---
namespace: aiwg
platforms: [all]
name: research-gap-detect-f85610f2ea2b
description: Build the mutual citation graph, find connected components, identify isolated clusters, and optionally search for bridge candidates and file gap issues.
commandHint:
  argumentHint: "[--clusters-only] [--file-issues] [--search-bridges] [--format full|summary|json]"
  allowedTools: Read, Write, Glob, Grep, Bash, Agent, WebSearch
  model: sonnet
  category: research-analysis
  modelRole: coding
  modelTier: standard
---

# Research Gap Detect

Analyze the research corpus citation graph to find disconnected clusters, isolated papers, and gap opportunities. Optionally searches for bridge paper candidates and files gap issues.

## Triggers

- "find research gaps"
- "detect clusters"
- "cluster analysis"
- "find isolated papers"
- "bridge candidate search"
- `/research-gap-detect`

## Parameters

### `--clusters-only` (optional)
Only run cluster detection — skip bridge search and issue filing.

### `--file-issues` (optional)
Auto-file gap issues for each disconnected cluster pair.

### `--search-bridges` (optional)
Search external databases for papers that could bridge disconnected clusters.

### `--min-cluster-size N` (optional)
Minimum papers in a cluster to report. Default: 2.

### `--format` (optional)
Output format: `full` (default), `summary`, or `json`.

## Execution Flow

### Phase 1: Build Citation Graph

1. Read the citation-network index (from `/corpus-index-build --graph citation-network`)
   - If stale or missing: run `/corpus-index-build --graph citation-network` first
2. Build an adjacency list from outgoing + incoming edges
3. Treat as undirected for cluster detection (A cites B ≡ A connected to B)

### Phase 2: Connected Components (BFS)

Run BFS/connected-components on the undirected citation graph:

1. Initialize: all nodes unvisited
2. For each unvisited node: BFS to find its connected component
3. Collect components sorted by size (largest first)

**Output**:
```
Connected Components: 9

Cluster 1: "Agentic Workflows" (124 papers)
  Hub: REF-016 (34 connections)
  Topics: agentic-workflows, multi-agent, orchestration
  Sample: REF-001, REF-016, REF-024, REF-121 ...

Cluster 2: "GUI Agents" (31 papers)
  Hub: REF-198 (12 connections)
  Topics: gui-agents, web-agents, screen-understanding
  Sample: REF-198, REF-201, REF-215 ...

...

Cluster 9: "Isolated" (3 papers)
  No hub (all degree 1)
  REF-299, REF-312, REF-350
```

### Phase 3: Gap Analysis

For each pair of clusters, assess the gap:

1. **Topic overlap** — do the clusters share any tags?
2. **Temporal overlap** — do they cover the same years?
3. **Author overlap** — do any authors appear in both clusters?
4. **Bridgeability** — could a single paper connect them?

Prioritize gaps by:
- **Size product** — larger clusters disconnected = higher priority
- **Topic proximity** — clusters with related but not identical topics
- **Recency** — newer clusters may simply be missing recent cross-citations

**Output**:
```
Gap Analysis: 12 cluster pairs

Priority 1: "Agentic Workflows" ↔ "GUI Agents"
  Gap: 124 × 31 = 3,844 (size product)
  Topic overlap: agent, llm (2 shared tags)
  Bridge opportunity: HIGH
  Suggested search: "LLM agent GUI interaction orchestration"

Priority 2: "Evaluation" ↔ "Reproducibility"
  Gap: 45 × 28 = 1,260
  Topic overlap: evaluation, benchmark (2 shared tags)
  Bridge opportunity: MEDIUM
  Suggested search: "reproducible LLM evaluation benchmarks"
...
```

### Phase 4: Bridge Search (if --search-bridges)

For each high-priority gap:

1. Generate search queries from cluster topic overlap
2. Search external databases (Semantic Scholar, arXiv, Google Scholar)
3. Filter candidates by:
   - Cites papers from BOTH clusters
   - Published in overlapping time range
   - High citation count (likely to be connecting work)
4. Rank candidates by bridge potential

