number of triple-structured facts. Many applications require abridged versions of entity descriptions, called entity summaries. Existing solutions to entity summarization are mainly unsupervised. In this paper, we present a supervised approach NEST that is based on our novel neural model to jointly encode graph structure and text in KGs and generate high-quality diversified summaries. Since it is costly to obtain manually labeled summaries for training, our supervision is weak as we train with programmatically labeled data which may contain noise but is free of manual work. Evaluation results show that our approach significantly outperforms the state of the art on two public benchmarks.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Ontology-guided Semantic Composition for Zero-Shot Learning

Zero-shot learning (ZSL) is a popular research problem that aims at predicting for those classes that have never appeared in the training stage by utilizing the inter-class relationship with some side information. In this study, we propose to model the compositional and expressive semantics of class labels by an OWL (Web Ontology Language) ontology, and further develop a new ZSL framework with ontology embedding. The effectiveness has been verified by some primary experiments on animal image classification and visual question answering.

0 citations0 reviewsNo code linkedOpen access