SARS-CoV-2 related
Collection
This collection contains some models and datasets about SARS-CoV-2, including deep mutation scanning (DMS) data of some important variants.
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11 items
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Updated
Base model: westlake-repl/SaProt_35M_AF2
Model Card for Model ID
This model is used to predict the spike receptor-binding domain (RBD) expression of SARSCoV-2 Omicron XBB.1.5 variants.
Task type
protein level regression
Dataset description
The dataset is from Deep mutational scans of XBB.1.5 and BQ.1.1 reveal ongoing epistatic drift during SARSCoV-2 evolution.
Label means the delta level of RBD expression (log-mean fluorescence intensity) compre to wildtype, ranging from minus infinity to positive infinity. Zero means wildtype expression, lager means higher expression and smaller means lower expression.
Model input type
Amino acid sequence
Performance
0.70 Spearman's ρ
LoRA config
lora_dropout: 0.0
lora_alpha: 16
target_modules: ["query", "key", "value", "intermediate.dense", "output.dense"]
modules_to_save: ["classifier"]
Training config
class: AdamW
betas: (0.9, 0.98)
weight_decay: 0.01
learning rate: 5e-4
epoch: 100
batch size: 200
precision: 16-mixed