maestro-flow 0.5.35 → 0.5.37

package/.agents/skills/scholar-ideation/phases/02-gap-analysis.md

@@ -1,249 +1,249 @@
-# Phase 2: Gap Analysis
-
-Systematically identify and evaluate research gaps from the literature review to find valuable research opportunities.
-
-## Objective
-
-- Analyze literature across 5 gap types (literature, methodological, application, interdisciplinary, temporal)
-- Evaluate gaps along 5 analysis dimensions
-- Prioritize gaps by importance, novelty, and feasibility
-- Produce a structured gap analysis with actionable research opportunities
-
-## Input
-
-- **literatureResults**: Papers, trends, and key findings from Phase 1
-- **workflowPreferences.topic**: Research topic
-- **workflowPreferences.scope**: Research scope
-
-## Execution
-
-### Step 2.1: Systematic Literature Analysis
-
-Build a comparison matrix from the papers discovered in Phase 1.
-
-**Comparison matrix**:
-
-| Paper | Method | Dataset | Performance | Key Innovation | Limitations |
-|-------|--------|---------|-------------|----------------|-------------|
-| Paper A | Method X | Dataset 1 | Metric: value | Innovation A | Limitation A |
-| Paper B | Method Y | Dataset 2 | Metric: value | Innovation B | Limitation B |
-| ... | ... | ... | ... | ... | ... |
-
-Focus on:
-- What methods are used and how they compare
-- What datasets and benchmarks are standard
-- What performance levels are achieved
-- What each paper identifies as limitations or future work
-
-### Step 2.2: Five-Type Gap Identification
-
-Analyze the literature systematically across five gap types.
-
-**Type 1: Literature Gaps**
-
-Topics or questions not yet sufficiently studied.
-
-Identification methods:
-- Find sub-areas with few papers (< 20 relevant publications)
-- Analyze "Future Work" sections of survey/review papers
-- Identify low-citation but potentially important research directions
-- Discover emerging topics with limited coverage
-
-Questions to answer:
-- Which sub-topics within the field have received minimal attention?
-- Are there important questions that no paper directly addresses?
-- What have review papers flagged as under-explored?
-
-**Type 2: Methodological Gaps**
-
-Limitations and improvement opportunities in existing methods.
-
-Identification methods:
-- Analyze common weaknesses across papers (from comparison matrix Limitations column)
-- Identify scenarios where methods fail or degrade
-- Find computational efficiency or scalability problems
-- Spot gaps between theoretical guarantees and practical performance
-
-Questions to answer:
-- What limitations do ALL current methods share?
-- In what specific scenarios do existing approaches fail?
-- Are there well-known theoretical results with no practical implementation?
-
-**Type 3: Application Gaps**
-
-Theory-to-practice transfer opportunities and new application domains.
-
-Identification methods:
-- Identify theoretical work lacking real-world validation
-- Find successful methods that haven't been applied to relevant new domains
-- Spot disconnects between industry needs and academic research
-- Discover technology transfer possibilities
-
-Questions to answer:
-- Which promising methods have not been tested in practical settings?
-- What industry problems could benefit from existing academic methods?
-- Are there successful cross-domain transfers that haven't been attempted?
-
-**Type 4: Interdisciplinary Gaps**
-
-Research opportunities at the intersection of different fields.
-
-Identification methods:
-- Identify similar problems solved differently across fields
-- Find methods that could transfer across disciplines
-- Discover complex problems requiring multi-disciplinary collaboration
-- Spot emerging cross-disciplinary areas
-
-Questions to answer:
-- Are there related fields with transferable methods?
-- Do similar problems appear in different domains with different solutions?
-- What new fields are emerging at discipline boundaries?
-
-**Type 5: Temporal Gaps**
-
-New research needs arising from changes over time.
-
-Identification methods:
-- Identify new problems created by recent technology advances
-- Find data distribution shifts that affect existing methods
-- Discover new challenges from changing social/regulatory requirements
-- Spot opportunities from recent technological breakthroughs
-
-Questions to answer:
-- What new technologies have created previously impossible research directions?
-- Have recent developments invalidated assumptions in older work?
-- What regulatory or societal changes demand new research?
-
-### Step 2.3: Five-Dimension Analysis
-
-For each identified gap, evaluate along five dimensions.
-
-**Dimension 1: Research Topic Coverage**
-- How many high-quality papers exist on this topic?
-- Thresholds: Sufficient (>100), Moderate (20-100), Under-researched (<20), Unexplored (~0)
-- How many active research groups are working on it?
