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Metagenomic studies have increasingly utilized sequencing technologies in order to analyze DNA fragments found in environmental samples.One important step in this analysis is the taxonomic classification of the DNA fragments. Conventional…

Genomics · Quantitative Biology 2020-02-11 Andreas Georgiou , Vincent Fortuin , Harun Mustafa , Gunnar Rätsch

Biomedical association studies are increasingly done using clinical concepts, and in particular diagnostic codes from clinical data repositories as phenotypes. Clinical concepts can be represented in a meaningful, vector space using word…

Quantitative Methods · Quantitative Biology 2018-11-06 Brett K. Beaulieu-Jones , Isaac S. Kohane , Andrew L. Beam

Multimodal classification research has been gaining popularity in many domains that collect more data from multiple sources including satellite imagery, biometrics, and medicine. However, the lack of consistent terminology and architectural…

Machine Learning · Computer Science 2021-09-21 William C. Sleeman , Rishabh Kapoor , Preetam Ghosh

Many high-dimensional and large-volume data sets of practical relevance have hierarchical structures induced by trees, graphs or time series. Such data sets are hard to process in Euclidean spaces and one often seeks low-dimensional…

Machine Learning · Computer Science 2021-09-16 Eli Chien , Chao Pan , Puoya Tabaghi , Olgica Milenkovic

Hyperbolic spaces, which have the capacity to embed tree structures without distortion owing to their exponential volume growth, have recently been applied to machine learning to better capture the hierarchical nature of data. In this…

Machine Learning · Computer Science 2021-03-18 Ryohei Shimizu , Yusuke Mukuta , Tatsuya Harada

Continual learning has traditionally focused on classifying either instances or classes, but real-world applications, such as robotics and self-driving cars, require models to handle both simultaneously. To mirror real-life scenarios, we…

Computer Vision and Pattern Recognition · Computer Science 2025-06-13 Melika Ayoughi , Mina Ghadimi Atigh , Mohammad Mahdi Derakhshani , Cees G. M. Snoek , Pascal Mettes , Paul Groth

Recent neuroimaging studies that focus on predicting brain disorders via modern machine learning approaches commonly include a single modality and rely on supervised over-parameterized models.However, a single modality provides only a…

This paper proposes a learning model, based on rank-fusion graphs, for general applicability in multimodal prediction tasks, such as multimodal regression and image classification. Rank-fusion graphs encode information from multiple…

Computer Vision and Pattern Recognition · Computer Science 2020-07-06 Icaro Cavalcante Dourado , Salvatore Tabbone , Ricardo da Silva Torres

Hyperbolic embeddings have demonstrated their effectiveness in capturing measures of uncertainty and hierarchical relationships across various deep-learning tasks, including image segmentation and active learning. However, their application…

Machine Learning · Computer Science 2024-08-12 Paolo Mandica , Luca Franco , Konstantinos Kallidromitis , Suzanne Petryk , Fabio Galasso

Large-scale multi-relational embedding refers to the task of learning the latent representations for entities and relations in large knowledge graphs. An effective and scalable solution for this problem is crucial for the true success of…

Machine Learning · Computer Science 2017-07-07 Hanxiao Liu , Yuexin Wu , Yiming Yang

Different cell types aggregate and sort into hierarchical architectures during the formation of animal tissues. The resulting spatial organization depends (in part) on the strength of adhesion of one cell type to itself relative to other…

Quantitative Methods · Quantitative Biology 2023-08-02 Dhananjay Bhaskar , William Y. Zhang , Alexandria Volkening , Björn Sandstede , Ian Y. Wong

Hyperbolic geometry is an effective geometry for embedding hierarchical data structures. Hyperbolic learning has therefore become increasingly prominent in machine learning applications where data is hierarchically organized or governed by…

Artificial Intelligence · Computer Science 2025-11-27 Melika Ayoughi , Pascal Mettes , Paul Groth

Fine-grained emotion classification (FEC) is a challenging task. Specifically, FEC needs to handle subtle nuance between labels, which can be complex and confusing. Most existing models only address text classification problem in the…

Computation and Language · Computer Science 2023-06-27 Chih-Yao Chen , Tun-Min Hung , Yi-Li Hsu , Lun-Wei Ku

3D-aware visual pretraining has proven effective in improving the performance of downstream robotic manipulation tasks. However, existing methods are constrained to Euclidean embedding spaces, whose flat geometry limits their ability to…

Robotics · Computer Science 2026-03-13 Jin Yang , Ping Wei , Yixin Chen , Nanning Zheng

Nickel and Kiela (2017) present a new method for embedding tree nodes in the Poincare ball, and suggest that these hyperbolic embeddings are far more effective than Euclidean embeddings at embedding nodes in large, hierarchically structured…

Computation and Language · Computer Science 2021-09-17 Sameer Bansal , Adrian Benton

Recent advances in single cell sequencing and multi-omics techniques have significantly improved our understanding of biological phenomena and our capacity to model them. Despite combined capture of data modalities showing similar progress,…

Molecular Networks · Quantitative Biology 2025-03-13 Marcello Barylli , Joyaditya Saha , Tineke E. Buffart , Jan Koster , Kristiaan J. Lenos , Louis Vermeulen , Vivek M. Sheraton

Many real-world graphs involve different types of nodes and relations between nodes, being heterogeneous by nature. The representation learning of heterogeneous graphs (HGs) embeds the rich structure and semantics of such graphs into a…

Machine Learning · Computer Science 2021-09-16 Costas Mavromatis , George Karypis

Concept Bottleneck Models (CBMs) have become a popular approach to enable interpretability in neural networks by constraining classifier inputs to a set of human-understandable concepts. While effective, current models embed concepts in…

Machine Learning · Computer Science 2026-05-13 Daniel Uyterlinde , Swasti Shreya Mishra , Pascal Mettes

Recent research in representation learning has shown that hierarchical data lends itself to low-dimensional and highly informative representations in hyperbolic space. However, even if hyperbolic embeddings have gathered attention in image…

Computer Vision and Pattern Recognition · Computer Science 2023-09-20 Gabriel Moreira , Manuel Marques , João Paulo Costeira , Alexander Hauptmann

Most previous heterogeneous graph embedding models represent elements in a heterogeneous graph as vector representations in a low-dimensional Euclidean space. However, because heterogeneous graphs inherently possess complex structures, such…

Machine Learning · Computer Science 2024-04-16 Jongmin Park , Seunghoon Han , Soohwan Jeong , Sungsu Lim