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	<title>gnTEAM &#187; Search Results  &#187;  &#8220;Negation&#8221;</title>
	<atom:link href="http://gnteam.cs.manchester.ac.uk/search/%22Negation%22/feed/rss2" rel="self" type="application/rss+xml" />
	<link>http://gnteam.cs.manchester.ac.uk</link>
	<description>Text extraction, analytics, mining</description>
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		<title>CliNER</title>
		<link>http://gnteam.cs.manchester.ac.uk/resources/cliner/</link>
		<comments>http://gnteam.cs.manchester.ac.uk/resources/cliner/#comments</comments>
		<pubDate>Wed, 10 Feb 2016 13:07:39 +0000</pubDate>
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		<description><![CDATA[<p>About CliNER CliNER is a command line tool for identification of mentions of four categories of clinically relevant events: Problems, Tests, Treatments and Clinical Departments. It also recognises and normalises clinical temporal expressions. It was developed as part of the i2b2 2012 text mining challenge and therefore has been trained&#8230; </p>
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]]></description>
				<content:encoded><![CDATA[<h2>About CliNER</h2>
<p>CliNER is a command line tool for identification of mentions of four categories of clinically relevant events: Problems, Tests, Treatments and Clinical Departments. It also recognises and normalises clinical temporal expressions. It was developed as part of the <a href="https://www.i2b2.org/NLP/TemporalRelations/">i2b2 2012 text mining challenge</a> and therefore has been trained and optimised on the i2b2 data.</p>
<p>For example, for input:</p>
<p align="center">He had surgery about 3 weeks ago and had the lining cleaned and a biopsy was performed.</p>
<p>CliNER will produce the following output (stand-off):</p>
<div class="xml">
<pre>&lt;?xml version="1.0" encoding="UTF-8" ?&gt;
&lt;ClinicalNarrativeTemporalAnnotation&gt;
&lt;TEXT&gt;&lt;![CDATA[
He had surgery about 3 weeks ago and had the lining cleaned and a biopsy was performed.
]]&gt;&lt;/TEXT&gt;
&lt;TAGS&gt;
&lt;EVENT id="E1" start="65" end="73" text="a biopsy" modality="FACTUAL" polarity="POS" type="TEST" /&gt;
&lt;EVENT id="E1" start="8" end="15" text="surgery" modality="FACTUAL" polarity="POS" type="TREATMENT" /&gt;
&lt;TIMEX3 id="T1" start="22" end="33" text="3 weeks ago" type="DATE" val="2014-07-29" mod="NA" /&gt;
&lt;/TAGS&gt;
</pre>
</div>
<p>System Architecture</p>
<ul>
<li>Implemented in Java, using <a href="http://ctakes.apache.org/">cTAKES</a>, <a href="http://crfpp.googlecode.com/">CRF++</a> and <a href="https://github.com/filannim/clinical-norma">Clinical NorMA</a></li>
<li>Support for multiple formats, currently supporting:
<ul>
<li>standoff XML</li>
<li>character offset-based format</li>
</ul>
</li>
</ul>
<p>Algorithm details<br />
Conditional random fields with IO scheme and five groups of features:</p>
<ul>
<li>Lexical features included the token itself, its lemma, and POS tag, as well as lemmas and POS tags of the surrounding tokens. Each token was also assigned features from its associated chunk (phrase): the type of phrase (nominal, verbal, etc), tense and aspect (if the phrase was verbal), the location of the token within the chunk (beginning or inside), and the presence of negation.</li>
<li>Domain features capture mentions of specific clinical/healthcare concepts. Mentions of Problem, Test, and Treatment (as generated by cTAKES) were assigned to the token.</li>
<li>Semantic role features model dependencies between the token and associated verb. Each token is assigned the role, the verb, and their combination (eg, ‘object+perform’) in order to capture particular verb–role preferences.</li>
<li>Section type feature represents the section type in which the token appeared.</li>
<li>Temporal expression (TE) features represent five features that indicated the presence of the five common types of constituents of TEs in a given token.</li>
</ul>
<p>More details on the architecture and the performance of the tool can be found in the paper below. Please cite this publication if you use CliNER:</p>
<p>Kovačević, A., Dehghan, A., Filannino, M., Keane, J. A., &amp; Nenadic, G. (2013). Combining rules and machine learning for extraction of temporal expressions and events from clinical narratives. <em>Journal of the American Medical Informatics Association</em>, 20(5), 859-866.</p>
<div>Contact <a href="http://gnteam.cs.manchester.ac.uk/staff/akovacevic/">Aleksandar Kovacevic</a> (<a href="http://informatika.ftn.uns.ac.rs/AleksandarKovacevic/">http://informatika.ftn.uns.ac.rs/AleksandarKovacevic/</a>, <a href="mailto:kocha78@gmail.com">kocha78@gmail</a>) with any questions, bugs and/or suggestions.</div>
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		<item>
		<title>Contrasts and contradictions in scientific texts</title>
		<link>http://gnteam.cs.manchester.ac.uk/project/contrasts-and-contradictions-in-scientific-texts/</link>
		<comments>http://gnteam.cs.manchester.ac.uk/project/contrasts-and-contradictions-in-scientific-texts/#comments</comments>
		<pubDate>Thu, 02 Jul 2015 10:07:07 +0000</pubDate>
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		<guid isPermaLink="false">http://gnode.dev/?post_type=project&#038;p=1538</guid>
		<description><![CDATA[<p>Detecting and analysing contrasts and contradictions in scientific texts is essential for suggesting further research potentials and discoveries. Finding contrasts and contradictions in text by means of automatic methods is a relatively new area in text mining. Specifically, most biological text mining research has so far focused on mining affirmative&#8230; </p>
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]]></description>
				<content:encoded><![CDATA[<p>Detecting and analysing contrasts and contradictions in scientific texts is essential for suggesting further research potentials and discoveries. Finding contrasts and contradictions in text by means of automatic methods is a relatively new area in text mining. Specifically, most biological text mining research has so far focused on mining affirmative statements about the relations amongst entities, although it is of growing interest to find reports on weak or negative relations, or lack there of. Negation detection is a middle step to finding contrasts and contradictions, and has been of special interest in medical text mining, because of the abundance of negative patterns in medical descriptions. The aim of this research is to develop text mining methods to detect and analyse contrasting facts in the biomedical literature and specifically in molecular interactions.</p>
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		<title>Information for prospective postgraduate students</title>
		<link>http://gnteam.cs.manchester.ac.uk/contact/prospective-postgraduates/</link>
		<comments>http://gnteam.cs.manchester.ac.uk/contact/prospective-postgraduates/#comments</comments>
		<pubDate>Mon, 22 Jun 2015 12:21:04 +0000</pubDate>
