scientify 1.1.5 → 1.2.1

package/skills/idea-generation/references/idea-template.md

@@ -1,217 +1,82 @@
 # Idea Template
 
-Use this template for each idea in `~/.openclaw/workspace/ideas/`.
+Use this template for each generated idea (`$WORKSPACE/ideas/idea_N.md`).
 
----
+## Required Sections
 
-# Idea N: [Short Descriptive Title]
+```markdown
+# Idea N: [Title]
 
-## One-Line Summary
-
-[A single sentence that captures the core innovation. Should be understandable without context.]
-
----
+## One-line Summary
+[Single sentence describing the core innovation]
 
 ## Challenges Addressed
+1. [Challenge 1]
+2. [Challenge 2]
 
-What problems in the current research landscape does this idea solve?
-
-- **[Challenge 1]**: [Brief description of the technical limitation]
-- **[Challenge 2]**: [Brief description of unsolved problem]
-- **[Challenge 3]**: [Brief description of key bottleneck]
-
----
+## Existing Methods & Limitations
 
-## Existing Methods & Their Limitations
+### Method A [arXiv:XXXX.XXXXX]
+- **Approach**: [Brief description]
+- **Limitation**: [Why insufficient]
 
-| Method | Paper/Source | Strength | Weakness This Idea Addresses |
-|--------|--------------|----------|------------------------------|
-| [Method A] | [Citation] | [What it does well] | [Limitation] |
-| [Method B] | [Citation] | [What it does well] | [Limitation] |
-| [Method C] | [Citation] | [What it does well] | [Limitation] |
-
----
+### Method B [arXiv:XXXX.XXXXX]
+- **Approach**: [Brief description]
+- **Limitation**: [Why insufficient]
 
 ## Motivation
-
-### Why is this problem important?
-
-[Explain the significance of solving this problem. Who benefits? What applications are enabled?]
-
-### What gap does this fill?
-
-[Describe the specific research gap this idea addresses. Reference the limitations above.]
-
-### Potential impact
-
-[Quantify if possible: "Could improve X metric by Y%" or "Enables new application Z"]
-
----
+[Why this gap matters, what opportunity exists]
 
 ## Proposed Method
 
-### Core Insight
-
-[2-3 sentences describing the key innovation. What is the "aha" moment?]
+### Core Idea
+[Main innovation in 2-3 sentences]
 
 ### Technical Approach
+[Detailed description]
 
-**Overview:**
-
-[1 paragraph high-level description]
-
-**Step-by-step methodology:**
-
-1. **[Step 1 Name]**: [Description]
-   - Input: [what this step takes]
-   - Output: [what this step produces]
-   - Key operation: [main computation]
-
-2. **[Step 2 Name]**: [Description]
-   - Input: ...
-   - Output: ...
-   - Key operation: ...
-
-3. **[Step 3 Name]**: [Description]
-   - ...
-
-### Mathematical Formulation
-
-**Problem Setup:**
-
-Let $X \in \mathbb{R}^{n \times d}$ denote [description]...
-
-**Core Equations:**
-
-```latex
-% Main loss function
-\mathcal{L} = \mathcal{L}_{task} + \lambda \mathcal{L}_{reg}
-
-% Where task loss is:
-\mathcal{L}_{task} = ...
-
-% And regularization term is:
-\mathcal{L}_{reg} = ...
-```
-
-**Key derivations (if applicable):**
-
-[Show important mathematical steps that justify the approach]
-
-### Architecture / Algorithm
-
-```
-Algorithm: [Name]
-Input: [inputs]
-Output: [outputs]
-
-1. Initialize [parameters]
-2. For each [iteration]:
-   a. Compute [something]
-   b. Update [something]
-3. Return [result]
-```
-
-Or for neural architectures:
-
-```
-[Input] → [Layer 1] → [Layer 2] → ... → [Output]
-         (dim: ...)   (dim: ...)         (dim: ...)
-```
+### Key Equations
+$$
+\mathcal{L} = ...
+$$
 
----
+## How This Improves on Cited Papers
+| Paper | Their Limitation | Our Improvement |
+|-------|------------------|-----------------|
+| [A]   | ...              | ...             |
+| [B]   | ...              | ...             |
 
