@monoes/monomindcli 2.15.3 → 2.15.4

package/org-skills/scientific-brainstorming/references/facilitation_workflows.md

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+# Facilitation Workflows and Records
+
+These workflows make a session reproducible without turning facilitation into
+an automatic scientific decision. Adapt timing and accessibility needs, but
+record adaptations.
+
+## Minimum session record
+
+Create one record with:
+
+- session ID, date, title, focal question, and decision owner;
+- facilitator, participant pseudonyms, represented perspectives, missing
+  perspectives, and relevant conflicts;
+- in-scope/out-of-scope boundaries and constraints;
+- information and examples shown before independent generation;
+- idea, assumption, cluster, criterion, review, evidence-check, gate, and
+  decision-log entries;
+- method, timing, anonymization, voting, merge, and stopping rules;
+- AI tool/version/purpose when used, without storing sensitive prompt content;
+- deviations from the planned process and their reasons.
+
+Use `scripts/session_scaffold.py` to create a deterministic JSON starting
+point. It intentionally omits a generated timestamp: provide `--date` when a
+date belongs in the record.
+
+## Provenance templates
+
+### Idea
+
+```json
+{
+  "id": "I001",
+  "statement": "A concise candidate research direction.",
+  "provenance": {
+    "origin": "human",
+    "contributor_ids": ["P01"],
+    "recorded_stage": "independent",
+    "source_refs": [],
+    "ai_tool": null
+  },
+  "assumption_ids": ["A001"],
+  "predicted_observations": ["What would be expected if the idea were useful"],
+  "uncertainties": ["The main unresolved uncertainty"],
+  "evidence_status": "not-checked",
+  "status": "candidate"
+}
+```
+
+Allowed origin labels in the bundled validator are `human`, `ai-assisted`,
+`literature-inspired`, `mixed`, and `other`. An origin label documents process;
+it does not determine quality or ownership.
+
+### Assumption
+
+```json
+{
+  "id": "A001",
+  "statement": "The measurement reflects the proposed construct.",
+  "category": "measurement",
+  "status": "untested",
+  "test_or_check": "Compare with an orthogonal measure.",
+  "owner_id": "P01",
+  "evidence_refs": []
+}
+```
+
+Useful categories include `causal`, `mechanistic`, `measurement`, `sampling`,
+`operational`, `statistical`, `feasibility`, `ethical`, and `value`.
+
+### Literature check
+
+```json
+{
+  "idea_id": "I001",
+  "checked_on": "2026-07-23",
+  "queries": ["Exact query or protocol identifier"],
+  "sources_screened": ["DOI or stable URL"],
+  "support": [],
+  "challenges": [],
+  "search_limits": ["Databases, date, language, or access limits"],
+  "status": "search-incomplete",
+  "reviewer_id": "P02"
+}
+```
+
+Do not store copyrighted full text, confidential reviews, credentials, or
+personal data in the register.
+
+## 30-minute individual or pair workflow
+
+### Minute 0–5: scope
+
+1. Write one question and one decision the session can inform.
+2. List real and assumed constraints separately.
+3. Check whether clinical, ethics, safety, dual-use, privacy, or regulatory
+   concerns require a different process.
+
+### Minute 5–12: independent generation
+
+- Work silently, even as a pair.
+- Generate one idea per record.
+- Attach at least one assumption and one uncertainty.
+- Do not search or ask an AI system during this first round unless the session
+  explicitly studies AI anchoring.
+
+### Minute 12–17: share and expand
+
+- Read ideas without ranking.
+- Clarify wording.
+- Run a second two-minute private round for additions and contradictions.
+
+### Minute 17–23: cluster and criteria
+
+- Cluster by one declared relation.
+- Define three to five criteria with directions and scale anchors.
+- Identify any noncompensatory safety or ethics gates.
+
+### Minute 23–28: challenge
+
+- Write one disconfirming observation and one alternative explanation for each
+  leading candidate.
