{"entity":{"id":"embedding","kind":"term","name":"Embedding (learned representation)","aka":["embeddings","learned embedding","embedding vector","patient embedding","tile embedding","gene embedding","frozen embeddings","mean pooling of embeddings"],"tldr":"An embedding is a list of numbers a model produces to stand for an input (a tile, a gene, a patient), placed so that similar inputs land near each other.","summary":"In machine learning an embedding maps complex high-dimensional data into a lower-dimensional vector space (Wikipedia). Foundation models are mostly used as embedding machines: a frozen encoder turns each tile or cell into a vector, mean or attention pooling aggregates them into a slide or sample vector (Wikipedia on pooling layers), and a small model on top does the prediction. Whether the embedding groups samples by tissue or subtype without any labels (cluster purity) is the first check of its quality.","asOf":"2026-09-24","wikipedia":"https://en.wikipedia.org/wiki/Embedding_(machine_learning)","links":[{"label":"Wikipedia: pooling layer","url":"https://en.wikipedia.org/wiki/Pooling_layer"},{"label":"Wikipedia","url":"https://en.wikipedia.org/wiki/Embedding_(machine_learning)"}],"tags":["cansim-terms"],"related":["cancer-ai-vocabulary"],"cancers":[],"sections":[],"technologies":[],"targets":[],"drugs":[],"companies":[],"institutions":[],"pathways":[],"terms":["transformer-architecture","fine-tuning-vs-frozen","linear-probe","pca"],"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/embedding."],"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/embedding/","neighbours":{"term":[{"id":"cancer-ai-vocabulary","kind":"term","name":"Cancer AI vocabulary (CanSim terms map)","route":"/terms/cancer-ai-vocabulary/"},{"id":"contrastive-learning","kind":"term","name":"Contrastive learning (InfoNCE)","route":"/terms/contrastive-learning/"},{"id":"fine-tuning-vs-frozen","kind":"term","name":"Fine-tuning versus frozen features, and LoRA","route":"/terms/fine-tuning-vs-frozen/"},{"id":"linear-probe","kind":"term","name":"Linear probe","route":"/terms/linear-probe/"},{"id":"pca","kind":"term","name":"Principal component analysis (PCA) as a feature compressor","route":"/terms/pca/"},{"id":"tokenisation","kind":"term","name":"Tokenisation (genes, tiles and sequence as tokens)","route":"/terms/tokenisation/"},{"id":"transformer-architecture","kind":"term","name":"Transformer and attention","route":"/terms/transformer-architecture/"},{"id":"zero-shot","kind":"term","name":"Zero-shot prediction","route":"/terms/zero-shot/"}]}}