Recommended outline and guidelines for M.S. theses

Prof. Neil Rowe

Version of January 2021

Abstract (10-22 lines)

• Summarize the methods and results of the thesis, with particular emphasis on the methods and resultsGive some motivation for the work, but don't write a second introductionUsually you need not describe prior work unless it was really important.
• Many readers will read only the abstract and not the rest of the thesis, so the abstract should be self-containedConsistent with that, do not use specialized terms, acronyms, or citations in the abstract.
• The abstract is not included in the templates for theses, but you should include it anyway at the front of your thesis file to make it easier to compare to the thesisOnce it is agreed upon, you can copy it into the introductory material form and delete it from the thesis.

Chapter 1: Introduction (2 to 4 pages)

• Describe the need (problem) your thesis tries to address. Convince the reader that it is a serious need (that is, motivate the reading of the thesis)This requires finding relevant citations to publications of experts, and summarizing their pointsDo not just state your own opinions about why the problem is important, as experts usually have a broader perspective.
• Explain why a computer program, system, or methodology can help this need.
• Explain why previous work (if any) hasn't solved this need, or else hasn't solved it completely.
• Explain what new ideas you had for solving this needOnly describe these ideas in general terms here; do not give names or details of tools or products you use.
• Briefly describe the remaining chapters of the thesisThis should usually be the only place you describe chapters.

Chapter 2: Previous attempts by other people not at NPS to solve this problem, and other problems like it, with computer programs or methodologies (4 to 12 pages)

• Describe other attempts to solve the problem or problems that you are trying to solve ("previous work") using different methods than yours, by people not at NPSGive citations, but not names of papers, full author names, or other reference details that will be in the reference listWork done at NPS should go in chapter 3.
• Generally, you need at least six examples of previous work from refereed publications (which are, generally speaking, conference proceedings, journals, and book chapters)Web sites are usually unrefereed, so avoid referencing them unless they have key information (such as software details) not available elsewhere. Key software downloads and relevant Web sites should be cited too, but they don't count as one of the six publicationsEvery publication listed should have a specified author or authors; organizations can be authors too.
• Point out the key features of each example of previous work. Usually one paragraph per reference is enough, but important references may require more.
• Describe any general mathematical background necessary for your program or methodologyHowever, the specific mathematical methods you used should go in chapter 3 or 4.

Chapter 3: More precise description of the problem you tried to solve and the general approach that you used (3 to 20 pages)

• Describe the problems in the real world that your program or methodology will try to addressDescribe the setting of those problems, and note things that aren't done as well as they could be, either because they aren't using digital technology or they aren't using it the right wayFocus on the problems, not the solution.
• Describe the major software and data you used in your work at a high level of detail. This can include work at NPS. However, references to previous work on problems similar to yours that used methods different from yours should go in chapter 2, and details of your particular experimental plan should go in chapter 4.
• Describe the specific assumptions you made in writing your program or formulating your methodology, as for instance the situations they try to address, the sort of people that will use the program or method, applicable orders and regulations that define the task environment, and so on

Chapter 4: Description of your methodology or program (5 to 40 pages, plus some figures)

• Generally speaking, this chapter should give enough detail so that a reader could duplicate your workBut if there are too many details, or you need to give lengthy detailed instructions necessary to install or run a program, those should be moved to appendices or (in some cases) separate "design" documentsThe actual names of software variables and subroutines, and the format of your data structures, are usually too many details.
• If you have created or modified a program, system, or methodology, say what computer your program runs on, what programming language it is written in, and what special facilities it requires.
• Describe the input and output of your program, system, or methodology.
• Give a block diagram of the main parts for your program, system, or methodology, and describe the main interactions between the partsTry to avoid procedure names, variable names, etc.; explain in a high-level way.
• Mention any programs or subroutines or sub-methodologies that you use that were written by other people, and explain where they go in the block diagram.
• Describe the data structures used in your program if you created them.
• Give details of the components of your program or methodology that you created, each in a separate section (this may take many pages if it is complicated).
• Describe the error checking and other user-friendliness features of your program or methodology.
• If you experimented with more than one algorithm, program, or methodology, do the same thing above for the othersThis may be best done in separate chapters, particularly if you have much to say about each.
• Usually write in the past tense in this chapter as if your work is finished.

