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.gitattributes

@@ -31,3 +31,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 *.zip filter=lfs diff=lfs merge=lfs -text
 *.zst filter=lfs diff=lfs merge=lfs -text
 *tfevents* filter=lfs diff=lfs merge=lfs -text
+world.mp4 filter=lfs diff=lfs merge=lfs -text

README.txt

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+---
+title: 🧬CTMap - Clinical Terminology AutoMap AI
+emoji: ⚗️🧠🔬🧬
+colorFrom: yellow
+colorTo: green
+sdk: gradio
+sdk_version: 3.5
+app_file: app.py
+pinned: false
+license: mit
+---
+
+Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference

Readme.md

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+Files Directory - drop in examples here to ref by app.py

app.py

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+import pandas_profiling as pp
+import pandas as pd
+import tensorflow as tf
+
+from datasets import load_dataset
+from tensorflow.python.framework import tensor_shape
+
+#LOINC
+datasetLOINC = load_dataset("awacke1/LOINC-CodeSet-Value-Description.csv", split="train")
+#SNOMED:
+datasetSNOMED = load_dataset("awacke1/SNOMED-CT-Code-Value-Semantic-Set.csv", split="train")
+#eCQM:
+dataseteCQM = load_dataset("awacke1/eCQM-Code-Value-Semantic-Set.csv", split="train")
+
+# map using autotokenizer
+from transformers import AutoTokenizer
+tokenizer = AutoTokenizer.from_pretrained("bert-base-cased")
+dataset = datasetLOINC.map(lambda examples: tokenizer(examples["Description"]), batched=True)
+JSONOBJ2=dataset[0]
+print(JSONOBJ2)
+
+sw = datasetLOINC.filter(lambda example: example["Description"].startswith("Allergy"))
+len(sw)
+print(sw)
+print(datasetLOINC)
+print(datasetSNOMED)
+print(dataseteCQM)
+
+# play with some dataset tools before the show:
+
+#print(start_with_ar["Description"])
+
+#---
+#Main Stage - Begin!
+#---
+
+import os
+import json
+import numpy as np
+import gradio as gr
+
+HF_TOKEN = os.environ.get("HF_TOKEN")
+CHOICES = ["SNOMED", "LOINC", "CQM"]
+JSONOBJ = """{"items":{"item":[{"id": "0001","type": null,"is_good": false,"ppu": 0.55,"batters":{"batter":[{ "id": "1001", "type": "Regular" },{ "id": "1002", "type": "Chocolate" },{ "id": "1003", "type": "Blueberry" },{ "id": "1004", "type": "Devil's Food" }]},"topping":[{ "id": "5001", "type": "None" },{ "id": "5002", "type": "Glazed" },{ "id": "5005", "type": "Sugar" },{ "id": "5007", "type": "Powdered Sugar" },{ "id": "5006", "type": "Chocolate with Sprinkles" },{ "id": "5003", "type": "Chocolate" },{ "id": "5004", "type": "Maple" }]}]}}"""
+
+
+def profile_dataset(dataset=datasetSNOMED, username="awacke1", token=HF_TOKEN, dataset_name="awacke1/SNOMED-CT-Code-Value-Semantic-Set.csv"):
+    df = pd.read_csv(dataset.Description)
+    if len(df.columns) <= 15:
+        profile = pp.ProfileReport(df, title=f"{dataset_name} Report")
+    else:
+        profile = pp.ProfileReport(df, title=f"{dataset_name} Report", minimal = True)
+    
+    repo_url = create_repo(f"{username}/{dataset_name}", repo_type = "space", token = token, space_sdk = "static", private=False)
+    
+    profile.to_file("./index.html")
+
+    upload_file(path_or_fileobj ="./index.html", path_in_repo = "index.html", repo_id =f"{username}/{dataset_name}", repo_type = "space", token=token)
+    readme = f"---\ntitle: {dataset_name}\nemoji: ✨\ncolorFrom: green\ncolorTo: red\nsdk: static\npinned: false\ntags:\n- dataset-report\n---"    
+    with open("README.md", "w+") as f:
+        f.write(readme)