+- Mark literature work as `not-checked` unless a real search was performed.
+
+### Minute 28–30: log
+
+- Select the next information-gathering action, not a scientific conclusion.
+- Record owner, due/revisit condition, and unresolved concerns.
+
+## 60–90 minute facilitated group workflow
+
+### Before the session
+
+- Obtain a neutral focal question from the decision owner.
+- Recruit complementary perspectives and identify missing voices.
+- Send constraints and definitions, not example solutions.
+- Choose an anonymous contribution path.
+- Predeclare how ideas are retained, clustered, rated, and escalated.
+- Decide what information must not enter shared notes or external tools.
+
+### Opening (10 minutes)
+
+- State purpose, boundaries, and what the session cannot establish.
+- Explain the sequence: independent generation, sharing, clustering,
+  evaluation, challenge, then next-step logging.
+- Ask leaders and sponsors to withhold preferences.
+- Invite conflict and accessibility disclosures.
+
+### Independent round (10–15 minutes)
+
+- Same prompt and time for all.
+- Require stable idea IDs, assumptions, and uncertainty.
+- Allow private submission to the facilitator.
+
+### Round robin and second round (15–20 minutes)
+
+- One item per person per turn; passing is permitted.
+- Clarify without advocacy.
+- Display all items simultaneously only after initial capture.
+- Add a short second private generation round.
+
+### Clustering (10–15 minutes)
+
+- Name the relationship used for each cluster.
+- Keep originals visible.
+- Log every merge and preserve minority interpretations.
+- Do not use lexical similarity as a claim of semantic equivalence.
+
+### Independent evaluation (10 minutes)
+
+- Publish criteria, definitions, directions, and weights first.
+- Rate privately; permit uncertainty ranges and abstention.
+- Reveal distributions before discussion.
+
+### Challenge and gate (15 minutes)
+
+- Assign each candidate to a non-originator.
+- Record falsifiers, alternatives, bias risks, harm/misuse potential, and
+  mitigations.
+- Route triggered reviews to the responsible office; do not resolve them by
+  vote.
+
+### Close (5–10 minutes)
+
+- Log candidate dispositions and dissent.
+- Assign literature, feasibility, consultation, or protocol tasks.
+- State that any score or rank is provisional.
+- Schedule a revisit after evidence checks or external review.
+
+## Asynchronous workflow
+
+Use for distributed teams or when status differences make live contribution
+difficult.
+
+1. Freeze the prompt, definitions, scope, and deadline.
+2. Collect independent entries without showing the current pool.
+3. Release a de-identified pool at the same time to all participants.
+4. Collect clarification requests and second-round ideas.
+5. Publish a merge log and let originators contest merges.
+6. Collect ratings and rationales independently.
+7. Return distributions, dissenting reasons, and missing responses.
+8. Collect revisions once; more rounds require a stated stopping rule.
+9. Record attrition and whether late participants saw different information.
+
+If iterative anonymous judgment and convergence are the actual objective, use
+a documented Delphi design rather than calling any online survey “Delphi.”
+
+## Literature-aware reopening workflow
+
+This pattern reduces premature literature anchoring while keeping ideation
+connected to evidence.
+
+1. Complete and freeze an independent human-first idea set.
+2. Run a documented search for each shortlisted idea.
+3. Separate located evidence, interpretations, and unknowns.
+4. Record search limits and contradictory or null findings.
+5. Give all participants the same bounded evidence packet.
+6. Run a new private round asking for revisions, alternatives, and
+   disconfirming studies.
+7. Link new ideas to their parent IDs without overwriting the initial record.
+
+Never label an idea “novel” solely because no result appeared in one search.
+
+## Leader and authority controls
+
+- The most senior person speaks after independent capture.
+- The facilitator is not the scientific decision owner when avoidable.
+- Ask for ratings before discussion and show distributions.
+- Provide a confidential dissent channel.
+- Separate factual corrections from preference statements.
+- Record who can veto and on what grounds.
