thesis-structure

name

thesis-structure

description

Thesis architecture & defense-prep KNOWLEDGE — BSc, MSc, PhD structure; classic 5-chapter + cumulative (article-based) variants; RQ↔chapter mapping with word_budget.py --rq-trace; Turkish thesis (YÖK) requirements (front-matter order, Özet↔Abstract equivalence, ethics declaration, acknowledgments, approval page); institute guideline ingestion; the concepts behind defense prep (viva questions, answer skeletons, presentation outline). Use when structuring or auditing a thesis, or preparing Özet/Abstract. To actually RUN guided defense preparation (jury question bank + presentation scaffold) use the /defense-prep command — this skill is its underlying knowledge, not the command.

1. Thesis Architecture Types

1.1 Classic 5-Chapter Structure

Standard for all thesis levels (BSc, MSc, PhD). Each chapter has a defined purpose and typical word proportion:

Chapter	Purpose	Typical %	Content core
1. Introduction	Frame problem, state RQs, claim novelty	15%	background, gap, research questions, thesis outline
2. Literature Review	Map prior work, position your contribution	20%	thematic synthesis (not annotated bibliography), identifies gaps, hypotheses
3. Methodology	Describe design, methods, tools, data	25%	study design, participants/data, procedures, analysis strategy, validity measures
4. Results/Findings	Present outcomes, data analysis results	20%	organized per RQ (headings must mirror RQ statements), tables, figures, no interpretation
5. Discussion & Conclusion	Interpret, compare, claim contributions	20%	answer each RQ, situate vs literature, limitations, future work, practical implications

RQ-Mapping Rule (enforced by word_budget.py --rq-trace):
Every RQ stated in Ch.1 must have a corresponding Results section heading in Ch.4 and a claim in Ch.5. Execute:

python scripts/word_budget.py --rq-trace

Returns mapping: RQ1 → Section 4.1.1 heading → Discussion answer, or FLAG if missing.

Typical word counts (adjust per institution, field, degree):

• BSc: 8,000–15,000 words
• MSc: 25,000–50,000 words
• PhD: 80,000–150,000 words

1.2 Cumulative (Article-Based) Thesis

Structure when your thesis comprises ≥2 peer-reviewed / submitted journal papers:

Ch.1: General Introduction (framing, overall RQ, synthesis of papers' motivation)
Ch.2: Literature Review (cross-cutting themes across the papers)
Paper 1 (standalone Methods + Results, verbatim or lightly adapted)
Paper 2 (standalone Methods + Results)
Ch.5: General Discussion (synthesize across papers, implications, limitations, future work)

Front-matter (same as classic) + binding narrative between papers. Each paper retains its own abstract; the dissertation gains an Özet + Abstract at the start. Common in STEM fields where students have multiple publications by completion.

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2. Cross-Chapter Logic Chain

Integrity checks (audit before finalization)

1. Novelty cascade:

   • Ch.1 Literature Review identifies a gap.
   • Ch.3 Methodology describes your unique approach to close it.
   • Ch.4 Results present the outcome.
   • Ch.5 claims this outcome answers the gap.

2. RQ traceability:

   • Ch.1: "RQ1: Does method X outperform baseline Y under constraint Z?"
   • Ch.4: Heading "4.2.1 Performance Comparison: Method X vs Baseline Y" (no rewording).
   • Ch.5: "RQ1 was answered via [comparison table 5]: X achieved ±% better accuracy…"

3. Limitation honesty:

   • Ch.3 methodology describes scope, participant/data size, design choice rationale.
   • Ch.5 explicitly names what you couldn't do and why (sample size, generalizability, confounds).

4. Consistency across languages (if bilingual):

   • Özet (Turkish) Ch.1–Ch.5 structure mirrors English Abstract word for word. See reference/yok-tr.md Section 2.

