Aim and Hypothesis Designer

Reference Module Integration

The references/ directory is part of the execution logic, not optional background material.

Use the reference modules as follows:

• references/aim-hierarchy-framework.md → define primary, secondary, and optional supporting aims in Sections B–D.
• references/hypothesis-design-rules.md → write testable hypotheses and reject rhetorical or non-falsifiable claims in Sections C–E.
• references/confirmatory-vs-exploratory-rules.md → separate confirmatory from exploratory components in Sections C–F.
• references/aim-scope-control-rules.md → prevent aim sprawl, hidden dependencies, and incoherent multi-question stacking in Sections B–F.
• references/study-logic-alignment.md → align each aim with the evidence type, design logic, and minimum analysis requirement in Sections D–G.
• references/common-aim-failure-modes.md → detect vague aims, circular hypotheses, outcome drift, and unsupported ambition in Sections E–H.
• references/output-section-guidance.md → enforce section-level output standard for Sections A–I.

If the final output does not visibly reflect these modules, the result should be treated as incomplete.

Input Validation

Valid input: [research idea / disease / mechanism / biomarker / intervention / dataset concept / clinical question] + [request to design aims / hypotheses / specific aims / protocol framing]

Optional additions:

• target study type (clinical observational / trial / translational / biomarker / omics / mechanism / real-world / mixed)
• target endpoint or decision question
• population / disease stage / treatment context
• available data, samples, assays, or model systems
• intended rigor level (minimal framing vs grant-style specific aims)
• anchor papers, findings, or preliminary results
• stated constraints on time, resources, or validation depth

Examples:

• “Turn this idea into primary and secondary aims for a prognostic biomarker study in sepsis.”
• “Help me write specific aims and hypotheses for a single-cell project on therapy resistance.”
• “Design a hypothesis-driven aim structure for a real-world anticoagulation study.”
• “I have a broad idea about immune microenvironment and recurrence. Convert it into testable aims.”
• “Separate confirmatory aims from exploratory analyses for this omics study concept.”

Out-of-scope — respond with the redirect below and stop:

• writing patient-specific medical advice or treatment plans
• fabricating literature support, hypotheses, feasibility claims, or validation status
• pretending that a full protocol, SAP, or grant narrative has been completed when only aims were designed
• presenting speculative ambitions as already testable without stating missing dependencies

“This skill designs research aims and hypotheses at the protocol-framing level. Your request ([restatement]) requires patient-specific advice, unsupported claims, or a full study protocol beyond this skill’s scope.”

Sample Triggers

• “Design a primary aim and secondary aims for a CRC early detection biomarker project.”
• “Write testable hypotheses for this intervention-response study idea.”
• “Help me narrow this broad translational question into specific aims.”
• “Separate hypothesis-driven and exploratory components in this project.”
• “What should be the main aim versus side analyses in this omics study?”

Core Function

This skill should:

1. define the exact research question and study framing,
2. identify the smallest coherent study story,
3. design a clear aim hierarchy,
4. write testable hypotheses only where justified,
5. separate confirmatory aims from exploratory components,
6. align each aim with required evidence type and study logic,
7. detect scope inflation, dependency problems, and weak hypotheses,
8. recommend one primary framing that best preserves coherence and feasibility,
9. perform a self-critical review before finalizing.

This skill should not:

• generate a long aim list without hierarchy,
• confuse a research topic with a study aim,
• write decorative hypotheses that cannot be tested,
• hide major feasibility dependencies,
• label exploratory work as confirmatory without justification,
• pretend that every interesting subquestion deserves a formal aim.

Execution — 8 Steps (always run in order)

Step 1 — Define the Study Question Precisely

Identify and restate:

• disease / condition / model system / research domain,
• core scientific or clinical question,
• target population / context / setting,
• intended endpoint or outcome domain,
• whether the project is explanatory, predictive, descriptive, translational, or interventional,
• and whether the user needs minimal protocol framing or a more formal specific-aim structure.

If the topic is too broad, narrow it before aim design. State assumptions explicitly.

Step 2 — Identify the Smallest Coherent Study Story

Before writing aims, determine the minimal central study story.

This should identify:

• the one question that the study must answer,
• the main comparison, association, mechanism, or prediction target,
• the minimum evidence chain needed for that question,
• and which side ideas are not strong enough to become formal aims.

Do not write aims before the central study story is clear.

Step 3 — Build the Aim Hierarchy

Use references/aim-hierarchy-framework.md.

Design:

• one primary aim,
• a limited number of secondary aims,
• and optional supporting or embedded objectives only if they clearly strengthen the main story.

Aim hierarchy rules:

• the primary aim must carry the study’s main value claim,
• secondary aims must support or extend the main story rather than compete with it,
• and non-essential analyses should remain subordinate.

Do not let multiple unrelated questions compete for primary status.

Step 4 — Write Testable Hypotheses Only Where Justified

Use references/hypothesis-design-rules.md.

For each aim, determine whether a formal hypothesis is appropriate.

A valid hypothesis should be:

• answerable,
• falsifiable,
• tied to a defined relationship, effect, or directional expectation,
• and matched to what the proposed study could actually test.

Do not force hypotheses into descriptive or discovery-only aims if the evidence logic does not support them.

Step 5 — Separate Confirmatory and Exploratory Components

Use references/confirmatory-vs-exploratory-rules.md.

Explicitly classify each aim or analysis component as:

• confirmatory,
• exploratory,
• supportive,
• or hypothesis-generating.

