init

README.md

@@ -10,3 +10,11 @@ pinned: false
 ---
 
 Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference
+
+
+用streamlit做一个网站。
+1. 输入是文本。
+   1. 先用mockData.json的text测试。
+2. 功能是进行调用api对文本进行实体识别，得到list of entity。
+   1. 先mock这个功能。输出mockData.json的entities。
+3. 一个输出模块，使用streamlit_text_label，高亮文本中的list of entity。

app.py

@@ -1,4 +1,46 @@
 import streamlit as st
+from streamlit_text_label import label_select, Selection
 
-x = st.slider('Select a value')
-st.write(x, 'squared is', x * x)
+
+def mock_entity_recognition(text):
+    # Simulate entity recognition functionality
+    entities = [
+        Selection(start=0, end=12, text="FINAL REPORT",
+                  labels=["REPORT_TYPE"]),
+        Selection(start=22, end=33, text="Pseudomonas", labels=["DISEASE"]),
+        Selection(start=39, end=49, text="intubation", labels=["PROCEDURE"]),
+        Selection(start=62, end=67, text="study", labels=["EXAM"]),
+        Selection(start=116, end=126, text="Substantial", labels=["SEVERITY"]),
+        Selection(start=127, end=145, text="bilateral pleural",
+                  labels=["ANATOMY"]),
+        Selection(start=146, end=155, text="effusions", labels=["OBSERVATION"])
+    ]
+    return entities
+
+
+def main():
+    st.title("Medical Text Entity Recognition")
+
+    # 1. Text input
+    text = st.text_area("Enter medical text:", value="FINAL REPORT HISTORY : Pseudomonas with intubation . FINDINGS : In comparison with the study of ___ , there is little change in the monitoring and support devices . Substantial bilateral pleural effusions , more prominent on the right with bibasilar atelectasis .")
+
+    if st.button("Recognize Entities"):
+        # 2. Call the simulated entity recognition function
+        entities = mock_entity_recognition(text)
+
+        # 3. Use streamlit_text_label to highlight recognized entities
+        st.subheader("Recognition Results:")
+        labeled_text = label_select(
+            body=text,
+            labels=["REPORT_TYPE", "DISEASE", "PROCEDURE",
+                    "EXAM", "SEVERITY", "ANATOMY", "OBSERVATION"],
+            selections=entities
+        )
+
+        st.write("Recognized entities:")
+        for entity in entities:
+            st.write(f"{entity.text} ({entity.labels[0]})")
+
+
+if __name__ == "__main__":
+    main()

