Ibex BCR Deep Encoders

Ibex

This is a series of 72 Keras3-based amino acid encoders for Heavy and Light chains of the B cell Receptor (BCR). These are the individual trained models for larger Ibex package that will be available after review from BioConductor. The package itself has the functionality to employ these models and interact with single-cell data, but due to the size of the trained models, the keras objects are stored here.Sequence inputs 

Human Heavy: 10000000

Human Light: 5000000

Human Heavy-Expanded: 5000000

Human Light-Expanded: 2500000

Mouse Heavy: 5000000

Mouse Heavy-Expanded: 5000000

Model details

Architecture: 512-256-128-256-512

Parameters: 

Batch Size = 128

Latent Dimensions = 128

Epochs = 128

Loss = Mean Squared Error (CNN) & KL Divergence (VAE)

Activation = ReLU

Learning rate = 1e-6

Optimizers: Adam

Early stopping was set to patients of 10 for minimal validation loss and restoration of best weights

CNN autoencoders have batch normalization layers between the dense layers. 

More information available at the GitHub Repo