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            <!--<div class="header-content mx-auto">-->
              <h1 class="title-heading">DeepVet: Automating Veterinary Disease Coding</h1>
            <br>
            <p>Annotate veterinary clinical notes with SNOMED-CT codes</p>
            <!--class="mb-5"-->
              <!--<a href="#download" class="btn btn-outline btn-xl js-scroll-trigger">Start Now for Free!</a>-->
            </div>
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          <div class="col-md-12">
              <div>
                <textarea class="form-control" id="clinicalNotes" rows="4" placeholder="Input text here..."
                style="height: 300px"></textarea>
                <select class="form-control" id="exampleSelect">
                <option>Choose an example...</option>
                <option>Cancer example</option>
                <option>Genitourinary disorder example</option>
                </select>
                <br>
                <div class="row ml-auto" id="submitButtonRow">
                  <button type="button" class="btn btn-primary" id="submitButton">Submit</button>
                  <!--<div class="spinner-border text-danger ml-3" role="status">-->
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    <section class="bg-gray features">
      <div class="row">
        <div class="col-6 justify-content-around ml-auto share" id="predictionResult">
        </div>
        <div class="section-heading text-left col-4 mx-auto">
          <h3>Inferring SNOMED-CT codes through the hierarchy</h3>
           <br>
          <p class="text-muted">We develop the first large-scale algorithm to automatically predict all 4577 standard veterinary diagnosis codes from free text.</p>
          <br>
          <p class="text-muted">We trained our algorithm on a curated dataset of over 100K expert labeled veterinary clinical notes and over one million unlabeled notes.</p>
          <hr>
        </div>
      </div>
    </section>

    <section id="features">
      <div class="row">
        <div class="section-heading text-left col-4 ml-auto">
          <h3>Interpreting result</h3>
           <br>
          <p class="text-muted">In order to better understand how DeepVet predicts diagnosis codes from clinical notes, we implement a simple saliency-based interpretation method</p>
            <hr>
        </div>
        <div class="col-5 justify-content-around mx-auto">
          <p>$PET_NAME$, a 2 year old male neutered boxer , presented to CSU dermatology service for a recheck of <span class="highlight">allergic dermatitis</span> .
            It was reported that $PET_NAME$ 's  <span class="highlight">pruritus</span> is relatively seasonal , worse in the spring and summer , but does not completely go away
            in the winter . $PET_NAME$'s main problem  <span class="highlight">areas</span> were his  <span class="highlight">paws</span> and his muzzle .
          </p>
        </div>
      </div>
    </section>

    <section class="bg-gray">
      <div class="row">
        <div class="col-4 justify-content-around ml-auto">
          <img src="/assets/img/best-abstainsion-2.jpg" class="img-fluid" alt="">
        </div>
         <div class="section-heading text-left col-4 mx-auto">
          <h3>Automatic Abstention</h3>
           <br>
          <p class="text-muted">DeepVet also learns to abstain in examples when it is uncertain and defers them to human experts, fostering human-machine collaboration.</p>
           <br>
           <p class="text-muted">In order to not mislead further clinical research, having the ability to abstain from making very erroneous predictions and ensuring highly precise tagging is an important feature.</p>
            <hr>
        </div>
      </div>
    </section>


     <section class="learnmore" id="contact">
      <div class="row">
        <div class="col-4 justify-content-around ml-auto text-center section-heading">
          <h2>Learn more</h2>
          <p>Contact: <EMAIL></p>
        </div>
        <div class="text-left col-4 mx-auto">
          <p>
            <b>Large-scale Generative Modeling to Improve Automated Veterinary Disease Coding.</b> <br>
          <NAME>, <NAME>, and <NAME>. <br>
            <b>NeurISP Machine Learning for Health Workshop (2018).</b>
          </p> <br>
          <p> <b> DeepTag: inferring diagnoses from veterinary clinical notes. </b> <br>
            <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>ante, and <NAME>. <br>
            <b> npj Digital Medicine 1, no. 1 (2018): 60. </b> </b></p>
          <hr>
        </div>
      </div>
    </section>

