# Week 10 — annotation agreement and analysis

[**Full learning notebook: explanations, step-by-step challenges, stashes and evidence**](./learning-notebook.md) · [NotebookLM export](./notebooklm.txt)

Status: NOT_STARTED. Calendar dates: not assigned. Owner: Peter Ciancaglini. Planning authority: v5 Part 6 with retained v4 details. Deeper walkthrough: [v6 · Week 10 · Inter-annotator agreement and the first real analysis](../../../LABLOOP-Master-Plan-v6.md#week-10--inter-annotator-agreement-and-the-first-real-analysis). Active project/repository: fermlit.

[Programme](../../README.md) · [Model instructions](../../specs.md) · [Decisions](../../DECISIONS.md) · [Resources](../../SOURCES.md) · [**v6 walkthrough**](../../../LABLOOP-Master-Plan-v6.md#week-10--inter-annotator-agreement-and-the-first-real-analysis) · [Previous week review](../week-09-fermlit-scale-up/review.md) · [Next week](../week-11-fermlit-dataset-engineering/specs.md)

## Outcome and relevance

This week delivers the three concrete artifacts below and the supporting learning/branding/opportunity pack. The scientific or commercial outcome follows the preserved source brief, while the acceptance checks make its evidence testable. The career objective is to turn this work into something a scientist, hiring manager or buyer can inspect.

- Scientific/build priority: Receive the second human's independent 30-paper annotations, calculate categorical agreement/kappa and numeric tolerance agreement, then adjudicate.
- Public/profile priority: Prepare a two-human agreement explanation; publish actual overlap and metrics only after labels arrive.
- Career/relationship/commercial priority: Give the annotator credit appropriate to contribution; prepare a follow-up scientific-feedback message using one figure.

## Deeper walkthrough (v6)

Read [v6 · Week 10 · Inter-annotator agreement and the first real analysis](../../../LABLOOP-Master-Plan-v6.md#week-10--inter-annotator-agreement-and-the-first-real-analysis) before Monday. It carries this week's v5 brief unchanged and adds the **Welcome** analogy, **Learn it** (▶ core and ＋ deeper sources), **Run it** (repos with a 20-40 minute exercise), the **NotebookLM kit** and the mentor check below. Standing v6 rules: [resource rules](../../../LABLOOP-Master-Plan-v6.md#prologue-3--the-resource-rules-so-you-never-waste-an-evening-on-a-bad-source), [NotebookLM protocol](../../../LABLOOP-Master-Plan-v6.md#prologue-4--the-notebooklm-protocol-one-notebook-per-week-zero-decisions), [chapter anatomy](../../../LABLOOP-Master-Plan-v6.md#prologue-5--how-to-read-a-chapter-the-anatomy-identical-for-all-41). v6 adds depth only; it does not change a goal, gate, output or the 600-minute cap, so this specification still governs execution.

**Act III · Threads: B, M, FL · Next gate: 13**

**Where this week sits.**
- ← **From:** week 6 gold set + second annotator; week 9 2,000 records.
- → **Feeds:** week 11 (formal completeness result), week 13 (Paper 1 skeleton figures), week 14 (Methods), week 16 (conformal prediction extends the GP's uncertainty idea), week 34 (judge-human agreement in labdocs).
- ⟳ **Returns in:** Paper 1 "Annotation agreement" paragraph and figures 1-4.

**Goals.**
- 🎯 **This week:** kappa per field in `eval/README.md`; gold v1 frozen; descriptive notebook; `make figs` regenerates figures 1-4.
- 🏁 **Next milestone:** Gate 13.
- 🌟 **Final:** the trust number in Paper 1's abstract.

