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Unique identifier: 0e8d3b46-e411-4c12-8003-b07bb12ce221

1. Descrição do cargo/posição/bolsa
1. Job description

Job:
One research grant with reference number BI|2020/092 is now available under the scope of project ICARE4U - PTDC/EME-SIS/31474/2017 | LISBOA- 01-0145-FEDER-031474, funded by FEDER, PORL-PROGRAMA OPERACIONAL REGIONAL DE LISBOA E FUNDAÇÃO PARA A CIÊNCIA E A TECNLOGIA

Job/Fellowship Reference: One research grant with reference number BI|2020/092 is now available under the scope of project ICARE4U - PTDC/EME-SIS/31474/2017 | LISBOA- 01-0145-FEDER-031474, funded by FEDER, PORL-PROGRAMA OPERACIONAL REGIONAL DE LISBOA E FUNDAÇÃO PARA A CIÊNCIA E A TECNLOGIA

Main research field: Engineering

Sub research field:

Job summary:

ICare4U is a project that proposes the development of a decision support system based on intelligent modelling and patient sub-group analysis, to provide personalized therapy for critically ill patients.

It is hypothesized that the 'Collective Experience' from large clinical databases, where clinical decisions are linked with patient outcomes, can be used to identify specific patient sub-groups and build personalized therapy models towards a new era of personalized medicine, allowing the improvement of patient outcomes in the ICU. The validity of the proposed systems will be tested using two case studies where generalized severity scoring systems have consistently performed poorly: patients admitted to the ICU who then develop acute kidney injury, where two-thirds of these patients require renal support therapy; and severe sepsis a typical heterogeneous disease among critically ill patients, in which the immune response is highly dynamic

and variable, and likely to need complex therapies to improve patient outcomes.

One of the tasks of the project involves using existing text-based information, such as medical reports and physicians and nurses’ notes, to improve the decision-making process. The work to be developed by the researcher will be in the context of this task, and consists of implementing and integrating a technique called “Fuzzy Fingerprints” in the decision support system, and to enhance and integrate Fuzzy Fingerprints with Deep Learning.

Digital fingerprints aim to extract information about a user that he/she has not provided knowingly, and represent such information in a compact and efficient form. Fuzzy fingerprints based on the order of top-k events have been successfully applied in many areas, including text mining, and will be used in this project to help identifying critically ill patients (by creating patient sub-group fingerprints). The technique presents a simple but extremely effective and robust way to evaluate and compare the relevant features of event patterns, which in the present case would be the text contained in the physicians/nurses notes. Important phrases and/or keywords will be used as events and event patterns. A text based fingerprint will be created for each admitted patient. A sliding window top-k algorithm will be adapted to create an evolving patient fingerprint algorithm to cope with patients’ evolving condition. Patients will be attributed to patient sub-groups based on fuzzy fingerprint similarity.

The MIMIC II database will be used for this project. All text data will have to be “cleaned up” on a pre-processing phase since textual medical databases have several particularities that prevent its immediate and effective use.



Job description:

Public notice for research grant

PTDC/EME-SIS/31474/2017 | LISBOA-01-0145-FEDER-031474

iCare4U

INESC-ID - Instituto de Engenharia de Sistemas e Computadores, Investigação e Desenvolvimento em Lisboa is a R&D institute dedicated to advanced research and development in the fields of Information Technologies, Electronics, Communications, and Energy. INESC-ID has participated in more than 50 research projects funded by the European Union and more than 190 funded by national entities. Until today, our researchers have published more than 700 papers in international journal papers, more than 3000 papers in international conferences, and have registered 15 patents and/or brands.

1  RESEARCH GRANT TYPE

One research grant with reference number BI|2020/092 is now available under the scope of project iCare4U - PTDC/EME-SIS/31474/2017 | LISBOA- 01-0145-FEDER-031474, funded by FEDER, PORL-PROGRAMA OPERACIONAL REGIONAL DE LISBOA  e FUNDAÇÃO PARA A CIÊNCIA E A TECNLOGIA and under the following conditions:

2  DURATION

5 months, starting in January 2021

-     Renewable, if the candidate is enrolled in a PhD program -  art. 6º, n.4 c)

(https://www.fct.pt/apoios/bolsas/docs/RegulamentoBolsasFCT2019.pdf )

subject to suitable performance within the period of the project, not exceeding the maximum period set by FCT for such grants –4 years (included contract renewals)