+    upload_file(path_or_fileobj ="./README.md", path_in_repo = "README.md", repo_id =f"{username}/{dataset_name}", repo_type = "space", token=token)
+    return f"Your dataset report will be ready at {repo_url}"
+
+#def lowercase_title(example):
+#    return {"Description": example[title].lower()}
+
+# demonstrate map function of dataset
+#JSONOBJ_MAP=datasetLOINC.map(lowercase_title)
+#JSONOBJ_MAP=datasetLOINC.filter(lambda example: example["Description"].startswith("Mental health")) 
+
+
+
+
+def concatenate_text(examples):
+    return {
+        "text": examples["Code"]
+        + " \n "
+        + examples["Description"]
+        + " \n "
+        + examples["Purpose: Clinical Focus"]
+    }
+
+def cls_pooling(model_output):
+    return model_output.last_hidden_state[:, 0]
+    
+def get_embeddings(text_list):
+    encoded_input = tokenizer(
+        text_list, padding=True, truncation=True, return_tensors="tf"
+    )
+    encoded_input = {k: v for k, v in encoded_input.items()}
+    model_output = model(**encoded_input)
+    return cls_pooling(model_output)
+
+
+def fn(    text1,    text2,    num,    slider1,    slider2,    single_checkbox,    checkboxes,    radio,    dropdown,    im1,    im2,    im3,    im4,
+    video,    audio1,    audio2,    file,    df1,    df2,):
+#def fn(    text1,    text2,    single_checkbox,    checkboxes,    radio,    im4,  file,    df1,    df2,):
+
+    searchTerm = text1
+    searchTermSentence = text2
+    
+    start_with_searchTermLOINC = datasetLOINC.filter(lambda example:example["Description"].startswith('Allergy'))    #Allergy
+    
+    
+    # FAISS
+    columns = start_with_searchTermLOINC.column_names
+    columns_to_keep = ["Value Set Name", "Code", "Description", "Purpose: Clinical Focus", "Code System OID"]
+    columns_to_remove = set(columns_to_keep).symmetric_difference(columns)
+    start_with_searchTermLOINC = start_with_searchTermLOINC.remove_columns(columns_to_remove)
+    start_with_searchTermLOINC 
+    start_with_searchTermLOINC.set_format("pandas")
+    df = start_with_searchTermLOINC[:]
+
+    df["Purpose: Clinical Focus"][0]
+    
+    df4 = df.explode("Purpose: Clinical Focus", ignore_index=True)
+    df4.head(4)
+    
+    from datasets import Dataset
+    clinical_dataset = Dataset.from_pandas(df4)
+    clinical_dataset
+    
+    clinical_dataset = clinical_dataset.map(lambda x: {"c_length": len(x["Description"].split())})
+    
+    clinical_dataset = clinical_dataset.filter(lambda x: x["c_length"] > 15)
+    clinical_dataset
+    
+    
+    clinical_dataset = clinical_dataset.map(concatenate_text)
+    #embedding = get_embeddings(clinical_dataset["text"][0])
+    #embedding.shape
+    
+    from transformers import AutoTokenizer, TFAutoModel
+
+    model_ckpt = "sentence-transformers/multi-qa-mpnet-base-dot-v1"
+    tokenizer = AutoTokenizer.from_pretrained(model_ckpt)
+    model = TFAutoModel.from_pretrained(model_ckpt, from_pt=True)
+    
+#    TensorShape([1, 768])
+    tf.shape([1, 768])
+    
+    embeddings_dataset = clinical_dataset.map(
+    lambda x: {"embeddings": get_embeddings(x["text"]).numpy()[0]})
+    
+#    embeddings_dataset.add_faiss_index(column="embeddings")
+
+#    question = "How can I load a dataset offline?"
+#    question_embedding = get_embeddings([question]).numpy()
+#    question_embedding.shape
+    
+#    scores, samples = embeddings_dataset.get_nearest_examples("embeddings", question_embedding, k=5)
+    
+#    import pandas as pd
+
+#    samples_df = pd.DataFrame.from_dict(samples)
+#    samples_df["scores"] = scores
