Transcript Slide 1

Week 5. Writing the PhD thesis,
proposal and research papers
PhD seminar
Dr. Felipe Orihuela-Espina
Outline
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4.
How to elaborate a PhD thesis
The thesis protocol
Parts of a thesis
Writing abstracts
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HOW TO ELABORATE A PHD
THESIS
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How to elaborate a thesis
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Definition: What is a thesis?
What has a thesis got to demonstrate?
How to choose a thesis topic
The actors
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The student
The supervisor
The thesis committee
The panel
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Developing the project
Periodic monitoring by the supervisor and the committee
Writing the document
Formatting
 How to write the thesis
 Legal authorship (Institution) and intellectual authorship
(student)
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Some references for this section
 [Camacho2003] Camacho Mejía, Felipe;
Herrera Barrera, Armando; Guía para la
elaboración de una tesis (2003)
Universidad Autónoma del Estado de
México (UAEMex)
 [Sloman??] Sloman, Aaron “Writing a
thesis” University of Birmingham
 [??] “How to write a PhD thesis”
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Definition of a thesis
 A thesis is a scientific text describing a an
in-depth description of a phenomenon
(that includes computing) together with a
set of solutions/hypothesis to yet unsolved
problems or questions about the
phenomena, and that further provides
extensive support and evidence to back up
any claims made. [Self definition]
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What has a thesis got to demonstrate?
 That the student is capable of:
 Carrying out innovative research by himself
 Criticism; both towards other’s work and to his
own work
 Planning, executing and finishing a long term
project
 Communicating knowledge and ideas
 …in an organised fashion understandable by nonexperts
 …yet without sacrificing accuracy
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How to choose a thesis topic
 Proposed by the department or the supervisor
 Often as a result of a research project, a
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necessity/research priority of the institution or sometimes
from a collaboration with an industrial partner
Pros:
 Saves some headaches such as questioning one-self what do I
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do?
The problem definition, extension and coverage are often well
studied and defined
Motivation and justification is clear
There is already a researcher interested or involved, almost
certainly with expertise on the topic
 Cons:
 You might not love the topic
 You might not get on well with the supervisor
 You risk just following instructions, and not demonstrating
initiative (necessary for obtaining the degree)
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How to choose a thesis topic
 Proposed by the student
 Often as a result of the student’s interests
 Pros:
 You are likely to love the topic
 You are free to find a supervisor which you want to
work with
 You are already demostrating drive and initiative
 Cons:
 There might not be any researcher willing to supervise
the thesis or with enough knowledge about the topic
 You’ll have to work on the problem definition,
motivation, etc
 Funding?
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The actors
 The student
 The supervisor
 The thesis committee
 The panel
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The student
 You! The one carrying out the thesis project
 Responsible for:
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Solving all problems related to the thesis research
Carry out the experiments
Proposing the solutions
Writing and submitting the protocol, the thesis and any papers that may
result
Successful finalization of the research
 If something goes wrong it is your fault, so do not blame your supervisor.
The scientific quality of the work (legal)
Finding funding for his/her conference attendance
 Entitled to:
 Institutional support
 An adequate supervision
 That’s not mean babysitting
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The supervisor
 Whether the one who originally offered the topic or
chosen by the student.
 That’s not your boss, just your companion!
 In every aspect of the research, you have the last word.
It’s your thesis, not his/hers.
 Responsible for:
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Providing adequate guidance all throughout
Providing starting knowledge/context about the problem
The scientific quality of the work (moral)
Ensuring that the student finishes in time and form
 …despite the student’s best efforts not to…
 Entitled to:
 When appropriate, co-authorships in publications
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The supervisor
 NOT responsible for solving anything at all about the
thesis.
 The student shall not assume that his supervisor knows
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everything about the topic
Moreover, after a year or so the student ought to have
surpass his supervisor in knowledge about the topic.
 Often can recommend bibliography and references
 May help to a degree in the writing and proof reading
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of the thesis
May suggest a publication strategy
May help in funding search for conference attendance
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The supervisor
 The supervisor is responsible for the
scientific quality of the work, as in time it
will become part of his CV and
consequently linked to his/her reputation
 However
 This responsibility is only moral, not legal.
 The student is free to submit his work even
without the consent of the supervisor and it is
not obliged to comply with any of the
supervisor recommendations.
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The thesis committee
 4 members of the faculty plus 1 external
 Not all will have expertise related to the thesis topic, this
offers a different point of view
 Ultimately chosen by the faculty,
 …but the student and (perhaps) the supervisor may
proposed alternatives
 Responsible for:
 Periodically evaluating the student progress
 Detecting weaknesses in the research
 Providing suggestions for amending deviations menacing
the finalization within time constraints
 Entitled to:
 Being provided with the advances with enough time
 …in English if Spanish is not their first language!
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The panel
 Peers assessing the final workpiece
 Experts on the field
 Responsible for:
 Evaluating the final thesis
 Rejecting works which do not exhibit originality, or
do not reach scientific standards
 Entitled to:
 Being provided with the advances with enough
time
 …in English if Spanish is not their first language!
