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Browse files
app.py
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@@ -215,7 +215,7 @@ with gr.Blocks() as demo:
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with gr.Tab("Genus Prediction"):
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gr.Markdown("""
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-
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A demo of predicting the genus of a DNA sequence using multiple
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approaches (method dropdown):
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that we precomputed and stored in a Pinecone index. Thie method
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DOES NOT examine ecological layer data.
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""")
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gr.Interface(
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fn=predict_genus,
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inputs=[
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inp_dna,
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inp_lat,
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inp_lng,
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],
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outputs=["image"],
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allow_flagging="never",
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)
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with gr.Tab("DNA Embedding Space Visualizer"):
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gr.Markdown("""
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-
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We show a 2D t-SNE plot of the DNA embeddings of the five most common
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genera in our dataset. This shows that the DNA Transformer model is
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learning to cluster similar DNA sequences together.
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""")
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gr.Interface(
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fn=cluster_dna,
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inputs=
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label="Number of top genera to visualize")
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],
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outputs=["image"],
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allow_flagging="never",
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)
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demo.launch()
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with gr.Tab("Genus Prediction"):
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gr.Markdown("""
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## Genus prediction
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A demo of predicting the genus of a DNA sequence using multiple
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approaches (method dropdown):
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that we precomputed and stored in a Pinecone index. Thie method
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DOES NOT examine ecological layer data.
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""")
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# gr.Interface(
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# fn=predict_genus,
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# inputs=[
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# gr.Dropdown(choices=["cosine", "fine_tuned_model"], value="fine_tuned_model"),
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# inp_dna,
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# inp_lat,
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# inp_lng,
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# ],
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# outputs=["image"],
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# allow_flagging="never",
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# )
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method_dropdown = gr.Dropdown(choices=["cosine", "fine_tuned_model"], value="fine_tuned_model")
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predict_button = gr.Button("Predict Genus")
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genus_output = gr.Image()
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predict_button.click(
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fn=predict_genus,
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inputs=[method_dropdown, inp_dna, inp_lat, inp_lng],
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outputs=genus_output
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)
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with gr.Tab("DNA Embedding Space Visualizer"):
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gr.Markdown("""
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## DNA Embedding Space Visualizer
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We show a 2D t-SNE plot of the DNA embeddings of the five most common
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genera in our dataset. This shows that the DNA Transformer model is
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learning to cluster similar DNA sequences together.
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""")
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# gr.Interface(
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# fn=cluster_dna,
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# inputs=[
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# gr.Slider(minimum=1, maximum=10, step=1, value=5,
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# label="Number of top genera to visualize")
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# ],
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# outputs=["image"],
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# allow_flagging="never",
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# )
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top_k_slider = gr.Slider(minimum=1, maximum=10, step=1, value=5, label="Number of top genera to visualize")
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visualize_button = gr.Button("Visualize Embedding Space")
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visualize_output = gr.Image()
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visualize_button.click(
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fn=cluster_dna,
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inputs=top_k_slider,
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outputs=visualize_output
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)
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demo.launch()
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