Inference Demo

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import sys
# from os import path
# sys.path.append(path.abspath(path.join(path.dirname(__file__),
# '../../..')))
import marimo as mo
import pandas as pd
from dnallm import load_config, load_model_and_tokenizer, DNAInference

import sys # from os import path # sys.path.append(path.abspath(path.join(path.dirname(__file__), # '../../..'))) import marimo as mo import pandas as pd from dnallm import load_config, load_model_and_tokenizer, DNAInference

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model_df = pd.read_excel("./plant_DNA_LLMs_finetune_list.xlsx")

model_df = pd.read_excel("./plant_DNA_LLMs_finetune_list.xlsx")

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tasks = model_df.Task.unique()
print("Available tasks:", tasks, sep="\n")

tasks = model_df.Task.unique() print("Available tasks:", tasks, sep="\n")

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task_dropdown = mo.ui.dropdown(
    tasks,
    value='open chromatin',
    label='Predict Task'
)

task_dropdown = mo.ui.dropdown( tasks, value='open chromatin', label='Predict Task' )

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models = model_df.Model.unique()
print("Available models:", models, sep="\n")

models = model_df.Model.unique() print("Available models:", models, sep="\n")

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model_dropdown = mo.ui.dropdown(
    models,
    value='Plant DNABERT',
    label='Model'
)

model_dropdown = mo.ui.dropdown( models, value='Plant DNABERT', label='Model' )

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tokenizers = model_df.Tokenzier.unique()
print("Available models:", tokenizers,sep="\n")

tokenizers = model_df.Tokenzier.unique() print("Available models:", tokenizers,sep="\n")

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tokenizer_dropdown = mo.ui.dropdown(
    tokenizers,
    value='BPE',
    label='Tokenizer'
)

tokenizer_dropdown = mo.ui.dropdown( tokenizers, value='BPE', label='Tokenizer' )

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source_dropdown = mo.ui.dropdown({'modelscope':'modelscope',
                                  'huggingface':'huggingface'
                                 }, value='modelscope', label='Model Source')

source_dropdown = mo.ui.dropdown({'modelscope':'modelscope', 'huggingface':'huggingface' }, value='modelscope', label='Model Source')

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placeholder = 'GGGCAGCGGTTACACCTTAATCGACACGACTCTCGGCAACGGATATCTCG\
GCTCTTGCATCGATGAAGAACGTAGCAAAATGCGATACCTGGTGTGAATTGCAGAAT\
CCCGCGAACCATCGAGTTTTTGAACGCAAGTTGCGCCCGAAGCCTTCTGACGGA\
GGGCACGTCTGCCTGGGCGTCACGCCAAAAGACACTCCCAACACCCCCCCGCGGGGC\
GAGGGACGTGGCGTCTGGCCCCCCGCGCTGCAGGGCGAGGTGGGCCGAAGCAGGGGCTGCC\
GGCGAACCGCGTCGGACGCAACACGTGGTGGGCGACATCAAGTTGTTCTCGGTGCAGCGT\
CCCGGCGCGCGGCCGGCCATTCGGCCCTAAGGACCCATCGAGCGACCGAGCTTGCCCTCG\
GACCACGACCCCAGGTCAGTCGGGACTACCCGCTGAGTTTAAGCATATAAATAAGCGGAGGAG\
AAGAAACTTACGAGGATTCCCCTAGTAACGGCGAGCGAACCGGGAGCAGCCCAGCTTGA\
GAATCGGGCGGCCTCGCCGCCCGAATTGTAGTCTGGAGAGGCGT'
dnaseq_entry_box = mo.ui.text_area(
    placeholder=placeholder,
    full_width=True,
    label='DNA Sequence:',
    rows=5
)