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How to write the thesis
 Developing the project
 Periodic monitoring by the supervisor and
the committee
 Writing the document
 Formatting
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Developing the project
 A coarse overview:
 Reading about the background
 Establish a calendar
 Tentative: if no special constraints applied. Admit deviations
 Imposed: when special project constraints applied. Does not
admit deviations.
 If in engineering; then budget proposal
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 Inc. materials and human resources
Launch hypothesis and analyse project requisites and
demands
Design and execute experiments
Analyse your data
Write your final thesis document
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Periodic monitoring
 The goal is to ensure that the thesis is finished in
due time and form guaranteeing minimal scientific
quality (and engineering if it is the case)
 Advances should be check periodically
 The most common way for this monitoring are the
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bi/weekly meetings with the supervisor
Thesis committee meetings often take place every 6
months and are exceptional occassions to assess the
real progress of the thesis
 Other forms of monitoring include:
 Seminar giving
 Technical reports writing
 Periodic report writing as requested by the
programme
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Periodic monitoring
 How often should I meet my supervisor?:
 It really depends on your needs…
 However:
 Do NOT allow your supervisor to avoid meeting
you for long periods
 Do NOT relax yourself and “forget” to meet you
supervisor for long periods
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Periodic monitoring
 What should I take to/prepare the meetings?
 Read in depth about the specific topic to discuss that week
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 Ensure that you have your questions ready
Organize any results (figures and tables) that you will show
 It is rude to do it at the expense of the time of your supervisor
 If you have become stuck onto a particular problem
 Do not tell your supervisor until you have at least seriously tried to solve it
 …but if really stuck, then spend the most of the meeting on this.
 Remember that your supervisor may not know the solution!
 Have a list of non-research issues that ought to be disscussed: admin,
conference attendance, scholarship problems, etc
 Do not expect your supervisor to remember from one meeting to the next you
current needs
 If presenting a document (paper, report, protocol, etc) be sure that the
draft is polished to your best
 It is rude to use your supervisor as a spellchecker or as a primary school teacher
who has to tell you that every sentence you write is correct
 Respect the time of your supervisor!
 …during the meeting, and out of the meeting
 If exceptionally arriving late then apologize in advance by mail/phone
 Do not go beyond your scheduled time; perhaps other students are waiting
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Periodic monitoring
 Your supervisor should in turn:
 Read whatever you sent prior to the meeting
BEFORE the meeting
 Be up-to-date with your research
 Not impose his will or point of view; but
instead give his/her best advice and let the
student take the decision
 Tell the student if other meetings and
responsibilities comes in the way
 Reallocate time if necessary so that the student do
not miss his meeting
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Writing the document
 Who is it written for?
 Scientific peers
 The thesis is a scientific document:
 Be precise and concise
 Effort to ensure efficient and effective communication
 Avoid colloquial laguage
 Be scrupulous on correctness (lexical, orthographical, syntax,
grammar, etc)
 Artistics licences are valid as long as they do not prevent
clear communication of ideas
 Long sentences are often a bad idea
 Take care of the flow of ideas
 The reader does not know:
 your nomenclature, nor your acronyms, etc
 the details of your research and specifically of your
experimentation. Provide enough details for replicability.
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Writing the document
 Assume knowledge only within expectable limits
 Level of detail
 Basic concepts
 If truly trivial, then omit them
 …but remember that the reader knowledge does not match
exactly yours!
 Things which are trivial for you, may not be trivial for him.
 Advanced concepts
 If fairly known, mention and provide adequate references.
 Concepts developed in your thesis
 They ought to be perfectly/accurately defined, and if
necessary with proper mathematical formulation.
 Avoid explining then in several places
 …however readability may demand some repetition
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Writing the document
 Level of details
 Experimental description
 The secret is simple: Replicability
 Every aspect of your experiment has to be replicable with absolute
fidelity by the reader.
Not replicable from your text, not good enough
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 Often convenient to provide justification for arbitrary decisions.
 Mathematical development, proofs and
demonstrations
 Omit if they are trivial (although they almost never are)
 Explain them as they unfold; do not only state them
 A thesis is not better or more complex conceptually just because
it has more maths and looks like more formal
 …that may scare a bachelor but not your panelist, and in turn it may
actually irritate them
 Ensure that they are utterly correct and coherent thorughout the
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document
Appendix are a good place for long developments and proofs
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Formatting
 Compulsory: Most times, the institutions have
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regulations about the formatting (inc. front
cover, style, fonts, interline space, margins,
paper size (and weight!), etc). Be sure you
comply with them.
Availability; We may not have always the
software we like. Use whatever you need to
guarantee the best possible presentation.
 Never excuse a bad presentation blaming the
software/hardware tool you have used!
 Portability: The format chosen has to be
easily portable to other formats.
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Authorship
 Legal authorship (Institution)
 The institution is the legal responsible for the
results.
 The institution can legally protect the intellectual
property of the knowledge generated by the
research and/or commercially exploit the
research
 …but in turn any damage that your research may
cause is the institution’s responsibility
 Silly example: If the bridge falls, its not your fault, but the
institution!