    <!--<section class="contact" id="contact">-->
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  <!-- Custom scripts for this template -->
  <script src="/assets/js/new-age.min.js"></script>
  <script type="text/javascript">

    // Example selection
    var cancer_example = "$Pet_Name$ is a 10 year old male castrated hound mix that was presented for continuation of chemotherapy for previously diagnosed B-cell multicentric lymphoma. $Pet_Name$ was started on CHOP chemotherapy last week and has been doing very well since receiving doxorubicin. The owners have noted his lymph nodes have gotten much smaller. He has some loose stool, yet improved with metronidazole. Current medications include prednisolone. Assessment: $Pet_Name$ is in a strong partial remission based on today’s physical exam. He is also doing very well since starting chemotherapy. A CBC today was unremarkable and adequate for chemotherapy. She was dispensed oral cyclophosphamide and furosemide that the owners were instructed to give at home.";
    var metabolism_example = "$Person_Name$ cc : recheck hypercalcemia responding to pred - iCa has dropped - is on 10 milligram twice a day pred 25 milligram twice a day lasix eating human food on own feeling better blood urea nitrogen down from 89 -- > 62 today Vit D still pending wt stable has residual brisket edema from Fluids on Wed patient : Treating symptomatically discontinue fluids since drinking well on own lower pred to 10 milligram once daily and lasix 25 milligram once daily recheck on Tues pred appears to be treating underlying cause so strong suspicion for LSA E. Ellis VMD wt : 62.5 lbs . temperature : 101.3f"
    var psvg_excample = "$Pet_Name$ initially presented on 9/30 with lethargy and fever. She was diagnosed with bilateral renomegaly. An ultrasound had revealed possible cyst in a small left kidney and probable ureteral obstruction with secondary hydronephrosis of the right kidney. $Pet_Name$ was transfered to our care on the evening of 10/2."

    $('#exampleSelect').change(function(){
      var data= $(this).val();
      if (data === "Cancer example") {
        $("#clinicalNotes").val(cancer_example)
      } else if (data === "Genitourinary disorder example") {
          $("#clinicalNotes").val(psvg_excample)
      } else if (data === "Choose an example...") {
          $("#clinicalNotes").val("")
        }
    });

    var spinning_wheel_html = "<div class=\"spinner-border text-danger ml-3\" role=\"status\" id=\"spinWheel\"><span class=\"sr-only\">Loading...</span></div>";


    // Submission
    $("#submitButton").click(function() {
      var text = $("#clinicalNotes").val();
      var inp = {text: text};

      // add loading spinning
      $("#submitButtonRow").append(spinning_wheel_html);

      $.ajax({
          url: 'https://cors-anywhere.herokuapp.com/http://172.16.58.3/api/predict',  //real server address: http://172.16.58.3
          type: 'POST',
          data: JSON.stringify(inp),
          contentType: 'application/json; charset=utf-8',
          dataType: 'json',
          async: true,
          success: function(msg) {

              //also remove spin wheel
              $("#spinWheel").remove()

              //first we reset
              if ($("#predictionResult").children().length > 0) {
                  $("#predictionResult").empty()
              }

              // we then append result
              $("#predictionResult").append(msg['output_html']);
              console.log(msg);
          }
      });
    });
  </script>

  </body>

</html>
<commit_msg>Update deepvet.html<commit_after><!DOCTYPE html>
<html lang="en">

  <head>

    <meta charset="utf-8">
    <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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    <title>New Age - Start Bootstrap Theme</title>