Chapter 5: Discussion of results (3 to 20 pages of text, plus 1 to 20 figures or tables)

• If your results can be quantified, summarize the performance of your program or methodology in whatever way is appropriateThat usually includes how long it took to run or do, how much space or resources it required, and how accurate its results were.
• Use tables and figures wherever you can to simplify the discussion(Put actual computer runs in appendices.). Bear in mind there is a limit to how many tables and figures a reader can be expected to look at, particularly if they look similar.
• If your results are not quantifiable, discuss them and try to draw conclusions from themHowever, major conclusions should go in the last chapter.
• Discuss any insights you obtained from your dataIf your focus is on data analysis, categorize the data in a variety of ways and assess differences between the categories.
• If you experimented with more than one algorithm, program, or methodology, do the same thing above for the othersThis may be best done in separate chapters.

Chapter 6: Conclusion (1 to 3 pages)

• State the major achievements of your program or methodologyTry to compare your program to similar previous workAvoid repeating statements made earlier, and try to give a new perspective based on the results you have obtained.
• Honestly admit the major weaknesses of your program or methodology, and how they might be fixed by future researchers.

Possible appendices

· Instructions on downloading and installing software you wroteIf third-party software was important for this thesis and was not straightforward to download and install, give instructions for it too.

· Results of test runs or examples if interesting to the reader and too big to include earlierIf there are several types of these, make them different appendices.

· Text of your programs or data if interesting to the reader (but this should not exceed 50 pages)Do not include programs or data not written by you, even if they were important to the thesis.

Note: The page minima are for theses involving programming and large experimentsA thesis focused on concepts should be longer than that.

Some general guidelines for thesis writing

Thesis writing is a form of technical writing. Technical writing tries to convey difficult concepts, and so it needs to be especially clear compared to other kinds of writing. That means sentences should be kept short and should use the minimum number possible of specialized words.

1. A thesis should represent 360 hours of work if you have three schedule slots for it (3 quarters * 12 weeks/quarter * 10 hours/week), and 480 hours of work if you have four schedule slots for it.

2. Use words you would use to explain things to fellow students who are not necessarily familiar with your fieldAvoid fancy words just because they sound "academic". A helpful resource on improving clarity of your language is http://plainlanguage.gov.

3. Try to use the same term for the same thing; don't try to be poetic. This makes it easier for readers trying to understand the technical ideasHowever, if you are mentioning the same term quite a bit, a pronoun can provide variety when it clearly has only one meaning.

4. The purpose of a thesis is to describe interesting things you did. So don't spend many pages on other peoples' work unless you need it to make points about itOn the other hand, it is important to refer to at least some related work to show you understand how your work fits into a culture of academic inquirySo as a minimum, you should have at least six references to refereed papers by other researchers or academics.

5. Do not assume the reader remembers something you said earlier; cross-reference instead. Technical papers are not usually read in orderAlso, avoid repeating statements since readers can page backward if they need to. Things are different with spoken language, for which repetition is necessary.

6. Avoid one-sentence paragraphs except for numbered or bulleted items of a listSimilarly, avoid one-paragraph sections and subsections, though an acceptable exception can be the last paragraph of chapter 1 that describes the remaining chapters of the thesisCombine text as necessary to avoid these situations.

7. Use past tense to describe what you didUse "we", "us", "our", and "ours" so you can clarify what you didAnd prefer active voice for verbs, not passiveSome examples:

· Replace "Results in path planning were investigated" by "We investigated path planning".

· Replace "the code that was developed" by "our code".

· Replace "Some examples are shown in Figure 3-1" by "Figure 3-1 shows some examples".

Some conferences and journals disagree with this and prefer you use passive voice to sound more scientific. But in a thesis, it is more important to identify what you did.

