This Repo design for article that submmit in MIE 2024
1.0
release, ONLY run this repository on devices without sensitive information or access to paid services.
Clone repository:
git clone https://github.com/mjafarpour87/medical-insights.git
or
git clone [email protected]:mjafarpour87/medical-insights.git
Create environment variable:
python -m venv venv
Activate environment variable:
Windows
$ .\venv\Scripts\activate
Linux
$ source venv/bin/activate
pip install -r requirements.txt
You can install last version of triplea with this command
pip install git+https://github.com/EhsanBitaraf/triple-a.git
python -m spacy download en_core_web_sm
For run web view of article:
Windows
streamlit run web.py --server.port 7186
# | File Name | Description |
---|---|---|
Step 1 | step01_check_config.py | Check TripleA Configuration |
step 2 | step02_get_pubmed.py | |
Step 3 | step03_move_state_forward.py | |
Step 4 | step04_extract_topic_textrank.py | Extract topic from abstract and title with method textrank |
Step 5 | step05_extract_topic_with_llm.py | Extract topic from abstract and title with LLM |
Step 6 | step06_repair_response.py | Repair Json format in response of LLM |
Step 7 | step07_export_dataset.py | Export Dataset |
Step 8 | step08_generate_co_occurrence_graph.py | Generate Co-occurrence graph and export graphml and vosviewer |
method | Graph Nodes | Graph Edges | Graph Average Degree | Graph Density | Graph Average Clustering Coefficient | Graph Degree Assortativity Coefficient | Components |
---|---|---|---|---|---|---|---|
LLM | 45806 | 357482 | 7.804261450465004 | 0.00034076024235192684 | 0.9052766558811535 | -0.06969792652358299 | 514 |
Keyword | 15555 | 337659 | 21.707425265188043 | 0.0027912338003327816 | 0.8692939688222773 | -0.1513162822347413 | 69 |
Textrank | 41185 | 288024 | 6.9934199344421515 | 0.00033961829518464216 | 0.8905241147162223 | -0.07659374291256468 | 86 |
g_textrank_topic Elapsed Time Calculation Report : 34.7201886177063 Graph Type: Undirected Graph Nodes: 41185 Graph Edges: 288024 Graph Average Degree : 6.9934199344421515 Graph Density : 0.00033961829518464216 Graph Transitivity : 0.050903166471327685 Graph max path length : NaN Graph Average Clustering Coefficient : 0.8905241147162223 Graph Degree Assortativity Coefficient : -0.07659374291256468 Graph Radius : NaN Found infinite path length because the graph is not connected SCC: Can not calculate in undirected graph. WCC: Can not calculate in undirected graph. Reciprocity : Can not calculate in undirected graph. Graph Diameter : Number of Components : 86
g_llm_topic Elapsed Time Calculation Report : 44.90726280212402 Graph Type: Undirected Graph Nodes: 45806 Graph Edges: 357482 Graph Average Degree : 7.804261450465004 Graph Density : 0.00034076024235192684 Graph Transitivity : 0.062294261111459366 Graph max path length : NaN Graph Average Clustering Coefficient : 0.9052766558811535 Graph Degree Assortativity Coefficient : -0.06969792652358299 Graph Radius : NaN Found infinite path length because the graph is not connected SCC: Can not calculate in undirected graph. WCC: Can not calculate in undirected graph. Reciprocity : Can not calculate in undirected graph. Graph Diameter : Number of Components : 514
g_keyword Elapsed Time Calculation Report : 125.76658606529236 Graph Type: Undirected Graph Nodes: 15555 Graph Edges: 337659 Graph Average Degree : 21.707425265188043 Graph Density : 0.0027912338003327816 Graph Transitivity : 0.045427854941359314 Graph max path length : NaN Graph Average Clustering Coefficient : 0.8692939688222773 Graph Degree Assortativity Coefficient : -0.1513162822347413 Graph Radius : NaN Found infinite path length because the graph is not connected SCC: Can not calculate in undirected graph. WCC: Can not calculate in undirected graph. Reciprocity : Can not calculate in undirected graph. Graph Diameter : Number of Components : 69
3-7
Graph Nodes | Graph Edges | Graph Average Degree | Graph Density | Graph Transitivity | Graph Average Clustering Coefficient | Graph Degree Assortativity Coefficient | Graph Radius | Number of Components |
---|---|---|---|---|---|---|---|---|
180 | 1869 | 10.383333333333333 | 0.11601489757914339 | 0.33822583239504583 | 0.6287495176290473 | -0.26864279905481586 | 2 | 1 |
1106 | 23179 | 20.95750452079566 | 0.037932134879268165 | 0.18028782814226374 | 0.8656427256105894 | -0.3634106013533251 | 1 | 1 |
85 | 441 | 5.188235294117647 | 0.12352941176470589 | 0.35589388001205907 | 0.5677863710428314 | -0.14805472645939238 | 2 | 1 |
0-7
Graph Nodes | Graph Edges | Graph Average Degree | Graph Density | Graph Transitivity | Graph Average Clustering Coefficient | Graph Degree Assortativity Coefficient | Graph Radius | Number of Components |
---|---|---|---|---|---|---|---|---|
45741 | 356983 | 7.80444240397018 | 0.00034125240069830256 | 0.062251828346278654 | 0.9051982234160808 | -0.06977365378359335 | NaN | 509 |
10995 | 248968 | 22.643747157798998 | 0.004119291824231217 | 0.11401194246943137 | 0.823940403480553 | -0.2240567505762541 | NaN | 2 |
37023 | 270895 | 7.316938119547308 | 0.00039527514016246063 | 0.054351639999606426 | 0.8842263711703248 | -0.07624538974062134 | NaN | 43 |
Please see our contributing guidelines for more details on how to get involved.