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]]></description>
				<content:encoded><![CDATA[<div class="osc-res-tab tabbable   osc-tabs-left"><div style="clear:both;width: 100%;"><ul class="nav osc-res-nav nav-pills osc-tabs-left-ul" id="oscitas-restabs-1-prospective-postgraduates-78957"><li class="active"><a href="./#general-information" data-toggle="tab">General information</a></li><li class=""><a href="./#themes" data-toggle="tab">Themes</a></li><li class=""><a href="./#application-steps" data-toggle="tab">Application steps</a></li><li class=""><a href="./#funding" data-toggle="tab">Funding</a></li><li class=""><a href="./#environment" data-toggle="tab">Environment</a></li></ul></div><div style="clear:both;width: 100%;"><ul class="tab-content" id="oscitas-restabcontent-1-prospective-postgraduates-78957"><li class="tab-pane active" id="general-information"></p>
<h3>General information</h3>
<p>We are always keen to have postgraduate research students in various areas of text mining and natural language processing. As a rule of thumb, you will need to have an xmaplesxcellent first degree in computer science or related area (e.g. computational lingustics, mathematics, physics, bioinformatics), with very good programming experience and some experience in natural language processing (e.g. final year project, summer internship, an ad-hoc project). An MSc or publications in a related area will be also a distinctive advanatage <a href="https://writing-help.org/blog/domestic-terrorism-essay" style="text-decoration: none; color: inherit;">try terrorism essay for free</a>.</p>
<p>The main theme of our research is <strong>feature engineering</strong> from unstructured documents written in natural languages. We investigate methodologies for the extraction of both explicit and implicit features from large collections of textual documents. Features can be terms, names, relations, co-occurances, events, etc. Once engineered from text, the features can be used to provide understanding and reasoning over knowledge (e.g. by applying machine learning or data mining) &#8211; this discipline is referred to as text analytics, text mining or more generally natural language processing (NLP).</p>
<p></li><li class="tab-pane " id="themes"></p>
<h3>Themes</h3>
<p>Here are some core <strong>text mining themes</strong> (please see below for details) that are currently the focus in our TEAM:</p>
<ul>
<li><strong>Text analytics and sentiment analysis</strong>: identification of subjective opinion and sentiment features from user-generated content (e.g. blog mining, tweets, etc.);</li>
<li><strong>Extracting negations, contrasts and contradictions</strong>: identification of utterances that are negated, or contrast or contradict some other expressions (both explicit and implicit);</li>
<li><strong>Concept mining and structuring</strong>: learning and identification of concepts and terminology from text, including their structuring (internal and external);</li>
<li><strong>Temporal text analytics</strong>: identification of temporal expressions and their scope in text;</li>
<li><strong>Integrated text and data mining</strong>: combining the results from different perspectives using various methods from machine learning;</li>
<li><strong>Text processing midleware for the Semantic Web</strong>: building an infrastructure to support building text mining solutions for the Semantic Web (identification of concepts, links, etc);</li>
</ul>
<p>and these are preferred <strong>application areas</strong>:</p>
<ul>
<li>Biology and biomedicine (molecular interactions, cancer studies, characterisation of molecular events, etc.)</li>
<li>Bioinformatics and computational biology (tools, services, resources, methods)</li>
<li>Clinical medicine and health-care (clinical decision support, quality of life monitoring)</li>
<li>E-science, e-commerce and e-government (e.g. monitoring, tracking, dissemination of information)</li>
<li>Engineering (knowledge management)</li>
</ul>
<p>You would typically &#8216;select&#8217; a topic that consist of a particular theme in a specific application area. I&#8217;d be also happy to consider proposals in the areas of <strong>multi-lingual text mining</strong> and <strong>NLP for Serbian</strong>.</p>
<p></li><li class="tab-pane " id="application-steps"></p>
<h3>Application steps</h3>
<p>You will be expected to have passion for text processing, in addition to an excellent first degree in computer science or related area. Some experience in natural language processing is very useful, whereas very good programming experience (in a combination of programming languages) is a must. If you belive you&#8217;ve got all these, send an email to Goran Nenadic (see below) with a full CV and a brief note as why you would like to do PhD in our TEAM. Please allow some time for us to reply. Contact email: <a href="mailto:G.Nenadic@manchester.ac.uk">G.Nenadic@manchester.ac.uk</a>.</p>
<p></li><li class="tab-pane " id="funding"></p>
<h3>Funding</h3>
<p>PhD studies are between 3 and 4 years, typically closer to 4 than to 3 years. There is only one route for securing funding: the candidate needs to be outstanding. There are 3 possible sources of funding:</p>
<ul>
<li>specific, pre-defined projects (NONE CURRENTLY),</li>
<li>funding from the School of Computer Science (see <a href="http://cdt.cs.manchester.ac.uk/" target="_blank">here</a> for details) and</li>
<li>external funding (private, external bodies &#8211; e.g. foreign governments, etc).</li>
</ul>
<p></li><li class="tab-pane " id="environment"></p>
<h3>Environment</h3>
<p>The School of Computer Science is one of the leading Schools in the UK reknown for the excellence of its research. The world&#8217;s first computer with internal memory was build in the School and Alan Turing has laid the foundations of Computer Science and Artificial intelligence while in Manchester. The international reputation of our research reflects on its high ranking in the last national Research Assessment Exercise (RAE), which places the School among the best five Computer Science departments in the UK and top in England for research power. The School has a vibrant research environment with more than 150 PhD students, 90 research staff and 70 academic staff.</p>
<p>Our research <a href="http://gnode.dev/people/">TEAM</a> is part of the Text Mining/NLP research group, which hosts the UK National Centre for Text Mining. We are also affiliated to <a href="http://www.mib.ac.uk/" target="_blank">the Manchester Interdisciplinary BioCentre</a>. The team is vibrant, diverse and very much international.</p>
<p></li></ul></div></div>
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		<item>
		<title>Training</title>
		<link>http://gnteam.cs.manchester.ac.uk/training/</link>
		<comments>http://gnteam.cs.manchester.ac.uk/training/#comments</comments>
		<pubDate>Mon, 22 Jun 2015 12:04:38 +0000</pubDate>
		<dc:creator><![CDATA[admin]]></dc:creator>
		