 

-     Renewable, if the candidate is enrolled in a non-degree programme – art. 6º, n. 4 a)

(https://www.fct.pt/apoios/bolsas/docs/RegulamentoBolsasFCT2019.pdf )

subject to suitable performance within the period of the project, not exceeding the maximum period set by FCT for such grants – 1 year (included contract renewals)

 

3  LEGISLATION

A fellowship contract will be celebrated according to:

1.       Law 40/2004 of 18th of August (Scientific Research Fellow Status) and its successive amendments, including the amendments introduced by the Decree Law n. 123/2019 of 28 th of August 
https://dre.pt/web/guest/legislacao-consolidada/-/lc/124281176/201912061112/73740605/diploma/indice?lcq=estatuto+do+bolseiro,

2.       Regulations for Research Grants of the Foundation for Science and Technology in force  (https://www.fct.pt/apoios/bolsas/docs/RegulamentoBolsasFCT2019.pdf )

3.       INESC-ID Lisboa Grant Regulations

https://www.inesc-id.pt/scholarship-regulations/

The fellowship contract is awarded on an exclusive dedication basis – art. 5 of Scientific Research Fellow Status and art. 16 of Regulations for Research Grants of the Foundation for Science and Technology.

4  MONTLY AMOUNT

The monthly amount of the grant 1 074,64 s in accordance with the values stipulated in the “Regulations for Research Grants of the Foundation for Science and Technology” in force (https://www.fct.pt/apoios/bolsas/docs/Tabela_Valores_SMM_LOE_2020.pdf)  and shall be rendered through a monthly bank transfer to an account held by the grantee.

5 4 OBJECTIVES/WORKPLAN

ICare4U is a project that proposes the development of a decision support system based on intelligent modelling and patient sub-group analysis, to provide personalized therapy for critically ill patients.

It is hypothesized that the 'Collective Experience' from large clinical databases, where clinical decisions are linked with patient outcomes, can be used to identify specific patient sub-groups and build personalized therapy models towards a new era of personalized medicine, allowing the improvement of patient outcomes in the ICU. The validity of the proposed systems will be tested using two case studies where generalized severity scoring systems have consistently performed poorly: patients admitted to the ICU who then develop acute kidney injury, where two-thirds of these patients require renal support therapy; and severe sepsis a typical heterogeneous disease among critically ill patients, in which the immune response is highly dynamic

and variable, and likely to need complex therapies to improve patient outcomes.

One of the tasks of the project involves using existing text-based information, such as medical reports and physicians and nurses’ notes, to improve the decision-making process. The work to be developed by the researcher will be in the context of this task, and consists of implementing and integrating a technique called “Fuzzy Fingerprints” in the decision support system, and to enhance and integrate Fuzzy Fingerprints with Deep Learning.

Digital fingerprints aim to extract information about a user that he/she has not provided knowingly, and represent such information in a compact and efficient form. Fuzzy fingerprints based on the order of top-k events have been successfully applied in many areas, including text mining, and will be used in this project to help identifying critically ill patients (by creating patient sub-group fingerprints). The technique presents a simple but extremely effective and robust way to evaluate and compare the relevant features of event patterns, which in the present case would be the text contained in the physicians/nurses notes. Important phrases and/or keywords will be used as events and event patterns. A text based fingerprint will be created for each admitted patient. A sliding window top-k algorithm will be adapted to create an evolving patient fingerprint algorithm to cope with patients’ evolving condition. Patients will be attributed to patient sub-groups based on fuzzy fingerprint similarity.

The MIMIC II database will be used for this project. All text data will have to be “cleaned up” on a pre-processing phase since textual medical databases have several particularities that prevent its immediate and effective use.

6  SCIENTIFIC SUPERVISION

The activity will be supervised by João Paulo Baptista Carvalho, Associate Professor at Tecnico, ULisboa and researcher at INESC-ID.

INESC ID will integrate the grantee in the research team of the scientific advisor

7  ELIGIBILITY CONDITIONS

The candidate should have an MSC in Computer Science, Informatics, Electrical Engineering or related and have some experience in Natural Language Processing, Text Mining and Computational Intelligence and/or Machine Learning methods.

Required language skills: proficiency in English.