+- Ask an external reviewer to challenge ideas favored by the sponsor.
+- Do not force consensus; retain “no consensus” as a valid outcome.
+
+## Accessibility and inclusion
+
+- Offer spoken, typed, asynchronous, and private contribution modes.
+- Define jargon and distribute materials in accessible formats.
+- Allow processing time and breaks.
+- Do not infer silence as agreement.
+- Compensate or acknowledge stakeholder and lived-experience contributions
+  under applicable policy.
+- Record whose participation was constrained by language, time zone,
+  technology, hierarchy, or access.
+
+## Sensitive and unpublished work
+
+Before the session, classify what may be recorded and shared. Minimize detail:
+
+- use abstracted mechanisms instead of controlled operational parameters;
+- use participant IDs instead of personal identifiers;
+- store unpublished ideas only in approved systems with appropriate access;
+- do not paste unpublished manuscripts, grant reviews, patient information,
+  proprietary methods, security-sensitive details, or controlled data into
+  public AI or collaboration services;
+- follow contractual, institutional, community, and Indigenous data-governance
+  obligations.
+
+If safe abstraction would make the question meaningless, stop and use an
+approved closed process.
+
+## Decision-log entry
+
+```json
+{
+  "decision_id": "D001",
+  "date": "2026-07-23",
+  "owner_id": "P01",
+  "candidate_ids": ["I001", "I002"],
+  "decision": "Advance I001 to a bounded literature review; no study approved.",
+  "rationale": "Reason linked to criteria and qualitative review.",
+  "dissent": ["P02 preferred I002 because ..."],
+  "uncertainties": ["Feasibility estimate has not been checked."],
+  "gate_status": {
+    "ethics": "not-assessed",
+    "biosafety_or_dual_use": "not-applicable",
+    "regulatory": "not-assessed"
+  },
+  "next_action": "Run and document the search protocol.",
+  "revisit_when": "Evidence check and methods consultation are complete."
+}
+```
+
+The log should make the decision reconstructable, not merely defensible after
+the fact.

package/org-skills/scientific-brainstorming/references/idea_evaluation.md

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+# Transparent Idea Evaluation
+
+Evaluation narrows a candidate set; it does not convert ideas into evidence.
+Use explicit criteria, independent ratings, uncertainty, qualitative review,
+adversarial checks, and noncompensatory gates.
+
+## Define criteria before viewing scores
+
+For every criterion record:
+
+- name and decision relevance;
+- direction (`higher` or `lower`);
+- observable anchors for the minimum, midpoint, and maximum;
+- weight and who set it;
+- evidence required for a rating;
+- uncertainty representation;
+- conflicts or overlap with other criteria.
+
+Possible criteria include information gain, ability to distinguish mechanisms,
+importance to stakeholders, feasibility, reversibility, novelty relative to a
+documented search, methodological rigor, cost, time, equity, safety, and
+dual-use burden.
+
+Avoid:
+
+- “impact” or “quality” without anchors;
+- counting correlated criteria twice;
+- silently converting missing information to a zero;
+- changing weights after seeing which idea wins;
+- averaging away an ethics, safety, regulatory, or feasibility veto.
+
+## Rating process
+
+1. Train raters on two neutral examples that are not session candidates.
+2. Ask raters to score independently and cite the reason or source.
+3. Allow `not assessable` and abstention rather than forced precision.
+4. Collect a central score and plausible low/high values when uncertainty is
+   material.
+5. Reveal distributions and reasons.
+6. Discuss disagreements, then retain both original and revised ratings.
+7. Resolve factual errors separately from preference differences.
+
+Do not report inter-rater agreement as evidence that an idea is correct.
+Agreement can reflect shared information or shared bias.
+
+## Weighted additive matrix
+
+The bundled `scripts/evaluate_matrix.py` uses a simple, fully disclosed model.
