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

{
  "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. Criterion names must not collide with idea_id, qualitative_review, uncertainties, or another criterion's generated _low/_high columns. Scale widths must be finite.

Scores 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.

Missing central scores, including abstentions, are rejected. Keep them in the session record and defer the comparison or document a separate complete-case matrix; never impute zero or drop a criterion silently. Missing or jointly blank bounds hold the central rating fixed only for calculation. The output records bounds_supplied per criterion, lists criteria_without_uncertainty_bounds, and warns that this does not imply certainty. Even fully supplied bounds are plausibility judgments, not confidence or credible intervals.

Run:

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:

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:
6. directly relevant evidence;
7. indirect analogy;
8. conflicting or null evidence;
9. expert opinion;
10. no direct evidence located in this search.
11. 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.

Bounded pilot record for a shortlisted idea

Plan the smallest informative check before developing a full protocol:

Idea ID and source/target mapping (if analogical):
Target-domain baseline or current explanation:
Competing explanations and their differing predictions:
Observable, units, comparison, and measurement limitations:
Feasibility dependencies and required review:
Advance / revise / stop rule fixed before seeing pilot outcomes:
Outcomes that would be inconclusive (including failed controls):
Next evidence needed if the pilot succeeds:

Illustrative example, not an executed experiment: an optical signal rises after a sample treatment. One candidate explanation is a change in the target quantity; another is altered measurement response. A preliminary plan could compare the original readout with an orthogonal measurement and a response control. Define acceptable disagreement and control performance from assay characterization before inspecting outcomes. Concordant readings with adequate controls justify further investigation; a failed response control is inconclusive about the biological mechanism. No numeric threshold, sample size, or causal conclusion is supplied by this brainstorming example.

For an analogy, record what was demonstrated in the source system separately from what was observed in the target. A successful pilot establishes only the tested conditions and cannot by itself prove the transferred mechanism.

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.