2. pahelix.model_zoo¶
Table of Contents
2.1. pretrain_gnns_model¶
This is an implementation of pretrain gnns: https://arxiv.org/abs/1905.12265
- class pahelix.model_zoo.pretrain_gnns_model.AttrmaskModel(*args: Any, **kwargs: Any)[source]¶
This is a pretraning model used by pretrain gnns for attribute mask training.
- Returns
the loss variance of the model.
- Return type
loss
2.2. protein_sequence_model¶
Sequence-based models for protein.
- class pahelix.model_zoo.protein_sequence_model.LstmEncoderModel(vocab_size, emb_dim=128, hidden_size=1024, n_layers=3, padding_idx=0, epsilon=1e-05, dropout_rate=0.1)[source]¶
- class pahelix.model_zoo.protein_sequence_model.ResnetEncoderModel(vocab_size, emb_dim=128, hidden_size=256, kernel_size=9, n_layers=35, padding_idx=0, dropout_rate=0.1, epsilon=1e-06)[source]¶
- class pahelix.model_zoo.protein_sequence_model.TransformerEncoderModel(vocab_size, emb_dim=512, hidden_size=512, n_layers=8, n_heads=8, padding_idx=0, dropout_rate=0.1)[source]¶
- class pahelix.model_zoo.protein_sequence_model.PretrainTaskModel(class_num, model_config, encoder_model)[source]¶
- class pahelix.model_zoo.protein_sequence_model.SeqClassificationTaskModel(class_num, model_config, encoder_model)[source]¶
- class pahelix.model_zoo.protein_sequence_model.ClassificationTaskModel(class_num, model_config, encoder_model)[source]¶
- class pahelix.model_zoo.protein_sequence_model.RegressionTaskModel(model_config, encoder_model)[source]¶
- class pahelix.model_zoo.protein_sequence_model.ProteinEncoderModel(model_config, name='')[source]¶
ProteinSequenceModel
2.3. seq_vae_model¶
- class pahelix.model_zoo.seq_vae_model.VAE(vocab, model_config)[source]¶
The sequence VAE model
- Parameters
vocab – the vocab object.
model_config – the json files of model parameters.
- sample(n_batch, max_len=100, z=None, temp=1.0)[source]¶
Generating n_batch samples in eval mode (z could be not on same device)
- Parameters
n_batch – number of sentences to generate
max_len – max len of samples
z – (n_batch, d_z) of floats, latent vector z or None
temp – temperature of softmax
- Returns
list of tensors of strings, samples sequence x
2.4. Helpful Link¶
Please refer to our GitHub repo to see the whole module.