{"entity":{"id":"masked-modelling","kind":"term","name":"Masked autoencoders and masked gene modelling","aka":["masked autoencoder","masked autoencoders","masked gene modelling","masked gene modeling","masked reconstruction","cross-modal masked reconstruction","autoencoder"],"tldr":"A masked autoencoder hides a random part of the input (image patches, or half the genes in a profile) and learns to reconstruct it from the rest.","summary":"An autoencoder learns an encoding that compresses the input and a decoding that recreates it (Wikipedia); the masked variant reconstructs only the hidden portion, which forces the encoder to learn the structure that relates parts of the input. For expression data the hidden parts are genes, so the model learns co-expression structure; for multimodal data one modality's token can be reconstructed from the others. It is the pretraining objective behind many pathology and transcriptome foundation models.","asOf":"2026-09-24","wikipedia":"https://en.wikipedia.org/wiki/Autoencoder","links":[{"label":"Wikipedia","url":"https://en.wikipedia.org/wiki/Autoencoder"}],"tags":["cansim-terms"],"related":["cancer-ai-vocabulary"],"cancers":[],"sections":[],"technologies":[],"targets":[],"drugs":[],"companies":[],"institutions":[],"pathways":[],"terms":["self-supervised-pretraining","gene-co-expression","tokenisation"],"trials":[],"people":[],"bottlenecks":[],"keyPapers":[],"journals":[],"dependsOn":[],"notes":["Listed in the CanSim terms map 1.0.0 (docs/onco/terms.json, generated 2026-09-24), CC BY 4.0, attribution: CanSim project, an open, public-data-first cancer foundation-model programme; CanSim page path /terms/masked-autoencoder."],"provenance":{"editedBy":"OnCo CanSim terms wave (Wikipedia summaries, standards and project pages, GDC and FDA pages, Europe PMC)","editedOn":"2026-09-24","note":"CanSim terms map 1.0.0 (docs/onco/terms.json, generated 2026-09-24), CC BY 4.0, attribution: CanSim project, an open, public-data-first cancer foundation-model programme"},"category":"Methods and models"},"route":"/terms/masked-modelling/","neighbours":{"term":[{"id":"cancer-ai-vocabulary","kind":"term","name":"Cancer AI vocabulary (CanSim terms map)","route":"/terms/cancer-ai-vocabulary/"},{"id":"gene-co-expression","kind":"term","name":"Gene co-expression structure","route":"/terms/gene-co-expression/"},{"id":"cross-entropy-mse","kind":"term","name":"Loss functions: cross-entropy and mean squared error","route":"/terms/cross-entropy-mse/"},{"id":"self-supervised-pretraining","kind":"term","name":"Self-supervised pretraining (SSL)","route":"/terms/self-supervised-pretraining/"},{"id":"tokenisation","kind":"term","name":"Tokenisation (genes, tiles and sequence as tokens)","route":"/terms/tokenisation/"}]}}