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Biomedical Nomic Embedding Surgery
This project modifies the tokenizer and embedding layer of:
nomic-ai/nomic-embed-text-v1-unsupervised
Changes
- Added 15 biomedical domain tokens:
- glioblastoma
- immunohistochemistry
- pharmacogenomics
- angiogenesis
- neurodegeneration
- bioavailability
- oncogenesis
- metastasis
- cytokinemia
- microvasculature
- electrophysiology
- histopathology
- chemoresistance
- osteogenesis
- hepatocarcinogenesis
Method
New embeddings were initialized by averaging existing sub-token embeddings.
Example:
glioblastoma: [g, ##lio, ##bla, ##sto, ##ma]
The resulting embedding was inserted into the expanded embedding matrix.
Verification
Original embeddings unchanged: True
New vocabulary size: 30537 tokenizer tokens
Embedding matrix: 30592 x 768
End-to-end inference verified successfully.
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