-
-**Dimension 2: Method Strengths/Weaknesses Comparison**
-- What are the theoretical foundations of existing methods?
-- How do they perform experimentally?
-- What is the computational complexity?
-- How well do they generalize and scale?
-
-**Dimension 3: Experimental Setup Completeness**
-- Are experimental scenarios diverse enough?
-- Do benchmarks cover the full problem space?
-- Are evaluation metrics comprehensive?
-- Are ablation studies thorough?
-
-**Dimension 4: Dataset and Benchmark Availability**
-- Are there public datasets of sufficient quality?
-- Are there standardized benchmarks?
-- Are datasets diverse and representative?
-- Is data annotation quality adequate?
-
-**Dimension 5: Theory-Practice Gap**
-- Do theoretical assumptions match real conditions?
-- Are methods practically deployable?
-- Do theoretical guarantees hold in experiments?
-- Is there industry adoption?
-
-### Step 2.4: Gap Prioritization
-
-Score each identified gap on three criteria (1-5 scale):
-
-**Importance**: Academic and practical value of filling this gap
-- 5: Breakthrough potential, affects the entire field
-- 4: Important, multiple groups would benefit
-- 3: Valuable, relevant to a significant subset
-- 2: Marginal, limited audience
-- 1: Trivial, minimal impact
-
-**Novelty**: Whether others are already addressing this gap
-- 5: Completely unexplored
-- 4: Very few attempts, mostly unsuccessful
-- 3: Some work exists but significant room remains
-- 2: Active area, incremental contribution possible
-- 1: Well-covered, minimal novelty
-
-**Feasibility**: Whether the gap can be addressed with available resources
-- 5: Fully feasible with current resources
-- 4: Feasible with some effort
-- 3: Challenging but possible
-- 2: Difficult, requires significant resources
-- 1: Nearly infeasible with available resources
-
-**Priority decision matrix**:
-
-| Importance | Novelty | Feasibility | Recommendation |
-|-----------|---------|-------------|----------------|
-| High | High | High | Top priority — pursue |
-| High | High | Medium | Worth attempting |
-| High | Medium | High | Safe choice |
-| Medium | High | High | Consider |
-| Low | * | * | Reconsider |
-
-### Step 2.5: Gap Validation
-
-Before finalizing, validate top gaps:
-- Search for very recent work (last 3 months) that might address the gap
-- Check arXiv preprints for ongoing related work
-- Verify no technical or data blockers exist
-- Consider whether the gap is a genuine research opportunity or a dead end
-
-```
-web_search: "{gap description keywords} {current year} arxiv"
-```
-
-If validation reveals the gap is being actively closed, downgrade priority or refine the gap definition.
-
-### Step 2.6: Gap Analysis Document
-
-Compile results into a structured analysis:
-
-```markdown
-## Gap Analysis: {Topic}
-
-### Identified Gaps
-
-#### Gap 1: {Title}
-- **Type**: Literature / Methodological / Application / Interdisciplinary / Temporal
-- **Description**: {Detailed description}
-- **Evidence**: {Papers/trends that reveal this gap}
-- **Importance**: {score}/5 — {justification}
-- **Novelty**: {score}/5 — {justification}
-- **Feasibility**: {score}/5 — {justification}
-- **Priority**: {Top / High / Medium / Low}
-
-#### Gap 2: {Title}
-...
-
-### Prioritized Opportunities
-1. {Top priority gap} — {one-line rationale}
-2. {Second priority} — {one-line rationale}
-3. {Third priority} — {one-line rationale}
-
-### Research Direction Recommendations
-- **Recommended focus**: {primary gap to pursue}
-- **Alternative directions**: {backup options}
-- **Combination opportunities**: {gaps that could be addressed together}
-```
-
-Present gap analysis to user for feedback (unless autoYes):
-```
-ask_user:
-  question: "Here is the gap analysis. Which gaps interest you most? Would you like to adjust priorities?"
-  → Incorporate user feedback into final priorities
-```
-
-## Output
-
-- **Variable**: `gapAnalysis` containing:
-  - `gaps[]` — List of identified gaps with type, description, evidence, and scores
-  - `opportunities[]` — Ranked research opportunities
-  - `prioritizedGaps[]` — Top 3-5 gaps sorted by priority
-  - `recommendedFocus` — Primary recommended research direction
-- **track_tasks**: Mark Phase 2 completed, Phase 3 in_progress
-
-## Next Phase
-
-Return to orchestrator, then proceed to [Phase 3: Research Question Formulation](03-research-question.md).