+#    samples_df.sort_values("scores", ascending=False, inplace=True)
+    
+    
+    #        "text": examples["Code"]
+    #    + " \n "
+    #    + examples["Description"]
+    #    + " \n "
+    #    + examples["Purpose: Clinical Focus"]
+        
+        
+#    for _, row in samples_df.iterrows():
+#        print(f"Code: {row.Code}")
+#        print(f"Description: {row.Description}")
+#        #print(f"Purpose: Clinical Focus: {row.Purpose: Clinical Focus}")
+#        #print(f"URL: {row.html_url}")
+#        print("=" * 50)
+#        print()
+    
+    # SNOMED and CQM ---------------
+    start_with_searchTermSNOMED = datasetSNOMED.filter(lambda example: example["Description"].startswith('Hospital'))    #Hospital
+    start_with_searchTermCQM = dataseteCQM.filter(lambda example: example["Description"].startswith('Telephone'))    #Telephone
+    
+    print(start_with_searchTermLOINC )
+    print(start_with_searchTermSNOMED )
+    print(start_with_searchTermCQM)
+    
+    #print(start_with_searchTermLOINC["train"][0] )
+    #print(start_with_searchTermSNOMED["train"][0] )
+    #print(start_with_searchTermCQM["train"][0] )
+        
+    #returnMsg=profile_dataset()
+    #print(returnMsg)
+    
+#    try:
+        #top1matchLOINC = json.loads(start_with_searchTermLOINC['train'])
+        #top1matchSNOMED = json.loads(start_with_searchTermSNOMED['train'])
+        #top1matchCQM = json.loads(start_with_searchTermCQM['train'])
+#        top1matchLOINC = json.loads(start_with_searchTermLOINC)
+#        top1matchSNOMED = json.loads(start_with_searchTermSNOMED)
+#        top1matchCQM = json.loads(start_with_searchTermCQM)
+#    except:
+#        print('Hello')
+        #print(start_with_searchTermLOINC[0])
+        #print(start_with_searchTermSNOMED[0] )
+        #print(start_with_searchTermCQM[0] )
+        
+    #print(returnMsg)
+ #   print("Datasets Processed")
+    
+    return (
+        (text1 if single_checkbox else text2)
+        + ", selected:"
+        + ", ".join(checkboxes),  # Text
+        {
+            "positive": num / (num + slider1 + slider2),
+            "negative": slider1 / (num + slider1 + slider2),
+            "neutral": slider2 / (num + slider1 + slider2),
+        },  # Label
+        (audio1[0], np.flipud(audio1[1]))
+        if audio1 is not None  else os.path.join(os.path.dirname(__file__), "files/cantina.wav"),  # Audio
+        np.flipud(im1)
+        if im1 is not None  else os.path.join(os.path.dirname(__file__), "files/cheetah1.jpg"),  # Image
+        video
+        if video is not None  else os.path.join(os.path.dirname(__file__), "files/world.mp4"),  # Video
+        [
+            ("The", "art"),
+            ("quick brown", "adj"),
+            ("fox", "nn"),
+            ("jumped", "vrb"),
+            ("testing testing testing", None),
+            ("over", "prp"),
+            ("the", "art"),
+            ("testing", None),
+            ("lazy", "adj"),
+            ("dogs", "nn"),
+            (".", "punc"),
+        ]   + [(f"test {x}", f"test {x}") for x in range(10)],  # HighlightedText        
+        [
+            ("The testing testing testing", None),
+            ("over", 0.6),
+            ("the", 0.2),
+            ("testing", None),
+            ("lazy", -0.1),
+            ("dogs", 0.4),
+            (".", 0),
+        ]   + [(f"test", x / 10) for x in range(-10, 10)],  # HighlightedText
+        #json.loads(JSONOBJ),  # JSON
+        start_with_searchTermLOINC.to_json(orient="records", path_or_buf="None"),