 ## Expected Advantages
-
-Why should this approach work better than existing methods?
-
-- **[Advantage 1]**: [Explanation with reasoning]
-- **[Advantage 2]**: [Explanation with reasoning]
-- **[Advantage 3]**: [Explanation with reasoning]
-
-**Theoretical justification (if applicable):**
-
-[Brief argument for why this should work]
-
----
-
-## Potential Challenges
-
-What could go wrong? How to mitigate?
-
-| Challenge | Risk Level | Mitigation Strategy |
-|-----------|------------|---------------------|
-| [Challenge 1] | High/Med/Low | [How to address] |
-| [Challenge 2] | High/Med/Low | [How to address] |
-| [Challenge 3] | High/Med/Low | [How to address] |
-
----
+1. [Advantage 1]
+2. [Advantage 2]
 
 ## Evaluation Plan
 
 ### Datasets
-
-| Dataset | Task | Size | Why Chosen |
-|---------|------|------|------------|
-| [Dataset 1] | [Task] | [Size] | [Reason] |
-| [Dataset 2] | [Task] | [Size] | [Reason] |
+- [Dataset 1]: [Why chosen]
 
 ### Baselines
-
-| Method | Paper | Why Compare |
-|--------|-------|-------------|
-| [Baseline 1] | [Citation] | [Reason] |
-| [Baseline 2] | [Citation] | [Reason] |
+- [Method from Paper A]
+- [Method from Paper B]
 
 ### Metrics
+- [Metric 1]: [What it measures]
 
-| Metric | Description | Expected Improvement |
-|--------|-------------|---------------------|
-| [Metric 1] | [What it measures] | [X% over baseline] |
-| [Metric 2] | [What it measures] | [Y% over baseline] |
-
-### Ablation Studies
-
-What components to ablate to understand contribution?
-
-1. [Component 1]: Remove/replace to test [hypothesis]
-2. [Component 2]: Remove/replace to test [hypothesis]
-
----
-
-## Scores
-
-| Criterion | Score (1-5) | Justification |
-|-----------|-------------|---------------|
-| **Novelty** | [X] | [Why this score] |
-| **Feasibility** | [X] | [Why this score] |
-| **Impact** | [X] | [Why this score] |
-| **Total** | [Sum] | |
-
----
-
-## Implementation Notes
-
-### Recommended Libraries
-
-- [Library 1]: For [purpose]
-- [Library 2]: For [purpose]
-
-### Reference Code
-
-- [Repo 1](URL): [What to reference]
-- [Repo 2](URL): [What to reference]
-
-### Estimated Effort
-
-- Model implementation: [X days]
-- Data pipeline: [X days]
-- Training & evaluation: [X days]
-- Total: [X days]
+## Scores (1-5)
+- **Novelty**: X/5 - [Justification]
+- **Feasibility**: X/5 - [Justification]
+- **Impact**: X/5 - [Justification]
+- **Total**: XX/15
+```
 
----
+## Idea Strategies
 
-## Related Ideas
+Generate 5 ideas using different strategies:
 
-- **Idea [M]**: [How it relates - could be combined? alternative approach?]
-- **Future extension**: [What could come next after this idea]
+| Idea | Strategy | Description |
+|------|----------|-------------|
+| 1 | Combination | Merge techniques from 2+ papers |
+| 2 | Simplification | Simplify complex method |
+| 3 | Generalization | Extend to new domain/task |
+| 4 | Constraint Relaxation | Remove limiting assumption |
+| 5 | Architecture Innovation | Novel model design |

package/skills/idea-generation/references/reading-long-papers.md

@@ -0,0 +1,43 @@
+# Reading Long Papers Strategy
+
+For papers >50KB or >15k tokens, use chunked reading.
+
+## Step 1: Structure Scan
+
+```bash
+ls -la $WORKSPACE/papers/{arxiv_id}/
+wc -l $WORKSPACE/papers/{arxiv_id}/*.tex
+```
+
+## Step 2: Chunked Reading
+
+Use Read tool with `offset` and `limit`:
+
+```
+Tool: Read
+Arguments:
+  file_path: "$WORKSPACE/papers/2404.04429/main.tex"
+  offset: 1
+  limit: 500    # First 500 lines
+```
+
+## Priority Sections
+
+| Priority | Section | Why |
+|----------|---------|-----|
+| 1 | Abstract | Core contribution |
+| 2 | Method | Technical details |
+| 3 | Experiments | Results |
+| 4 | Conclusion | Limitations |
+
+## Skip These
+
+- Appendix, Acknowledgments
+- Detailed hyperparameter tables
+
+## Quick Extraction
+
+```bash
+grep -n "\\\\section{" main.tex
+sed -n '/\\begin{abstract}/,/\\end{abstract}/p' main.tex
+```

