[protege-user] PhD Position in model-driven data analytics (for the biomedical domain)
"Sahay, Ratnesh" <[email protected]> Fri, 2 Oct 2015 19:01:13 +0000
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--===============6488379478347260267== Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_DB5PR01MB09019E07010A2A48AC60FBF28F4B0DB5PR01MB0901eurp_" --_000_DB5PR01MB09019E07010A2A48AC60FBF28F4B0DB5PR01MB0901eurp_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable [Apologies for cross-posting] PhD Position in model-driven data analytics (for the biomedical domain) Mathematical models for biomedical data are a powerful means to infer compl= ex mechanisms from experimental data. Such models are applied to infer reg= ulatory networks from experimental data for cells, but also for the assignm= ent of functional states cells and tissues derived from experimental time s= eries. The healthcare and Life Sciences (HCLS) domains are developing into data dr= iven sciences, which gather and contribute the public biomedical knowledge = in standardized representations throughout the world. Increasingly semantic= Web technologies are being applied in these knowledge rich domains to achi= eve interoperability of data and the semantic normalisation of the data res= ources for subsequent interpretation. This data is available as an integra= ted knowledge graph to contribute to the prior knowledge in the mathematica= l model, but also serves as a validation infrastructure, since the known kn= owledge should be replicated through the mathematical model. Expert knowledge in the form of mathematical models can be considered suffi= cient statistics of prior experimentation in the domain, embodying abstract= knowledge of it. When used in a probabilistic framework, such models provi= de a sound foundation for data mining, inference, and decision making under= uncertainty. The PhD position will focus on new analytical methods in the biomedical dom= ain that can exploit both the knowledge graph and relevant mathematical mod= els, with application to the prediction of states for cells, tissues and mo= re complex regulatory processes. The prior knowledge results from publicly = available data in terms of network information, but also on assumptions on = the underlying mechanisms and complex semantic annotations for the involved= components. Part of the research work is the participation into public cha= llenges and the analysis of standard data sets for the prediction of the kn= own states. Particular focus will be set on the molecular and phenotypic ch= aracterisation of cellular, tissues and other organismal states based on th= e full integration of the biomedical knowledge graph for particular disease= s. The Insight Centre for Data Analytics and the Information Technology Discip= line at the National University of Ireland, Galway, invite applications for= a PhD position in the area of mathematical modelling, machine learning, st= atistical models, and development of prediction models. The PhD student wil= l be hosted by the Information Technology discipline in the National Univer= sity of Ireland in Galway (NUIG) and the Insight Institute at NUIG. The sel= ected candidate will be embedded in international collaborations and possib= ly also European research projects. The candidate will be enabled to publis= h in high impact international conferences and journals and to participate = in world leading research. Eligibility * Four Years Bachelor's Degree or Master's Degree in Computer Scienc= e, Statistics, Applied Mathematics, Data Analytics, Operations Research, In= formation Technology, or Bioinformatics * Good knowledge of data analytics principles, for example machine l= earning, data mining, and/or statistics for data analysis * Good background in Java, Python or R programming * Strong interest in building