+For criterion \(j\), observed score \(x_{ij}\), minimum \(L_j\), maximum \(U_j\),
+and positive weight \(w_j\):
+
+- higher-is-better: \(n_{ij}=(x_{ij}-L_j)/(U_j-L_j)\)
+- lower-is-better: \(n_{ij}=(U_j-x_{ij})/(U_j-L_j)\)
+- normalized weight: \(p_j=w_j/\sum_j w_j\)
+- displayed score: \(100\sum_j p_j n_{ij}\)
+
+This compensatory formula means a high value on one criterion can offset a low
+value on another. Keep hard gates outside the formula.
+
+### Criteria configuration
+
+```json
+{
+  "schema_version": "1.0",
+  "criteria": [
+    {
+      "name": "information_gain",
+      "description": "Ability to discriminate plausible mechanisms",
+      "weight": 3,
+      "direction": "higher",
+      "minimum": 1,
+      "maximum": 5
+    },
+    {
+      "name": "resource_burden",
+      "description": "Relative time, cost, and scarce-resource burden",
+      "weight": 2,
+      "direction": "lower",
+      "minimum": 1,
+      "maximum": 5
+    }
+  ]
+}
+```
+
+Weights must be explicit, finite, and positive. They need not sum to one; the
+script reports both supplied and normalized values.
+
+### Scores CSV
+
+```csv
+idea_id,information_gain,information_gain_low,information_gain_high,resource_burden,resource_burden_low,resource_burden_high,qualitative_review,uncertainties,evidence_status,ethics_status
+I001,4,3,5,3,2,4,"Distinguishing prediction is clear","Assay performance unknown",search-incomplete,review-required
+I002,3,2,4,2,2,3,"Lower burden but less discriminating","Population transfer uncertain",mixed,not-assessed
+```
+
+Required columns are `idea_id`, every configured criterion,
+`qualitative_review`, and `uncertainties`. Low/high columns are optional but
+must appear as pairs and contain `low <= score <= high`. Extra columns are
+preserved as qualitative context.
+
+Run:
+
+```bash
+python scripts/evaluate_matrix.py scores.csv \
+  --config criteria.json \
+  --weight-delta 0.10 \
+  --output matrix.json
+```
+
+The output includes:
+
+- raw and normalized criterion scores;
+- supplied and normalized weights;
+- base score and deterministic presentation rank;
+- score interval implied by input low/high values;
+- minimum/maximum score and rank when each weight is perturbed one at a time
+  by the requested fraction and all weights are renormalized;
+- qualitative fields, limitations, formula, and tie rule;
+- `decision: null` and an explicit notice that no scientific conclusion or
+  automatic selection was made.
+
+The sensitivity analysis is local and one-factor-at-a-time. It does not explore
+all possible weights, criterion dependence, model-form uncertainty, correlated
+ratings, or uncertainty in the scale anchors.
+
+## Interpreting sensitivity
+
+Treat a ranking as fragile when:
+
+- rank changes under small, plausible weight perturbations;
+- score intervals overlap materially;
+- one criterion dominates the result;
+- rankings change after a reasonable alternative definition;
+- missing evidence is driving optimistic ratings;
+- qualitative review or a gate conflicts with the numeric order.
+
+Do not “fix” fragility by choosing weights that stabilize a preferred result.
+Use it to identify value judgments, missing information, or candidates that
+need further comparison.
+
+## Adversarial review template
+
+For every shortlisted idea record:
+
+```text
+Idea ID:
+Reviewer (not an originator):
+Strongest version of the idea:
+Observation that would count against it:
+At least two alternative explanations:
+Measurement or analysis failure:
+Sampling or generalizability failure:
+Prior evidence that challenges it:
+Potential harm, inequity, or misuse:
+Mitigation:
+Residual uncertainty:
+Disposition: retain / revise / pause / stop / external review
+```
+
+Review the strongest version before attacking it. Avoid performative “devil's
+advocacy” with no follow-up; every challenge needs a response, owner, and
+status.
+
+## Literature check
+
+For each idea:
+
+1. Translate the idea into searchable concepts and alternative terminology.
