Variational autoencoders (VAEs) compress high resolution CT volumes into compact latents while preserving clinically relevant structure. However, training CT-specific VAEs from scratch or heavily fine-tuning them incurs substantial computational and engineering cost, and often degrades under heterogeneous scanners, protocols, and diseases. This paper makes a progressive stride toward training-free medical VAEs by leveraging a critical observation: a single Foundation VAE, pretrained at scale on natural images and videos, can serve as a unified interface for CT Reconstruction, Augmentation, and Generation. With both encoder and decoder frozen, the Foundation VAE reconstructs CT volumes with preserved anatomy while suppressing acquisition noise; training segmentation models on these reconstructions improves surface accuracy by 3.9% NSD on average for pancreatic tumor and lung tumor. Within the same Foundation VAE latent space, a conditional latent diffusion model achieves 3.9% lower average FVD with 36.2% higher CT CLIP score, and improves multi-disease generation faithfulness across 18 types by 2.76% AUC. These results demonstrate Foundation VAEs as a practical interface for scalable CT representation reuse and faithful CT generation. Our code and demo are available at https:\/\/github.com\/qic999\/Foundation-VAE.<\/p>\n","protected":false},"excerpt":{"rendered":"
Variational autoencoders (VAEs) compress high resolution CT volumes into compact latents while preserving clinically relevant structure. However, training CT-specific VAEs from scratch or heavily fine-tuning them incurs substantial computational and engineering cost, and often degrades under heterogeneous scanners, protocols, and diseases. This paper makes a progressive stride toward training-free medical VAEs by leveraging a critical […]<\/p>\n","protected":false},"featured_media":0,"template":"","meta":{"msr-url-field":"","msr-podcast-episode":"","msrModifiedDate":"","msrModifiedDateEnabled":false,"ep_exclude_from_search":false,"_classifai_error":"","msr-author-ordering":null,"msr_publishername":"","msr_publisher_other":"","msr_booktitle":"","msr_chapter":"","msr_edition":"","msr_editors":"","msr_how_published":"","msr_isbn":"","msr_issue":"","msr_journal":"","msr_number":"","msr_organization":"","msr_pages_string":"","msr_page_range_start":"","msr_page_range_end":"","msr_series":"","msr_volume":"","msr_copyright":"","msr_conference_name":"ICML 2026","msr_doi":"","msr_arxiv_id":"","msr_s2_paper_id":"","msr_mag_id":"","msr_pubmed_id":"","msr_other_authors":"","msr_other_contributors":"","msr_speaker":"","msr_award":"","msr_affiliation":"","msr_institution":"","msr_host":"","msr_version":"","msr_duration":"","msr_original_fields_of_study":"","msr_release_tracker_id":"","msr_s2_match_type":"","msr_citation_count_updated":"","msr_published_date":"2026-05-29","msr_highlight_text":"","msr_notes":"","msr_longbiography":"","msr_publicationurl":"","msr_external_url":"","msr_secondary_video_url":"","msr_conference_url":"","msr_journal_url":"","msr_s2_pdf_url":"","msr_year":0,"msr_citation_count":0,"msr_influential_citations":0,"msr_reference_count":0,"msr_s2_match_confidence":0,"msr_microsoftintellectualproperty":false,"msr_s2_open_access":false,"msr_s2_author_ids":[],"msr_pub_ids":[{"provider":"s2","id":"eb38cda483d8576d382c714386e13aaca30ae29e"},{"provider":"arxiv","id":"2605.30893"}],"msr_hide_image_in_river":null,"footnotes":""},"msr-research-highlight":[],"research-area":[13562],"msr-publication-type":[193716],"msr-publisher":[],"msr-focus-area":[],"msr-locale":[268875],"msr-post-option":[],"msr-field-of-study":[246691,263185],"msr-conference":[260284],"msr-journal":[],"msr-impact-theme":[],"msr-pillar":[],"class_list":["post-1175019","msr-research-item","type-msr-research-item","status-publish","hentry","msr-research-area-computer-vision","msr-locale-en_us","msr-field-of-study-computer-science","msr-field-of-study-computer-vision-and-pattern-recognition"],"msr_publishername":"","msr_edition":"","msr_affiliation":"","msr_published_date":"2026-05-29","msr_host":"","msr_duration":"","msr_version":"","msr_speaker":"","msr_other_contributors":"","msr_booktitle":"","msr_pages_string":"","msr_chapter":"","msr_isbn":"","msr_journal":"","msr_volume":"","msr_number":"","msr_editors":"","msr_series":"","msr_issue":"","msr_organization":"","msr_how_published":"","msr_notes":"","msr_highlight_text":"","msr_release_tracker_id":"","msr_original_fields_of_study":"","msr_download_urls":"","msr_external_url":"","msr_secondary_video_url":"","msr_longbiography":"","msr_microsoftintellectualproperty":0,"msr_main_download":"","msr_publicationurl":"","msr_doi":"","msr_publication_uploader":[{"type":"url","viewUrl":"false","id":"false","title":"https:\/\/arxiv.org\/abs\/2605.30893","label_id":"243109","label":0}],"msr_related_uploader":"","msr_citation_count":0,"msr_citation_count_updated":"","msr_s2_paper_id":"","msr_influential_citations":0,"msr_reference_count":0,"msr_arxiv_id":"","msr_s2_author_ids":[],"msr_s2_open_access":false,"msr_s2_pdf_url":null,"msr_attachments":[],"msr-author-ordering":[{"type":"user_nicename","value":"Qi Chen","user_id":36990,"rest_url":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/microsoft-research\/v1\/researchers?person=Qi Chen"},{"type":"name","value":"Shuhan Ding","user_id":0,"rest_url":false},{"type":"user_nicename","value":"Yu Gu","user_id":44020,"rest_url":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/microsoft-research\/v1\/researchers?person=Yu Gu"},{"type":"user_nicename","value":"Ning Liu","user_id":33110,"rest_url":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/microsoft-research\/v1\/researchers?person=Ning Liu"},{"type":"user_nicename","value":"Jiang Bian","user_id":38481,"rest_url":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/microsoft-research\/v1\/researchers?person=Jiang Bian"},{"type":"name","value":"Alan L. 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