 Any other (internal) researcher can continue your
work (e.g. use your data!) without asking for
permission
 Although it is considered polite to ask for it…
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Authorship
 Intellectual authorship (student)
 As the original author of the thesis, the student
keeps the intellectual property
 The student is therefore entitled to (and in fact
more often than not, encouraged to) publish your
work
 After published, any other (external) researcher can
continue your work without asking for permission
 The student can self-cite himself without
committing plagiarism (but beware of selfplagiarism and salami slicing issues!)
 The student can continue its research on the
topic even after finishing its liase with the
institution.
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THE THESIS PROTOCOL
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The thesis protocol
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Title
Abstract
Introduction and related work
Justification and Motivation
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Defining limits and assessment
The research questions
Goals; Main and specific
Theoretical and reference frameworks (literature review)
Methodology; Materials and Methods
 Research hypothesis statement
 Planning and description of tasks and experiments
 Scheduling
 Publications derived from this thesis (Optional)
 Conclusions
 References
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Title
 It is convinient to set a working title early in
your PhD
 This might not necessarily be the one at the
end of your thesis (in fact, it will likely not
coincide)
 It helps centering the thesis main topic
 Try to be as concise as posible to delimit the
phenomenon
 A rather generic title may give a wrong impression
to the thesis committee
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Title
 Example:
 Orihuela-Espina PhD Thesis
 Working title: “Interpretation of fundus images
using physics based models.”
 Final (Real) thesis title: “Modelling and verification
of the diffuse reflectance of the ocular fundus”.
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Abstract
 It has to include:
 The purpose or specific aim of the project
 The methodology or experimentation
procedure
 The expected results
 The main expected conclusion and impact
 Writing abstracts is an art: we will learn
more later
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Abstract
 Examples:
 Prahl89 - PhD Thesis – Example for a thesis
 Berenschot2002, Costa2000, DeLint2000 –
Structured abstracts
 Cheong90 - Review, therefore it lacks results;
A fantastic example of short and concise
 Edelsbrunner83 – Short and concise
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Introduction and related work
 It should describe some relevant prior
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knowledge
It should very briefly summarised the state of
the art
 A rather naive way of doing it is by enumeration:
“This fellow did this. This fellow did that, …”
 You’ll be shouting that you’re a novice in the field
 A more elegant/smart way is to tell the story with
a good flow of ideas, and simply drop the key
references where suitable
 In computer science, related work is often
written in a separate section.
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Justification and Motivation
 You do not take over a PhD because you are
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bored at home…
…but because there is a real need to
understand a phenomena
 Economical
 Scientific
 Academic
 Others
 Nope! “…because I need it to get my degree” is
NOT a valid justification even if it is the only real
one
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Justification and Motivation
 Research hypothesis statement
 It demands a good analysis of the requisites.
 They may change as you progress, but the
more honest way to proceed is to keep it fixed
and if necessary when writing your thesis
state both, the original hypothesis and the
new one explaining why the change of mind
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Defining limits and assessment
 Clearly indicate the limits of your work
 The PhD is not the moment to get a Nobel prize
 Try to be realistic, it is easy to under-/overestimate your capacity
 It is at times hard to differentiate limits from
your goal
 If too short; maybe not enough to get the degree
 If too ambituous; maybe unfeasible and unable to
defend
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Defining limits and assessment
 Limits are often stated in terms of what’s
goind to be excluded
 In engineering it often comes bounded by
the project itself
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The research questions
 They represent open problems regarding the phenomenon of
interest
 Arguably the most important part of your protocol
 They ought to guide your research
 All goals (main and specific) are collateral consequences of
them
 All experiments are driven to answer them
 All experimental hypothesis are stated to (educatedly) guess
about them
 All conclusions are stated to satisfy them
 A rather bad habit is to state them (just because you’ve been
told to), and ignore them the next minute…
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Goals; Main and specific
 The main goal states what is to be
achieved during the thesis
 It is a long term goal
 It may fall BEYOND the reach and limits of the
project
 A thesis may be part of a more ambitious or bigger
project
 …that’s why establishing the limits is so critical
 It should be stated in one or two paragraphs
at most.
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Goals; Main and specific
 Main goal
 Here at INAOE they like it as:
 “Develop an algorithm that bla, bla, bla… and that is
competitive with the state of the art”
 That is only acceptable if you understand that’s NOT
the real goal but only a collateral goal
 The real goal in science is to understand a
phenomenon (that includes computer science!),
 …that is; to establish a relationship between dependent and
independent variables under given constraints (i.e. controlled
variables)
 …therefore developing/implementing anything is an
engineering goal
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Goals; Main and specific
 Specific goals
 Short term goals
 They will be covered during the thesis
 They may include developing specific
tools/algorithms etc
 They often/should also include validation as
one of them
 Each one of them has to be describable in at
most 1 paragraph
 It is not enough to state them, it is necessary
to describe them
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Theoretical and reference frameworks
 This/These chapter/s summarise/s all foundational
and similar techniques related to the thesis
 Theoretical framework: All necessary background to
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make the thesis self-contained; transdisciplinary
Reference framework: Literature review on the state
of the art of the phenomenon under study
 Beware! Depending on the scientific discipline these
may receive different names and be reported in
different manners; yet they ought to be always
present
 For instance, the reference framework in computer science is
often called related work.
