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The complete characterization of enzymatic activities between molecules remains incomplete, hindering biological engineering and limiting biological discovery. We develop in this work a technique, Enzymatic Link Prediction (ELP), for…

Molecular Networks · Quantitative Biology 2020-02-11 Julie Jiang , Li-Ping Liu , Soha Hassoun

Entity linking - connecting entity mentions in a natural language utterance to knowledge graph (KG) entities is a crucial step for question answering over KGs. It is often based on measuring the string similarity between the entity label…

Computation and Language · Computer Science 2020-02-27 Rostislav Nedelchev , Debanjan Chaudhuri , Jens Lehmann , Asja Fischer

Capturing associations for knowledge graphs (KGs) through entity alignment, entity type inference and other related tasks benefits NLP applications with comprehensive knowledge representations. Recent related methods built on Euclidean…

Computation and Language · Computer Science 2020-10-06 Zequn Sun , Muhao Chen , Wei Hu , Chengming Wang , Jian Dai , Wei Zhang

Large Language Models (LLMs) have demonstrated remarkable capabilities in natural language understanding and generation. However, they often struggle with complex reasoning tasks and are prone to hallucination. Recent research has shown…

Computation and Language · Computer Science 2024-12-17 Xue Wu , Kostas Tsioutsiouliklis

Knowledge Graphs (KGs) have long served as a fundamental infrastructure for structured knowledge representation and reasoning. With the advent of Large Language Models (LLMs), the construction of KGs has entered a new paradigm-shifting from…

Artificial Intelligence · Computer Science 2025-10-24 Haonan Bian

Although Large Language Models achieve strong success in many tasks, they still suffer from hallucinations and knowledge deficiencies in real-world applications. Many knowledge graph-based retrieval-augmented generation (KG-RAG) methods…

Artificial Intelligence · Computer Science 2025-05-28 Hairu Wang , Yuan Feng , Xike Xie , S Kevin Zhou

A common solution to the semantic heterogeneity problem is to perform knowledge graph (KG) extension exploiting the information encoded in one or more candidate KGs, where the alignment between the reference KG and candidate KGs is…

Artificial Intelligence · Computer Science 2024-07-09 Daqian Shi , Xiaoyue Li , Fausto Giunchiglia

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…

Computation and Language · Computer Science 2026-04-21 Yujie Luo , Zhuoyun Yu , Xuehai Wang , Yuqi Zhu , Ningyu Zhang , Lanning Wei , Lun Du , Da Zheng , Huajun Chen

API recommendation methods have evolved from literal and semantic keyword matching to query expansion and query clarification. The latest query clarification method is knowledge graph (KG)-based, but limitations include out-of-vocabulary…

Software Engineering · Computer Science 2023-09-29 Qing Huang , Zhenyu Wan , Zhenchang Xing , Changjing Wang , Jieshan Chen , Xiwei Xu , Qinghua Lu

Fact-checking is a crucial task as it ensures the prevention of misinformation. However, manual fact-checking cannot keep up with the rate at which false information is generated and disseminated online. Automated fact-checking by machines…

Artificial Intelligence · Computer Science 2023-10-12 Gustav Nikopensius , Mohit Mayank , Orchid Chetia Phukan , Rajesh Sharma

Link prediction with knowledge graphs has been thoroughly studied in graph machine learning, leading to a rich landscape of graph neural network architectures with successful applications. Nonetheless, it remains challenging to transfer the…

Machine Learning · Computer Science 2025-06-10 Xingyue Huang , Miguel Romero Orth , Pablo Barceló , Michael M. Bronstein , İsmail İlkan Ceylan

Temporal Knowledge Graph (TKG) reasoning that forecasts future events based on historical snapshots distributed over timestamps is denoted as extrapolation and has gained significant attention. Owing to its extreme versatility and variation…

Artificial Intelligence · Computer Science 2024-07-01 Jinchuan Zhang , Bei Hui , Chong Mu , Ling Tian

Recommender systems are pivotal in enhancing user experiences across various web applications by analyzing the complicated relationships between users and items. Knowledge graphs(KGs) have been widely used to enhance the performance of…

Information Retrieval · Computer Science 2024-07-02 Guangsi Shi , Xiaofeng Deng , Linhao Luo , Lijuan Xia , Lei Bao , Bei Ye , Fei Du , Shirui Pan , Yuxiao Li

Rule mining on knowledge graphs allows for explainable link prediction. Contrarily, embedding-based methods for link prediction are well known for their generalization capabilities, but their predictions are not interpretable. Several…

Artificial Intelligence · Computer Science 2024-06-17 N'Dah Jean Kouagou , Arif Yilmaz , Michel Dumontier , Axel-Cyrille Ngonga Ngomo

For many years, link prediction on knowledge graphs (KGs) has been a purely transductive task, not allowing for reasoning on unseen entities. Recently, increasing efforts are put into exploring semi- and fully inductive scenarios, enabling…

Machine Learning · Computer Science 2021-07-13 Mehdi Ali , Max Berrendorf , Mikhail Galkin , Veronika Thost , Tengfei Ma , Volker Tresp , Jens Lehmann

Recent studies on knowledge graphs (KGs) show that path-based methods empowered by pre-trained language models perform well in the provision of inductive and explainable relation predictions. In this paper, we introduce the concepts of…

Computation and Language · Computer Science 2023-05-02 Zhixiang Su , Di Wang , Chunyan Miao , Lizhen Cui

Current knowledge graph (KG) construction methods are confirmatory, focusing on recovering known relationships rather than identifying novel or context-dependent nodes. This paper proposes a phenotype-driven and evidence-governed framework…

Artificial Intelligence · Computer Science 2026-04-21 Adela Bâra , Simona-Vasilica Oprea

Knowledge graphs (KGs) are valuable for representing structured, interconnected information across domains, enabling tasks like semantic search, recommendation systems and inference. A pertinent challenge with KGs, however, is that many…

Computation and Language · Computer Science 2024-12-17 Haji Gul , Abdul Ghani Naim , Ajaz A. Bhat

Explaining neural model predictions to users requires creativity. Especially in enterprise applications, where there are costs associated with users' time, and their trust in the model predictions is critical for adoption. For link…

We propose KGT5-context, a simple sequence-to-sequence model for link prediction (LP) in knowledge graphs (KG). Our work expands on KGT5, a recent LP model that exploits textual features of the KG, has small model size, and is scalable. To…

Machine Learning · Computer Science 2023-06-01 Adrian Kochsiek , Apoorv Saxena , Inderjeet Nair , Rainer Gemulla
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