mathematical models for prediction * Alternative skills: semantic web technologies, knowledge graphs Stipend: PhD scholarship stipend of 18,000 per year, no tax. The duration o= f the contract will be 4 years as a fully funded PhD. Application procedure Informal enquiries about these positions may be made to: Prof. Dr. Dietrich Rebholz-Schuhmann Insight Centre for Data Analytics NUI Galway, The DERI building IDA Business Park, Lower Dangan Galway, IRELAND Email: [email protected]<mailto:[email protected]> Dr. Michael Madden Machine Learning & Data Mining Research Group, College of Engineering & Informatics National University of Ireland, Galway Galway, IRELAND Email: [email protected]<mailto:[email protected]> When applying, please use the same email addresses above and put " PhD Posi= tion in data modelling and simulation" in the subject line of your email. C= andidates are requested to submit (1) a cover letter explaining your intent= ions, and (2) a CV (in PDF format) giving details on your academic degrees,= working experiences and IT skills (maximum 2 pages). It is difficult but s= till advantageous, if you can write a paragraph (e.g. in the cover letter, = or extra), what ambitions in the PhD position appeal most to you. Interviews will be carried out towards middle and end of October via skype = conference call, and the position can be filled without much delay if requi= red. We expect the successful candidate to start at the earliest possible d= ate, ideally towards December 2015. INSIGHT Centre for Data Analytics (previously DERI http://deri.ie/) http://= www.insight-centre.org/ is a leading research institute in Semantic Web/Lin= ked Data technologies that offers a stimulating, dynamic and multi-cultural= research environment, excellent ties to research-groups worldwide, close c= ollaboration with industrial partners and up-to-date infrastructure and res= ources. The Information Technology Discipline (http://www.it.nuigalway.ie/) is NUI = Galway's Computer Science department and has a 20-year track record in inno= vative teaching, research, and engagement with industry and community. It i= s the largest academic discipline in the College of Engineering & Informati= cs, and has an established track record of excellence in research and techn= ology development, leading to numerous successful research groups with rese= arch ranging from theoretical advances to applications in science, engineer= ing, business, and medicine. ---------------------------------------------------------------------------= ---------------------------------- Regards, Ratnesh Sahay, PhD Research Unit Leader Semantics in eHealth and Life Sciences (SeLS) Insight Centre for Data Analytics NUI Galway, The DERI building IDA Business Park, Lower Dangan Galway, IRELAND Tel: + 353 91 495253 Fax: + 353 91 495541 Web: http://sels.insight-centre.org/ Web: http://www.ratneshsahay.org/ --_000_DB5PR01MB09019E07010A2A48AC60FBF28F4B0DB5PR01MB0901eurp_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable <html xmlns:v=3D"urn:schemas-microsoft-com:vml" xmlns:o=3D"urn:schemas-micr= osoft-com:office:office" xmlns:w=3D"urn:schemas-microsoft-com:office:word" = xmlns:m=3D"http://schemas.microsoft.com/office/2004/12/omml" xmlns=3D"http:= //www.w3.org/TR/REC-html40"> <head> <meta http-equiv=3D"Content-Type" content=3D"text/html; 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mso-level-number-position:left; text-indent:-18.0pt; font-family:"Courier New";} @list l0:level9 {mso-level-number-format:bullet; mso-level-text:\F0A7; mso-level-tab-stop:none; mso-level-number-position:left; text-indent:-18.0pt; font-family:Wingdings;} ol {margin-bottom:0cm;} ul {margin-bottom:0cm;} --></style><!--[if gte mso 9]><xml> <o:shapedefaults v:ext=3D"edit" spidmax=3D"1026" /> </xml><![endif]--><!