thesis writing - fke · james hayton, \your uncommon guide to thesis writing and phd life" ...

$: Thesis Writing - FKE · James Hayton, \Your uncommon guide to thesis writing and PhD life" Michalis Faloutsos, ... an active eld of research$
What is a Thesis? Getting it Done Writing from Scratch? Rule of Thumb Paper Structure Ethical Writing Conclusion

Thesis Writing

Tips on how to get it done, fast

M.N. MarsonoPostgraduate Academic Manager FKE

May 8, 2014

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Outline

1 What is a Thesis?

2 Getting it Done

3 Writing from Scratch?

4 Rule of Thumb

5 Paper Structure

6 Ethical Writing

7 Conclusion

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Disclaimer

An abridged version from materials taken from these sources

Douglas E. Comer, “How To Write A Dissertation or BedtimeReading For People Who Do Not Have Time To Sleep”https://www.cs.purdue.edu/homes/dec/essay.dissertation.html

Ian M Bird, “Preparing a Thesis”http://www.erp.wisc.edu/profdev/thesis04.pdf

James Hayton, “Your uncommon guide to thesis writing andPhD life”http://jameshaytonphd.com/

Michalis Faloutsos, “The structure of paper/report inSystems”http://www.cs.unm.edu/˜michalis/TECHWRITING/structure.html

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Miguel Roig, “Avoiding plagiarism, self-plagiarism, and otherquestionable writing practices: A guide to ethical writing”http://facpub.stjohns.edu/˜roigm/plagiarism/Index.html

Universiti Teknologi Malaysia Academic Regulation booklet

http://www.phdcomics.com

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What is a Thesis?

It is a documented evidence of defined scope and length that

You are capable of making original, valuable contributions inan active field of research.

You have comprehensive knowledge on you specific area ofresearch

The broad landscape of your fieldCurrent (competing) works being done elsewhereYour professional opinions are well-informed and backed up byyour knowledge and legitimate reasoning.

The body of work you submit in your thesis is comprehensive

(For PhD) You are ready for independent researches.

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Master’s vs. PhD.

The philosophical nature of a thesis takes a question aboutthe unknown, investigates it, and reports the findings and themeaning of the findings.

Both Masters and PhD require

Formulation of a questionInvestigation of the questionReporting of the resultsA discussion of the immediate implications.

The difference (Masters vs PhD) are the “originality” and“substantialness” in the context of the research and the thesis.

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A Master’s thesis is to assess that a candidate is

Technically competentAble to conduct scholarly researchHas critical-thinking abilityUnderstand relevant theoretical issues

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A PhD thesis is to assess that a candidate has:

All the above attributes, plusAn original contribution to knowledgeThe authority underlying the thesis – extensive (breadth) andintensive (depth) knowledge of their subject.

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What to Assess?

A thesis is an exit examination document

The quality of the research, the structure of your argument,the quality, relevance and depth of your references

In short, “Are you capable of discussing your work on aprofessional academic level?”

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Thesis Organization

In general, every thesis must have a solidly defined problem thatmotivated the research

Why the problem is important

What others have done

Describe the (novel) contribution and findings

Document the experiments that validate the contribution

Draw conclusions.

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Each thesis is unique and depends on the writer and the editor(your SV). The following example a good starting point:

Abstract: A short (few paragraphs) summary of the thedissertation. Describe the problem and the research approach.Emphasize the original contributions.

Chapter 1: Introduction: An overview of the problem; whyit is important; problem definition; a summary of extant workand a statement of your hypothesis or specific question to beexplored. Make it readable by anyone.

Chapter 2: Literature Review: Critical review of extantworks. Research gaps to be exploited. Make the definitionsprecise, concise, and unambiguous.

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Chapter 3: Conceptual Model Describe the central conceptunderlying your work. Make it a unified theme that tiestogether all your arguments. It should provide an answer tothe question posed in the introduction at a conceptual level.

Chapter 4: Experimental Setup and MeasurementsDescribe the results of experiments that provide evidence insupport of your thesis. Usually experiments or simulations

Could be proof-of-conceptTo show better efficiency

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Chapter 5: Corollaries And Consequences Describevariations, extensions, or other applications of the central idea.

Chapter 6: Conclusions Summarize what was learned andhow it can be applied. Mention the possibilities for futureresearch.

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Suggested Order For Writing

Begin by writing the chapters that describe your research (2,3,4, and 5 in the above outline). Define all technical terms.

Organize the problem description and definitions into aseparate chapter when appropriate. Make the definitionsprecise and formal.

After reading the main chapters to verify terminology, writethe conclusions.