+2. Search primary literature, systematic reviews, methods guidance, negative
+   findings, and adjacent disciplines.
+3. Record databases, exact queries, dates, filters, and screening limits.
+4. Verify each source, DOI, sample, design, and relevant result.
+5. Separate:
+   - directly relevant evidence;
+   - indirect analogy;
+   - conflicting or null evidence;
+   - expert opinion;
+   - no direct evidence located in this search.
+6. Update assumptions and ratings without overwriting the original record.
+
+Do not use citation counts as a validity score. Do not let an AI-generated
+summary substitute for reading the source.
+
+## Feasibility and rigor gate
+
+Ask a relevant methods expert to review:
+
+- research question, unit of inference, and proposed comparison;
+- discriminating predictions and plausible alternatives;
+- sampling frame, controls, randomization, blinding, and replication;
+- measurement validity and resource authentication;
+- nuisance variables, batch effects, missingness, and analytic flexibility;
+- sample-size or information requirements;
+- feasibility, dependencies, cost, skills, and failure recovery;
+- value and interpretability of null or contradictory outcomes.
+
+This is a gate to protocol development, not approval to collect data.
+
+### NIH-funded biomedical work
+
+When NIH guidance applies, the later application or protocol should address:
+
+- rigor of prior published and unpublished research;
+- robust and unbiased design, methodology, analysis, interpretation, and
+  reporting;
+- relevant biological variables;
+- authentication of key biological or chemical resources.
+
+NIH's SABV policy expects sex to be considered in research questions, design,
+analysis, and reporting for vertebrate animal and human studies, with strong
+justification for a single-sex scope. “Include both sexes” alone is not an
+analysis plan, and an inappropriate underpowered comparison can reduce rather
+than improve rigor. Consult current NIH instructions and program staff.
+
+## Ethics, safety, and regulatory gate
+
+Ask whether the idea involves:
+
+- people, identifiable or sensitive data, vulnerable groups, or clinical care;
+- animals;
+- pathogens, toxins, engineered biological systems, or environmental release;
+- dual-use capabilities, dangerous optimization, or security-sensitive
+  details;
+- controlled technologies, export restrictions, or research-security duties;
+- Indigenous, community, cultural, or data-sovereignty obligations;
+- proprietary information or unpublished work;
+- environmental, distributive, or accessibility harms.
+
+Record `not-assessed`, `not-applicable`, `review-required`, `approved under
+identifier ...`, `redesign-required`, or `stop`. Only the authorized body can
+issue approval. Current policies vary by jurisdiction and can change.
+
+## Decision log
+
+Record the decision while alternatives and uncertainty are still visible:
+
+- date, owner, and decision scope;
+- candidate IDs and versions;
+- criteria, anchors, weights, and sensitivity settings;
+- raw ratings, ranges, dissent, missing ratings, and abstentions;
+- evidence-check protocol and results;
+- adversarial review and responses;
+- feasibility and ethics/safety/regulatory gate status;
+- selected next action and why;
+- rejected or deferred alternatives and why;
+- revisit trigger, owner, and deadline.
+
+Do not rewrite the log after outcomes are known. Append corrections and
+reasons.
+
+## Preregistration and open science handoff
+
+Ideation is normally exploratory. When a candidate becomes a confirmatory
+study:
+
+1. distinguish hypotheses formed before versus after seeing relevant outcomes;
+2. specify design, primary outcomes, exclusions, stopping, and analysis
+   decisions before outcome inspection;
+3. use a time-stamped registry appropriate to the field;
+4. document amendments and label departures and new analyses as exploratory;
+5. consider a Registered Report when protocol review before results is useful;
+6. follow consent, privacy, intellectual-property, security, and community
+   constraints when sharing.
+
+Preregistration supports transparency; it does not guarantee a good question,
+adequate power, correct analysis, reproducibility, ethics approval, or truthful
+execution. Exploratory research remains valuable when reported as exploratory.