Guidelines DOCTORAL PROGRAMME

Faculty of Engineering

D O C T O R A L P R O G R A M M E

Doc.

04/11/02

Name: Sheng...… Doctorate in Applied Science....

First name: Qizheng... Department: Electrical Engineering...

Nationality: Chinese... Official starting date: 8/12/2003... PHOTOGRAPH Place of birth: Shanghai, China... Supervisor(s): Bart De Moor...…...

Date of birth: May 13, 1977... Yves Moreau...

Guidelines

The total required study time is 1500 hours.

A. Direct tuition (assessment by the lecturer of the study subject)

Category Type Study time

(hours) A.1. Doctorate courses and doctoral seminars: intra-university as well as extra-

university courses (incl. Academic English) and seminar series, interuniversity programmes, symposia, workshops, etc. recognised by the Doctorate

Commission of the Faculty of Engineering as A1 modules of the doctoral programme.

5 h/h

A.2. Seminars at a doctoral level presented by the doctoral candidate 100h/seminar A.3. General doctoral training

Methodology, epistemology, experiment design, advanced statistics, ... 5 h/h A.4. "Second cycle" courses, incl. 2nd cycle "GAS"-courses 4 h/h A.5. "Third cycle"-courses, incl. "GGS"- and 3rd cycle "GAS"-courses 5 h/h Remark:

- For courses taken without assessment, the study time equals 1h/h.

B. Other activities and achievements (evaluated by the advisory committee)

Category Type Study time

(hours) B.1. Publications (as author or co-author):

- in an international journal or book (with review) - full paper in proceedings of an international congress - in a national journal or book

- project reports, project proposals and approved logistic tasks (with prior approval)

200 h 150 h 80 h 50 h B.2. Reporting to the advisory committee (only the first reporting should be

communicated to the Doctorate Commission) ^{50 h}

B.3. Participation in scientific meetings (congresses, workshops, ...) - participation without reporting

- participation with reporting

- paper presentation, lecture or poster presentation

10 h/day 20 h/day 100 h B.4. Didactical activities

- advisor for student theses (a maximum of 3 theses)

- teaching tasks and didactical training (maximum 150 h) 150 h/thesis

2 h/h

B.5. Formal contacts with the advisor(s) (maximum 200 h) ^{1 h/h}

A. Direct tuition (minimally one course with evaluation from category A1 and two units with evaluation from category A2)

Course Title Lecturer Period Hours Category Assessm

ent Signature of the

Lecturer Study time

Academic English Caroline Greenman 2001 – 2002 20 A1 None 20h

G0M8B2 Algorithmic data analysis Emmanuel Lesaffre 2001 – 2002 26 A5 Passed 26x5=130h

Seminar: ‘Markov chain Monte Carlo methods for pattern recognition problem in microarray data’ in the Brainstorm session of SISTA, ESAT

Qizheng Sheng 2001 – 2002 A2 100h

H0P30A Signal processing, identification, system theory and automation

Johan Suykens 2001 – 2002 26 A1 None 26h

I0E76A Genetics, Genetic Evolution Mechanisms and Genetic Nomenclature

F. Volckaert, J.

Michiels, A.

Roebroek, A.

Vandamme, F.

2002 – 2003 26 A5 None 26h

H0P30A Signal processing, identification, system theory and automation:

(Seminar presented by the student: ‘Biclustering microarray data by Gibbs sampling’, 27/02/2003)

Johan Suykens 2002 – 2003 26 A1 Evaluated 26x5=130h

H0P30A Signal processing, identification, system theory and automation

Johan Suykens 2003 – 2004 26 A1 None 26h

Seminar: ‘Biclustering strategies in microarray data analysis’ in the Department of Psycology, K.U.Leuven

Qizheng Sheng 04/05/2004 A2 100h

MS. Statistical Data-Analysis (Gent)

Bioinformatics, Statistical Genetics and Computational Biology

Robert Gentleman 2004-2005 22.5 (theory) 40 (practise)

A5 None 62.5h

Total study time for direct tuition 620.5h

B1. Publications (only published and accepted papers can be included; minimally one publication at the international level)

T i t l e Authors Journal Acceptance

Date Year/Edition/Nr of the Publication

Study time

Biclustering microarray data by Gibbs sampling Qizheng Sheng, Yves Moreau, and Bart De Moor

Bioinformatics 18/05/2003 2003/19/2 200h

Advances in cluster analysis of microarray data Qizheng Sheng, Yves Moreau, Frank De Smet, Kathleen Marchal, and Bart De Moor

Data analysis and visualization in genomics and proteomics (book)

April 2005 200h

Applications of Gibbs sampling in bioinformatics Qizheng sheng, Gert Thijs, Yves Moreau and Bart De Moor

Proceedings of Workshop on Mathematica

Programming in Data Mining and Machine Learning, McMaster Univ., Hamilton, Canada

28/03/2005 June 1, 2005 150h

Total study time for publications

550h

B2. Reporting to the advisory committee (minimally: presentation of the doctoral plan after 1

year)