Write the introduction.

Complete an abstract.

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Criteria of a Good thesis

Content: Spend more time and effort writing about thestrengths of your work, and making clear, confidentstatements wherever possible to emphasize your bestresults.

Style: Read some of your supervisor’s work, so you can geta sense of their style. Keep the style simple and avoiddense, dry, monotonous text blocks. Thesis writing isnot a creative writing, although you need to becreative and be aware of the rhythm of your writing.

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Clarity: Clarity is king. Make your expression clear. Theexaminer can disagree with you, but they shouldnever misunderstand you. Always check forambiguous the statements.

Honesty: An ethical writer always acknowledges thecontributions of others and the source of his/herideas. Others ideas, data, and conclusions are usuallyborrowed and used as the foundation of one’s owncontribution.

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Thesis Writing Cycle

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Thesis Writing Tips

Writing requires solid blocks of uninterrupted time

Create a protected time and space to write.Focus onto one task, idea or sub-section at a time.

Have a routine:

Begin and end the day productively.Build momentum early.End the day by preparing for the next (day).Have a sound sleep and rest.

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Set your PhD thesis writing goals.

Writing is a acquired skills. Continuous writing helps.

Set a thesis submission deadline

Typically takes 3 to 6 months, could be longer.Set your own deadlines and stick to them.Do not underestimate the time your supervisor will read yourthesis (and for how many rounds)

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See it through to completion

Too often, things are left “70% done”, with the intention ofcoming back to finish it later. A mad scramble during the lastfew weeks trying to go back and fill in all the gaps (guaranteedstress).Get things completed and ready to submit one-by-one untilthere’s nothing left to do.

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Reading papers for your PhD thesis

Thesis writing requires a lot of reading and a lot of references(sometimes over two hundreds). Trying to rearrange your ideasand supporting them with references can be difficult.Use tools to sort your references (Mendeley, EndNote, Jabref)Focus only on the very best literatures. Select top n referencesthat are really solid (and recent) and know them inside-out.

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Writing your PhD thesis:

Collating and formatting figures can be one of the most timeconsuming parts of writing up. It is worth to spend timeworking on decent figures and illustration than writing athousand words to explain a figure.Use standard modeling diagrams when appropriate. It will addthe feel of quality thesis and be consistent.Preparing your data in advance will also show you where youare lacking data. Try to visualize how the results can be bestrepresented.Write down a concise version of your materials and methods.More than likely you will have to edit this come thesis time,but you will save time in sifting through notes.

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Writing your PhD thesis (cont’d):

Adjusting your writing style will save you time in the long run.Understand your supervisor’s style and what he/she likes anddislikes.Write about what you know about, which made the thesisshorter, faster and easier to write, and of higher qualityUse writing SW that helps you produce good quality thesis(LATEX/LYX, MS Word with EndNote). Make sure you use asmany functionalities as possible (dynamic linking, auto pagenumbering etc.).

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Cut anything sub-standard (literature, figures, diagrams).Compare them against the best you have read in literatures.

Take a break from thesis writing:

After reading ten papers or more finding a point to start or agood open line to a chapter can be tiresome. Allowing thedata from the papers to settle in your head will allow you torun through some opening lines in your head and allow you toformulate some ideas or hypothesis regarding the subject.

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Review your thesis/dissertation before submission

Reviewing your work also helps you to generate ideas for thenext sections or chapters and determine what you need towrite about next.Check spelling mistakes, bad sentencing and bad scientificphrasing. Your SV is the first flood-gate. Making him/herinterested is vital.The review process can add weeks to how long it takes.Submit your chapters regularly to your supervisor for correctionand critique.

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Do We Need to Write a Thesis from Scratch?

You may not realize that 75% of your thesis is already done, youjust need to take advantage of it!

Technical papers

Research proposal

Presentations

It requires careful considerations (see the Caveat Emptorslides)

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Do not Reinvent the Wheel

Don’t reinvent the wheel! Why spend sleepless nightsrewriting sections and paragraphs again

You’ve already written/published some papers, these make upto most of your thesis!

Do not let your supervisor to go through the process ofcorrecting your thesis, again!

Most institutions do not accept thesis as a collection ofpapers (such as the Scandinavian countries, Japan).

Traditional thesis formatting and organization is required(UTM included).

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A Lazy Man’s Guide to Fast Thesis Writing

Get the UTM thesis template and learn how to format your workproperly (if you need to use LATEX, learn it).

Define the thesis title. Tie all important keywords into oneunified title.

Write the thesis abstract.