8. When you finish chapters, run the spelling corrector in your word-processing software, and then run the program in http://faculty.nps.edu/ncrowe/coursematerials/deadwood_program.zipThis is a Python program that identifies over 12,000 cases of unnecessary wording in a text document. If you install a Python interpreter and unzip deadwood.zip, you can run deadwood.py from the command line as with one argument, the name of the text fileIt covers well-known problems like:

· "utilize" (use "use" instead)

· "employ the use of" (use "use" instead)

· "employ" (use "use" instead)

· "take advantage of" (use "use" instead)

· "leverage" (use "use" instead)

· "perform" (use "do" instead)

· "be used to" (eliminate)

· "in order to" (use "to" instead)

· "as a way to" (use "to" instead)

· "one of the" (use "one" instead)

· "some of the" (use "some" instead)

· "the entirety of" (use "all" instead)

· "a kind of" (use "a" instead)

· "a type of" (use "a" instead)

· "in fact" (delete)

· "actually" (delete)

· "simply" (delete)

· "vice" as a preposition (used "instead of" or "versus")

· "whether or not" (use "whether")

· "with regard to" (use "for" or "about")

· "for the purposes of" (use "to")

· "have the option to" (use "could")

· "have the ability to" (use "can")

· "are required to" (use "must")

· "and/or" (use "or" since the default meaning in English is inclusive-or)

· "a wide variety of" (use "many")

· "a large number of" (use "many")

· "a large fraction of" (use "most")

· "in such a way" (use "so")

· "this paper" (use "this thesis")

9. Colons and semicolons are more helpful in academic writing than elsewhere since they make it easier to see the sentence structure when conveying difficult conceptsTry to use them when you can, but be sure you are using them properlyColons are used to introduce lists and closely related ideas; semicolons are like periods but where you want to group two related statements together.

10. Hyphenate a sequence of words functioning together as an adjective. For instance, in "large artificial-intelligence program" you should hyphenate the two middle words since a reader unfamiliar with your topic might think you mean an "intelligence program" that is "large" and "artificial". Some more examples:

· computer-science department

· Navy fighter aircraft

· intelligent computer-aided instruction

· ten-procedure fire-fighting program

· problem-dependent forward-chaining Python code

· large integrated nonbacktracking Java program

This means that the same sequence of words is sometimes hyphenated and sometimes not depending on whether it functions like an adjectiveFor instance, you should write "I used artificial intelligence" but also "I used artificial-intelligence programs".

11. Minimize acronyms as much as possible since they make a thesis harder to understand.

a. For example, write "NPS" as "Naval Postgraduate School" or by its principal capitalized noun as "School".

b. An acceptable exception is for acronyms that are used many times in a thesis, like an acronym for the name of your subject or program that you refer to 20 times in the thesis.

c. When use an acronym, write out its words in parentheses the first time you use it.

d. The plural of an acronym can be made by adding a lower-case "s" to its end, e.g. "ICSs" from "ICS" for "industrial control system"Do not use apostrophes in making plurals.

e. Do not make a hyperlink to an acronym table, though it is OK to have an acronym tableHyperlinks are difficult to navigate in PDF, your final thesis format.

12. Capitalization seems to be a problem for many students today.

a. Generally speaking, words should only be capitalized if they comprise a "proper noun" or something of which there is only one instance in the world, like "NPS", "Internet", and "Web" (a shortened form of "World Wide Web")Names of computer programs, subroutines, and protocols are proper nouns and should be capitalized.

b. Although acronyms are written with all capital letters, the words on which an acronym is based are not necessarily capitalized when written out, only if the phrase refers to a single instance in the real world For instance, you should write out the acronym "AI" as "artificial intelligence", not "Artificial Intelligence", and "ICS" as "industrial control system", but "HTTP" should be written as "Hypertext Transfer Protocol" since there is only one such protocol.

13. About fonts:

a. Commands to an operating system or software that are to be typed online should be given in Courier New font or other fixed-width font.

b. The Thesis Processing Office likes terms you are defining to be in italics font at their first occurrenceThis is only useful if you have a large number of them, which is usually too confusing for the reader; otherwise, put things you define in quotation marks.

c. Avoid boldface fonts except in titles and section headings.

14. Avoid hyperbolic language (e.g. "vast", "incredibly", and "disaster"), emotional language (e.g. "terrible" and "peril"), and exclamation points, because academic writing should try to be objective about its subject.

15. Some nouns in English like "software", "mail", and "traffic" are inherently plural ("mass nouns") and should not have an "s" on the end"Data" is another inherently plural mass noun, but it does have a singular of "datum" if you need it.

16. About figures, tables, and equations:

a. Put them just after the first paragraph in which they are referenced

b. All figures and tables should have captionsPut the caption below a figure but above a table.

c. If you are using Microsoft Word, insert captions with the "Reference" tab, and then set a link to them on the "Insert" menu. This will allow figure and table numbers to be automatically updated if you insert or delete some

d. Only include figures or tables not created by you if they are very necessary, since a thesis is intended to show your own work.