+# Phase 2: Gap Analysis
+
+Systematically identify and evaluate research gaps from the literature review to find valuable research opportunities.
+
+## Objective
+
+- Analyze literature across 5 gap types (literature, methodological, application, interdisciplinary, temporal)
+- Evaluate gaps along 5 analysis dimensions
+- Prioritize gaps by importance, novelty, and feasibility
+- Produce a structured gap analysis with actionable research opportunities
+
+## Input
+
+- **literatureResults**: Papers, trends, and key findings from Phase 1
+- **workflowPreferences.topic**: Research topic
+- **workflowPreferences.scope**: Research scope
+
+## Execution
+
+### Step 2.1: Systematic Literature Analysis
+
+Build a comparison matrix from the papers discovered in Phase 1.
+
+**Comparison matrix**:
+
+| Paper | Method | Dataset | Performance | Key Innovation | Limitations |
+|-------|--------|---------|-------------|----------------|-------------|
+| Paper A | Method X | Dataset 1 | Metric: value | Innovation A | Limitation A |
+| Paper B | Method Y | Dataset 2 | Metric: value | Innovation B | Limitation B |
+| ... | ... | ... | ... | ... | ... |
+
+Focus on:
+- What methods are used and how they compare
+- What datasets and benchmarks are standard
+- What performance levels are achieved
+- What each paper identifies as limitations or future work
+
+### Step 2.2: Five-Type Gap Identification
+
+Analyze the literature systematically across five gap types.
+
+**Type 1: Literature Gaps**
+
+Topics or questions not yet sufficiently studied.
+
+Identification methods:
+- Find sub-areas with few papers (< 20 relevant publications)
+- Analyze "Future Work" sections of survey/review papers
+- Identify low-citation but potentially important research directions
+- Discover emerging topics with limited coverage
+
+Questions to answer:
+- Which sub-topics within the field have received minimal attention?
+- Are there important questions that no paper directly addresses?
+- What have review papers flagged as under-explored?
+
+**Type 2: Methodological Gaps**
+
+Limitations and improvement opportunities in existing methods.
+
+Identification methods:
+- Analyze common weaknesses across papers (from comparison matrix Limitations column)
+- Identify scenarios where methods fail or degrade
+- Find computational efficiency or scalability problems
+- Spot gaps between theoretical guarantees and practical performance
+
+Questions to answer:
+- What limitations do ALL current methods share?
+- In what specific scenarios do existing approaches fail?
+- Are there well-known theoretical results with no practical implementation?
+
+**Type 3: Application Gaps**
+
+Theory-to-practice transfer opportunities and new application domains.
+
+Identification methods:
+- Identify theoretical work lacking real-world validation
+- Find successful methods that haven't been applied to relevant new domains
+- Spot disconnects between industry needs and academic research
+- Discover technology transfer possibilities
+
+Questions to answer:
+- Which promising methods have not been tested in practical settings?
+- What industry problems could benefit from existing academic methods?
+- Are there successful cross-domain transfers that haven't been attempted?
+
+**Type 4: Interdisciplinary Gaps**
+
+Research opportunities at the intersection of different fields.
+
+Identification methods:
+- Identify similar problems solved differently across fields
+- Find methods that could transfer across disciplines
+- Discover complex problems requiring multi-disciplinary collaboration
+- Spot emerging cross-disciplinary areas
+
+Questions to answer:
+- Are there related fields with transferable methods?
+- Do similar problems appear in different domains with different solutions?
+- What new fields are emerging at discipline boundaries?
+
+**Type 5: Temporal Gaps**
+
+New research needs arising from changes over time.
+
+Identification methods:
+- Identify new problems created by recent technology advances
+- Find data distribution shifts that affect existing methods
+- Discover new challenges from changing social/regulatory requirements
+- Spot opportunities from recent technological breakthroughs
+
+Questions to answer:
+- What new technologies have created previously impossible research directions?
+- Have recent developments invalidated assumptions in older work?
+- What regulatory or societal changes demand new research?
+
+### Step 2.3: Five-Dimension Analysis
+
+For each identified gap, evaluate along five dimensions.
+
+**Dimension 1: Research Topic Coverage**
+- How many high-quality papers exist on this topic?
+- Thresholds: Sufficient (>100), Moderate (20-100), Under-researched (<20), Unexplored (~0)
+- How many active research groups are working on it?
