AI Prompt Template for Scientific Hypothesis Generation and Ranking

Objective: Equip researchers with a modular AI prompt that systematically breaks down literature findings, surfaces research gaps, generates testable hypotheses, and ranks them by feasibility, novelty, and potential impact for use in biology, materials science, and social sciences.

The base prompt was formed through these deliberate steps:

Isolate the core workflow into sequential stages so the model cannot skip gap identification or jump straight to speculation.
Insert domain flexibility early so the same structure works across biology, materials science, and social sciences without rewriting.
Separate fixed methodological guidance into reusable snippets to keep the main prompt clean and consistent.
Expose ranking criteria and output quantity as variables so users can tune rigor and volume without editing the template.
Require explicit justification for each rank so the model produces transparent, auditable reasoning rather than opaque scores.

Prompt Template

You are a senior research methodologist specializing in {{field}}.

Analyze the following literature findings:
{{literature_summary}}

{{snippet:literature_breakdown}}

Identify the most significant unresolved gaps. From those gaps, generate exactly {{number_of_hypotheses}} clearly testable hypotheses.

{{snippet:hypothesis_evaluation}}

Rank the hypotheses from highest to lowest priority according to the criteria of feasibility, novelty, and potential impact. For each ranked hypothesis provide a short justification that references the original literature and the identified gap.

Element	Type	Example value
{{field}}	variable	materials science
{{literature_summary}}	variable	Recent studies show graphene oxide membranes achieve 90 percent salt rejection yet suffer from swelling-induced flux decline after 200 hours of operation.
{{number_of_hypotheses}}	variable	4
{{snippet:literature_breakdown}}	snippet	Break the findings into key claims, supporting evidence strength, methodological limitations, and stated future directions.
{{snippet:hypothesis_evaluation}}	snippet	Evaluate each hypothesis for operationalizability, required resources, expected timeline, and alignment with open research questions.

Prompt Example

You are a senior research methodologist specializing in materials science.

Analyze the following literature findings:
Recent studies show graphene oxide membranes achieve 90 percent salt rejection yet suffer from swelling-induced flux decline after 200 hours of operation.

Break the findings into key claims, supporting evidence strength, methodological limitations, and stated future directions.

Identify the most significant unresolved gaps. From those gaps, generate exactly 4 clearly testable hypotheses.

Evaluate each hypothesis for operationalizability, required resources, expected timeline, and alignment with open research questions.

Rank the hypotheses from highest to lowest priority according to the criteria of feasibility, novelty, and potential impact. For each ranked hypothesis provide a short justification that references the original literature and the identified gap.

Note

Keep the literature summary concise and citation-free inside the prompt. Supply full references in a separate context window if the model supports it.

Extended example values for the same elements:

{{field}}
- biology
- social sciences
- polymer chemistry
{{literature_summary}}
- CRISPR base-editing efficiency drops below 30 percent in primary human T cells when targeting loci with high chromatin density.
- Longitudinal surveys indicate that remote-work policies increase reported autonomy yet correlate with a 12 percent rise in after-hours communication volume.
{{number_of_hypotheses}}
- 3
- 5
- 6
{{snippet:literature_breakdown}}
- Extract the central mechanistic claims, quantify the strength of supporting data, list experimental constraints, and note any contradictory results.
- Summarize observed patterns, confidence intervals, sample limitations, and explicit calls for further investigation.
{{snippet:hypothesis_evaluation}}
- Score each hypothesis on measurability, cost of required instrumentation, ethical feasibility, and potential to resolve the stated gap.
- Assess testability via available methods, estimated sample size needs, and expected contribution to theoretical frameworks.

Tip

After the model returns ranked hypotheses, feed the top-ranked item back into a follow-up prompt that asks for a minimal experimental protocol. This keeps the generation and evaluation stages cleanly separated.