Write two or three sentences introducing the motivation andproblem statementsWrite a concise contribution of each of your papersHighlight significance of your overall work.

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Chapter 1.

The hardest part as it will set the tone for the readers.Put all of your original work in the context of your broad andspecific fields of research.This includes giving a broad (and well-referenced) overview ofyour sub-field, how it fits into the broad context of your fieldand why it’s important, and how your specific research hasaddressed some of these particular issues.It should allow seamless transition from the end of this chapter(thesis organization) into the main chapters.

Chapter 2

A proper Literature Review chapter is required. Adapt fromresearch proposal and papers.Focus on extant works and how they fit into the thesisframework.Highlight the gaps.

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Main chapters

Adapt from your research papers.Possible if a consistent paper writing style is used. See theslides on Paper Structure.Some rearrangements are required. Strip the introduction andconclusion sections (from the paper).Do not rewrite paragraphs, unless necessary.

Final Chapter

Thesis findings and statement of contributions. This section isvery critical to highlight novelty of your findings in the broadcontext of your research.Challenges remain in your field, with some detailed plans forfuture directions.

The rest — acknowledgments, dedication, references, etc. —take practically no time or effort.

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Caveat Emptor (at Own’s Risk)

The preparation of papers and the preparation of a thesis maycreate conflicts.

Originality: A paper after several revisions may have lostoriginality, especially when edited by the SV. Hence, the thesisreproduced from papers may not be the original writing bystudents.

Mutual exclusiveness: The papers must be mutuallyexclusives. Overlap papers (e.g., short conference and longjournal versions) will create conflict. Use the mostcomprehensive and recent version.

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Methods: A journal may want you to minimize methods tosave pages but a thesis requires demonstration ofunderstanding of methods as well as information needed forcritical evaluation of the methods used.

Results: Not much of an issue but some data may berelevant yet missing for publication purposes (a big array tablefor instance, or method validation). Consider the use ofappendices for this purpose.

Conclusions: The thesis may end up with repetitiveconclusion when taken verbatim from papers. Somerearrangements may be required.

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Follow Good Thesis Writing Practices

Thesis is an exit examination document. The good thing is,you can set the tone yourself

Set high standards

Show that you care. Else, why should us?

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Terms and Phrases To Avoid

Mostly adverbs, they are very often overly used. Use strong wordsinstead.

Avoid judgmental words such as “bad”, “good”. Use“incorrect/correct” to refer to factual correctness or errors.

Use precise words or phrases to assess quality (e.g., “methodA requires less computation than method B”).

Avoid all qualitative judgments such as “true”, “pure”,“good”, “perfect”, “an ideal solution”

Avoid vague phrases such as “as the basis of” , “different” vs.“various”, “in light of”, “lots of”, “obviously”, “clearly” etc.

See more athttps://www.cs.purdue.edu/homes/dec/essay.dissertation.html

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Voices and Tense

Voice: Use active constructions. For example, say “theoperating system starts the device” instead of “the device isstarted by the operating system”.

Tense: Write in the present tense. For example, say “Thesystem writes a page to the disk and then uses the frame...”instead of “The system will use the frame after it wrote thepage to disk...”

Define Negation Early: Example: say “no data block waitson the output queue” instead of “a data block awaitingoutput is not on the queue.”

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Grammar and Logic

Grammar and Logic: Be careful that the subject of eachsentence really does what the verb says it does.

“RPC requires programs to transmit large packets” is not thesame as “RPC requires a mechanism that allows programs totransmit large packets”.“There is a compiler that translates the N languages by...”means a single compiler exists that handles all the languages,while the sentence “For each of the N languages, there is acompiler that translates...” means that there may be 1compiler, 2 compilers, or N compilers.

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Focus On Results

Stick to the plain facts. Avoid

“After working eight hours in the lab that night, werealized...”.“If that cat had not crawled through the hole in the floor, wemight not have discovered the power supply error indicator onthe network bridge”Never attribute such events to mystical causes or imply thatstrange forces may have affected your results.

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Avoid Self-Assessment

Avoid self-assessment (both praise and criticism)

“The method outlined in Section 2 represents a majorbreakthrough in the design of distributed systems because...”“Although the technique in the next section is notearthshaking,...”“This novel architecture ...”

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References to Extant Work

Always cites papers, not authors.

Avoid the phrase “the authors claim that X”. If you agree onX correct, simply state X followed by a reference.

If one absolutely must reference a paper instead of a result,say “the paper states that...” or “reference [1] presentsevidence that...”.

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Concept vs. Instance

A reader can become confused when a concept and aninstance of it are blurred.