+
+**Dimension 2: Method Strengths/Weaknesses Comparison**
+- What are the theoretical foundations of existing methods?
+- How do they perform experimentally?
+- What is the computational complexity?
+- How well do they generalize and scale?
+
+**Dimension 3: Experimental Setup Completeness**
+- Are experimental scenarios diverse enough?
+- Do benchmarks cover the full problem space?
+- Are evaluation metrics comprehensive?
+- Are ablation studies thorough?
+
+**Dimension 4: Dataset and Benchmark Availability**
+- Are there public datasets of sufficient quality?
+- Are there standardized benchmarks?
+- Are datasets diverse and representative?
+- Is data annotation quality adequate?
+
+**Dimension 5: Theory-Practice Gap**
+- Do theoretical assumptions match real conditions?
+- Are methods practically deployable?
+- Do theoretical guarantees hold in experiments?
+- Is there industry adoption?
+
+### Step 2.4: Gap Prioritization
+
+Score each identified gap on three criteria (1-5 scale):
+
+**Importance**: Academic and practical value of filling this gap
+- 5: Breakthrough potential, affects the entire field
+- 4: Important, multiple groups would benefit
+- 3: Valuable, relevant to a significant subset
+- 2: Marginal, limited audience
+- 1: Trivial, minimal impact
+
+**Novelty**: Whether others are already addressing this gap
+- 5: Completely unexplored
+- 4: Very few attempts, mostly unsuccessful
+- 3: Some work exists but significant room remains
+- 2: Active area, incremental contribution possible
+- 1: Well-covered, minimal novelty
+
+**Feasibility**: Whether the gap can be addressed with available resources
+- 5: Fully feasible with current resources
+- 4: Feasible with some effort
+- 3: Challenging but possible
+- 2: Difficult, requires significant resources
+- 1: Nearly infeasible with available resources
+
+**Priority decision matrix**:
+
+| Importance | Novelty | Feasibility | Recommendation |
+|-----------|---------|-------------|----------------|
+| High | High | High | Top priority — pursue |
+| High | High | Medium | Worth attempting |
+| High | Medium | High | Safe choice |
+| Medium | High | High | Consider |
+| Low | * | * | Reconsider |
+
+### Step 2.5: Gap Validation
+
+Before finalizing, validate top gaps:
+- Search for very recent work (last 3 months) that might address the gap
+- Check arXiv preprints for ongoing related work
+- Verify no technical or data blockers exist
+- Consider whether the gap is a genuine research opportunity or a dead end
+
+```
+web_search: "{gap description keywords} {current year} arxiv"
+```
+
+If validation reveals the gap is being actively closed, downgrade priority or refine the gap definition.
+
+### Step 2.6: Gap Analysis Document
+
+Compile results into a structured analysis:
+
+```markdown
+## Gap Analysis: {Topic}
+
+### Identified Gaps
+
+#### Gap 1: {Title}
+- **Type**: Literature / Methodological / Application / Interdisciplinary / Temporal
+- **Description**: {Detailed description}
+- **Evidence**: {Papers/trends that reveal this gap}
+- **Importance**: {score}/5 — {justification}
+- **Novelty**: {score}/5 — {justification}
+- **Feasibility**: {score}/5 — {justification}
+- **Priority**: {Top / High / Medium / Low}
+
+#### Gap 2: {Title}
+...
+
+### Prioritized Opportunities
+1. {Top priority gap} — {one-line rationale}
+2. {Second priority} — {one-line rationale}
+3. {Third priority} — {one-line rationale}
+
+### Research Direction Recommendations
+- **Recommended focus**: {primary gap to pursue}
+- **Alternative directions**: {backup options}
+- **Combination opportunities**: {gaps that could be addressed together}
+```
+
+Present gap analysis to user for feedback (unless autoYes):
+```
+ask_user:
+  question: "Here is the gap analysis. Which gaps interest you most? Would you like to adjust priorities?"
+  → Incorporate user feedback into final priorities
+```
+
+## Output
+
+- **Variable**: `gapAnalysis` containing:
+  - `gaps[]` — List of identified gaps with type, description, evidence, and scores
+  - `opportunities[]` — Ranked research opportunities
+  - `prioritizedGaps[]` — Top 3-5 gaps sorted by priority
+  - `recommendedFocus` — Primary recommended research direction
+- **track_tasks**: Mark Phase 2 completed, Phase 3 in_progress
+
+## Next Phase
+
+Return to orchestrator, then proceed to [Phase 3: Research Question Formulation](03-research-question.md).