 

By the grant start date, the candidate must be enrolled in:

a)       a PhD programme art. 6º, n.1
(https://www.fct.pt/apoios/bolsas/docs/RegulamentoBolsasFCT2019.pdf)

or

b)       a non-degree programme – art. 6º, n. 2
(
https://www.fct.pt/apoios/bolsas/docs/RegulamentoBolsasFCT2019.pdf )

8  EVALUATION CRITERIA AND COMMITEE

The selection will be according to the following criteria:

         I.            30%: Academic record

        II.            35%: Scientific record in areas relevant for the task

      III.            20%: Personal references

     IV.            15%:English language level

The jury may also decide not to assign the scholarship, if none of candidates meets the required conditions

Jury

name

Professional Status

Institutions

 

 

 

 

 

President

João Paulo Baptista de Carvalho

Associate Professor

INESC ID | Tecnico Ulisboa

Member

Maria Luísa Torres Ribeiro Marques da Silva Coheur

Assistant Professor

INESC ID | FCULisboa

Member

Susana Margarida da Silva Vieira

Assistant Professor

IDMEC | Tecnico Ulisboa

Substitute member

Isabel Maria Martins Trancoso

Full Professor

INESC-ID | Tecnico Ulisboa

Substitute member

Fernando Manuel Marques Batista

Associate Professor

INESC-ID | ISCTE-IUL








9  COMPLAIN AND APPEAL DEADLINES AND PROCEDURES

The jury has the faculty not to select a candidate who does not prove the requirements mentioned in required education Level and research experience

 

The admitted and excluded candidates will be notified by email of the final ranking list, including the copy of the Preliminary Report of the jury.

 

Prior Hearing and Deadline for Final Decision: After being notified, candidates have 10 working days to submit, if applicable, a formal rebuttal.

 

After that period, the jury notifies the candidates of the Final Report.

 

Excluded applicants may complain about the jury's final report for 15 working days after notification or appeal the jury's decision to the INESC ID Board of Directors for 30 working days after notification.

 

According to the Portuguese Law, a disabled candidate has a preference when in equal classification, which prevails over any other legal preference. Candidates must declare their respective degree of disability, the type of disability and the means of communication / expression to be used in the selection process, under the law.

10  FORMALISATION OF APPLICATIONS

Applications are formalised by sending an email to rh@inesc-id.pt with the documents stated bellow and in pdf form. 

The application email should clearly state the reference of the research grant and project.

 

 

 

 

 

1

Single copy of official academic degree certificate in the required education level  

 

 

 

a) In the application submission, the candidates from portuguese education institutions may replace this document by a declaration of honour stating that they have the required academic degree.

 

 

It is mandatory for the approval of the fellowship contract that the selected candidate presents a single copy of the official academic degree certificate, required in education level

 

 

b) In the application submission, the candidates from foreigner education institutions may replace this document by a declaration of honour stating that they have the required academic degree.

 

 

 

It is mandatory for the approval of the fellowship contract that the selected candidate presents a single copy of the official diploma recognition, required in education level

 

 

 

For more information about diploma recognition please press here

 

 

 

 

2

Detailed list of grades (pdf form);

 

 

 

 

3

Proof of enrolment required on  7 a) or 7 b) (pdf form);

 

 

 

In the application submission, the candidates may replace this document by a declaration of honour stating that they are/will be enrolled required in  7 a) or 7 b)

 

 

It is mandatory for the approval of the fellowship contract that the selected candidate presents an official  copy of the enrolment, required in 7 a) or 7 b)

 

 

 

4

Detailed curriculum vitae (pdf form);

 

 

 

 

5

Motivation letter explaining the interest in the position (pdf form);

 

 

 

 

6

Name of two personal references (pdf form).

 






 

Application Dates

 

From

 

To

 

30-11-2020

 

15-12-2020

 

 

 




Vacant posts: 1

Type of contract: Information not available

Job country: Portugal

Job city: Lisbon

Job company/institute: INESC-ID


Application deadline: 15 Dezembro 2020
(The Application's deadline must be confirmed on the Job Description)

2. Dados de contactos da organização
2. Organization contact data

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3. Habilitações académicas
3. Required education Level


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4. Línguas exigidas
4. Required languages


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5. Experiência exigida em investigação
5. Required research experience


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