:PROPERTIES:
:ID: 6294e2be-6189-4473-b363-a1dd9a75ff9b
:END:

#+title: thesis
#+filetags: :project: :knowledge:

* thesis

BGU MSc thesis on the ROLL method (Rate Optimized Likelihood Loss). See [[id:d23011c5-d925-4f14-b05a-0a1f4bdbe860][impl]] for the implementation project this thesis documents.

** Architecture

- =main.tex= — root document; defines all title/author/supervisor commands, includes all chapters
- =Main_pages/= — cover_page, title_page, abstract, acknowledgements, abstract_heb, cover_heb
- =content/<chapter>/= — one folder per chapter with its own .tex file
- =content/images/= — shared image path (set via =\graphicspath=)
- =bibliography/thesis.bib= — references
- =bibliography/unsrtnat_adjusted_for_bgu_thesis.bst= — custom BGU bibliography style (do not edit)

** Conventions

- Thesis metadata (title, author, supervisor, month, year) defined as commands at top of =main.tex=
- Hebrew title/author/supervisor have =he= suffix commands (=\thesistitlehe=, etc.)
- Both English and Hebrew ToC, abstract, and cover pages are required by BGU
- Chapters added via =\input{content/<chapter>/<chapter>}= with a matching =\addtocontents{tocheb}= line
- Build engine: pdflatex (uses =\usepackage[utf8x]{inputenc}=, not xelatex)
- Math notation: data points are bold (=\mathbf{x}_i=); batches are =\mathcal{B}_0= / =\mathcal{B}_1=
- KDE background (general technique) in Ch. 2 (=sec:kde-background=); Ch. 3 back-references it
- =sec:imbalanced-tpr-fpr= and =sec:neyman-pearson= live in Ch. 2; Ch. 3 =sec:problem-formulation= \Cref's them — do not rename

** Mentor Direction (2026-08-17)

Primary narrative focus agreed with mentor:
- *Main story*: noise resistance and AUC optimization — this is the thesis core
- *Hero method*: =roll-aoc= (AUC variant) — primary contribution
- *Primary competitor*: =libauc-auroc= (Yuan et al. AUCMLoss + PESG) — already implemented
- *Single-point optimization* (=roll-tpr90=): touch on briefly as secondary result
- *Pacing*: get to the differentiating, strong results quickly — don't bury the lede

** Baselines (all in =impl/src/roll.py= + =impl/experiments/keel/_base.py=)

| Experiment name | Class | What it is |
|---|---|---|
| =bce-weighted= | BCE + pos_weight | Standard imbalance fix |
| =libauc-auroc= | =libauc_auc_loss= + PESG | Yuan et al. 2021 compositional AUC — primary AUC competitor |
| =gce-0.7= | =gce_loss= | Generalized Cross-Entropy (noise-robust) |
| =mae= | =mae_loss= | MAE loss (noise-robust) |
| =focal-loss= | =focal_loss= | Focal Loss |
| =roll-aoc= | =kernelized_roll_aoc= | *ROLL AUC variant — hero method* |
| =roll-tpr90= | =kernelized_roll_tpr= | ROLL TPR@FPR variant — secondary result |

Note: =libauc-auroc= requires PESG optimizer (not Adam) — already wired up in impl.

** Chapter Structure

See subnodes for per-chapter guidelines and section details.

| Ch. | Title | File | Target |
|-----|-------|------|--------|
| 1 | Introduction | =content/introduction/introduction.tex= | 4–6 pp |
| 2 | Background / Related Work | =content/related_work/related_work.tex= | 15–20 pp |
| 3 | Method | =content/method/method.tex= | ~30 pp |
| 4 | Experiments | =content/experiments/experiments.tex= | 15–20 pp |
| 5–6 | Discussion + Conclusion | =content/discussion_and_conclusions/= | 8–12 pp |

** Gotchas

- Template uses =utf8x= inputenc, which requires the =ucs= nix/texlive package
- Hebrew rendering via =babel-hebrew= (pdflatex approach, not fontspec/xelatex)
- Example images in =content/related_work/images/= are from the template — safe to delete
- =flake.nix= uses =rec= on the derivation so =buildInputs= is in scope for PATH export
- =nix develop= devShell includes python3+sympy — use it to verify math claims, never check mentally
- KDE backward pass uses inverse-function-theorem approach deliberately (user must explain it verbally)
- Correct gradient of threshold w.r.t. negative-class score: σ'(τ−x_i) / Σ_j σ'(τ−x_j) — sympy-verified
- *(NIX BUILD) New .tex files must be =git add='ed before =nix build=.* Nix flakes use git to enumerate source files; untracked files are invisible to the build. Symptom: silent LaTeX failure — TOC, LoF, and LoT all appear empty in the output PDF. Fix: =git add <new-file>=, then rebuild.

** Key Files

- =flake.nix= — Nix build; =nix build= produces =result/main.pdf=; =nix develop= for dev shell
- =flake.lock= — pinned to nixpkgs-unstable as of 2026-06-16
- =main.tex= — fill in =\thesistitle=, =\thesisauthorname=, =\thesissupervisername=, =\thesismonth=, =\thesisyear=

** Subnodes

- [[id:c4a0d60f-49d3-4185-8c5b-f8a5a10a2ccc][thesis/introduction]] — Ch. 1 guidelines: structure, length, what to include
- [[id:cd785954-008e-4b64-957d-25d1dbeac127][thesis/related-work]] — Ch. 2 section structure, placement markers, label conventions
- [[id:0543ac39-af9b-40fd-9973-e60576a20695][thesis/method]] — Ch. 3 section status table, derivation gotchas
- [[id:c41756b5-fd5f-456e-ab2b-18f27db7d61d][thesis/experiments]] — Ch. 4 data sources, key results, section status
- [[id:9b50caf2-d259-4848-b7f5-22a9288e8ba2][thesis/discussion]] — Ch. 5–6 guidelines: failure modes, future work
- [[id:151159e8-1105-4a84-af9c-72d31c5e0660][thesis/todos]] — project TODOs
- [[id:bd98ede2-d6ec-4e93-8d10-4800fe528ff7][thesis/citations]] — sources justifying implementation choices (architectures, baselines)
- [[id:2c598296-d2f0-4333-9cdd-3625f8375e03][thesis/work-history/recent]] — session work log

* todo

** TODO Basic structure - take it into account
** TODO Import and make sense of all references
** TODO Continue to auto-summarize references continuously