+        #json.dumps(json.loads(start_with_searchTermLOINC['train'].to_json(orient="records", path_or_buf="None"))),
+        "<button style='background-color: red'>Click Me: " + radio + "</button>",  # HTML
+        os.path.join(os.path.dirname(__file__), "files/titanic.csv"),
+        df1,  # Dataframe
+        np.random.randint(0, 10, (4, 4)),  # Dataframe
+        df2,  # Timeseries
+    )
+
+
+
+demo = gr.Interface(
+    fn,
+    inputs=[
+        gr.Textbox(value="Allergy", label="Textbox"),
+        gr.Textbox(lines=3, value="Bathing", placeholder="Type here..", label="Textbox 2"),
+        gr.Number(label="Number", value=42),
+        gr.Slider(10, 20, value=15, label="Slider: 10 - 20"),
+        gr.Slider(maximum=20, step=0.04, label="Slider: step @ 0.04"),
+        gr.Checkbox(label="Check for NER Match on Submit"),
+        gr.CheckboxGroup(label="Clinical Terminology to Check", choices=CHOICES, value=CHOICES[0:2]),
+        gr.Radio(label="Preferred Terminology Output", choices=CHOICES, value=CHOICES[2]),
+        gr.Dropdown(label="Dropdown", choices=CHOICES),
+        gr.Image(label="Image"),
+        gr.Image(label="Image w/ Cropper", tool="select"),
+        gr.Image(label="Sketchpad", source="canvas"),
+        gr.Image(label="Webcam", source="webcam"),
+        gr.Video(label="Video"),
+        gr.Audio(label="Audio"),
+        gr.Audio(label="Microphone", source="microphone"),
+        gr.File(label="File"),
+        gr.Dataframe(label="Filters", headers=["Name", "Age", "Gender"]),
+        gr.Timeseries(x="time", y=["price", "value"], colors=["pink", "purple"]),
+    ],
+    outputs=[
+        gr.Textbox(label="Textbox"),
+        gr.Label(label="Label"),
+        gr.Audio(label="Audio"),
+        gr.Image(label="Image"),
+        gr.Video(label="Video"),
+        gr.HighlightedText(label="HighlightedText", color_map={"punc": "pink", "test 0": "blue"}),
+        gr.HighlightedText(label="HighlightedText", show_legend=True),
+        gr.JSON(label="JSON"),
+        gr.HTML(label="HTML"),
+        gr.File(label="File"),
+        gr.Dataframe(label="Dataframe"),
+        gr.Dataframe(label="Numpy"),
+        gr.Timeseries(x="time", y=["price", "value"], label="Timeseries"),
+    ],
+    examples=[
+        [
+            "Allergy",
+            "Admission",
+            10,
+            12,
+            4,
+            True,
+            ["SNOMED", "LOINC", "CQM"],
+            "SNOMED",
+            "bar",
+            os.path.join(os.path.dirname(__file__), "files/cheetah1.jpg"),
+            os.path.join(os.path.dirname(__file__), "files/cheetah1.jpg"),
+            os.path.join(os.path.dirname(__file__), "files/cheetah1.jpg"),
+            os.path.join(os.path.dirname(__file__), "files/cheetah1.jpg"),
+            os.path.join(os.path.dirname(__file__), "files/world.mp4"),
+            os.path.join(os.path.dirname(__file__), "files/cantina.wav"),
+            os.path.join(os.path.dirname(__file__), "files/cantina.wav"),
+            os.path.join(os.path.dirname(__file__), "files/titanic.csv"),
+            [[1, 2, 3], [3, 4, 5]],
+            os.path.join(os.path.dirname(__file__), "files/time.csv"),
+        ]
+    ]
+    * 3,
+    theme="default",
+    title="⚗️🧠🔬🧬 Clinical Terminology Auto Mapper AI 👩‍⚕️🩺⚕️🙋",
+    cache_examples=False,
+    description="Clinical Terminology Auto Mapper AI",
+    article="Learn more at [Yggdrasil](https://github.com/AaronCWacker/Yggdrasil)",
+#    live=True,
+)
+
+if __name__ == "__main__":
+    demo.launch(debug=True)