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Theoretical and reference frameworks
 In writing these:
 Analyze, summarise and criticise the existing
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knowledge
Acknowledge the authorship of other authors
(otherwise it is plagiarism)
Ensure that you cite all key works in your area
 Often, at the time of writing your protocol
experiments may not have been run1 but a good
knowledge of the topic is expected. This includes:
 Domain
 Subdomains
1.
At INAOE this is NOT the case; you are expected to have some preliminary results by the
time you write your protocol
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Methodology; materials and methods
 Planning and description of tasks and
experiments
 They should refer to the achievement and
solving of the research questions and goals
 That does NOT mean 1-to-1 mapping!
 It is important both; identification and
description
 The more detailed, the easier will be to carry
out them later on
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Methodology; materials and methods
 Scheduling
 This is the chronological timing in weeks or
months of the expected times when the tasks
will be carried out.
 Always leave enough time for reading and
writing
 As a rule of thumb; reading NEVER ends
 The Gantt chart or chronogram is often a
good tool to express your scheduling
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Publications derived from this thesis
 If by this time, any publication has been
secured then indicate.
 …but remember, no one expects that you
have yet publish a lot…
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Conclusions
 At the time of writing the protocol it is early
to have final or definitive conclusions
 …so these do not refer to the intermediate
results in case you have some
 … they more often refer to the feasiblity of the
thesis, the foreseen hinders, a brief
discussion over the literature read so far, etc
 It should state the impact of your thesis
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References
 Cite ALL relevant references read so far
 …so that the thesis committee can assess whether you are
reading sufficiently and effectively
 Be coherent with the style format thorughout the
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document
Include:
 Scientific papers
 Books
 Other thesis (regardless of the degree)
 Technical reports
 Web sites
 Other sources of information; private communications from other
researchers, public documents, standards, patents, etc
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PARTS OF A THESIS
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Parts of a thesis
 Title
 Abstract
 Preliminaries
 Table of contents, figure and table listing, abbreviations and acronyms
 Chapters
 Introductory chapter
 Theoretical and reference frameworks
 Experimental chapters
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 Introduction
 Methodology
 Description of the work developed
 Results and analysis
 Discussion of results
Conclusions, Recommendations, and future work
References
Appendixes
 Others
 Index of terms, Source code, maps, circuits, etc
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Parts of a thesis
 The thesis final document is rather different
from the protocol
 The protocol describes what is it intended, what
tantatively is it going to be achieved, and a plan
for it. It emphasizes the research questions
 In constrast, the thesis describes what has been
done, the results and the conclusions. It
emphasizes the findings and scientific evidence
brought
 …consequently, these documents have a
different structure.
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Parts of a thesis
 The thesis document, as a scientific
document is far more strict than the
protocol
 Normally every institution imposes a
certain structure and format to be followed
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Parts of a thesis
 Title page
Chapter numbering and structure is indicative
 Abstract
 Prelimaries
 Ch. 1: Introductory chapter
 Ch. 2-3: Theoretical and reference framework
 Ch. 4-7: Experimental chapters
 Ch. 8: Discussion, Conclusions and future
work
 Appendixes
 References
 Other material
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Title
 The title must strictly stick to the
developed research
 …and not to the phenomenon or general field
investigated
 Accuracy should reign over generality
 Be scrupulously precise in the use of
technical terms
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Title
 A weak title might be misleading
 …specifically, it might lead to false
expectations
 …and that include your panel!
 A good title might help a correct search
 Rules are similar to those of the protocol
 …however this is final! This is what would be
indexed by engines
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Title
 Do not worry if title is a bit long
 …as long as it is justified
 …but if you find yourself having a rather long title,
suspect that you are not being concise
 If the more important part of the research is
the methodology itself over its application,
then subtitles are often a convinience
 Example: Database access through the web
using ASP: Application to Probesi
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Abstract
 The abstract opens your thesis document.
 In a thesis, it is about 1 pg long
 After reading the abstract the reader must know:
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

What was the problem before this thesis
What has been your contribution
The highlights of your findings
How this thesis impact science
 We will see a section about writing abstracts later
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Ch.1: Introductory chapter
 The first chapter is often an introductory chapter.
 It would be expected to cover the following:










Project framing; registry number, funding, conflicts of interests,
Preliminaries and description of the phenomenon
Justification and motivation
Research questions
Goals
Limits
Research hypothesis
Contributions
Publications derived from the thesis
Assessment; how should the thesis be understood and
evaluated
 Thesis outline
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Ch.1: Introductory chapter
 By the end of the first chapter, the reader
should know exactly:
 what have you addressed
 what have you achieved
 how this work moved science forward
 It may be appropriate to use your protocol
as an starting reference
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Ch.1: Introductory chapter
 Preliminaries include a brief yet fully
descriptive introduction to the topic,
problem and open questions
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Ch.1: Introductory chapter
 Justification and motivation
 Indicate the need for your work
 It is not the reason why you want to do the
thesis, but the society/market need to gain
that knowledge
 For an engineering project, a market analysis is
usually a good starting point, although that
analysis is not part of the project itself
 It will be necessary to expand over what you
wrote in your protocol
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Ch.1: Introductory chapter
 Research questions:
 Hopefully they will be fundamentally the same
that you stated in your protocol
 …but this is research! Justified deviations are
acceptable
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Ch.1: Introductory chapter
 Goals and limits
 Restate your original goals if necessary but try to
keep them as the originally stated in the protocol
 Time and money affecting the goals constraints
should be explicitly declared
 In engineering, and as well in computer science,
they should be quantitative if possible
 Limits can still be described in terms of what it
has not been done
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Ch.1: Introductory chapter
 Goals and limits
 Not complying with a goal is a severe fault if not
justified
 Again, justified deviations are acceptable
 …but even more acceptable is to stick to original statements
and describe why haven’t they been achieved as planned
 A time limitation is, more often than not, insufficient
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 …that’s why you put your limits in the protocol!