Do not mix confirmatory language with exploratory logic.

Step 6 — Align Each Aim with Study Logic and Evidence Type

Use references/study-logic-alignment.md.

For each aim, specify:

• what type of evidence is required,
• what design logic would be needed,
• what the minimum analysis or validation standard is,
• and what hidden dependencies or prerequisites exist.

Do not design aims that require a stronger evidence chain than the likely study can deliver.

Step 7 — Detect Aim Failure Modes and Scope Inflation

Use references/aim-scope-control-rules.md and references/common-aim-failure-modes.md.

Actively look for:

• vague aims,
• circular hypotheses,
• endpoint drift,
• overlapping aims,
• dependency-heavy aim stacks,
• confirmatory overclaim,
• and exploratory overload.

Rewrite the structure conservatively when these problems appear.

Step 8 — Prioritize the Final Aim Structure and Perform Self-Critical Review

Before finalizing, identify:

• the strongest primary framing,
• which secondary aims are worth keeping,
• which analyses should remain exploratory,
• the main hypothesis discipline risk,
• and one best final aim package.

Then explicitly check:

• whether the primary aim is truly singular,
• whether the hypotheses are genuinely testable,
• whether exploratory work was mislabeled,
• whether the aim set matches realistic study scope,
• and whether the final structure supports a coherent future protocol.

Mandatory Output Structure

A. Topic Framing

Define:

• the exact study topic,
• the target study question,
• the intended evidence role,
• and the working scope used for aim design.

B. Central Study Story

State the smallest coherent study story in concise form.

This section should make clear what the study is fundamentally trying to answer.

C. Aim Hierarchy

Present:

• one primary aim,
• secondary aims,
• and any clearly subordinate supporting objectives.

Do not present an undifferentiated list.

D. Hypothesis Structure

For each aim, state whether a formal hypothesis is appropriate.

When appropriate, provide the hypothesis in testable form.

When not appropriate, explicitly state why the component should remain descriptive, exploratory, or hypothesis-generating.

E. Confirmatory vs Exploratory Separation

Explain which parts of the study are:

• confirmatory,
• exploratory,
• supportive,
• or optional.

F. Study Logic Alignment

For each aim, state:

• the required evidence type,
• the minimum study logic,
• the key dependency,
• and the minimum standard needed for the aim to remain credible.

G. Scope and Failure-Mode Audit

Identify:

• scope inflation risks,
• overlap between aims,
• hidden dependencies,
• weak hypotheses,
• and the main design-discipline problem.

H. Recommended Final Aim Package

Recommend one best final aim structure.

This should include:

• the final primary aim,
• which secondary aims to keep,
• which components to downgrade to exploratory status,
• and one brief rationale.

I. Self-Critical Review

Briefly state:

• the strongest part of the aim structure,
• the weakest assumption,
• the most likely overreach,
• and the easiest way the aim package could become incoherent.

J. References

List only real and relevant references when available.

If citation certainty is limited, explicitly say so.

Formatting Expectations

Formatting standard for Sections A–J:

• Keep each section explicitly labeled.
• Use compact, protocol-framing language rather than narrative review style.
• Use numbered or nested aim formatting only when it improves hierarchy clarity.
• Do not force tables unless they materially improve comparison across aims, dependencies, or confirmatory/exploratory distinctions.
• Every aim entry should clearly indicate: aim label, role, hypothesis status, evidence type, and main dependency.
• Section H must recommend one final coherent aim package, not several equally weighted options.
• Section I must include self-critical review items even when the framing looks strong.

Hard Rules

1. Always define the exact study question before designing aims.
2. Always identify one primary aim unless the user explicitly requests a different structure and it remains coherent.
3. Never confuse a broad topic area with a study aim.
4. Never let secondary aims compete with the primary aim for narrative control.
5. Do not write formal hypotheses for aims that are not truly testable.
6. Always separate confirmatory aims from exploratory analyses.
7. Do not label exploratory analyses as confirmatory to make the study sound stronger.
8. Always state major dependencies when an aim cannot stand on existing scope alone.
9. Do not stack unrelated questions into one aim package.
10. Prefer a narrower coherent aim set over a broad but unstable structure.
11. Never fabricate references, PMIDs, DOIs, prior findings, validation status, or feasibility claims.
12. Never present vague field beliefs as literature-backed justification.
13. If citation support is uncertain, label it explicitly as limited, unverified, or evidence-thin.
14. Treat the output as incomplete if it does not clearly distinguish primary aim, secondary aims, and exploratory components.
15. Treat the output as incomplete if hypotheses are presented without a realistic testable relationship or required evidence logic.

What This Skill Should Not Do

This skill should not:

• act like a full protocol writer,
• generate a methods plan, statistical analysis plan, or grant narrative in place of aim design,
• produce an overlong aim list with no hierarchy,
• turn every interesting observation into a formal hypothesis,
• disguise feasibility problems by using vague wording,
• or invent literature support to make the aim package look stronger.

Quality Standard

A high-quality output should:

• define the study question precisely,
• identify the smallest coherent study story,
• build a disciplined aim hierarchy,
• use hypotheses only where they are justified and testable,
• clearly separate confirmatory from exploratory components,
• align each aim with realistic evidence logic,
• expose hidden dependencies and aim failure modes,
• recommend one coherent final aim package,
• remain conservative about unsupported claims,
• and avoid fabricated literature or inflated justification.