requirements.txt

@@ -0,0 +1,7 @@
+datasets
+transformers
+pandas-profiling
+huggingface-hub
+gradio
+Tensorflow
+torch

time.csv

@@ -0,0 +1,8 @@
+time,value,price
+1,1,4
+2,3,8
+3,6,12
+4,10,16
+5,15,20
+6,21,24
+7,28,28

titanic.csv

@@ -0,0 +1,892 @@
+PassengerId,Survived,Pclass,Name,Sex,Age,SibSp,Parch,Ticket,Fare,Cabin,Embarked
+1,0,3,"Braund, Mr. Owen Harris",male,22,1,0,A/5 21171,7.25,,S
+2,1,1,"Cumings, Mrs. John Bradley (Florence Briggs Thayer)",female,38,1,0,PC 17599,71.2833,C85,C
+3,1,3,"Heikkinen, Miss. Laina",female,26,0,0,STON/O2. 3101282,7.925,,S
+4,1,1,"Futrelle, Mrs. Jacques Heath (Lily May Peel)",female,35,1,0,113803,53.1,C123,S
+5,0,3,"Allen, Mr. William Henry",male,35,0,0,373450,8.05,,S
+6,0,3,"Moran, Mr. James",male,,0,0,330877,8.4583,,Q
+7,0,1,"McCarthy, Mr. Timothy J",male,54,0,0,17463,51.8625,E46,S
+8,0,3,"Palsson, Master. Gosta Leonard",male,2,3,1,349909,21.075,,S
+9,1,3,"Johnson, Mrs. Oscar W (Elisabeth Vilhelmina Berg)",female,27,0,2,347742,11.1333,,S
+10,1,2,"Nasser, Mrs. Nicholas (Adele Achem)",female,14,1,0,237736,30.0708,,C
+11,1,3,"Sandstrom, Miss. Marguerite Rut",female,4,1,1,PP 9549,16.7,G6,S
+12,1,1,"Bonnell, Miss. Elizabeth",female,58,0,0,113783,26.55,C103,S
+13,0,3,"Saundercock, Mr. William Henry",male,20,0,0,A/5. 2151,8.05,,S
+14,0,3,"Andersson, Mr. Anders Johan",male,39,1,5,347082,31.275,,S
+15,0,3,"Vestrom, Miss. Hulda Amanda Adolfina",female,14,0,0,350406,7.8542,,S
+16,1,2,"Hewlett, Mrs. (Mary D Kingcome) ",female,55,0,0,248706,16,,S
+17,0,3,"Rice, Master. Eugene",male,2,4,1,382652,29.125,,Q
+18,1,2,"Williams, Mr. Charles Eugene",male,,0,0,244373,13,,S
+19,0,3,"Vander Planke, Mrs. Julius (Emelia Maria Vandemoortele)",female,31,1,0,345763,18,,S
+20,1,3,"Masselmani, Mrs. Fatima",female,,0,0,2649,7.225,,C
+21,0,2,"Fynney, Mr. Joseph J",male,35,0,0,239865,26,,S
+22,1,2,"Beesley, Mr. Lawrence",male,34,0,0,248698,13,D56,S
+23,1,3,"McGowan, Miss. Anna ""Annie""",female,15,0,0,330923,8.0292,,Q
+24,1,1,"Sloper, Mr. William Thompson",male,28,0,0,113788,35.5,A6,S
+25,0,3,"Palsson, Miss. Torborg Danira",female,8,3,1,349909,21.075,,S
+26,1,3,"Asplund, Mrs. Carl Oscar (Selma Augusta Emilia Johansson)",female,38,1,5,347077,31.3875,,S
+27,0,3,"Emir, Mr. Farred Chehab",male,,0,0,2631,7.225,,C
+28,0,1,"Fortune, Mr. Charles Alexander",male,19,3,2,19950,263,C23 C25 C27,S
+29,1,3,"O'Dwyer, Miss. Ellen ""Nellie""",female,,0,0,330959,7.8792,,Q
+30,0,3,"Todoroff, Mr. Lalio",male,,0,0,349216,7.8958,,S
+31,0,1,"Uruchurtu, Don. Manuel E",male,40,0,0,PC 17601,27.7208,,C