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		<description><![CDATA[<p>gnTEAM provides traninig in topics related to text mining for undergraduate (BSc final year projects) and postgraudate students (MSc, MPhil, PhD and EngD projects). Final year undergraduate and MSc projects associated with the team are announced annually as part of the School of Computer Science taught programmes. The current research post-graduate&#8230; </p>
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]]></description>
				<content:encoded><![CDATA[<p>gnTEAM provides traninig in topics related to text mining for undergraduate (BSc final year projects) and postgraudate students (MSc, MPhil, PhD and EngD projects).<br />
Final year undergraduate and MSc projects associated with the team are announced annually as part of the School of Computer Science taught programmes.</p>
<p>The current <strong>research post-graduate themes</strong> include:</p>
<ul>
<li>Integrated and Contrastive Text and Data Mining</li>
<li>Text Analytics and Blog/Forum Sentiment Analysis</li>
<li>Extracting negations, contrasts and contradiction from biomedical literature</li>
<li>Clinical text mining</li>
<li>Text mining in engineering</li>
</ul>
<p>More specific post-graduate information is available <a href="http://gnode.dev/contact/prospective-postgraduates/">here</a>. For PhD funding opportunities see <a href="http://www.cs.manchester.ac.uk/study/postgraduate-research/programmes/cdt/" target="_blank">CDT in Computer Science</a>.</p>
<h2>Selected completed student projects</h2>
<div class="table-responsive"><table  style="width:100%; "  class="easy-table easy-table-default " border="0">
<thead>
<tr><th >Student Name</th>
<th >Project Title</th>
<th >Year</th>
</tr>
</thead>
<tbody>
<tr><td >E. Hein</td>
<td > EDViC: a web application to visualise and explore epidemiological literature (BSc project)</td>
<td > 2013</td>
</tr>

