Automated Adverse Drug Event (ADE) Detection from Text in Spark NLP with BioBert

Adverse Drug Reactions (ADRs) or Adverse Drug Events (ADEs) are potentially very dangerous to patients and are amongst the top causes of morbidity and mortality [1]. Many ADRs are hard to discover as they happen to certain groups of people in certain conditions and they may take a long time to expose. Healthcare providers conduct clinical trials to discover ADRs before selling the products but normally are limited in numbers. Thus, post-market drug safety monitoring is required to help discover ADRs after the drugs are sold on the market [2].

Recently unstructured data such as medical reports [3] or social network data [4] have been used to detect content that contains ADRs. Case reports published in the scientific biomedical literature are abundant and generated rapidly. Social networks are another source of redundant data with unstructured format. While an individual tweet or Facebook status that contains ADRs may not be clinically useful, a large volume of these data can expose serious or unknown consequences.

Given the need for collecting ADRs from various resources that are not composed in a structured manner (i.e. tweet, news, web forum etc.) as well as scientific papers (i.e. PubMed, arxiv, white papers, clinical trials, etc.), we wanted to build an end-2-end NLP pipeline to detect if a text contains possible ADRs, and extracting the ADR and Drug entities mentioned.

#tensorflow #naturallanguageprocessing #python #healthcare #apache-spark

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Automated Adverse Drug Event (ADE) Detection from Text in Spark NLP with BioBert

Navigating Between DOM Nodes in JavaScript

In the previous chapters you've learnt how to select individual elements on a web page. But there are many occasions where you need to access a child, parent or ancestor element. See the JavaScript DOM nodes chapter to understand the logical relationships between the nodes in a DOM tree.

DOM node provides several properties and methods that allow you to navigate or traverse through the tree structure of the DOM and make changes very easily. In the following section we will learn how to navigate up, down, and sideways in the DOM tree using JavaScript.

Accessing the Child Nodes

You can use the firstChild and lastChild properties of the DOM node to access the first and last direct child node of a node, respectively. If the node doesn't have any child element, it returns null.

Example

<div id="main">
    <h1 id="title">My Heading</h1>
    <p id="hint"><span>This is some text.</span></p>
</div>

<script>
var main = document.getElementById("main");
console.log(main.firstChild.nodeName); // Prints: #text

var hint = document.getElementById("hint");
console.log(hint.firstChild.nodeName); // Prints: SPAN
</script>

Note: The nodeName is a read-only property that returns the name of the current node as a string. For example, it returns the tag name for element node, #text for text node, #comment for comment node, #document for document node, and so on.

If you notice the above example, the nodeName of the first-child node of the main DIV element returns #text instead of H1. Because, whitespace such as spaces, tabs, newlines, etc. are valid characters and they form #text nodes and become a part of the DOM tree. Therefore, since the <div> tag contains a newline before the <h1> tag, so it will create a #text node.

To avoid the issue with firstChild and lastChild returning #text or #comment nodes, you could alternatively use the firstElementChild and lastElementChild properties to return only the first and last element node, respectively. But, it will not work in IE 9 and earlier.

Example

<div id="main">
    <h1 id="title">My Heading</h1>
    <p id="hint"><span>This is some text.</span></p>
</div>

<script>
var main = document.getElementById("main");
alert(main.firstElementChild.nodeName); // Outputs: H1
main.firstElementChild.style.color = "red";

var hint = document.getElementById("hint");
alert(hint.firstElementChild.nodeName); // Outputs: SPAN
hint.firstElementChild.style.color = "blue";
</script>

Similarly, you can use the childNodes property to access all child nodes of a given element, where the first child node is assigned index 0. Here's an example:

Example

<div id="main">
    <h1 id="title">My Heading</h1>
    <p id="hint"><span>This is some text.</span></p>
</div>

<script>
var main = document.getElementById("main");

// First check that the element has child nodes 
if(main.hasChildNodes()) {
    var nodes = main.childNodes;
    
    // Loop through node list and display node name
    for(var i = 0; i < nodes.length; i++) {
        alert(nodes[i].nodeName);
    }
}
</script>

The childNodes returns all child nodes, including non-element nodes like text and comment nodes. To get a collection of only elements, use children property instead.