**Mentor check.** *"I can explain kappa to a founder with a referee analogy and tell them which FermLit fields are trustworthy."*

## Required inputs and dependency check

- [Week 06](../week-06-human-gold-standard/specs.md): inspect its actual evidence and review; source/code artifacts must exist before the dependent task begins.
- [Week 09](../week-09-fermlit-scale-up/specs.md): inspect its actual evidence and review; source/code artifacts must exist before the dependent task begins.
- Read [commitment](./commitment.md), [evidence](./evidence.md), [review](./review.md) and the current root TODAY/PROGRESS/QUESTIONS files.
- Read this week's chapter, [v6 · Week 10 · Inter-annotator agreement and the first real analysis](../../../LABLOOP-Master-Plan-v6.md#week-10--inter-annotator-agreement-and-the-first-real-analysis), then the standing sections: [Part 0 · how to use the document](../../../LABLOOP-Master-Plan-v6.md#part-0--how-to-use-this-document-read-this-every-monday-for-the-first-month), [Part 3 · the scientific thesis](../../../LABLOOP-Master-Plan-v6.md#part-3--the-scientific-thesis-explained-twice-like-a-kid-then-like-a-reviewer), [Part 4 · curriculum](../../../LABLOOP-Master-Plan-v6.md#part-4--curriculum-from-zero-four-tracks-all-free-exact-units), [Part 8 · the prompt pack](../../../LABLOOP-Master-Plan-v6.md#part-8--the-prompt-pack-copy-paste-fill-the-brackets) and [Part 9 · branding and endorsement](../../../LABLOOP-Master-Plan-v6.md#part-9--branding-connection-ladder-endorsement). The same sections exist in the [v5 master](../../../LABLOOP-Master-Plan-v5.md), which remains the governing sequence; v6 reproduces them and adds depth. Retained commercial/instrument details come from [v4](../../../AI-Upskilling-Plan-Biotech-v4.md).
- Inspect the actual canonical repository state, available data, existing figures and required human/external inputs. Never assume a previous week succeeded from its folder name.
- Verify current resource links, versions, dataset rights and any live company/venue information before relying on them. Use [source catalog](../../SOURCES.md); explicitly record inaccessible resources.

## Seven-day plan: 600 minutes maximum

The model must turn these into exact physical actions using the observed files and available inputs. Each 90-minute block includes start/stop rituals. All calls, posts, debugging, reading and exercises consume this same capacity.

| Day | Budget | Work and stopping condition |
|---|---:|---|
| Monday | 90 min | Receive the second human's independent 30-paper annotations, calculate categorical agreement/kappa and numeric tolerance agreement, then adjudicate. Stop when: Pre-adjudication labels are retained and agreement is reported by field and support. |
| Tuesday | 90 min | NPTEL lectures 4-6 (Monod, yields, maintenance) Produce: Yield coefficients computed on IndPenSim |
| Wednesday | 90 min | Analyze titer/product/organism, scale and reporting patterns with denominators and comparable units. Stop when: Exploratory comparisons are labeled; no causal or cross-product efficacy claims. Reserve the last 10 minutes for the optional Wednesday note. |
| Thursday | 90 min | Rasmussen & Williams, *GPML* ch. 1-2 — gaussianprocess.org/gpml (free); scikit-learn GP examples Select material/exercise that fits 60 minutes; use the last 30 for the founder paper. |
| Friday | 90 min | Generate Paper 1 figures 1–4 with frozen data/version and export static versions plus captions. Stop when: One command regenerates each plot and caption N agrees with the table. |
| Saturday | 90 min | Resolve the earliest critical spillover or dependency. Prepare any long-form publication draft from existing figures here if needed. Sandbox only after commitments are met. |
| Sunday | 60 min | 20 min build-log draft/publication when authorized; 5 min evidence/checklist; 20 min source-grounded gap review; 15 min next week's six physical actions. |

The source lists more material than necessarily fits. Select exact excerpts for the learning objective and park the remainder; no full-course completion requirement.

## Learning specification

### Biology/domain unit

Source unit: B10 · Bioreactors II: kinetics and yields

Material: NPTEL lectures 4-6 (Monod, yields, maintenance)

Produce: Yield coefficients computed on IndPenSim

Understanding check: You can explain Yx/s and Yp/x

During preparation, write one worked example connected to the week's actual task, one exercise with a separate answer key and five questions. Peter supplies answers; score explanation quality and flag misconceptions in QUESTIONS. Numeric/scientific conclusions require actual data or explicitly synthetic teaching values.

### AI/scientific-method unit

Source unit: M10 · Gaussian processes

Material: Rasmussen & Williams, *GPML* ch. 1-2 — gaussianprocess.org/gpml (free); scikit-learn GP examples

Produce: GP soft sensor with uncertainty bands

Understanding check: You can explain a kernel as "similarity"

Use the [prompt pack](../../../LABLOOP-Master-Plan-v6.md#part-8--the-prompt-pack-copy-paste-fill-the-brackets): P1 explanation ladder, P2 concept-to-project bridge and P3 quiz. Coding practice belongs within the allocated study/build block. Where the source asks for a favorable scientific result, substitute an honest measured comparison as explained below.