17. The Thesis Processing Office has ideas about citations and references inconsistent with computer science, so do not necessarily follow them.

a. Standard citation formats in computer science and related fields are either in the APA format of parenthesized of author_last_name-year pairs (e.g. "(Rowe, 2008)") or the IEEE format of numbers in brackets (e.g. "[7]") where the number is that of an item in your reference listI prefer APA format in a thesis because it is clearer and more flexible, and because a reader may want to know the name of the author without having to go to the reference listNeither format uses footnotes, so you should avoid them.

b. Try to avoid reference-management tools like Zotero since they are more trouble than they are worth for science and engineering disciplines, making mistakes that are work to correctIf you must use it, an important mistake that Zotero makes is putting a period after the name of an author that is an organization when using APA format.

c. A citation should usually go at the end of the first sentence referring to the ideas contained in the reference, and should occur before the period ending the sentence with a space before itHowever in a long sentence, an earlier location in the sentence is acceptable and may be better.

d. Citations of papers in APA format with more than two authors should use "et al." after a comma and the last name of the second author.

e. Citations of two or more references related to the same idea should go in the same pair of parentheses in APA format, separated by semicolons.

f. Do not cite the same reference more than once in the same paragraph, despite what the thesis processing office saysScience and engineering writing does not do this. Their practice is to assume that a citation refers to everything in its paragraph until the next citation.

g. Do not abbreviate names of journals and conferences in the reference list. You want to make it easy for readers to locate the reference, and abbreviations like "Comput" can mean "computer", "computers", "computation", or "computability".

h. Technical-writing practice is not to use names of authors and vendors outside of citations and reference lists, since you should focus on ideas and not people.

i. Your reference-list format must be consistent with the citation format.

j. A reference list in APA format should have references in alphabetical order of the first author's last name.

k. Every item in a reference list must list an author; use the name of the responsible organization as the author if no human author is listedNever give a title first in the reference.

l. Prefer to cite refereed publications rather than unrefereed publicationsThat means that references to journal papers, conference papers, and chapters in books where different people write each chapter are preferable; references to entire books are OK but not quite as goodPreferred references are mostly in the ACM and IEEE digital libraries. Avoid Archiv because it has mostly unpublished material, and avoid Web pages if you can, especially pages like Wikipedia without listed human authors or without a dateHowever, if you used some software or data, its Web page may be the only information about it, and you should cite itIn some cases you get critical information from talking to or getting email from someone, and you should cite that as a "personal communication".

m. When you have a final draft, check that every citation in your text is matched by a reference in the reference list at the end of the thesis, and every reference in the reference list is matched by at least one citation in the text.

18. Minimize the use of quotations and graphics from other peopleA thesis is supposed to be original work, and if you are quoting other people or copying their pictures, you are not doing original workIt is better to paraphraseIf you do use quotations, enclose them in quotation marks and give a formal citation at their endThis is important because universities treat plagiarism seriously. Try to avoid using other people's figures.

19. You may need to refer to software products, but don't feel you need to repeat everything the vendor says about their product. Subject their claims to the same scrutiny as any scientific hypothesisIf they claim the product is fast, effective, or easy to use, test it and report what you discovered rather than repeating what they said about itYou also do not need to follow nonstandard punctuation of products, if it violates the usual rule of capitalization of proper nouns, so use "IPhone", not "iPhone".

20. Programs you wrote go in appendicesDetailed output, figures, and tables that would make the results chapter too long also should go in appendicesAppendices should not contain programs or documents that someone else wrote

21. Comments written into your thesis document by your advisors and readers should be deleted once you have answered them if you agree with themIf you disagree, keep the original comment and write your own comment after it about why you disagree.

22. Do not assume that once a thesis is checked and edited by your advisors or the Writing Center that it is fineIt takes multiple passes to fix a thesisCheck everything yourself after others have looked at it. Important things to check on the final draft are extra words, missing words, whether every citation has a reference, and whether every reference has a citationAlso check things like incorrect terms, missing explanations, unnecessary repetition, insufficient captions, and overuse of acronyms

23. The Thesis Processing Office and the Writing Center only make suggestions. Your advisors and second readers can overrule them.