An algorithm vs. a particular program that implements itA programming language vs. a compilerA general abstraction vs. its particular implementation in acomputer systemA data structure vs. a particular instance of it in memory.

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Drawing Only Warranted Conclusions

Draw conclusions that the evidence supports.

If programs run much slower on computer A than on computerB, one cannot conclude that the processor in A is slower thanthe processor in B unless one has ruled out all differences inthe computers’ operating systems, input or output devices,memory size, memory cache, or internal bus bandwidth.

Refrain from doing judgment unless one has the results from acontrolled experiment (e.g., running a set of several programsmany times, each when the computer is otherwise idle).

Even if the cause of some phenomenon seems obvious, onecannot draw a conclusion without solid, supporting evidence.

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Science and What’s Not

In a scientific thesis, one never draws conclusions about theeconomic viability or commercial success of an idea/method.

Avoid statements such as “over four hundred vendors makeproducts using technique Y”.

Politics And Science: A scientist avoids all political andideological influence when assessing ideas.

One must assess the idea independent of the source.

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Structure of a Good Paper

A properly structured paper helps thesis writing (refer toWriting from Scratch section)

When writing technical papers, keep in mind of overall thesisframework.

Partition ideas structurally to allow nice fitting to the thesisstructure

A properly written technical papers can be easily adapted asthe thesis main chapters.

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Structure of a Good Paper

Some rules by Michalis Faloutsos (UNM)

Recursiveness 1: In every section, the first paragraph shouldbe a summary/overview of the section. You can actually startby saying: “In this section, we present...”

Recursiveness 2: In every paragraph, the first (or secondline) should correspond to summary of the paragraph.

Top-Down: Start from high level and start increasing thedetails slowly.

Prepare the reader: Papers and reports are not suspensethrillers. The reader should have an idea of where you aretrying to get at.

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Adapt: These rules are meant as guidelines. Paperrequirements can differ. However, when you break one ofthese rules, be aware of it and have a good justification.

Huge introduction: if you can not say it in 1.5 pageprobably it is not very clear in your mind or you don’t use theright level of abstraction.

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Basic Structure

Basic structure:

Our Idea

Model and analysis

Experiments and verification

Discussion and deduction.

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Abstract

1 paragraph 200-300 word. This is the ad and trailer for thepaper: it has to be an executive summary of your work

1-2 lines: goal of this paper

1-2 lines: motivation and importance of work

1-2 lines: per result or contribution of our work. Quantifiableif possible e.g., 50% faster.

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Introduction

At paragraph level:

* indicates one or at most two paragraphs** means as many paragraphs area needed,

Introduction [1-1.5 pages]

* What is the problem, motivation, importance, maincontribution

* The problem: high level definition, significance

* Previous work [at most one line per relevant paper, leavedetails for next section]

* Our contribution: possibly list of results and contributions

* “The rest of this paper is structured as follows. In section2,.....”

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Background and Model

Background and Model [1-1.5 pages]

* Definitions, scenario, model

* Previous work [provide details only if this will help showwhere your work is different or better. Make sure youreference all related work and especially that by people in thecommittee!]

* Weaknesses of previous work or the absence of the thing youare proposing

* Assumptions and limitations of your work. [Be honest, butdon’t condemn your work].

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Our Idea

The Idea [as required]

* The innovation in brief

* New definitions, if necessary

** What it is and how it works

** Explanation of fine points, clarifications

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Analysis

Analysis [as required]

* Overview of what we prove in this section

* Analysis-specific definitions [i.e. a graph structure that youwill use in the proof]

** Analysis - proofs

* Comments - Meaning of proofs at an intuitive or practicallevel

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Experimental Results

Experimental Results [ as required]

* Overview of experiments: what we do measure, what wedon’t, why* Simulation model or measuring infrastructure** Experimental Results

Use a heading (in bold) to distinguish experiments (e.g., Theeffect of size on performance or even better The size does notaffect the performance..)Each plot should have a clear reason for appearing (e.g., withmore load we get worse throughput). Explain each plot: theaxis, what we see, what is the trend, why this is the trendStatistical comments will strengthen your results: confidenceinterval, correlation coefficient etc.Each figure should be fairly stand alone and self explanatory:captions should be readable and understandable.Comments, discussion, explanations

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Discussion

Discussion [1-2 pages]

* Overview of section

** Paragraphs according to needs

If you have space and ideas, you can strengthen theimportance of your work by showing:

significance,relation to other pieces of work,possible practical applications

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Conclusion

Conclusions [1-1.5]

* Overview what this work was about.