### Founder/scientist paper

Select one verified founder/scientific-lead paper relevant to this week's domain. Use [P11](../../../LABLOOP-Master-Plan-v6.md#part-8--the-prompt-pack-copy-paste-fill-the-brackets); save the question, method, numerical result with context, data workflow, three author questions and one connection sentence in founder-paper.md. Keep abstract-only access limitations explicit. On source weeks with no study, prioritize the commercial/submission task and log any skipped digest.

## Artifact contracts

These filenames are outputs to prepare during this week's execution; this scaffold does not claim they already exist. Drafts and measured results have different states. Technical code/data stay in the canonical project repository and are referenced from these coordinating files.

| Artifact | Required content / acceptance | Primary responsibility |
|---|---|---|
| `agreement-report.md` | Receive the second human's independent 30-paper annotations, calculate categorical agreement/kappa and numeric tolerance agreement, then adjudicate. Acceptance: Pre-adjudication labels are retained and agreement is reported by field and support. | Model assists; Peter checks and owns the outcome |
| `descriptive-analysis.md` | Analyze titer/product/organism, scale and reporting patterns with denominators and comparable units. Acceptance: Exploratory comparisons are labeled; no causal or cross-product efficacy claims. | Model assists; Peter checks and owns the outcome |
| `figure-inventory.md` | Generate Paper 1 figures 1–4 with frozen data/version and export static versions plus captions. Acceptance: One command regenerates each plot and caption N agrees with the table. | Model assists; Peter checks and owns the outcome |
| `study-notes.md` | Selected exact free resources; bounded lesson/exercise; separate solution; quiz and grading rubric; Peter's answers and gaps when executed | Model prepares; Peter learns |
| `founder-paper.md` | Verified source and P11 digest; authentic question and connection sentence; access limitations | Model assists; Peter checks |
| `branding-pack.md` | Wednesday note, Sunday build log, X adaptation, figure/caption/alt text and the week's special asset; each claim linked to real proof | Model drafts; Peter owns voice/public claims |
| `opportunity-actions.md` | Qualified target/role, source/date, ladder stage, next action, message/interview/proposal draft and actual status | Model prepares; Peter owns external relationships |
| `evidence.md` | Actual paths/URLs, versions, checks/metrics, preparation versus execution state and external receipts when applicable | Updated after each deliverable |
| `review.md` | Checklist, learning assessment, gate status, shortfalls, next actions and carryover | Peter and reviewing model |

During preparation, future measured tables get column definitions, input requirements and run instructions with PENDING status. During execution, replace pending values only with measured outputs. Do not create realistic-looking fake evidence.

## Branding and opportunity execution brief

Branding: Prepare a two-human agreement explanation; publish actual overlap and metrics only after labels arrive.

Opportunity action: Give the annotator credit appropriate to contribution; prepare a follow-up scientific-feedback message using one figure.

Use [career asset contracts](../../CAREER-ASSETS.md). Publish at most the agreed cadence; one figure and one supported number or admitted failure can support multiple drafts. In long-form weeks, prepare a 1,500–2,500-word article from existing evidence within the build/buffer allocation. In release/demo weeks, prepare a 60-second script: problem, input, command/action, result, limitation and proof link.

Verify individuals, jobs and affiliations at execution time. The [GridX list](../../../GridX%20Startups.csv) and v4 company map are research seeds, not current facts. Do not reveal named company weaknesses or employer/client confidential information. Keep drafted/sent/replied/booked/held statuses separate. The planning request alone does not authorize external messages or publication; honor explicit authorization in the execution session.

## Quality risks and week-specific constraints

Kappa is not an agreement statistic for continuous raw measurements without justified categorization. If the second annotator is delayed, agreement stays pending and downstream release limitations must be explicit.

Apply the root scientific evidence contract: provenance; meaningful independent splits; no future-data leakage; baseline comparison; actual denominators/uncertainty; failed cases; human review where required. State whether data are simulated, public experimental, synthetic or partner-provided.