A deviation from the topic is a weak justification.
 In that case, a new protocol would have been required
Complications arise during research and errors on the
hypothesis based on new evidence collected during
the thesis are strong justifications
 That is what the thesis is all about!
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Ch.1: Introductory chapter
 Goals and limits
 Goals and limits should have been defined a
priori,
 …but truth is many do “adjust” them to what
has been achieved
 Watch out! This ensures that you comply but it is
often considered dishonest.
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Ch.1: Introductory chapter
 Research hypothesis:
 There may be more than one.
 This is what you defend
 Defend also include refuting!
 A thesis is the confirmation/refutation of a
hypothesisw
 Without yet getting into details (you’ll get to
this later), briefly highlight which hypothesis
are correct or wrong
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Ch.1: Introductory chapter
 Contributions
 Indicate what new knowledge have you
generated
 If collateral achievements are worth (specific
algorithms, databases/corpus, tools, etc), then
state these as well
 These by themselves are insufficient to guarantee
a degree
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Ch.1: Introductory chapter
 Publications derived from the thesis




Include all publications derived from the thesis
Clearly separate the journal from then conferences
Clearly separate peer-reviewed ones from others.
Show that you have read adequately by publishing
your theoretical and reference frameworks as a
review
 Rule of thumb;
 A thesis supported by outstanding record of publications is a
safe shot
 A thesis without published back up would be thoroughly
questioned and is unlikely to be enough to grant the degree
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Ch.1: Introductory chapter
 Assessment
 Do not underestimate including a good
assessment.
 Assessment is not about telling the panel the
qualification you expect for your work
 …but about telling the reader how should the
thesis be interpreted and contextualized
 The reader should be guided to what you are
interested in him to get from the thesis
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Ch.1: Introductory chapter
 Thesis outline
 Spend a few lines delineating the structure of
the rest of the document
 Example: “Chapter 2 describes …”
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Ch.1: Introductory chapter
 Acknowledgements may be part of this introductory chapter, or
made separately in a special section outside
 Acknowledgements are expected to include (and in this order)
 Yuor supervisor/s – regardless of whether it is deserved
 Your sponsor – whoever funded you (research council, business, etc)
 Your external (and perhaps even the internals) members of the




committee and panel – for the review!
Other external researchers that may have significantly help you with
your thesis – in whatever aspect (solving doubts, giving ideas, proof
reading, etc)
Other members of your research group who might have been invoved
with your work
Any other person which might have been important for your thesis
Finally, anyone else you want to thank (your family, your
girlfriend/wife/partner, your cat, aunties, etc)
 Sometimes, institutions formatting rules indicate the position where
the acknowledgements may appear
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Preliminaries
 Preliminaries include:
 Table of contents
 Figure and table listing,
 Abbreviations and acronyms lists
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Ch. 2-3: Theoretical and reference
frameworks
 Theoretical framework
 It gives a broad view of all the knowledge related
to your thesis ensuring it is self-contained
 This is where your panel will assess your “peripheral
vision”
 Includes the knowledge accepted by the research
community and all the theories that will support
our work
 It does not yet include any of your work, but some
cirticism on the evidence thrown by your thesis is
acceptable (and encouragable)
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Ch. 2-3: Theoretical and reference
frameworks
 Theoretical framework
 Do not include things which will not be used
 Example: If you include an alternative theory upon
which your thesis is not based, it is because you
will contextualize your finding against it
 Do not throw everything you know here;
 It is not about showing off or boasting how much
you know
 …yet ensure it transpires that you are a true expert
on your field
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Ch. 2-3: Theoretical and reference
frameworks
 Reference framework
 This is now fully focused on your specific topic
 This is where you show the reviewer that you:
 Know about your topic everything worth knowing
 Understand the subtleties of every aspect of the problem
 Analyze, discuss, criticise what other authors have
done
 Not everything published is true or correct
 Good criticism is constructive
 At INAOE a comparative table is often expected, but
this is not the only way to summarise…
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Ch. 2-3: Theoretical and reference
frameworks
 Reference framework
 Here is where you defend why you favoured
certain techniques or solutions over others.
 Defending your choice does not mean refuting
other theories or look down on other’s work
 Indicate the strengths and weaknesses on every
work considered
 Be open to critics to your own choice
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Ch. 2-3: Theoretical and reference
frameworks
 Reference framework
 The emphasis of your defence should be
proportional to the relevance for your work
 Example: If your work is not about optimization, but
for one of your experiments you needed
optmization; it doesn’t matter too much which
optimization have you used. Just indicate the one
you have chosen and briefly why you consider it to
be the appropriate.