placeholder = 'GGGCAGCGGTTACACCTTAATCGACACGACTCTCGGCAACGGATATCTCG\ GCTCTTGCATCGATGAAGAACGTAGCAAAATGCGATACCTGGTGTGAATTGCAGAAT\ CCCGCGAACCATCGAGTTTTTGAACGCAAGTTGCGCCCGAAGCCTTCTGACGGA\ GGGCACGTCTGCCTGGGCGTCACGCCAAAAGACACTCCCAACACCCCCCCGCGGGGC\ GAGGGACGTGGCGTCTGGCCCCCCGCGCTGCAGGGCGAGGTGGGCCGAAGCAGGGGCTGCC\ GGCGAACCGCGTCGGACGCAACACGTGGTGGGCGACATCAAGTTGTTCTCGGTGCAGCGT\ CCCGGCGCGCGGCCGGCCATTCGGCCCTAAGGACCCATCGAGCGACCGAGCTTGCCCTCG\ GACCACGACCCCAGGTCAGTCGGGACTACCCGCTGAGTTTAAGCATATAAATAAGCGGAGGAG\ AAGAAACTTACGAGGATTCCCCTAGTAACGGCGAGCGAACCGGGAGCAGCCCAGCTTGA\ GAATCGGGCGGCCTCGCCGCCCGAATTGTAGTCTGGAGAGGCGT' dnaseq_entry_box = mo.ui.text_area( placeholder=placeholder, full_width=True, label='DNA Sequence:', rows=5 )

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title = mo.md(
    "<center><h2>Model inference</h2></center>"
)
hstack=mo.hstack(
    [task_dropdown,
    model_dropdown,
    tokenizer_dropdown,
    source_dropdown],
    align='center',
    justify='center'
)
mo.vstack([title, dnaseq_entry_box, hstack])

title = mo.md( "<center><h2>Model inference</h2></center>" ) hstack=mo.hstack( [task_dropdown, model_dropdown, tokenizer_dropdown, source_dropdown], align='center', justify='center' ) mo.vstack([title, dnaseq_entry_box, hstack])

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try:
    model_name = model_df[
        (model_df.Task == task_dropdown.value)
        & (model_df.Model == model_dropdown.value)
        & (model_df.Tokenzier == tokenizer_dropdown.value)
    ].Name.tolist()[0]
    print("Current model:", model_name, sep="\n")
    callout = ""
except:
    callout = mo.callout("Cannot found the model", kind="warn")
    model_name = None
mo.vstack([callout], align="stretch")

try: model_name = model_df[ (model_df.Task == task_dropdown.value) & (model_df.Model == model_dropdown.value) & (model_df.Tokenzier == tokenizer_dropdown.value) ].Name.tolist()[0] print("Current model:", model_name, sep="\n") callout = "" except: callout = mo.callout("Cannot found the model", kind="warn") model_name = None mo.vstack([callout], align="stretch")

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dnaseq = ''
if dnaseq_entry_box.value:
    dnaseq = dnaseq_entry_box.value
else:
    dnaseq = placeholder
    print("No sequence found, use default sequence.")

dnaseq = '' if dnaseq_entry_box.value: dnaseq = dnaseq_entry_box.value else: dnaseq = placeholder print("No sequence found, use default sequence.")

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configs = load_config("./inference_config.yaml")

configs = load_config("./inference_config.yaml")

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# Set task type
task = task_dropdown.value
if task in ['core promoter', 'sequence conservation', 'enhancer', 
            'H3K27ac', 'H3K27me3', 'H3K4me3', 'lncRNAs']:
    data = task.split()[-1]
    configs['task'].task_type = 'binary'
    configs['task'].num_labels = 2
    configs['task'].label_names = ['Not '+data, data.capitalize()]
elif task in ['open chromatin']:
    configs['task'].task_type = 'multiclass'
    configs['task'].num_labels = 3
    configs['task'].label_names = ['Not '+task, 'Partial '+task, 'Full '+task]
elif task in ['promoter strength leaf', 'promoter strength protoplast']:
    configs['task'].task_type = 'regression'
    configs['task'].num_labels = 1
    configs['task'].label_names = [task]
else:
    pass

# Set task type task = task_dropdown.value if task in ['core promoter', 'sequence conservation', 'enhancer', 'H3K27ac', 'H3K27me3', 'H3K4me3', 'lncRNAs']: data = task.split()[-1] configs['task'].task_type = 'binary' configs['task'].num_labels = 2 configs['task'].label_names = ['Not '+data, data.capitalize()] elif task in ['open chromatin']: configs['task'].task_type = 'multiclass' configs['task'].num_labels = 3 configs['task'].label_names = ['Not '+task, 'Partial '+task, 'Full '+task] elif task in ['promoter strength leaf', 'promoter strength protoplast']: configs['task'].task_type = 'regression' configs['task'].num_labels = 1 configs['task'].label_names = [task] else: pass