Keep source gates intact, and log scope/time conflicts in review. Missing people, money, access or results must not be replaced with invented evidence. Reduce optional polish first. A specific essential external dependency stays pending while independent preparation continues.

## Completion and gate review

This is an enabling week. Its deliverables feed the next scheduled gate: 13. Complete the acceptance checklist below; do not promote reputation from a draft.

- [ ] Monday artifact satisfies: Pre-adjudication labels are retained and agreement is reported by field and support.
- [ ] Wednesday artifact satisfies: Exploratory comparisons are labeled; no causal or cross-product efficacy claims.
- [ ] Friday artifact satisfies: One command regenerates each plot and caption N agrees with the table.
- [ ] Study pack is prepared; Peter's actual learning/quiz result is recorded separately.
- [ ] Branding and opportunity drafts use supported claims and the correct external-action state.
- [ ] Reproduction or document checks are recorded with file/version references.
- [ ] This week's special gate, if any, has real evidence or remains explicitly pending.
- [ ] Review, root progress/log and the next physical action are updated.

## Minimum viable week and recovery

Source-preserving minimum: kappa.

Operational first step if stalled: open `agreement-report.md`, write the required inputs and produce the smallest checkable example in ten minutes. If a more urgent missing gate dependency controls the week, use the source minimum above.

If the full week does not fit, use [P14](../../../LABLOOP-Master-Plan-v6.md#part-8--the-prompt-pack-copy-paste-fill-the-brackets): retain one gate-critical deliverable and one directly supporting study exercise; record what is skipped versus moved. Do not mark the original full gate passed merely because the minimum was completed. After a missed week, reforecast from actual evidence and avoid a second unexamined lost week.

## Handoff to the next model

In review, state exactly what exists, what was verified, what Peter can now explain, which external events remain pending, where the canonical code/data live, and the next file/function or draft paragraph to touch. Link each fact to evidence. Carry scientific assumptions, split definitions and rights constraints forward explicitly.

## Ready-to-copy model prompt

```text
Prepare Week 10 of this LABLOOP execution plan.
Read execution-plan/specs.md, execution-plan/DECISIONS.md,
execution-plan/GATES.md and
execution-plan/weeks/week-10-annotation-agreement-and-analysis/specs.md, commitment.md, evidence.md and review.md.
Read prior prerequisite reviews and inspect actual repository/data state.
Use v5 as the governing sequence, the v6 Week 10 chapter
(LABLOOP-Master-Plan-v6.md) as the deeper walkthrough, and v4 only for
retained details.
Produce the full local preparation pack and the exact week-specific files named
in the artifact table. Give me a bounded lesson with exercises/answer key,
daily physical actions, technical runbook or draft, branding drafts and
career/commercial actions. Keep the total to 600 minutes.
Separate prepared artifacts from measured results and my learning completion.
Verify sources and do not invent metrics, citations, papers, people or outcomes.
Do not execute external communications, publication or spending unless the
current session already authorizes the specific action.
Finish by updating evidence/review and TODAY with the next physical action.
```

## Preserved original v5 weekly brief

v6 reproduces this brief unchanged inside [v6 · Week 10 · Inter-annotator agreement and the first real analysis](../../../LABLOOP-Master-Plan-v6.md#week-10--inter-annotator-agreement-and-the-first-real-analysis).
The following is source planning text, not a claim of completion. Apply the explicit evidence corrections in this specification and DECISIONS.md.

### Week 10 · Inter-annotator agreement and the first real analysis
- **Goal:** kappa reported; first descriptive science.
- **Tue (B10):** NPTEL 4-6; yields on IndPenSim.
- **Thu (M10):** GPML ch. 1-2; GP soft sensor with bands.
- **Build:** [ ] Mon: compute Cohen's kappa per field between you and the second annotator; adjudicate disagreements; freeze gold v1. Done when kappa is in `eval/README.md`. [ ] Wed: descriptive analysis notebook: titer by organism and product, productivity vs scale, reporting completeness by year and journal. [ ] Fri: figures 1-4 of Paper 1 drafted (Plotly to static). Done when `make figs` regenerates them.
- **Sun:** L-Sun: "Two humans, 30 papers, kappa = X: how much can you trust a dataset built by an LLM?" L-Wed.
- **Only one thing:** kappa.