Example

<div id="main">
    <h1 id="title">My Heading</h1>
    <p id="hint"><span>This is some text.</span></p>
</div>

<script>
var main = document.getElementById("main");

// First check that the element has child nodes 
if(main.hasChildNodes()) {
    var nodes = main.children;
    
    // Loop through node list and display node name
    for(var i = 0; i < nodes.length; i++) {
        alert(nodes[i].nodeName);
    }
}
</script>

#javascript 

Automated Adverse Drug Event (ADE) Detection from Text in Spark NLP with BioBert

Adverse Drug Reactions (ADRs) or Adverse Drug Events (ADEs) are potentially very dangerous to patients and are amongst the top causes of morbidity and mortality [1]. Many ADRs are hard to discover as they happen to certain groups of people in certain conditions and they may take a long time to expose. Healthcare providers conduct clinical trials to discover ADRs before selling the products but normally are limited in numbers. Thus, post-market drug safety monitoring is required to help discover ADRs after the drugs are sold on the market [2].

Recently unstructured data such as medical reports [3] or social network data [4] have been used to detect content that contains ADRs. Case reports published in the scientific biomedical literature are abundant and generated rapidly. Social networks are another source of redundant data with unstructured format. While an individual tweet or Facebook status that contains ADRs may not be clinically useful, a large volume of these data can expose serious or unknown consequences.

Given the need for collecting ADRs from various resources that are not composed in a structured manner (i.e. tweet, news, web forum etc.) as well as scientific papers (i.e. PubMed, arxiv, white papers, clinical trials, etc.), we wanted to build an end-2-end NLP pipeline to detect if a text contains possible ADRs, and extracting the ADR and Drug entities mentioned.

#tensorflow #naturallanguageprocessing #python #healthcare #apache-spark

8 Open-Source Tools To Start Your NLP Journey

Teaching machines to understand human context can be a daunting task. With the current evolving landscape, Natural Language Processing (NLP) has turned out to be an extraordinary breakthrough with its advancements in semantic and linguistic knowledge. NLP is vastly leveraged by businesses to build customised chatbots and voice assistants using its optical character and speed recognition techniques along with text simplification.

To address the current requirements of NLP, there are many open-source NLP tools, which are free and flexible enough for developers to customise it according to their needs. Not only these tools will help businesses analyse the required information from the unstructured text but also help in dealing with text analysis problems like classification, word ambiguity, sentiment analysis etc.

Here are eight NLP toolkits, in no particular order, that can help any enthusiast start their journey with Natural language Processing.


Also Read: Deep Learning-Based Text Analysis Tools NLP Enthusiasts Can Use To Parse Text

1| Natural Language Toolkit (NLTK)

About: Natural Language Toolkit aka NLTK is an open-source platform primarily used for Python programming which analyses human language. The platform has been trained on more than 50 corpora and lexical resources, including multilingual WordNet. Along with that, NLTK also includes many text processing libraries which can be used for text classification tokenisation, parsing, and semantic reasoning, to name a few. The platform is vastly used by students, linguists, educators as well as researchers to analyse text and make meaning out of it.


#developers corner #learning nlp #natural language processing #natural language processing tools #nlp #nlp career #nlp tools #open source nlp tools #opensource nlp tools

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Top Spark Development Companies | Best Spark Developers - TopDevelopers.co

An extensively researched list of top Apache spark developers with ratings & reviews to help find the best spark development Companies around the world.

Our thorough research on the ace qualities of the best Big Data Spark consulting and development service providers bring this list of companies. To predict and analyze businesses and in the scenarios where prompt and fast data processing is required, Spark application will greatly be effective for various industry-specific management needs. The companies listed here have been skillfully boosting businesses through effective Spark consulting and customized Big Data solutions.

Check out this list of Best Spark Development Companies with Best Spark Developers.

#spark development service providers #top spark development companies #best big data spark development #spark consulting #spark developers #spark application