def train_model(alignment_file, output_dir, ensemble=None):
if train_params["verbose"]:
print("Starting training")
if ensemble is not None:
model_params["r_seed"] += ensemble + 1
data_helper = helper.DataHelper(alignment_file=alignment_file,
calc_weights=True)
vae_model = model.VariationalAutoencoder(
data_helper,
batch_size=model_params["bs"],
encoder_architecture=[
model_params["encode_dim_zero"], model_params["encode_dim_one"]
],
decoder_architecture=[
model_params["decode_dim_zero"], model_params["decode_dim_one"]
],
n_latent=model_params["n_latent"],
logit_p=model_params["logit_p"],
sparsity=model_params["sparsity"],
encode_nonlinearity_type="relu",
decode_nonlinearity_type="relu",
final_decode_nonlinearity=model_params["final_decode_nonlin"],
final_pwm_scale=model_params["final_pwm_scale"],
conv_decoder_size=model_params["d_c_size"],
convolve_patterns=model_params["conv_pat"],
n_patterns=model_params["n_pat"],
random_seed=model_params["r_seed"],
)
job_string = helper.gen_job_string(
{"filename": os.path.basename(alignment_file).split(".")[0]},
model_params)
print(job_string)
date_prefix = os.path.basename(os.path.dirname(alignment_file))
path = os.path.join(output_dir, date_prefix)
if ensemble is not None:
path = path + "-ensemble" + str(ensemble)
if not os.path.exists(path):
os.mkdir(path)
train.train(data_helper,
vae_model,
num_updates=train_params["num_updates"],
save_progress=train_params["save_progress"],
save_parameters=train_params["save_parameters"],
verbose=train_params["verbose"],
job_string=job_string)
vae_model.save_parameters(file_prefix=job_string, path=path)
"n_pat" : 4,
"r_seed" : 12345,
"conv_pat" : True,
"d_c_size" : 40
}
train_params = {
"num_updates" : 300000,
"save_progress" : True,
"verbose" : True,
"save_parameters" : False,
}
if __name__ == "__main__":
data_helper = helper.DataHelper(alignment_file=data_params["alignment_file"],
calc_weights=True)
vae_model = model.VariationalAutoencoder(data_helper,
batch_size = model_params["bs"],
encoder_architecture = [model_params["encode_dim_zero"],
model_params["encode_dim_one"]],
decoder_architecture = [model_params["decode_dim_zero"],
model_params["decode_dim_one"]],
n_latent = model_params["n_latent"],
logit_p = model_params["logit_p"],
sparsity = model_params["sparsity"],
encode_nonlinearity_type = "relu",
decode_nonlinearity_type = "relu",
final_decode_nonlinearity = model_params["final_decode_nonlin"],
final_pwm_scale = model_params["final_pwm_scale"],
conv_decoder_size = model_params["d_c_size"],
def main(args):
if args.alignment_file != "":
data_params["dataset"] = os.path.basename(
args.alignment_file).split(".")[0]
data_helper = helper.DataHelper(dataset=data_params["dataset"],
calc_weights=False,
alignment_file=args.alignment_file,
working_dir=args.working_dir,
load_all_sequences=False)
vae_model = model.VariationalAutoencoder(
data_helper,
batch_size=model_params["bs"],
encoder_architecture=[
model_params["encode_dim_zero"], model_params["encode_dim_one"]
],
decoder_architecture=[
model_params["decode_dim_zero"], model_params["decode_dim_one"]
],
n_latent=model_params["n_latent"],
logit_p=model_params["logit_p"],
sparsity=model_params["sparsity"],
encode_nonlinearity_type="relu",
decode_nonlinearity_type="relu",
final_decode_nonlinearity=model_params["final_decode_nonlin"],
final_pwm_scale=model_params["final_pwm_scale"],
conv_decoder_size=model_params["d_c_size"],
convolve_patterns=model_params["conv_pat"],
n_patterns=model_params["n_pat"],
random_seed=model_params["r_seed"],
working_dir=args.working_dir)
print("Loading model parameters...")
vae_model.load_parameters(file_prefix=args.ckpt_path)
print("Computing delta elbo...")
mutant_name_list, delta_elbo_list = data_helper.single_mutant_matrix(
vae_model, N_pred_iterations=args.n_iters)
print("Done.")
# Result summary
outprefix = os.path.join(
args.working_dir,
os.path.basename(args.alignment_file).split(".")[0])
preds = pd.DataFrame(zip(mutant_name_list, delta_elbo_list),
columns=["Variant", "delta_elbo"])
preds.to_csv(outprefix + "_preds_raw.csv", index=False)
preds.loc[:, "Variant"] = preds["Variant"].apply(
lambda s: s[0] + str(int(s[1:-1]) + args.start_idx - 1) + s[-1])
variant_seq = pd.read_csv(args.variant_seq_csv)
variant_seq = variant_seq.loc[variant_seq["Variant"].apply(
lambda s: s[0] != s[-1])]
preds = preds.loc[preds["Variant"].isin(variant_seq["Variant"])]
org_len = len(variant_seq)
variant_seq = variant_seq.merge(preds, on="Variant", how="left")
assert len(variant_seq) == org_len
variant_seq[["Variant", "scaled_effect1",
"delta_elbo"]].to_csv(outprefix + ".csv", index=False)
print("Saved results to {}".format(outprefix + ".csv"))
correlation, _ = spearmanr(variant_seq["scaled_effect1"].values,
variant_seq["delta_elbo"].values)
print("Spearman's correlation: {}".format(correlation))
def getVAEDataHelper(ds_attributes):
return helper.DataHelper(
alignment_file=ds_attributes['alignment'],
working_dir=ds_attributes['alignment_directory'],
calc_weights=False,
)
"n_pat": 4,
"r_seed": 12345,
"conv_pat": True,
"d_c_size": 40
}
train_params = {
"num_updates": 300000,
"save_progress": True,
"verbose": True,
"save_parameters": False,
}
if __name__ == "__main__":
data_helper = helper.DataHelper(dataset=data_params["dataset"],
calc_weights=True)
vae_model = model.VariationalAutoencoder(
data_helper,
batch_size=model_params["bs"],
encoder_architecture=[
model_params["encode_dim_zero"], model_params["encode_dim_one"]
],
decoder_architecture=[
model_params["decode_dim_zero"], model_params["decode_dim_one"]
],
n_latent=model_params["n_latent"],
logit_p=model_params["logit_p"],
sparsity=model_params["sparsity"],
encode_nonlinearity_type="relu",
decode_nonlinearity_type="relu",
# "save_parameters" : False,
"save_parameters": 30000,
}
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument("--alignment_file", type=str, default="")
parser.add_argument("--working_dir", type=str, default=".")
args = parser.parse_args()
if args.alignment_file != "":
data_params["dataset"] = os.path.basename(
args.alignment_file).split(".")[0]
data_helper = helper.DataHelper(dataset=data_params["dataset"],
calc_weights=True,
alignment_file=args.alignment_file,
working_dir=args.working_dir)
n_seqs = data_helper.x_train.shape[0]
if n_seqs < model_params["bs"]:
msg = "Found {} sequences less than batch size: {}.".format(
n_seqs, model_params["bs"])
msg += " Setting to {}.".format(n_seqs)
print(msg)
model_params["bs"] = n_seqs
vae_model = model.VariationalAutoencoder(
data_helper,
batch_size=model_params["bs"],
encoder_architecture=[
model_params["encode_dim_zero"], model_params["encode_dim_one"]