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Ch. 2-3: Theoretical and reference
frameworks
 Reference framework
 The emphasis of your defence should be
proportional to the relevance for your work
(Cont.)
 Example: On the other hand, if you are working in
optimization, highlight why have you favoured that
technique over other alternatives. Clearly describe
the pros and cons in an objective manner (do not
try to bias the reader towards your choice; he may
be a strong defender of the alternative!!)
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Ch. 2-3: Theoretical and reference
frameworks
 Reference framework
 Show that you are up-to-date!
 Ensure thatb you have the latest references on the field
 Make extensice and intensive use of research
which has been peer reviewed
 Avoid using dubious references (specially from the
internet)
 Be comprehensive
 A common mistake is to forget about some
author/group’s work; an easy door for attack from the
panel!
 Use more than one reference for conflicting concepts
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Ch. 2-3: Theoretical and reference
frameworks
 Reference framework
 Try to follow some scheme, organization or
flow
 Chronological order: from the oldest to the more
recent
 By topic: First everything related to one subtopic,
then move to the next subtopic
 By acceptance: Review first the most widely
accepted theories and models
 By similarity or relevance to your topic; whether by
convergence (most distant first) or by divergence
(most similar first)
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Ch. 4-7: Experimental chapters
 Experimental chapters are the
fundamental/main part of your thesis
 This is your work!
 Each chapter is dedicated to answer
one research question
 Concomitantly, each chapter may comply with
some specific goal or afford a specific
contribution
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Ch. 4-7: Experimental chapters
 The emphasis of each chapter will however
depend on your thesis aim:
 Emphasize methodology if novel or scarcely used
 Emphasize experimental design and rigour if
exceptional
 Remember! Experiments have to be carefully designed
and planned even if this is not the goal of the chapter
 Emphasize the research hypothesis associated to
the question
 Emphasize the contribution of the chapter
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Ch. 4-7: Experimental chapters
 The emphasis of each chapter will
however depend on your thesis aim
(Cont.):
 Emphasize differences in experimental design
against other authors’ choices
 Emphasize optimization of resources if
applicable
 Sometimes a better experiment is easy to design
or foresee but practical limitations prevent their
implementation
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Ch. 4-7: Experimental chapters
 The emphasis of each chapter will
however depend on your thesis aim
(Cont.):
 Emphasize the description of the algorithms
and their parameterization if the experiments
involve a collection of simulations
 Emphasize the sequence of the experiments
and simulations if thie is relevant
 Do not assume that commutative does apply
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Ch. 4-7: Experimental chapters
 The description of your experiments ought
to be:
 scrupulous,
 rigorous,
 exhaustive
 utterly/brutally honest
 guaranteeing replicability of your results
 Non reproducible results are simply invalid!
 This is what science is all about!
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Ch. 4-7: Experimental chapters
 The description of your experiments ought
to be (Cont.):
 Indicate not only the factors you have
manipulated (independent variables) but also
everything that is kept constant (controlled
variables)
 Painstakingly describe all pre-processing,
processing and analysis of your data, and this
includes the statistics for hypothesis testing
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Ch. 4-7: Experimental chapters
 There is a full theory about experiment
design…
 It ensures your experiment reduces bias, cost
and time
 It has a strong statistical connotation that at
the end of the day is an optimization problem;
aiming to solve your unknowns with minimal
“effort” measured in some way
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Ch. 4-7: Experimental chapters
 Minutely describe all results with clear distinction
between quantitative and qualitate statements
 Do NOT include any judgement or adjective
 Stay objective at all times
 Stick to your results and do not extrapolate
 This is just a reporting exercise, the time to speculate will
come in your conclusions chapter if you want
 Do not be afraid of negative findings/results
 Most times, science advances through negative findings
 …although of course these requires even more thorough
attention to the way they are reported.
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Ch. 4-7: Experimental chapters
 Use but don’t abuse stats
 Example: If you did 10000 simulations you do
not need to report all 10000 results
independently, just use descriptive stats
 Graphs are a good way to summarise info
 Tables are more explicit that graphs and plots
but often more difficult to read.