package/skills/literature-survey/SKILL.md

@@ -0,0 +1,272 @@
+---
+name: literature-survey
+description: "Comprehensive literature survey (100+ papers). Searches, filters, clusters, and iterates for complete coverage. Use for: exploring new research areas, collecting papers systematically, building literature databases. NOT for: summarizing papers you have (use /write-review-paper), finding a specific paper (use arxiv_search), generating ideas (use /idea-generation)."
+metadata:
+  {
+    "openclaw":
+      {
+        "emoji": "🔍",
+      },
+  }
+---
+
+# Literature Survey
+
+Comprehensive literature discovery workflow for a research domain. This skill searches broadly, filters by relevance, clusters by direction, and iterates to ensure complete coverage.
+
+## Architecture: Isolated Sub-agent
+
+This survey runs in an **isolated sub-session** to avoid context pollution. The main session only receives the final report.
+
+```
+Main Session
+    ↓
+sessions_spawn(task: "执行文献调研...", label: "literature-survey")
+    ↓
+Sub-agent Session (隔离上下文)
+    ├── Phase 1: 生成检索词
+    ├── Phase 2: 批量检索
+    ├── Phase 3: 相关性筛选
+    ├── Phase 4: 聚类分组
+    ├── Phase 5: 迭代发现
+    └── Phase 6: 生成报告
+    ↓
+返回主 Session: 摘要 + 文件路径
+```
+
+---
+
+## When User Requests Literature Survey
+
+**Step 1: Spawn isolated sub-agent**
+
+When user says things like:
+- "调研 [topic] 领域的文献"
+- "帮我收集 [topic] 相关的论文"
+- "Survey papers on [topic]"
+
+Use `sessions_spawn` to run the survey in isolation:
+
+```
+sessions_spawn({
+  task: `你是一个文献调研专家。请为研究主题 "{TOPIC}" 执行完整的文献调研。
+
+## 调研目标
+{USER_REQUIREMENTS}
+
+## 执行流程
+
+### Phase 1: 生成检索词
+基于研究主题，生成 8-15 个检索词组合，覆盖：
+- 核心概念的不同表述
+- 相关技术方法
+- 应用场景
+- 英文和中文关键词（如适用）
+
+将检索词保存到 $WORKSPACE/survey/search_terms.json
+
+### Phase 2: 批量检索
+对每个检索词使用 arxiv_search tool：
+- max_results: 30-50 per query
+- 合并去重（按 arxiv_id）
+- 记录每篇论文的来源检索词
+
+将原始结果保存到 $WORKSPACE/survey/raw_results.json
+
+### Phase 3: 相关性筛选
+阅读每篇论文的标题和摘要，判断与 "{TOPIC}" 的相关性：
+- 5分：高度相关，直接研究此主题
+- 4分：相关，涉及关键方法或应用
+- 3分：部分相关，可作为参考
+- 2分：边缘相关
+- 1分：不相关
+
+保留 score >= 4 的论文。
+将筛选结果保存到 $WORKSPACE/survey/filtered_papers.json
+
+### Phase 4: 聚类分组
+分析筛选后论文的摘要，识别 3-6 个研究方向/子主题。
+为每个方向创建子文件夹并分配论文：
+
+$WORKSPACE/papers/
+├── {direction-1}/
+│   ├── paper_list.md
+│   └── [arxiv_ids...]
+├── {direction-2}/
+│   └── ...
+└── uncategorized/
+
+将聚类结果保存到 $WORKSPACE/survey/clusters.json
+
+### Phase 5: 迭代发现（1-2轮）
+检查高分论文的摘要，识别：
+- 提到的新方法名称
+- 引用的重要工作
+- 新的关键词
+
+如果发现新方向，补充检索并重复 Phase 2-4。
+最多迭代 2 轮。
+
+### Phase 6: 生成报告
+创建 $WORKSPACE/survey/report.md：
+
+# 文献调研报告: {TOPIC}
+
+## 调研概要
+- 检索词数量: X
+- 初始检索: Y 篇
+- 筛选后: Z 篇
+- 研究方向: N 个
+
+## 研究方向分布
+
+### 方向1: [名称]
+- 论文数量: X
+- 代表性工作: [列表]
+- 主要特点: [描述]
+
+### 方向2: [名称]
+...
+
+## 高影响力论文 (Top 10)
+| 排名 | 标题 | 年份 | 相关度 | 方向 |
+|-----|------|-----|-------|-----|
+| 1   | ... | ... | 5     | ... |
+
+## 研究趋势
+[基于论文年份分布的观察]
+
+## 发现的新方向
+[迭代中发现的额外关键词和方向]
+
+## 建议阅读顺序
+1. [入门级论文]
+2. [核心方法论文]
+3. [最新进展]
+
+---
+
+完成后，向主 session 报告：
+- 总共发现的论文数量
+- 识别的研究方向
+- 报告文件位置`,
+  label: "literature-survey-{TOPIC_SLUG}",
+  runTimeoutSeconds: 900,
+  cleanup: "keep"
+})
+```
+
+**Step 2: Wait and relay results**
+
+Sub-agent 完成后会自动 announce 结果到主 session。
+将结果摘要展示给用户，包括：
