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Motivation: Biological data and knowledge bases increasingly rely on Semantic Web technologies and the use of knowledge graphs for data integration, retrieval and federated queries. In the past years, feature learning methods that are…

Quantitative Methods · Quantitative Biology 2017-05-01 Mona Alshahrani , Mohammed Asif Khan , Omar Maddouri , Akira R Kinjo , Núria Queralt-Rosinach , Robert Hoehndorf

The ability to learn disentangled representations that split underlying sources of variation in high dimensional, unstructured data is important for data efficient and robust use of neural networks. While various approaches aiming towards…

Machine Learning · Statistics 2019-05-15 Raphael Suter , Đorđe Miladinović , Bernhard Schölkopf , Stefan Bauer

Connectivity structure shapes neural computation, but inferring this structure from population recordings is degenerate: multiple connectivity structures can generate identical dynamics. Recent work uses low-rank recurrent neural networks…

Neurons and Cognition · Quantitative Biology 2026-03-30 Timothy Doyeon Kim , Ulises Pereira-Obilinovic , Yiliu Wang , Eric Shea-Brown , Uygar Sümbül

A fundamental computation for statistical inference and accurate decision-making is to compute the marginal probabilities or most probable states of task-relevant variables. Probabilistic graphical models can efficiently represent the…

Machine Learning · Computer Science 2019-06-28 KiJung Yoon , Renjie Liao , Yuwen Xiong , Lisa Zhang , Ethan Fetaya , Raquel Urtasun , Richard Zemel , Xaq Pitkow

Machine learning, deep learning, and NLP methods on knowledge graphs are present in different fields and have important roles in various domains from self-driving cars to friend recommendations on social media platforms. However, to apply…

Machine Learning · Computer Science 2024-09-25 Elika Bozorgi , Sakher Khalil Alqaiidi , Afsaneh Shams , Hamid Reza Arabnia , Krzysztof Kochut

Complex textual information extraction tasks are often posed as sequence labeling or \emph{shallow parsing}, where fields are extracted using local labels made consistent through probabilistic inference in a graphical model with constrained…

Machine Learning · Computer Science 2018-10-01 Dung Thai , Sree Harsha Ramesh , Shikhar Murty , Luke Vilnis , Andrew McCallum

Graph Neural Networks (GNNs) have been extensively used in various real-world applications. However, the predictive uncertainty of GNNs stemming from diverse sources such as inherent randomness in data and model training errors can lead to…

Machine Learning · Computer Science 2025-03-11 Fangxin Wang , Yuqing Liu , Kay Liu , Yibo Wang , Sourav Medya , Philip S. Yu

We address the challenge of building domain-specific knowledge models for industrial use cases, where labelled data and taxonomic information is initially scarce. Our focus is on inductive link prediction models as a basis for practical…

Machine Learning · Computer Science 2023-01-03 Felix Hamann , Adrian Ulges , Maurice Falk

Large Language Models (LLMs) demonstrate an impressive capacity to recall a vast range of factual knowledge. However, understanding their underlying reasoning and internal mechanisms in exploiting this knowledge remains a key research area.…

Computation and Language · Computer Science 2024-08-07 Marco Bronzini , Carlo Nicolini , Bruno Lepri , Jacopo Staiano , Andrea Passerini

Although deep neural networks have shown well-performance in various tasks, the poor interpretability of the models is always criticized. In the paper, we propose a new interpretable neural network method, by embedding neurons into the…

Machine Learning · Computer Science 2022-11-16 Wei Han , Yangqiming Wang , Christian Böhm , Junming Shao

The development and evaluation of graph neural networks (GNNs) generally follow the independent and identically distributed (i.i.d.) assumption. Yet this assumption is often untenable in practice due to the uncontrollable data generation…

Machine Learning · Computer Science 2025-03-06 Yiming Xu , Bin Shi , Zhen Peng , Huixiang Liu , Bo Dong , Chen Chen

Knowledge graph embedding methods learn embeddings of entities and relations in a low dimensional space which can be used for various downstream machine learning tasks such as link prediction and entity matching. Various graph convolutional…

Machine Learning · Computer Science 2021-02-16 Nasrullah Sheikh , Xiao Qin , Berthold Reinwald , Christoph Miksovic , Thomas Gschwind , Paolo Scotton

Social and information networks are gaining huge popularity recently due to their various applications. Knowledge representation through graphs in the form of nodes and edges should preserve as many characteristics of the original data as…

Machine Learning · Computer Science 2021-02-08 Rucha Bhalchandra Joshi , Subhankar Mishra

Although static networks have been extensively studied in machine learning, data mining, and AI communities for many decades, the study of dynamic networks has recently taken center stage due to the prominence of social media and its…

Social and Information Networks · Computer Science 2020-12-21 Tony Gracious , Shubham Gupta , Arun Kanthali , Rui M. Castro , Ambedkar Dukkipati

Temporal Knowledge Graphs have emerged as a powerful way of not only modeling static relationships between entities but also the dynamics of how relations evolve over time. As these informational structures can be used to store information…

Machine Learning · Computer Science 2025-10-29 Edward Markai , Sina Molavipour

Knowledge graphs have emerged as an important model for studying complex multi-relational data. This has given rise to the construction of numerous large scale but incomplete knowledge graphs encoding information extracted from various…

Machine Learning · Computer Science 2018-07-24 Rakshit Trivedi , Bunyamin Sisman , Jun Ma , Christos Faloutsos , Hongyuan Zha , Xin Luna Dong

In recent years, the use of edge information provided by knowledge graphs together with the advantages of higher-order connectivity in graph neural networks for recommendation systems has become an important research direction. However,…

Information Retrieval · Computer Science 2026-05-12 Zhifei Hu , Feng Xia

Traditionally, graph neural networks have been trained using a single observed graph. However, the observed graph represents only one possible realization. In many applications, the graph may encounter uncertainties, such as having…

Machine Learning · Computer Science 2024-10-10 See Hian Lee , Feng Ji , Kelin Xia , Wee Peng Tay

Knowledge graphs have garnered significant research attention and are widely used to enhance downstream applications. However, most current studies mainly focus on static knowledge graphs, whose facts do not change with time, and disregard…

Computation and Language · Computer Science 2024-03-11 Li Cai , Xin Mao , Yuhao Zhou , Zhaoguang Long , Changxu Wu , Man Lan

In this study, we design a low-complexity and generalized AI model that can capture common knowledge to improve data reconstruction of the channel decoder for semantic communication. Specifically, we propose a generative adversarial network…

Machine Learning · Computer Science 2025-07-25 Minh-Duong Nguyen , Quoc-Viet Pham , Nguyen H. Tran , Hoang-Khoi Do , Duy T. Ngo , Won-Joo Hwang
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