* Main results and contributions

* Comments on importance or

* Tips for practical use and how your results or experience canhelp someone in practice or another researcher to use yoursimulator or avoid pitfalls]

* Future work. Reinforce the importance of work, but avoidgiving out your ideas.

Conclusions are very important. Do not expect that the readerremembers everything you told him/her. Having stated thedefinitions, you can now be more specific than in the introduction

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Other Sections

References

It has to be complete, accurate, and recent

Appendices

As requiredProof, data parameters

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Why Unethical Writing

Not enough resources to write proper -> unethical writing

Time

Results

Language prowess

Brain power

Supervision time

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Plagiarism

Item 27 UTM Academic Regulation

“Plagiarism in academic includes producing thesis, dissertation,project report, article, coursework and research findingswithout acknowledging or referring to the original sources andclaiming as one’s own work. It involves the submission of thewhole or part of the work towards a degree. ”

American Association of University Professors(September/October, 1989)

“...taking over the ideas, methods, or written words ofanother, without acknowledgment and with the intention thatthey be taken as the work of the deceiver.”

In-short: Writing inappropriation with intention to deceive

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Plagiarism of ideas

An ethical writer always acknowledges the contributions ofothers and the source of his/her ideas.

Others Ideas, data, and conclusions are usually borrowed andused as the foundation of one’s own contribution

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Plagiarism of text

Any verbatim text (word-by-word) taken from another authormust be enclosed in quotation marks.

Must be in proper context as in the original publication

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Inappropriate paraphrasing

Always identify the source of our information whenparaphrasing or summarizing.

Reproduce the exact meaning of the other author’s ideas orfacts using our words and sentence structure.

To properly paraphrase, the author must have a thoroughunderstanding of the ideas and terminology being used.

Whenever possible, to use one’s own words whenparaphrasing.

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Plagiarism and Common knowledge

Give credit to those whose ideas and facts we are using.

One general exception for the ideas that represent commonknowledge

When in doubt, always provide a citation

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Ethically Questionable Citation Practices

Double-check your citations.

If done manually, check citations against citation listed in thereference section and vice versa.Can be sloppy, use mechanized method (EndNote, BibTex)when writing

Ensure that all elements of a citation (e.g., spelling ofauthors’ names, volume number of journal, pagination) arederived directly from the original paper

Do not cite that appears on a secondary source.Make sure the the publication is traceable

Must ensure that credit is given to those authors who firstreported the phenomenon being studied.

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Inappropriate Manipulation of References

The references used in a paper should only be those that aredirectly related to its contents.

When borrowing heavily from a source, authors should alwayscraft their writing in a way that makes clear to readers, whichare theirs and which are borrowed.

Try to obtain the actual published paper. When the publishedpaper cannot be obtained, cite the specific version of thematerial being used.

When describing others’ work, do not rely on a secondarysummary of that work.

It is a deceptive practice, reflects poor scholarly standards, andcan lead to a flawed description of the work described.Always consult the primary literature.

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Selective reporting

Authors is responsibility to report evidence that runs contraryto their point of view.

Evidence that support of our position/stand must bemethodologically sound.When citing supporting studies that suffer frommethodological, statistical, or other types of shortcomings,such flaws must be pointed out to the reader.

Authors have an ethical obligation to report all aspects of thestudy that may impact the independent repeatability of theirresearch.

Researchers have an ethical responsibility to report the resultsof their studies.

Any post hoc manipulations that may alter the initial results(e.g., elimination of outliers, or the use of alternative statisticaltechniques) must be rationalized.

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A Thesis is a Scientific Document

The scientific method starts with a hypothesis and thencollecting evidence to support or deny it. The most difficultaspect of writing a thesis consists of organizing the evidenceand associated discussions into a coherent form.

The essence of a thesis is critical thinking, not experimentaldata. Analysis and concepts form the heart of the work.

A thesis concentrates on principles: it states the lessonslearned, and not merely the facts behind them.

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In general, every statement in a thesis must be supportedeither by a reference to published scientific literature or byoriginal work.

Each sentence in a thesis must be complete and correct in agrammatical sense and must be crystal clear.

Each statement in a thesis must be correct and defensible in alogical and scientific sense.

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The Bottom Line is

Develop a topic based on what has already been said andwritten

BUT write something new and original

Rely on experts’ and authorities’ opinions

BUT improve upon and/or disagree with those same opinions

Give credit to previous researchers

BUT make your own significant contribution

Improve your English to fit into a discourse community bybuilding upon what you hear and read

BUT use your own words and your own voice

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thesis writing - fke · james hayton, \your uncommon guide to thesis writing and phd life" ...

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