**Output**:
```
Bridge Candidates Found: 8

For gap "Agentic Workflows" ↔ "GUI Agents":
  1. "WebAgent: World-Centric Web Navigation" (2024)
     Cites: REF-016 (Cluster 1), REF-198 (Cluster 2)
     Citations: 87
     Bridge potential: HIGH

  2. "Agent-E: Vision-Language Planning for Web Tasks" (2024)
     Cites: REF-024 (Cluster 1), REF-201 (Cluster 2)
     Citations: 45
     Bridge potential: MEDIUM
```

### Phase 5: File Issues (if --file-issues)

For each gap with bridge candidates, file a research induction issue:

```markdown
## Research Gap: [Cluster A] ↔ [Cluster B]

**Gap Size**: [N × M papers disconnected]
**Bridge Candidates**: [list]
**Suggested Action**: Induct [top candidate] to connect clusters

### Bridge Papers to Induct
- [ ] "WebAgent: World-Centric Web Navigation" — arxiv:2401.XXXXX
- [ ] "Agent-E: Vision-Language Planning" — arxiv:2403.XXXXX
```

### Phase 6: Report

```
Research Gap Detection
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━

Graph: 372 nodes, 1,247 edges
Connected components: 9
Largest cluster: 124 papers ("Agentic Workflows")
Isolated papers: 3

Gap analysis: 12 cluster pairs
  HIGH priority: 4 (bridge candidates available)
  MEDIUM priority: 5
  LOW priority: 3

Bridge candidates found: 8 papers
Issues filed: 4
Papers recommended for induction: 8
```

## Distinction from research-gap

| Tool | Approach | Output |
|------|----------|--------|
| `research-gap` | **Intellectual** — topic coverage, missing areas, GRADE gaps | Gap report with search queries |
| `research-gap-detect` | **Structural** — citation graph topology, disconnected components | Cluster map, bridge candidates, filed issues |

`research-gap` answers "what topics are we missing?" while `research-gap-detect` answers "which existing papers don't cite each other but should?"

## Examples

```bash
# Full analysis with bridge search
/research-gap-detect --search-bridges

# Just show clusters
/research-gap-detect --clusters-only

# Detect and auto-file issues
/research-gap-detect --file-issues

# Combined: search + file
/research-gap-detect --search-bridges --file-issues

# JSON for visualization
/research-gap-detect --format json
```

## References

- @$AIWG_ROOT/agentic/code/frameworks/research-complete/skills/corpus-index-build/SKILL.md — Builds the citation-network graph
- @$AIWG_ROOT/agentic/code/frameworks/research-complete/skills/citation-backfill/SKILL.md — Prerequisite: complete bidirectional edges
- @$AIWG_ROOT/agentic/code/frameworks/research-complete/skills/research-gap/SKILL.md — Complementary intellectual gap analysis
- @$AIWG_ROOT/agentic/code/frameworks/research-complete/skills/induct-research/SKILL.md — Inducts bridge candidates


---
Source attribution: jmagly
Original project: https://github.com/jmagly/aiwg/blob/bc0cd4d707708593ef15781cb9d38364ea29bdd5/agentic/code/frameworks/research-complete/skills/research-gap-detect/SKILL.md
License: MIT
License information: https://opensource.org/license/mit
Original upstream instructions; downloaded from Mega AI Hub.

## Upstream license notice

MIT License

Copyright (c) 2024 Joe Magly

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.



# Mega AI Hub resource metadata

Creator / publisher: jmagly
Original project: https://github.com/jmagly/aiwg/blob/bc0cd4d707708593ef15781cb9d38364ea29bdd5/agentic/code/frameworks/research-complete/skills/research-gap-detect/SKILL.md
Attribution basis: Source repository record

Fields of work: Data & Analytics, Education & Research
Roles: Data Analyst, Market Research Analyst, Researcher
Specialties: API
Tools: Semantic Scholar
Country applicability: Country not specified
Classification basis: Source catalog labels
Instruction SHA-256: ebae86a68820ae1cb5c8d3f8981c0cc4d2a9261538601559aa8dd128251e2ec3