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if model_name:
    # Load the model and tokenizer
    model, tokenizer = load_model_and_tokenizer(
        model_name,
        task_config=configs['task'],
        source=source_dropdown.value
    )
    # Instantiate the inference engine
    inference_engine = DNAInference(
        model=model,
        tokenizer=tokenizer,
        config=configs
    )
    # Predict the sequence
    predict_button = mo.ui.button(label="Predict",
                                  on_click=lambda value: inference_engine.infer_seqs(
                                    dnaseq, output_attentions=True)
                                 )
else:
    predict_button = mo.ui.button(label="Predict")
    inference_engine = None
mo.hstack([predict_button], align='center', justify='center')

if model_name: # Load the model and tokenizer model, tokenizer = load_model_and_tokenizer( model_name, task_config=configs['task'], source=source_dropdown.value ) # Instantiate the inference engine inference_engine = DNAInference( model=model, tokenizer=tokenizer, config=configs ) # Predict the sequence predict_button = mo.ui.button(label="Predict", on_click=lambda value: inference_engine.infer_seqs( dnaseq, output_attentions=True) ) else: predict_button = mo.ui.button(label="Predict") inference_engine = None mo.hstack([predict_button], align='center', justify='center')

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if predict_button.value:
    results = predict_button.value
else:
    results = None
results

if predict_button.value: results = predict_button.value else: results = None results

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if results:
    seqs = len(inference_engine.sequences)
    layers = len(inference_engine.embeddings['attentions'])
    heads = inference_engine.embeddings['attentions'][0].shape[1]
else:
    seqs = 1
    layers = 12
    heads = 12
seq_number = mo.ui.number(start=1, stop=seqs if seqs>0 else 1, label="Sequence index")
layer_slider = mo.ui.slider(start=1, stop=layers, step=1, label='Layer index',
                            show_value=True)
head_slider = mo.ui.slider(start=1, stop=heads, step=1, label='Head index',
                        show_value=True)
figure_size = mo.ui.number(start=200, stop=5120, step=10, label='Figure size',
                        value = 800)

if results: seqs = len(inference_engine.sequences) layers = len(inference_engine.embeddings['attentions']) heads = inference_engine.embeddings['attentions'][0].shape[1] else: seqs = 1 layers = 12 heads = 12 seq_number = mo.ui.number(start=1, stop=seqs if seqs>0 else 1, label="Sequence index") layer_slider = mo.ui.slider(start=1, stop=layers, step=1, label='Layer index', show_value=True) head_slider = mo.ui.slider(start=1, stop=heads, step=1, label='Head index', show_value=True) figure_size = mo.ui.number(start=200, stop=5120, step=10, label='Figure size', value = 800)

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plot_button = mo.ui.button(label="Plot attention map",
                        on_click=lambda value: inference_engine.plot_attentions(
                            seq_number.value-1, layer_slider.value-1, head_slider.value-1
                            )
                        )
plot_options = mo.hstack(
    [seq_number,
    layer_slider,
    head_slider,
    figure_size],
    align='center',
    justify='center'
)
mo.vstack([plot_options, plot_button], align='center', justify='center')

plot_button = mo.ui.button(label="Plot attention map", on_click=lambda value: inference_engine.plot_attentions( seq_number.value-1, layer_slider.value-1, head_slider.value-1 ) ) plot_options = mo.hstack( [seq_number, layer_slider, head_slider, figure_size], align='center', justify='center' ) mo.vstack([plot_options, plot_button], align='center', justify='center')

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plot_out = plot_button.value
if plot_out:
    chart = mo.ui.altair_chart(plot_out).properties(
        width=figure_size.value, height=figure_size.value
        )
else:
    chart = None
mo.vstack([chart], align='center', justify='center')

plot_out = plot_button.value if plot_out: chart = mo.ui.altair_chart(plot_out).properties( width=figure_size.value, height=figure_size.value ) else: chart = None mo.vstack([chart], align='center', justify='center')