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3. Chapter-by-Chapter Guidance

Chapter 1: Introduction (target: 12–18% of total)

Moves (in order):

1. Hook: Context — why the problem matters (broader field, practical need, or theoretical gap).
2. Problem statement: Specific gap or unresolved question.
3. Literature positioning: "Prior work has shown X and Y, but no one has studied [your angle]."
4. Explicit RQs: Numbered (RQ1, RQ2, etc.). Testable, not rhetorical.
5. Thesis outline: One sentence per chapter ("Ch.2 reviews…").

Discipline: Active voice, present tense for established fact, future for your work ("This thesis explores…").

Chapter 2: Literature Review (18–22%)

Synthesis, not summary. Group sources by theme, NOT by paper.

Structure option A (thematic):

2.1 Foundational Concept (3–4 sources in conversation)
2.2 Prior Approaches (contrast 2–3 methods)
2.3 Limitations and Gaps (what the literature misses)

Structure option B (chronological with themes):

2.1 Early Work (1990–2005)
  2.1.1 Methodological approaches in that era
  2.1.2 Key findings and limitations
2.2 Recent Developments (2006–present)
  2.2.1 Emerging methods
  2.2.2 Unresolved questions

Anti-pattern: "Author A says X. Author B says Y. Author C says Z." (annotated bibliography) → FWD: Replace with synthesis. One paragraph should reference ≥2 sources in substantive conversation.

Paragraph formula:
Topic sentence + Evidence (cite EV-cards or [@surname2024]) + Interpretation + Gap statement + Bridge to next paragraph.

Chapter 3: Methodology (22–28%)

Replicability standard: Another researcher must be able to reproduce your study using this chapter alone.

Sections (adjust per design type):

3.1 Study Design
    (observational, experimental, mixed, qualitative)
3.2 Participants / Data / Materials
    (recruitment, inclusion/exclusion, size justification, source)
3.3 Data Collection / Procedures
    (instruments, protocols, timeline, validation)
3.4 Data Analysis
    (statistical tests, thematic coding, software, version)
3.5 Validity Measures / Ethics
    (reliability/validity, ethical approval, informed consent)

For ML-based theses:

• Specify dataset(s): source, size, splits (train/val/test %), sampling strategy.
• Environment: Python version, libraries (versions!), hardware (GPU model if relevant).
• Hyperparameters: table of search range and final selection.
• Baselines: justify each baseline choice; why is it fair?
• Seeds: "N=5 independent runs with random seeds [list]."
• Ablations: what's being tested in each ablation, why?

Dispatch methodology-advisor before drafting this chapter (DESIGN mode) and again after drafting it (CRITIQUE mode) — it is the kit's read-only methodology expert and this chapter is exactly its INPUT CONTRACT's domain (classic empirical design + ML experiment design):

• What: "Propose a methodology for these RQs" (DESIGN, before Section 3.1 is written) or "Audit this Methods draft — run the replicability test" (CRITIQUE, after /draft methodology produces drafts/methodology.md)
• Mode: DESIGN | CRITIQUE | QUESTION (methodology-advisor's INPUT CONTRACT enum)
• Context: RQs/hypotheses from PROJECT.md, field, data availability/constraints; for ML theses also task type, datasets under consideration, candidate baselines
• Draft path (CRITIQUE only): drafts/methodology.md

The agent returns (read-only, no edits): verdict (sound | fixable | redesign-needed) or the recommended design, numbered issues/decisions, a validity-threat table, and the matching reporting-guideline pointer. Apply its fixes before /critique — reviewer-critic will independently re-score the same weaknesses if they reach a full peer review unaddressed.

Chapter 4: Results / Findings (18–25%)

No interpretation; facts only. All interpretation → Discussion.

Organization per RQ:

4.1 Results for RQ1
    4.1.1 [Specific outcome heading]
    [Table / Figure]
4.2 Results for RQ2
    [analogous structure]

Discipline:

• Heading text must match the RQ phrasing (word_budget.py --rq-trace checks this).
• Describe figures/tables in text (never: "see Figure 3").
• Report with precision: means ± std (over N runs), confidence intervals, p-values.
• For qualitative: theme labels + representative quotes with page numbers.

ML theses:

• Comparison table: method (rows) × criterion (columns); bold best per column.
• Include baseline results (necessary for fair comparison).
• Report N seeds, mean±std, statistical test of significance (if applicable).
• Ablation results (what happens when you remove component X?).