--[if gte mso 9]><xml> <o:shapelayout v:ext=3D"edit"> <o:idmap v:ext=3D"edit" data=3D"1" /> </o:shapelayout></xml><![endif]--> </head> <body lang=3D"EN-IE" link=3D"blue" vlink=3D"purple"> <div class=3D"WordSection1"> <p class=3D"MsoNormal">[Apologies for cross-posting]<o:p></o:p></p> <p class=3D"MsoNormal"><o:p> </o:p></p> <p class=3D"MsoNormal" style=3D"text-align:justify"><b><u>PhD Position in m= odel-driven data analytics (for the biomedical domain)<o:p></o:p></u></b></= p> <p class=3D"MsoNormal" style=3D"text-align:justify">Mathematical models for= biomedical data are a powerful means to infer complex mechanisms from expe= rimental data. Such models are applied to infer regulatory networks f= rom experimental data for cells, but also for the assignment of functional states cells and tissues derived from exp= erimental time series. <o:p></o:p></p> <p class=3D"MsoNormal" style=3D"text-align:justify">The healthcare and Life= Sciences (HCLS) domains are developing into data driven sciences, which ga= ther and contribute the public biomedical knowledge in standardized represe= ntations throughout the world. Increasingly semantic Web technologies are being applied in these knowledge rich domain= s to achieve interoperability of data and the semantic normalisation of the= data resources for subsequent interpretation. This data is available= as an integrated knowledge graph to contribute to the prior knowledge in the mathematical model, but also serv= es as a validation infrastructure, since the known knowledge should be repl= icated through the mathematical model. <o:p></o:p></p> <p class=3D"MsoNormal" style=3D"text-align:justify">Expert knowledge in the= form of mathematical models can be considered sufficient statistics of pri= or experimentation in the domain, embodying abstract knowledge of it. When = used in a probabilistic framework, such models provide a sound foundation for data mining, inference, and decision= making under uncertainty.<o:p></o:p></p> <p class=3D"MsoNormal" style=3D"text-align:justify">The PhD position will f= ocus on new analytical methods in the biomedical domain that can exploit bo= th the knowledge graph and relevant mathematical models, with application t= o the prediction of states for cells, tissues and more complex regulatory processes. The prior knowledge results= from publicly available data in terms of network information, but also on = assumptions on the underlying mechanisms and complex semantic annotations f= or the involved components. Part of the research work is the participation into public challenges and the a= nalysis of standard data sets for the prediction of the known states. Parti= cular focus will be set on the molecular and phenotypic characterisation of= cellular, tissues and other organismal states based on the full integration of the biomedical knowledge graph for= particular diseases. <i><o:p></o:p></i></p> <p class=3D"MsoNormal" style=3D"text-align:justify"><o:p> </o:p></p> <p class=3D"MsoNormal" style=3D"text-align:justify;background:white"><span = lang=3D"EN" style=3D"color:black;mso-fareast-language:EN-GB">The Insight Ce= ntre for Data Analytics and the Information Technology Discipline at the Na= tional University of Ireland, Galway, invite applications for a PhD position in the area of mathematical modelling, mac= hine learning, statistical models, and development of prediction models. Th= e PhD student will be hosted by the Information Technology discipline in th= e National University of Ireland in Galway (NUIG) and the Insight Institute at NUIG. The selected candidate= will be embedded in international collaborations and possibly also Europea= n research projects. The candidate will be enabled to publish in high impac= t international conferences and journals and to participate in world leading research. <o:p></o:p></span><= /p> <p class=3D"MsoNormal" style=3D"text-align:justify;background:white"><span = style=3D"mso-fareast-language:EN-US"><o:p> </o:p></span></p> <pre style=3D"text-align:justify"><b><u><span style=3D"font-size:11.0pt;fon= t-family:"Calibri","sans-serif"">Eligibility</span></u>= </b><span lang=3D"EN" style=3D"font-size:11.0pt;font-family:"Calibri&q= uot;,"sans-serif""> </span><b><u><span style=3D"font-size:11= .0pt;font-family:"Calibri","sans-serif""><o:p></o:p></s= pan></u></b></pre> <p class=3D"MsoListParagraphCxSpFirst" style=3D"margin-bottom:0cm;margin-bo= ttom:.0001pt;mso-add-space:auto;text-indent:-18.0pt;line-height:16.6pt;mso-= list:l0 level1 lfo2;background:white"> <![if !supportLists]><span lang=3D"EN" style=3D"font-family:Symbol;mso-fare= ast-language:EN-GB"><span style=3D"mso-list:Ignore">·<span style=3D"= font:7.0pt "Times New Roman"">  = ; </span></span></span><![endif]><span lang=3D"EN" style=3D"mso-fareast-langu= age:EN-GB">Four Years Bachelor’s Degree or Master’s Degree in C= omputer Science, Statistics, Applied Mathematics, Data Analytics, Operation= s Research, Information Technology, or Bioinformatics </span><span lang=3D"EN" style=3D"mso-fareast-language:EN-GB"><o:p></o:p></= span></p> <p class=3D"MsoListParagraphCxSpMiddle" style=3D"margin-bottom:0cm;margin-b= ottom:.0001pt;mso-add-space:auto;text-indent:-18.0pt;line-height:16.6pt;mso= -list:l0 level1 lfo2;background:white"> <![if !supportLists]><span lang=3D"EN" style=3D"font-family:Symbol;mso-fare= ast-language:EN-GB"><span style=3D"mso-list:Ignore">·<span style=3D"= font:7.0pt "Times New Roman"">  = ; </span></span></span><![endif]><span lang=3D"EN" style=3D"mso-fareast-langu= age:EN-GB">Good knowledge of data analytics principles, for example machine= learning, data mining, and/or statistics for data analysis<o:p></o:p></spa= n></p> <p class=3D"MsoListParagraphCxSpMiddle" style=3D"margin-bottom:0cm;margin-b= ottom:.0001pt;mso-add-space:auto;text-indent:-18.0pt;line-height:16.6pt;mso= -list:l0 level1 lfo2;background:white"> <![if !supportLists]><span lang=3D"EN" style=3D"font-family:Symbol;mso-fare= ast-language:EN-GB"><span style=3D"mso-list:Ignore">·<span style=3D"= font:7.0pt "Times New Roman"">  = ; </span></span></span><![endif]><span lang=3D"EN" style=3D"mso-fareast-langu= age:EN-GB">Good background in Java, Python or R programming <o:p></o:p= ></span></p> <p class=3D"MsoListParagraphCxSpMiddle" style=3D"margin-bottom:0cm;margin-b= ottom:.0001pt;mso-add-space:auto;text-indent:-18.0pt;line-height:16.6pt;mso= -list:l0 level1 lfo2;background:white"> <![if !supportLists]><span lang=3D"EN" style=3D"font-family:Symbol;mso-fare= ast-language:EN-GB"><span style=3D"mso-list:Ignore">·<span style=3D"= font:7.0pt "Times New Roman"">  = ; </span></span></span><![endif]><span lang=3D"EN" style=3D"mso-fareast-langu= age:EN-GB">Strong interest in building mathematical models for prediction<o= :p></o:p></span></p> <p class=3D"MsoListParagraphCxSpMiddle" style=3D"margin-bottom:0cm;margin-b= ottom:.0001pt;mso-add-space:auto;text-indent:-18.0pt;line-height:16.6pt;mso= -list:l0 level1 lfo2;background:white"> <![if !supportLists]><span lang=3D"EN" style=3D"font-family:Symbol;mso-fare= ast-language:EN-GB"><span style=3D"mso-list:Ignore">·<span style=3D"= font:7.0pt "Times New Roman"">  = ; </span></span></span><![endif]><span lang=3D"EN" style=3D"mso-fareast-langu= age:EN-GB">Alternative skills: semantic web technologies, knowledge graphs<= o:p></o:p></span></p> <p class=3D"MsoListParagraphCxSpLast" style=3D"margin-bottom:0cm;margin-bot= tom:.0001pt;mso-add-space:auto;line-height:16.6pt;background:white"> <span lang=3D"EN" style=3D"mso-fareast-language:EN-GB"><o:p> </o:p></s= pan></p> <p class=3D"MsoNormal" style=3D"text-align:justify;line-height:16.6pt;backg= round:white"> <b><span lang=3D"EN" style=3D"mso-fareast-language:EN-GB">Stipend:</span></= b><span lang=3D"EN" style=3D"mso-fareast-language:EN-GB"> PhD scholarship s= tipend of 18,000 per year, no tax. </span><span lang=3D"EN">The duration of the contract will be 4 years as a = fully funded PhD.