+- 发现的论文数量
+- 主要研究方向
+- 报告文件位置
+
+---
+
+## Workspace Structure
+
+```
+~/.openclaw/workspace/projects/{project-id}/
+├── project.json
+├── survey/                    # 调研过程数据
+│   ├── search_terms.json      # 检索词列表
+│   ├── raw_results.json       # 原始检索结果
+│   ├── filtered_papers.json   # 筛选后的论文
+│   ├── clusters.json          # 聚类结果
+│   ├── iterations.log         # 迭代记录
+│   └── report.md              # 最终报告
+├── papers/                    # 按方向组织的论文
+│   ├── {direction-1}/
+│   │   ├── paper_list.md
+│   │   └── 2401.12345/       # .tex 源文件
+│   ├── {direction-2}/
+│   └── uncategorized/
+└── ideas/                     # 后续 idea-generation 输出
+```
+
+---
+
+## Data Schemas
+
+### search_terms.json
+```json
+{
+  "topic": "battery life prediction",
+  "generated_at": "2024-01-15T10:00:00Z",
+  "terms": [
+    {"term": "battery remaining useful life", "category": "core"},
+    {"term": "lithium-ion degradation prediction", "category": "method"},
+    {"term": "SOH estimation neural network", "category": "technique"},
+    {"term": "EV battery health monitoring", "category": "application"}
+  ]
+}
+```
+
+### filtered_papers.json
+```json
+{
+  "filtered_at": "2024-01-15T10:30:00Z",
+  "total_raw": 245,
+  "total_filtered": 42,
+  "papers": [
+    {
+      "arxiv_id": "2401.12345",
+      "title": "...",
+      "abstract": "...",
+      "authors": ["..."],
+      "published": "2024-01-15",
+      "relevance_score": 5,
+      "source_terms": ["battery RUL", "degradation prediction"],
+      "notes": "直接研究锂电池RUL预测"
+    }
+  ]
+}
+```
+
+### clusters.json
+```json
+{
+  "clustered_at": "2024-01-15T11:00:00Z",
+  "clusters": [
+    {
+      "id": "data-driven",
+      "name": "数据驱动方法",
+      "description": "使用机器学习/深度学习的方法",
+      "paper_count": 15,
+      "paper_ids": ["2401.12345", "2401.12346", "..."],
+      "keywords": ["LSTM", "CNN", "transformer", "neural network"]
+    },
+    {
+      "id": "physics-based",
+      "name": "物理模型方法",
+      "description": "基于电化学机理的方法",
+      "paper_count": 8,
+      "paper_ids": ["..."]
+    }
+  ]
+}
+```
+
+---
+
+## Quick Mode (Without Sub-agent)
+
+For smaller surveys (< 50 papers), can run directly without spawning:
+
+User: "快速调研一下 [topic]，不超过 30 篇"
+
+→ Run Phase 1-4 directly in main session
+→ Skip iteration
+→ Generate simplified report
+
+---
+
+## Commands
+
+- "调研 [topic] 领域" → Full survey with sub-agent
+- "快速调研 [topic]" → Quick mode, 30 papers max
+- "继续上次的调研" → Resume from existing survey data
+- "扩展调研 [new direction]" → Add new search terms and iterate

package/skills/research-pipeline/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: research-pipeline
-description: "End-to-end research automation: from idea to code implementation with literature review, planning, and iterative refinement. Use arxiv, github_search, and exec tools."
+description: "End-to-end research automation: idea → literature → plan → implement → review → iterate. Use for: implementing a specific research idea, full ML research workflow. NOT for: just exploring literature (use /literature-survey), just generating ideas (use /idea-generation), just writing review (use /write-review-paper)."
 metadata:
   {
     "openclaw":