Type Date Date

Announcement to Doctorate Commission

Signature of the

Supervisor Study

time

Presentation doctoral plan after 1

year 11/06/2004 11/10/2004 50h

Presentation doctoral plan after 2

year not applicable Presentation doctoral plan after 3

year not applicable Presenation doctoral plan after 4

year not applicable Presentation doctoral plan after 5

year not applicable

Total study time for reporting 50h

B3. Participation in scientific meetings (minimally one active participation at an international congress) Meeting Title of the Presentation/Poster Date Days/ho

urs Signature of the

Supervisor Study

time NWO/IOP

Genomiocs winterschool, Wageningen, Netherlands

17/12/2001 – 19/12/2001

3 days 10x3 =

30h

Belgian bioinformatics conference 2002, Namur, Belgium

Poster: Applying Markov chain Monte Carlo methods to the two dimentional clusteirng problems of microarray data

12/04/2002 1 day 100h

IUAP study day, Leuven, Belgium

Poster: Applying Markov chain Monte Carlo methods to the two dimentional clusteirng problems of microarray data

15/05/2002 1 day 100h

Workshop:

Knowledge discovery meets drug discovery, Leuven, Belgium

23/10/2002 1 day 10h

IUAP study day, Louvain-la-Neuve, Belgium

26/11/2002 1 day 10h

Ph.D. symposium of the Faculty of Engineering, K.U.Leuven, Leuven, Belgium

Poster: Biclustering microarray data by Gibbs sampling

11/12/2002 4 hours 100h

Informal workshop on integrated text and data mining 2002, Leuven, Belgium

19/12/2002 – 20/12/2002

2 days 20h

IUAP study day, Louvain-la-Neuve, Belgium

Poster: Gibbs biclustering of microarray data

08/05/2003 1 day 100h

Belgian bioinformatics conference 2003, Leuven, Belgium

Poster: Gibbs biclustering of microarray data

13/05/2003 1 day 100h

ISMB 2003, Brisbane, Australia

Poster: Bclustering microarray data by Gibbs sampling

27/06/2003 – 03/07/2003

7 days 20x7+100

= 240h 3rd VIB microarray

users group meeting, Leuven, Belgium

10/11/2003 1 day 10h

ECCB2003, Paris, France

Presentation: Biclustering microarray data by Gibbs sampling

27/09/2003 – 30/09/2003

4 days 100h

Study day on machine learning in bioinformatics, Brussels, Belgium

17/10/2003 1 day 10h

Mathematics and genomics, Brussels, Belgium

18/10/2003 1 day 10h

Belgian bioinformatics conference 2004, Brussels, Belgium

23/04/2004 1 day 10h

Symposium, ‘Life, a Nobel Story’, Brussels, Belgium

28/04/2004 1 day 10h

ISMB/ECCB 2004, Glasgow, UK

Poster: Query-driven

biclustering of microarray data by Gibbs sampling

30/07/2004 – 04/08/2004

6 days 100h

1st Annual

conference on Life System Modelling and Simulation (for China), Shanghai, China

Presentation: Introduction to bioinformatics

28/10/2004 – 30/10/2004

3 days 100h

4th VIB microarray users group meeting, Brussels, Belgium

18/11/2004 – 19/11/2004

1.5 days 15h

Benelux Bioinformatics Conference 2005, Gent, Belgium

Presentation: Query-driven biclustering of microarray data by Gibbs sampling

14/04/2005 – 15/04/2005

2 days 100h

Workshop on Mathematica Programming in Data Mining and Machine Learning, McMaster Univ., Hamilton, Canada

Presentation: Applications of Gibbs sampling in bioinformatics

01/06/2005 – 04/06/2005

4 days 100h

Total study time for scientific meetings 1375h

B4. Didactical activities (advisor for student theses (max 3) and teaching activities (max 150 h)) Title of the thesis Academic Year Signature of the Thesis Advisor Study

time Simultaneous classifications of the

patients and the relevant genes

2003 – 2004 150h

Web implementation of the Gibbs sampling algorithm

2003 – 2004 150h

Title of the course unit Academic Year Signature of the Lecturer Study time

Total study time for didactical activities 300h

B5. Formal contacts with supervisor(s)

Total number of hours: 100h

Approval of the doctoral programme by the advisory committee:

Remarks: ...

...

...

...

...

Names and signatures of the supervisor(s) and the assessors:

Supervisors Name ... ...

Signature

Assessors Name ... ... ...

Signature

Heverlee, Date: ...

___________________________________________________________________________

The table below is reserved to the Doctorate Commission of the Faculty of Engineering.

Summary of the study time recognised by the Doctorate Commission of the Faculty of Engineering

Direct tuition Other activities and achievements

Hours Remarks Hours Remarks

A.1 B.1

A.2 B.2

A.3 B.3

A.4 B.4

A.5 B.5

Total Total

Total study time of the approved doctoral programme: ... hours.

Certificate of completion of the doctoral programme has been awarded on ...……

On behalf of the Doctorate Commission of the Faculty of Engineering,

the Secretary the Chairman

Heverlee, Date: ...