mockData.json

@@ -0,0 +1,138 @@
+{'data_source': 'MIMIC-CXR',
+ 'data_split': 'train',
+ 'entities': {'1': {'end_ix': 29,
+                    'label': 'OBS-DP',
+                    'relations': [['modify', '4']],
+                    'start_ix': 29,
+                    'tokens': 'Substantial'},
+              '10': {'end_ix': 44,
+                     'label': 'OBS-DP',
+                     'relations': [['suggestive_of', '16']],
+                     'start_ix': 44,
+                     'tokens': 'configuration'},
+              '11': {'end_ix': 47,
+                     'label': 'OBS-DP',
+                     'relations': [['modify', '12']],
+                     'start_ix': 47,
+                     'tokens': 'collection'},
+              '12': {'end_ix': 49,
+                     'label': 'OBS-DP',
+                     'relations': [['located_at', '14'],
+                                   ['suggestive_of', '16']],
+                     'start_ix': 49,
+                     'tokens': 'opacification'},
+              '13': {'end_ix': 52,
+                     'label': 'ANAT-DP',
+                     'relations': [['modify', '14']],
+                     'start_ix': 52,
+                     'tokens': 'left'},
+              '14': {'end_ix': 53,
+                     'label': 'ANAT-DP',
+                     'relations': [],
+                     'start_ix': 53,
+                     'tokens': 'base'},
+              '15': {'end_ix': 59,
+                     'label': 'OBS-U',
+                     'relations': [['modify', '16']],
+                     'start_ix': 59,
+                     'tokens': 'loculated'},
+              '16': {'end_ix': 60,
+                     'label': 'OBS-U',
+                     'relations': [],
+                     'start_ix': 60,
+                     'tokens': 'fluid'},
+              '17': {'end_ix': 67,
+                     'label': 'OBS-DP',
+                     'relations': [['modify', '20']],
+                     'start_ix': 67,
+                     'tokens': 'increased'},
+              '18': {'end_ix': 68,
+                     'label': 'ANAT-DP',
+                     'relations': [['modify', '19']],
+                     'start_ix': 68,
+                     'tokens': 'pulmonary'},
+              '19': {'end_ix': 69,
+                     'label': 'ANAT-DP',
+                     'relations': [],
+                     'start_ix': 69,
+                     'tokens': 'venous'},
+              '2': {'end_ix': 30,
+                    'label': 'ANAT-DP',
+                    'relations': [['modify', '3']],
+                    'start_ix': 30,
+                    'tokens': 'bilateral'},
+              '20': {'end_ix': 70,
+                     'label': 'OBS-DP',
+                     'relations': [['located_at', '19']],
+                     'start_ix': 70,
+                     'tokens': 'pressure'},
+              '21': {'end_ix': 79,
+                     'label': 'ANAT-DP',
+                     'relations': [['modify', '23']],
+                     'start_ix': 79,
+                     'tokens': 'left'},
+              '22': {'end_ix': 80,
+                     'label': 'ANAT-DP',
+                     'relations': [['modify', '23']],
+                     'start_ix': 80,
+                     'tokens': 'upper'},
+              '23': {'end_ix': 81,
+                     'label': 'ANAT-DP',
+                     'relations': [],
+                     'start_ix': 81,
+                     'tokens': 'zone'},
+              '24': {'end_ix': 87,
+                     'label': 'ANAT-DP',
+                     'relations': [],
+                     'start_ix': 87,
+                     'tokens': 'cavitary'},
+              '25': {'end_ix': 88,
+                     'label': 'OBS-DP',
+                     'relations': [['located_at', '24']],
+                     'start_ix': 88,
+                     'tokens': 'process'},
+              '3': {'end_ix': 31,
+                    'label': 'ANAT-DP',
+                    'relations': [],
+                    'start_ix': 31,
+                    'tokens': 'pleural'},
+              '4': {'end_ix': 32,
+                    'label': 'OBS-DP',
+                    'relations': [['located_at', '3']],
+                    'start_ix': 32,
+                    'tokens': 'effusions'},
+              '5': {'end_ix': 35,
+                    'label': 'OBS-DP',
+                    'relations': [['located_at', '6']],
+                    'start_ix': 35,
+                    'tokens': 'prominent'},
+              '6': {'end_ix': 38,
+                    'label': 'ANAT-DP',
+                    'relations': [['modify', '3']],
+                    'start_ix': 38,
+                    'tokens': 'right'},
+              '7': {'end_ix': 40,
+                    'label': 'ANAT-DP',
+                    'relations': [],
+                    'start_ix': 40,
+                    'tokens': 'bibasilar'},
+              '8': {'end_ix': 41,
+                    'label': 'OBS-DP',
+                    'relations': [['located_at', '6'], ['located_at', '7']],
+                    'start_ix': 41,
+                    'tokens': 'atelectasis'},
+              '9': {'end_ix': 43,
+                    'label': 'OBS-DP',
+                    'relations': [['modify', '10']],
+                    'start_ix': 43,
+                    'tokens': 'Unusual'}},
+ 'text': 'FINAL REPORT HISTORY : Pseudomonas with intubation . FINDINGS : In '
+         'comparison with the study of ___ , there is little change in the '
+         'monitoring and support devices . Substantial bilateral pleural '
+         'effusions , more prominent on the right with bibasilar atelectasis . '
+         'Unusual configuration to the collection of opacification at the left '
+         'base raises the possibility of some loculated fluid . There is again '
+         'evidence of increased pulmonary venous pressure . Overlapping '
+         'structures somewhat obscure visualization of the left upper zone and '
+         'simulate the appearance of cavitary process . This area should be '
+         'closely checked on subsequent radiographs .'}