{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/basisvae-translation-invariant-feature-level","title":"BasisVAE: Translation-invariant feature-level clustering with Variational Autoencoders","arxiv_id":"2003.03462","date":"2020-03-06","proceeding":null,"authors":["Kaspar Märtens","Christopher Yau"],"abstract":"Variational Autoencoders (VAEs) provide a flexible and scalable framework for non-linear dimensionality reduction. However, in application domains such as genomics where data sets are typically tabular and high-dimensional, a black-box approach to dimensionality reduction does not provide sufficient insights. Common data analysis workflows additionally use clustering techniques to identify groups of similar features. This usually leads to a two-stage process, however, it would be desirable to construct a joint modelling framework for simultaneous dimensionality reduction and clustering of features. In this paper, we propose to achieve this through the BasisVAE: a combination of the VAE and a probabilistic clustering prior, which lets us learn a one-hot basis function representation as part of the decoder network. Furthermore, for scenarios where not all features are aligned, we develop an extension to handle translation-invariant basis functions. We show how a collapsed variational inference scheme leads to scalable and efficient inference for BasisVAE, demonstrated on various toy examples as well as on single-cell gene expression data.","url_abs":"https://arxiv.org/abs/2003.03462v1","url_pdf":"https://arxiv.org/pdf/2003.03462v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"basisvae-translation-invariant-feature-level","repo_url":"https://github.com/kasparmartens/BasisVAE","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"clustering","task_name":"Clustering"},{"task_slug":"decoder","task_name":"Decoder"},{"task_slug":"dimensionality-reduction","task_name":"Dimensionality Reduction"},{"task_slug":"translation","task_name":"Translation"},{"task_slug":"variational-inference","task_name":"Variational Inference"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}