Chapter 5: Discussion & Conclusion (18–25%)

Structure:

5.1 Interpretation of Findings (per RQ)
5.2 Comparison with Prior Work
5.3 Limitations
5.4 Practical Implications
5.5 Future Work
5.6 Conclusion (summary statement)

5.1: Interpretation

• Restate each RQ, answer it with your result.
• Explain why the result occurred.
• Use hedging language appropriate to evidence strength (demonstrates > indicates > suggests).

5.2: Comparison

• How do your results align with / diverge from the literature?
• If conflict exists, propose an explanation (context differences, methodological, sample).
• Cite both supporting and contradicting prior work; don't hide conflicts.

5.3: Limitations

• Name constraints: sample size, generalizability scope, design trade-offs, confounds.
• For each, describe its impact: "This limits our ability to [X], relevant for [scenario]."
• NOT: "We had a small sample" (obvious). INSTEAD: "N=20 limits power to detect medium effects (β>0.20)."

5.4: Practical Implications

• Who benefits from this work? How?
• What should practitioners do differently based on these results?
• What should policymakers or institutions consider?

5.5: Future Work

• Logical next steps emerging from your findings or unresolved limitations.
• Avoid vague ("Further research is needed").
• INSTEAD: "Future work should test whether [mechanism] generalizes to [new population], which would require [design change]."

5.6: Conclusion

• 3–5 sentences. Restate the thesis claim, main finding, and significance.
• One-sentence vision: "This work opens the possibility of [X]."

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4. Turkish Theses (YÖK Compliance)

Full Turkish-specific requirements, guidelines for Özet↔Abstract equivalence, and how to ingest your institution's guideline are in reference/yok-tr.md. Key points:

• Front-matter order (non-negotiable in Türk univ.):

  1. Inner cover (iç kapak)
  2. Approval page (onay sayfası)
  3. Ethics declaration (etik beyan)
  4. Acknowledgments (teşekkür)
  5. Turkish summary (Özet) — if Turkish is the thesis language
  6. English summary (Abstract)
  7. Table of contents (İçindekiler)
  8. List of tables (Tablo listesi)
  9. List of figures (Şekil listesi)

• Özet↔Abstract equivalence: Same structure, same paragraph breaks, same keyword list (in respective languages). Not a free translation; a parallel rendering with identical claims and evidence markers.

• Institute guideline: Drop your PDF/DOCX guideline into templates/institution/GUIDELINE-NOTES.md (user manually extracts rules); this skill then references it as authoritative.

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5. Defense Preparation

Full committee-question templates, answer frameworks, and presentation outlines are in reference/defense.md. Quick summary:

• Likely questions by chapter:

  • Ch.1 (gap & novelty): "Why is this problem important? What makes your approach different?"
  • Ch.2 (prior work): "Which prior work is most relevant? How does it compare to yours?"
  • Ch.3 (methods): "Why did you choose this design? What are the limitations?"
  • Ch.4 (results): "What surprised you? How reliable are these findings?"
  • Ch.5 (claims): "What's the take-home message? Who benefits from this?"

• Presentation skeleton: 12–15 slides — one per chapter + outcomes slide. See reference/defense.md for detailed outline.

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6. Integrated Commands

Check thesis structure:

# Verify RQ ↔ Chapter 4 heading ↔ Chapter 5 answer mapping
python scripts/word_budget.py --rq-trace

# Summary of structure and word budget
/status

Audit Turkish Özet↔Abstract:

# Run style-auditor in TR mode
/critique  # or manual check against reference/yok-tr.md checklist

Export structure for defense prep:

# Load defense templates
reference/defense.md  # answer skeletons by likely question

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References

• Thesis types & architecture: This file.
• Turkish (YÖK) requirements: reference/yok-tr.md
• Defense prep: reference/defense.md
• Word budget & RQ tracing: Execute python scripts/word_budget.py --rq-trace
• Style guidance: Academic-writing skill
• Evidence card integration: Evidence-cards skill