</span><span lang=3D"EN" style=3D"mso-fareast-language:EN-= GB"><o:p></o:p></span></p> <pre style=3D"text-align:justify"><span lang=3D"EN" style=3D"font-size:11.0= pt;font-family:"Calibri","sans-serif";mso-fareast-langu= age:EN-GB"><o:p> </o:p></span></pre> <p class=3D"MsoNormal" style=3D"text-align:justify;line-height:16.6pt;backg= round:white"> <b><u><span lang=3D"EN">Application procedure </span></u></b><b><u><sp= an lang=3D"EN"><o:p></o:p></span></u></b></p> <p class=3D"MsoNormal" style=3D"text-align:justify;line-height:16.6pt;backg= round:white"> <span lang=3D"EN"> Informal enquiries about these positions may be mad= e to: <o:p></o:p></span></p> <p class=3D"MsoNormal" style=3D"text-align:justify;background:white"><b>Pro= f. Dr. Dietrich Rebholz-Schuhmann</b><b><o:p></o:p></b></p> <p class=3D"MsoNormal" style=3D"text-align:justify;background:white"><span = style=3D"color:black">Insight Centre for Data Analytics</span><o:p></o:p></= p> <p class=3D"MsoPlainText"><span style=3D"color:black">NUI Galway, The DERI = building</span><o:p></o:p></p> <p class=3D"MsoPlainText"><span style=3D"color:black">IDA Business Park, Lo= wer Dangan</span><o:p></o:p></p> <p class=3D"MsoPlainText"><span style=3D"color:black">Galway, IRELAND<o:p><= /o:p></span></p> <p class=3D"MsoPlainText"><span style=3D"color:black">Email: </span><a href= =3D"mailto:[email protected]">[email protected]</a><span = style=3D"color:black"> </span><o:p></o:p></p> <p class=3D"MsoNormal" style=3D"text-align:justify;line-height:16.6pt;backg= round:white"> <o:p> </o:p></p> <p class=3D"MsoNormal" style=3D"text-align:justify;background:white"><b>Dr.= Michael Madden<o:p></o:p></b></p> <p class=3D"MsoPlainText"><span style=3D"color:black">Machine Learning &= ; Data Mining Research Group, <br> College of Engineering & Informatics<o:p></o:p></span></p> <p class=3D"MsoPlainText"><span style=3D"color:black">National University o= f Ireland, Galway<o:p></o:p></span></p> <p class=3D"MsoPlainText"><span style=3D"color:black">Galway, IRELAND<o:p><= /o:p></span></p> <p class=3D"MsoPlainText"><span style=3D"color:black">Email: </span><a href= =3D"mailto:[email protected]">[email protected]</a> <o:p></o:p></p> <p class=3D"MsoPlainText"><o:p> </o:p></p> <p class=3D"MsoNormal" style=3D"text-align:justify;background:white"><span = lang=3D"EN">When applying, please use the same email addresses above and pu= t "</span> PhD Position in data modelling and simulation<span lang=3D"= EN">" in the subject line of your email. Candidates are requested to submit (1) a cover letter explaining your intentions, and= (2) a CV (in PDF format) giving details on your academic degrees, working = experiences and IT skills (maximum 2 pages). It is difficult but still adva= ntageous, if you can write a paragraph (e.g. in the cover letter, or extra), what ambitions in the PhD position a= ppeal most to you. <o:p></o:p></span></p> <p class=3D"MsoNormal" style=3D"text-align:justify;background:white"><span = lang=3D"EN"><o:p> </o:p></span></p> <p class=3D"MsoNormal" style=3D"text-align:justify;background:white"><span = lang=3D"EN">Interviews will be carried out towards middle and end of Octobe= r via skype conference call, and the position can be filled without much de= lay if required. We expect the successful candidate to start at the earliest possible date, ideally towards December= 2015. <o:p></o:p></span></p> <pre style=3D"text-align:justify"><span lang=3D"EN" style=3D"font-size:11.0= pt;font-family:"Calibri","sans-serif""><o:p> </o:p= ></span></pre> <pre style=3D"text-align:justify"><span lang=3D"EN" style=3D"font-size:11.0= pt;font-family:"Calibri","sans-serif"">INSIGHT Centre f= or Data Analytics (previously DERI </span><a