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    <nav class="navbar navbar-expand-lg navbar-light fixed-top" id="mainNav">
      <div class="container ml-auto">
        <a class="navbar-brand js-scroll-trigger" href="#page-top">Stanford Laboratory for Machine Learning, Genomics and Health</a>
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      <div class="container h-10">
        <div class="row h-10">
          <div class="col-lg-12 ml-auto">
            <!--<div class="header-content mx-auto">-->
              <h1 class="title-heading">DeepVet: Automating Veterinary Disease Coding</h1>
            <br>
            <p>Annotate veterinary clinical notes with SNOMED-CT codes</p>
            <!--class="mb-5"-->
              <!--<a href="#download" class="btn btn-outline btn-xl js-scroll-trigger">Start Now for Free!</a>-->
            </div>
          </div>
        </div>
      </div>
    </header>

    <section class="demo text-left" id="download">
      <div class="container">
        <div class="row">
          <div class="col-md-12">
              <div>
                <textarea class="form-control" id="clinicalNotes" rows="4" placeholder="Input text here..."
                style="height: 300px"></textarea>
                <select class="form-control" id="exampleSelect">
                <option>Choose an example...</option>
                <option>Cancer example</option>
                <option>Genitourinary disorder example</option>
                </select>
                <br>
                <div class="row ml-auto" id="submitButtonRow">
                  <button type="button" class="btn btn-primary" id="submitButton">Submit</button>
                  <!--<div class="spinner-border text-danger ml-3" role="status">-->
                    <!--<span class="sr-only">Loading...</span>-->
                  <!--</div>-->
                </div>

              </div>
          </div>
        </div>
      </div>
    </section>

    <section class="bg-gray features">
      <div class="row">
        <div class="col-6 justify-content-around ml-auto share" id="predictionResult">
        </div>
        <div class="section-heading text-left col-4 mx-auto">
          <h3>Inferring SNOMED-CT codes through the hierarchy</h3>
           <br>
          <p class="text-muted">We develop the first large-scale algorithm to automatically predict all 4577 standard veterinary diagnosis codes from free text.</p>
          <br>
          <p class="text-muted">We trained our algorithm on a curated dataset of over 100K expert labeled veterinary clinical notes and over one million unlabeled notes.</p>
          <hr>
        </div>
      </div>
    </section>

    <section id="features">
      <div class="row">
        <div class="section-heading text-left col-4 ml-auto">
          <h3>Interpreting result</h3>
           <br>
          <p class="text-muted">In order to better understand how DeepVet predicts diagnosis codes from clinical notes, we implement a simple saliency-based interpretation method</p>
            <hr>
        </div>
        <div class="col-5 justify-content-around mx-auto">
          <p>$PET_NAME$, a 2 year old male neutered boxer , presented to CSU dermatology service for a recheck of <span class="highlight">allergic dermatitis</span> .
            It was reported that $PET_NAME$ 's  <span class="highlight">pruritus</span> is relatively seasonal , worse in the spring and summer , but does not completely go away
            in the winter . $PET_NAME$'s main problem  <span class="highlight">areas</span> were his  <span class="highlight">paws</span> and his muzzle .
          </p>
        </div>
      </div>
    </section>

    <section class="bg-gray">
      <div class="row">
        <div class="col-4 justify-content-around ml-auto">
          <img src="/assets/img/best-abstainsion-2.jpg" class="img-fluid" alt="">
        </div>
         <div class="section-heading text-left col-4 mx-auto">
          <h3>Automatic Abstention</h3>
           <br>
          <p class="text-muted">DeepVet also learns to abstain in examples when it is uncertain and defers them to human experts, fostering human-machine collaboration.</p>
           <br>
           <p class="text-muted">In order to not mislead further clinical research, having the ability to abstain from making very erroneous predictions and ensuring highly precise tagging is an important feature.</p>
            <hr>
        </div>
      </div>
    </section>