+32,1,1,"Spencer, Mrs. William Augustus (Marie Eugenie)",female,,1,0,PC 17569,146.5208,B78,C
+33,1,3,"Glynn, Miss. Mary Agatha",female,,0,0,335677,7.75,,Q
+34,0,2,"Wheadon, Mr. Edward H",male,66,0,0,C.A. 24579,10.5,,S
+35,0,1,"Meyer, Mr. Edgar Joseph",male,28,1,0,PC 17604,82.1708,,C
+36,0,1,"Holverson, Mr. Alexander Oskar",male,42,1,0,113789,52,,S
+37,1,3,"Mamee, Mr. Hanna",male,,0,0,2677,7.2292,,C
+38,0,3,"Cann, Mr. Ernest Charles",male,21,0,0,A./5. 2152,8.05,,S
+39,0,3,"Vander Planke, Miss. Augusta Maria",female,18,2,0,345764,18,,S
+40,1,3,"Nicola-Yarred, Miss. Jamila",female,14,1,0,2651,11.2417,,C
+41,0,3,"Ahlin, Mrs. Johan (Johanna Persdotter Larsson)",female,40,1,0,7546,9.475,,S
+42,0,2,"Turpin, Mrs. William John Robert (Dorothy Ann Wonnacott)",female,27,1,0,11668,21,,S
+43,0,3,"Kraeff, Mr. Theodor",male,,0,0,349253,7.8958,,C
+44,1,2,"Laroche, Miss. Simonne Marie Anne Andree",female,3,1,2,SC/Paris 2123,41.5792,,C
+45,1,3,"Devaney, Miss. Margaret Delia",female,19,0,0,330958,7.8792,,Q
+46,0,3,"Rogers, Mr. William John",male,,0,0,S.C./A.4. 23567,8.05,,S
+47,0,3,"Lennon, Mr. Denis",male,,1,0,370371,15.5,,Q
+48,1,3,"O'Driscoll, Miss. Bridget",female,,0,0,14311,7.75,,Q
+49,0,3,"Samaan, Mr. Youssef",male,,2,0,2662,21.6792,,C
+50,0,3,"Arnold-Franchi, Mrs. Josef (Josefine Franchi)",female,18,1,0,349237,17.8,,S
+51,0,3,"Panula, Master. Juha Niilo",male,7,4,1,3101295,39.6875,,S
+52,0,3,"Nosworthy, Mr. Richard Cater",male,21,0,0,A/4. 39886,7.8,,S
+53,1,1,"Harper, Mrs. Henry Sleeper (Myna Haxtun)",female,49,1,0,PC 17572,76.7292,D33,C
+54,1,2,"Faunthorpe, Mrs. Lizzie (Elizabeth Anne Wilkinson)",female,29,1,0,2926,26,,S
+55,0,1,"Ostby, Mr. Engelhart Cornelius",male,65,0,1,113509,61.9792,B30,C
+56,1,1,"Woolner, Mr. Hugh",male,,0,0,19947,35.5,C52,S
+57,1,2,"Rugg, Miss. Emily",female,21,0,0,C.A. 31026,10.5,,S
+58,0,3,"Novel, Mr. Mansouer",male,28.5,0,0,2697,7.2292,,C
+59,1,2,"West, Miss. Constance Mirium",female,5,1,2,C.A. 34651,27.75,,S
+60,0,3,"Goodwin, Master. William Frederick",male,11,5,2,CA 2144,46.9,,S
+61,0,3,"Sirayanian, Mr. Orsen",male,22,0,0,2669,7.2292,,C
+62,1,1,"Icard, Miss. Amelie",female,38,0,0,113572,80,B28,
+63,0,1,"Harris, Mr. Henry Birkhardt",male,45,1,0,36973,83.475,C83,S
+64,0,3,"Skoog, Master. Harald",male,4,3,2,347088,27.9,,S
+65,0,1,"Stewart, Mr. Albert A",male,,0,0,PC 17605,27.7208,,C
+66,1,3,"Moubarek, Master. Gerios",male,,1,1,2661,15.2458,,C
+67,1,2,"Nye, Mrs. (Elizabeth Ramell)",female,29,0,0,C.A. 29395,10.5,F33,S
+68,0,3,"Crease, Mr. Ernest James",male,19,0,0,S.P. 3464,8.1583,,S
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