href=3D"http://deri.ie/"><span= lang=3D"EN" style=3D"font-size:11.0pt;font-family:"Calibri",&quo= t;sans-serif"">http://deri.ie/</span></a><span lang=3D"EN" style=3D"fo= nt-size:11.0pt;font-family:"Calibri","sans-serif"">) </= span><a href=3D"http://www.insight-centre.org/"><span lang=3D"EN" style=3D"= font-size:11.0pt;font-family:"Calibri","sans-serif"">ht= tp://www.insight-centre.org/</span></a><span style=3D"font-size:11.0pt;font= -family:"Calibri","sans-serif""> <span lang=3D"EN">is a= leading research institute in Semantic Web/Linked Data technologies that o= ffers a stimulating, dynamic and multi-cultural research environment, excel= lent ties to research-groups worldwide, close collaboration with industrial= partners and up-to-date infrastructure and resources.<o:p></o:p></span></s= pan></pre> <pre style=3D"text-align:justify"><span lang=3D"EN" style=3D"font-size:11.0= pt;font-family:"Calibri","sans-serif"">The Information = Technology Discipline (</span><a href=3D"http://www.it.nuigalway.ie/"><span= lang=3D"EN" style=3D"font-size:11.0pt;font-family:"Calibri",&quo= t;sans-serif"">http://www.it.nuigalway.ie/</span></a><span lang=3D"EN"= style=3D"font-size:11.0pt;font-family:"Calibri","sans-serif= "">) is NUI Galway’s Computer Science department and has a 20-ye= ar track record in innovative teaching, research, and engagement with indus= try and community. It is the largest academic discipline in the College of = Engineering & Informatics, and has an established track record of excel= lence in research and technology development, leading to numerous successfu= l research groups with research ranging from theoretical advances to applic= ations in science, engineering, business, and medicine.<o:p></o:p></span></= pre> <p class=3D"MsoNormal"><span style=3D"color:#1F497D"><o:p> </o:p></spa= n></p> <p class=3D"MsoNormal"><span style=3D"color:#1F497D">----------------------= ---------------------------------------------------------------------------= ------------<o:p></o:p></span></p> <p class=3D"MsoNormal"><span style=3D"color:#1F497D">Regards,<o:p></o:p></s= pan></p> <p class=3D"MsoPlainText"><span style=3D"color:#17375E">Ratnesh Sahay, PhD<= o:p></o:p></span></p> <p class=3D"MsoPlainText"><span style=3D"color:#17375E">Research Unit Leade= r<o:p></o:p></span></p> <p class=3D"MsoPlainText"><span style=3D"color:#17375E">Semantics in eHealt= h and Life Sciences (SeLS)<o:p></o:p></span></p> <p class=3D"MsoPlainText"><span style=3D"color:#17375E">Insight Centre for = Data Analytics<o:p></o:p></span></p> <p class=3D"MsoPlainText"><span style=3D"color:#17375E">NUI Galway, The DER= I building<o:p></o:p></span></p> <p class=3D"MsoPlainText"><span style=3D"color:#17375E">IDA Business Park, = Lower Dangan<o:p></o:p></span></p> <p class=3D"MsoPlainText"><span style=3D"color:#17375E">Galway, IRELAND<o:p= ></o:p></span></p> <p class=3D"MsoPlainText"><span style=3D"color:#17375E">Tel: + 353 91 4= 95253<o:p></o:p></span></p> <p class=3D"MsoPlainText"><span style=3D"color:#17375E">Fax: + 353 91 4= 95541<o:p></o:p></span></p> <p class=3D"MsoPlainText"><span style=3D"color:#17375E">Web: <a href=3D"htt= p://sels.insight-centre.org/"> <span style=3D"color:#17375E">http://sels.insight-centre.org/</span></a> &n= bsp; <o:p></o:p></span></p> <p class=3D"MsoNormal"><span style=3D"color:#17375E">Web: <a href=3D"http:/= /www.ratneshsahay.org/"> <span style=3D"color:#17375E">http://www.ratneshsahay.org/</span></a></span= ><span style=3D"color:#1F497D"><o:p></o:p></span></p> </div> </body> </html> --_000_DB5PR01MB09019E07010A2A48AC60FBF28F4B0DB5PR01MB0901eurp_-- --===============6488379478347260267== Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Disposition: inline _______________________________________________ protege-user mailing list [email protected] https://mailman.stanford.edu/mailman/listinfo/protege-user --===============6488379478347260267==--