     <section class="learnmore" id="contact">
      <div class="row">
        <div class="col-4 justify-content-around ml-auto text-center section-heading">
          <h2>Learn more</h2>
          <p>Contact: <EMAIL></p>
        </div>
        <div class="text-left col-4 mx-auto">
          <p>
            <b>Large-scale Generative Modeling to Improve Automated Veterinary Disease Coding.</b> <br>
          <NAME>, <NAME>, and <NAME>. <br>
            <b>NeurIPS Machine Learning for Health Workshop (2018).</b>
          </p> <br>
          <p> <b> DeepTag: inferring diagnoses from veterinary clinical notes. </b> <br>
            <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, and <NAME>. <br>
            <b> npj Digital Medicine 1, no. 1 (2018): 60. </b> </b></p>
          <hr>
        </div>
      </div>
    </section>

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  <script src="https://stackpath.bootstrapcdn.com/bootstrap/4.2.1/js/bootstrap.min.js" integrity="<KEY>" crossorigin="anonymous"></script>

  <!-- Plugin JavaScript -->
  <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery-easing/1.4.1/jquery.easing.min.js"></script>

  <!-- Custom scripts for this template -->
  <script src="/assets/js/new-age.min.js"></script>
  <script type="text/javascript">

    // Example selection
    var cancer_example = "$Pet_Name$ is a 10 year old male castrated hound mix that was presented for continuation of chemotherapy for previously diagnosed B-cell multicentric lymphoma. $Pet_Name$ was started on CHOP chemotherapy last week and has been doing very well since receiving doxorubicin. The owners have noted his lymph nodes have gotten much smaller. He has some loose stool, yet improved with metronidazole. Current medications include prednisolone. Assessment: $Pet_Name$ is in a strong partial remission based on today’s physical exam. He is also doing very well since starting chemotherapy. A CBC today was unremarkable and adequate for chemotherapy. She was dispensed oral cyclophosphamide and furosemide that the owners were instructed to give at home.";
    var metabolism_example = "$Person_Name$ cc : recheck hypercalcemia responding to pred - iCa has dropped - is on 10 milligram twice a day pred 25 milligram twice a day lasix eating human food on own feeling better blood urea nitrogen down from 89 -- > 62 today Vit D still pending wt stable has residual brisket edema from Fluids on Wed patient : Treating symptomatically discontinue fluids since drinking well on own lower pred to 10 milligram once daily and lasix 25 milligram once daily recheck on Tues pred appears to be treating underlying cause so strong suspicion for LSA E. Ellis VMD wt : 62.5 lbs . temperature : 101.3f"
    var psvg_excample = "$Pet_Name$ initially presented on 9/30 with lethargy and fever. She was diagnosed with bilateral renomegaly. An ultrasound had revealed possible cyst in a small left kidney and probable ureteral obstruction with secondary hydronephrosis of the right kidney. $Pet_Name$ was transfered to our care on the evening of 10/2."

    $('#exampleSelect').change(function(){
      var data= $(this).val();
      if (data === "Cancer example") {
        $("#clinicalNotes").val(cancer_example)
      } else if (data === "Genitourinary disorder example") {
          $("#clinicalNotes").val(psvg_excample)
      } else if (data === "Choose an example...") {
          $("#clinicalNotes").val("")
        }
    });

    var spinning_wheel_html = "<div class=\"spinner-border text-danger ml-3\" role=\"status\" id=\"spinWheel\"><span class=\"sr-only\">Loading...</span></div>";


    // Submission
    $("#submitButton").click(function() {
      var text = $("#clinicalNotes").val();
      var inp = {text: text};

      // add loading spinning
      $("#submitButtonRow").append(spinning_wheel_html);

      $.ajax({
          url: 'https://cors-anywhere.herokuapp.com/http://172.16.58.3/api/predict',  //real server address: http://172.16.58.3
          type: 'POST',
          data: JSON.stringify(inp),
          contentType: 'application/json; charset=utf-8',
          dataType: 'json',
          async: true,
          success: function(msg) {

              //also remove spin wheel
              $("#spinWheel").remove()

              //first we reset
              if ($("#predictionResult").children().length > 0) {
                  $("#predictionResult").empty()
              }

              // we then append result
              $("#predictionResult").append(msg['output_html']);
              console.log(msg);
          }
      });
    });
  </script>

  </body>

</html>

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