Spaces:
Running
Running
Erva Ulusoy
commited on
Commit
·
ec82ae1
1
Parent(s):
41634be
added info about upcoming features, fixed reset button
Browse files- ProtHGT_app.py +11 -2
ProtHGT_app.py
CHANGED
@@ -11,7 +11,7 @@ with st.spinner("Please wait while we prepare the environment. This may take a f
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start_time = time.time()
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os.system("bash setup.sh")
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end_time = time.time()
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-
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with open(".setup_done", "w") as f:
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f.write("done")
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@@ -26,6 +26,15 @@ if 'predictions_df' not in st.session_state:
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if 'submitted' not in st.session_state:
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st.session_state.submitted = False
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with st.sidebar:
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st.markdown("""
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@@ -317,4 +326,4 @@ with st.sidebar:
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if st.button("Reset"):
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st.session_state.predictions_df = None
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st.session_state.submitted = False
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st.
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start_time = time.time()
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os.system("bash setup.sh")
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end_time = time.time()
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print(f"Environment prepared in {end_time - start_time:.2f} seconds")
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with open(".setup_done", "w") as f:
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f.write("done")
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if 'submitted' not in st.session_state:
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st.session_state.submitted = False
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with st.expander("🚀 Upcoming Features"):
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st.info("""
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We are actively working on enhancing ProtHGT application with new capabilities:
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- **Real-time data retrieval for new proteins**: Currently, ProtHGT can only generate predictions for proteins that already exist in our knowledge graph. We are developing a new feature that will allow users to **predict functions for entirely new proteins starting from their sequences**. This will work by **retrieving relevant relationship data in real time from external source databases** (e.g., UniProt, STRING, and other biological repositories). The system will dynamically construct a knowledge graph for the query protein, incorporating its interactions, domains, pathways, and other biological associations before running function prediction. This approach will enable ProtHGT to analyze newly discovered or less-studied proteins even if they are not pre-annotated in our dataset.
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- **Expanded embedding options**: Currently, this application represents proteins using **TAPE embeddings**, which serve as the initial numerical representations of protein sequences before being processed in the heterogeneous graph model. We are working on integrating **ProtT5** and **ESM-2** as alternative initial embeddings, allowing users to choose different sequence representations that may enhance performance for specific tasks. A detailed comparison of how these embeddings influence function prediction accuracy will be included in our upcoming publication.
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Stay tuned for updates and future publications!
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""")
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with st.sidebar:
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st.markdown("""
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if st.button("Reset"):
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st.session_state.predictions_df = None
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st.session_state.submitted = False
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st.rerun()
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