How to structure a Ph.D. sandwich thesis?

Question

Although some guidelines can be taken from this post, additional details would be appreciated.

When building the introduction, I have difficulty trying to join and describe all the aspects of the 3 published articles I have. This will be also the same for the final discussion. In fact, it makes me feel that I'm repeating what I've already written in the papers. I like the DRY principle.

Here is a preliminary outline:

• TABLE OF CONTENTS

• ACKNOWLEDGEMENTS

• LIST OF ABBREVIATIONS USED

• SUMMARY

• INTRODUCTION

• HYPOTHESIS AND OBJECTIVES

• MATERIALS AND METHODS

• RESULTS

• Paper1

• Paper2

• Paper3

• DISCUSSION

• CONCLUSIONS

• REFERENCES

• ANNEXES

Answer 1

This is the structure that worked for me and number of my friends throughout western European universities:

Title: A title that reflects your contributions/publications.

Table of contents

ACKNOWLEDGEMENTS

ABBREVIATIONS

Abstract

INTRODUCTION

Note on Introduction: Most important of all is to highlight what you want to answer in your research. Also the problem/motivation should be discussed here.

Paper1 ... PaperN

Note On Paper-Based Chapters: The order of them are very important. Order them based on the content not the year of the publication.

Evaluation: In this chapter put both the discussion and results. Try to figure out the benefits and shortcomings of your research.

CONCLUSIONS and Future Work: conclude based on your contribution and highlight the future work.

REFERENCES

Note: Not so many students take time on organizing their references' style. Most of them just copy/paste the Bibtex code and don't look if all their references obey the same style rules.

ANNEXES

Answer 2

Your introduction has to wrap the rest of the thesis, not replace it. So, DRY partially applies here too.

A paper is directed towards other researchers working in your field, whereas a PhD thesis introduction usually is meant to be accessible by anyone in that discipline. Your aim is to write something that will allow your undergrad class mates to get up to speed and understand your papers. You should also give an overview of how all the pieces work together. For example,

"In paper I we showed that our new experimental technique works better than the previous ones, in Paper II we used it to solve a new problem that couldn't be tackled before, and in Paper III we combined it to improve another different technique".

So, a paper that uses machine learning in Bioitechnology would say "we used a SVM trained on this and that features over this dataset". The introduction to the thesis will include a chapter introducing machine learning, and explaining what a SVM is. If it were relevant, you could consider adding another one explaining why these features are relevant.

Discussion and conclusions are not a part of the sandwich thesis I am familiar with, because they would belong into the papers.