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Ch. 4-7: Experimental chapters
 When using graphs/plots:
 They must be representative of the
information you want to show
 The must be descriptive of the knowledge you
want to convey
 They must be clear, readable, properly
labelled, quickly interpretable and selfcontained (independent of the text)
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Ch. 4-7: Experimental chapters
 When using graphs/plots:
 Choosing the right plot might not be trivial
 …indeed! There is a whole research dedicated to
data visualization techniques
 Each plot type is better to highlight some kind of
information communication
 Data visualization is critical
 Sometimes visualization is improved if data are
previously transformed (e.g. use of logarithmic
scale)
 Sometimes it may be worthy to ghost some data to
emphasize some other aspect of the information
(e.g. outlier removal or hidding, axes cropping)
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Ch. 4-7: Experimental chapters
 When using graphs/plots:
 If you have more than 3 dimensions/variables
you may want to consider dimensionality
reduction techniques (e.g. PCA)
 3D plot interpretation maybe impressive but
not necessarily easy; at the end of the day,
paper is bidimensional
 Never, ever, sacrifice clarity for the sake of a more
aesthetically beautiful plot
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Ch. 4-7: Experimental chapters
 If the experiment is an indirect measure of
a non-observable phenomenon, then
clearly state your forward/inverse model
relating observable information to nononservable information
 Example: Image reconstruction
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Ch. 4-7: Experimental chapters
 NEVER, ever, manipulate your results
 As serious offence
 Do not force regressions, nor distributions
 Respect techniques assumptions and confine
your interpretation to these
 Victimism is not an option in science:
 Example:
 You say: “I cannot have more data. In my field collecting



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data is time consuming/costly/etc”
What I hear: “I’m lazy. I couldn’t care for carefully designing
my experiment to fit my circumstances”
You say: “Should I have more data, my results would have
been significat/better/more solid”
What I hear: “I have no idea about stats, so instead of doing
the right thing i.e. learning stats, let’s do the easy thing,
blame what everyone else does…”
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Ch. 4-7: Experimental chapters
 In engineering, you ought to include:
 Error analysis
 Cost analysis
 Many theoretically valid solutions may not be
feasible for practical constraints, and cost is
certainly one of these
 Pay special attention to:
 Units
 Type of variables
 Not all variables admit the same operations
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Ch. 4-7: Experimental chapters
 In engineering it is also necessary to
express intermediate needs and structures
 Example: Civil engineering; in improving a
motorway, you should not stop the motorway
for three months. You have to provide a
temporal diversion.
 Example: Computer science: If you are
updating the structure of a database provide
an intermediate repository and ensure you
have a plan for restoring/adding this
information to the new database.
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Ch. 4-7: Experimental chapters
 Discuss your results
 Subjectvity is not welcome, especially in exact
sciences
 Be cautious about leap of thinkings
 3 samples aren’t enough to demonstrate a trend
 Highlight both strengths but also weaknesses
 Compare, compare, compare
 Comparing is the basis of validation
 Important: Include those approaches who are
“better” than you. Not doing it opens a door for
attack from your panel.
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Ch. 4-7: Experimental chapters
 Analysis is more than just stating the obvious;
it is demonstrating that you understand the
subtleties and intricacies of your results
 Example: You have a data series following a
Gaussian distribution
 Does it fit to what you expected? Maybe you were
expecting some other distribution
 Is standard deviation too large? What about standard
error; too small?
 Is your positive result of the test a false positive?
 Is sample size adequate? Not too small, not too large
 Is this relation likely to be spurious?
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Ch. 4-7: Experimental chapters
 Demonstrate that you know how to interpret your
results
 Example: ¿Are your data against the laws of physics?
 ¿Turtles running 110m obstacles in 3 sg?
 ¿2+2=38?
 ¿Why did my genetic algorithm took 15 days to run if only
had a population of 3, 5 generations and fitness function was
trivial to evaluate?
 Did you design your experiment correctly? Was it
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actually executed correctly?
Since it is almost impossible to run a “perfect”
(unbiased) experiment, what biases might be
responsible for these observations?
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Ch. 4-7: Experimental chapters
 Do not anticipate conclusions!
 Consider alternative hypothesis
 If negative results, indicate why you think it
failed and how would you tackle the issue
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Ch. 4-7: Experimental chapters
 Particularly for software
 Just because it run once, it does not mean it would
run always
 Different hardware rounds in different manner even under the
same OS,
 If (pseudo-)random elements are present, initial conditions
may differ
 Home/lab testing is never exhaustive
 I don’t care if you took 8 months without eating or sleeping
 A good bunch of empirical simulations is not an analytical
proof of model checking!
 Blind/wild trial and testing? Or thoroughly/carefully

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plan tests?
Did you allocate sufficient time for design and
analysis (commesurate with the application size)?
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Ch. 4-7: Experimental chapters
 In science, you can’t hide from stats!
 …well, maybe you can: “If you need stats to
prove your hypothesis, you ought to have
done a better experiment” Lord Ernest
Rutherford
 Ensure you have the correct statistics, both
descriptive and inferential, according to your
experimental design
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Ch. 4-7: Experimental chapters
 Pay special attention to results changes
under different conditions
 Do you get the same or congruent results?
Are they disparate?
 Is what you have measured what you really
wanted to measure? Just a proxy?
 Check your boundary conditions
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Ch. 4-7: Experimental chapters
 A few unknowns can be estimated in
different ways with experiments having
slightly different (complementary) point of
view
 This is often a good way to confirm a result
 Just ensure your results do back up each
other
 If you got different results, then question why?
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Ch. 4-7: Experimental chapters
 When comparing to other works
 Make fair comparisons; homogeneous
groups, comparable treatments, etc
 In case of doubt, always give advantage to
the other methods
 Sometimes, repeating someone else’s
experiment is a good way to check your
approach (…as well as an excellent
opportunity to verify the other author’s results)
 If your results are outstanding, then be
skeptic!