<tr><td >T. Patel</td>
<td > Analysing Twitter Posts to Discover and Review New Software Tools (BSc project)</td>
<td > 2012</td>
</tr>

<tr><td >B. Dumitru</td>
<td > Mining twitter data to gather information about pharmaceutical drugs (BSc project)</td>
<td > 2012</td>
</tr>

<tr><td >I. Townend</td>
<td > Mapping of Clinical Data between Heterogeneous Terminologies and Classifications (MSc project)</td>
<td > 2011</td>
</tr>

<tr><td >S. Asif</td>
<td > An Analysis of Financial Blogs and Forums (MSc project)</td>
<td > 2010</td>
</tr>

<tr><td >A. Dehghan</td>
<td > A Rule-based Approach to External Context Extraction from Biomedical Literature: URL and Role Extraction (MSc project)</td>
<td > 2010</td>
</tr>

<tr><td >A. Tsoutsoumpi</td>
<td > A question answering system from FAQ pages (MSc project)</td>
<td > 2010</td>
</tr>

<tr><td >D. Yang</td>
<td > Extending Areca with Remote Backup Features (BSc project)</td>
<td > 2010</td>
</tr>

<tr><td >S. Latif</td>
<td >Automatic Summarisation As Pre-Processing For Document Clustering (PhD project)</td>
<td > 2010</td>
</tr>

<tr><td >M. Greenwood</td>
<td >Prioritising links for Topic-focused Web Crawling using Lexical and Terminological Profiling (MPhil project)</td>
<td > 2009</td>
</tr>

<tr><td >H. Afzal</td>
<td >A Literature-Based Framework for Semantic Descriptions of E-Science Resources (PhD project)</td>
<td > 2009</td>
</tr>
</tbody></table></div>
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		<title>Finding Conflicting Statements in the Biomedical Literature</title>
		<link>http://gnteam.cs.manchester.ac.uk/publication/157382-finding/</link>
		<comments>http://gnteam.cs.manchester.ac.uk/publication/157382-finding/#comments</comments>
		<pubDate>Tue, 10 Nov 2015 11:46:27 +0000</pubDate>
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		<title>Using SVMs with the Command Relation Features to Identify Negated Events in Biomedical Literature</title>
		<link>http://gnteam.cs.manchester.ac.uk/publication/113923-using/</link>
		<comments>http://gnteam.cs.manchester.ac.uk/publication/113923-using/#comments</comments>
		<pubDate>Tue, 10 Nov 2015 11:46:18 +0000</pubDate>
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