aksell commited on
Commit
b09c0bf
·
1 Parent(s): b5726b3

Fix links in documentation

Browse files
hexviz/pages/2_📄Documentation.py CHANGED
@@ -1,7 +1,9 @@
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  import streamlit as st
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  st.markdown(
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- """
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  ## Protein language models
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  There has been an explosion of capabilities in natural language processing models in the last few years.
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  These architectural advances from NLP have proven to work very well for protein sequences, and we now have protein language models (pLMs) that can generate novel functional proteins sequences [ProtGPT2](https://www.nature.com/articles/s42256-022-00499-z)
@@ -23,8 +25,8 @@ domain experts to explore and interpret the knowledge contained in pLMs.
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  ## How to use Hexviz
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  There are two views:
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- 1. [**Attention Visualization**](Attention_Visualization) Shows attention weights from a single head as red bars between residues on a protein structure.
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- 2. [**Identify Interesting Heads**](Identify_Interesting_Heads) Plots attention weights between residues as a heatmap for each head in the model.
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  The first view is the meat of the application and is where you can investigate how attention patterns map onto the structure of a protein you're interested in.
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  Use the second view to narrow down to a few heads that you want to investigate attention patterns from in detail.
@@ -50,5 +52,6 @@ Hexviz currently supports the following models:
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  ## FAQ
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  1. I can't see any attention- "bars" in the visualization, what is wrong? -> Lower the `minimum attention`.
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  2. How are sequences I input folded? -> Using https://esmatlas.com/resources?action=fold
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- """
 
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  )
 
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  import streamlit as st
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+ from hexviz.config import URL
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+
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  st.markdown(
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+ f"""
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  ## Protein language models
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  There has been an explosion of capabilities in natural language processing models in the last few years.
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  These architectural advances from NLP have proven to work very well for protein sequences, and we now have protein language models (pLMs) that can generate novel functional proteins sequences [ProtGPT2](https://www.nature.com/articles/s42256-022-00499-z)
 
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  ## How to use Hexviz
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  There are two views:
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+ 1. <a href="{URL}Attention_Visualization" target="_self">🧬Attention Visualization</a> Shows attention weights from a single head as red bars between residues on a protein structure.
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+ 2. <a href="{URL}Identify_Interesting_Heads" target="_self">🗺️Identify Interesting Heads</a> Plots attention weights between residues as a heatmap for each head in the model.
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  The first view is the meat of the application and is where you can investigate how attention patterns map onto the structure of a protein you're interested in.
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  Use the second view to narrow down to a few heads that you want to investigate attention patterns from in detail.
 
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  ## FAQ
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  1. I can't see any attention- "bars" in the visualization, what is wrong? -> Lower the `minimum attention`.
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  2. How are sequences I input folded? -> Using https://esmatlas.com/resources?action=fold
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+ """,
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+ unsafe_allow_html=True,
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  )