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Ch. 4-7: Experimental chapters
 Discussion: This is where you evaluate
your findings and contextualize them with
accepted knowledge
 Identify your own weaknesses, assumptions
(especially those hidden or not obvious),
biases, etc
 Be critical and objective to your own work
 Contextualize with accepted knowledge
(nomological validity)
 A strong discussion saves a weak thesis; a weak
discussion spoils a good thesis
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Conclusions, Recommendations, and future
work
 Conclusiones: This is a summary of your
findings
 Think how have you contributed to science
 It is not a mere summary of your results, but a
thought on their implications
 A common way to report them is by research
question (section) and then by specific finding
(subsection)
 It is here where you state if you have confirm
or refute your original hypothesis
 i.e. where your hypothesis becomes a thesis
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Conclusions, Recommendations, and future
work
 Recommendations:
 Highlight some of the difficulties and
challenges you faced during your
experimentation and how did you solve them
 Look beyond your own work; think how it does
impact other areas of science and technology
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Conclusions, Recommendations, and future
work
 Future work: A good research always led
to new open questions
 Show that you know how to continue your
research (when you no longer have a
supervisor)
 Identify ways in which your work can be
modified, improved, enlarged, generalized,
particularized, further verified/validated, etc
 A good way to extend your work is simply by
relaxing/attending some of the assumptions
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Conclusions, Recommendations, and future
work
 Future work:
 Identifiy how your work can seed other works
 Identify gaps that have to be more thoroughly
studied
 Launch new hypothesis on those yet
unresolved issues
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Appendixes
 It is also where you append your thesis with
supplementary material necessary for the
thesis to become self-contained
 Long mathematical proofs
 Specification sheets,
 Very large tables
 Consent forms
 Maps
 Budgets (compulsory for engineering projects)
 Code listing
 Photographs
 etc
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References
 Regardless of the chosen style (perhaps
imposed by the formatting rules of the
institution), it is necessary
 Sort your references in some way
 Keep a coherent citing/referencing style all
throughout the thesis
 Rule of thumb; In a 4 year thesis you shall
read about 450-600 papers of which 1/3-1/2
will be useful and will be included in your
thesis
 …less than that, and you haven’t read enough!
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References
 Common sorting.
 By order of appearance in the text (very
common in papers)
 By surname of the first author
 By year
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References
 Style
 There exists some standard styles: Chicago,
Vancouver, Harvard, etc
 In computer science the Vancouver style is
perhaps the most widely used
 These dictates not only the reference format,
but also the citation format
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Throughout the thesis
 Remember!:
 Avoid PLAGIARISM. The most severe offence in
academic work
 Use citations and quotations appropriately
 The rule is simple; Original authorship of every piece of work
must be crystal clear
 Avoid rambling and repeating concepts
 Use references to equations, sections, figures, tables, etc
 The thesis is written for your peers
 Avoid including trivial or basic material
 …but also remember that your peer may not be an expert on
you specific field.
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WRITING ABSTRACTS
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Writing Abstracts
 There exist 3 major types of abstracts:
 Descriptive
 Informative
 Critical
 A fourth type is the so called extended
abstracts; a longer than normal informative
abstract that acts as a substitute of a full
document
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Descriptive Abstracts
 Short – Usually less than 100 words
 Include:
 Purpose of the work (Goals)
 Methods
 Scope
 Does not include:
 Results, conclusions nor recommendations
 The reader will have to read the full
document to decide whether it is relevant for
him/her
 The kind of abstract you include in a review
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Informative Abstracts
 Mid size - Between 200 words and 1 pg
 Include:
 Background
 Aims
 Methods
 Results
 Conclusions and impact
 Communicates the content of the document.
Sufficient for a reader to decide its relevance.
 The kind of abstract you include in a paper
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Critical Abstracts
 Long – 500 words to 1000 words
 A non structured short summary of the
document
 Highlights the take away message of the
content
 The kind of abstract you include in your
thesis
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Dr. Peter Hancox/Trad. Dr. Felipe Orihuela
Espina
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Characteristics of a good abstract
 Concise
 Communication is effective and efficient
 Informative
 Regardless of the type the reader gets a quick
overview of the contents of the document
 Connected
 Flow is smooth and without breaks
 Conservative
 Does not include new material over the material
contained in the main document
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Common errors
 Title repetition
 Well, the title is a different part of the
document
 Boring
 Wasted invaluable space
 Starting with “This work…”
 Isn’t it obvious that you’ll talk about this
document?
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Dr. Peter Hancox/Trad. Dr. Felipe Orihuela
Espina
124
Common errors
 Making external references
 Title and abstracts should conform an selfcontained unit
 They have to be used for indexing the
document
 Avoid references to literature and figures or
tables
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Dr. Peter Hancox/Trad. Dr. Felipe Orihuela
Espina
125
Common errors
 Use of acronyms and abbreviations
 Leave those for the main text
 Only extremely well known acronyms may be
acceptable; USA, UK, etc
 Do you know what RTE, ATR, GSM, WAM or
LFG mean? Well, they are extremely well
known in their areas…so why should you
expect that someone knows the
acronyms/abbreviations in your field?
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Dr. Peter Hancox/Trad. Dr. Felipe Orihuela
Espina
126
THANKS, QUESTIONS?
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INAOE
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