Sequence Generation

In [1]:

from dnallm import load_config
from dnallm import load_model_and_tokenizer, DNAInference

from dnallm import load_config from dnallm import load_model_and_tokenizer, DNAInference

In [2]:

# Load configurations
configs = load_config("./generation_config.yaml")

# Load configurations configs = load_config("./generation_config.yaml")

In [ ]:

model_name = "zhangtaolab/plant-dnagpt-BPE"
model, tokenizer = load_model_and_tokenizer(model_name, task_config=configs['task'], source="modelscope")

model_name = "zhangtaolab/plant-dnagpt-BPE" model, tokenizer = load_model_and_tokenizer(model_name, task_config=configs['task'], source="modelscope")

Downloading Model from https://www.modelscope.cn to directory: /home/liuguanqing/.cache/modelscope/hub/models/zhangtaolab/plant-dnagpt-BPE
02:16:42 - dnallm.models.model - INFO - Model files are stored in /home/liuguanqing/.cache/modelscope/hub/models/zhangtaolab/plant-dnagpt-BPE
02:16:42 - dnallm.models.model - WARNING - Generation task does not require num_labels, but got 1. Setting to 0.
Downloading Model from https://www.modelscope.cn to directory: /home/liuguanqing/.cache/modelscope/hub/models/zhangtaolab/plant-dnagpt-BPE
Downloading Model from https://www.modelscope.cn to directory: /home/liuguanqing/.cache/modelscope/hub/models/zhangtaolab/plant-dnagpt-BPE

In [4]:

# Create inference engine
inference_engine = DNAInference(
    model=model,
    tokenizer=tokenizer,
    config=configs
)

# Create inference engine inference_engine = DNAInference( model=model, tokenizer=tokenizer, config=configs )

02:16:44 - dnallm.models.model - INFO - Using device: cuda

In [5]:

output = inference_engine.generate(["ACGT"], n_tokens=512, temperature=0.8, top_p=0.9)

output = inference_engine.generate(["ACGT"], n_tokens=512, temperature=0.8, top_p=0.9)

Setting `pad_token_id` to `eos_token_id`:8000 for open-end generation.

In [6]:

for seq in output:
    print(f"Input Sequence: {seq['Prompt']}")
    print(f"Generated Sequence: {seq['Output']}")
    print()

for seq in output: print(f"Input Sequence: {seq['Prompt']}") print(f"Generated Sequence: {seq['Output']}") print()

Input Sequence: ACGT
Generated Sequence: ACGTAGTAAAAAAGAAAGAAGGAAAGGGAAAAAGAGAAAGAGAAGGAAAAGGAAAAAGGAGAAAGGAAAGAAAGGGGAAAGAAGAAAAAAGGAAAGAAGAAAGAAAAAAAAGAAGGAAGAAAAAAAAAGGAGAAGGAGGGGGGAAAAAAAAGAAAGAAAAAAAAAGAAGAAAAAAAAAGAAAAAGAAAAAAAGAGAAAAAAAAAAAAAAAGAGGGAAAAAGAAAAAAGGAAGAGAAAGAGGAAAAAAGAAAAGAAGAAAAGGGAGAAGAGAAAAAAGAAAAAGGAAAGAAGAAAAGGAGAGAAAGGAAAAAAAAAAAGAAGGAAAAAAAAGAAGGAAGAAGAAAAAAAAAAAAAAAGAGAAAAGAAGAAGAAGGAAAAAGGAAAAGGGAAAAAAAGAAAAAGAAGGAAAGAAAAAAAAAAAAAGAAAGAAGAAGGAGAGAGAAAAAAGAGAGAAAGAAGAAAAAGAAAAAGGGAGAAAAAAGGGAAAAGGAAAAAAAAAAGAAAAAAGAGAAAAAGAA

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