scholar-agent

Scholar Agent

End-to-end automation: paper discovery → filtering → deep reading → feedback.

Two modes:

• Basic Mode: Pure CLI — fetch, filter, rate papers via REST API (no browser needed)
• Enhanced Mode: CLI + NotebookLM — deep-read papers with source-grounded answers from Gemini

Subcommands

Command	Description
/scholar-inbox	Today's papers → AI filtering → add to NotebookLM → deep read → report
/scholar-inbox <arXiv ID>	Add specific paper to NotebookLM and read
/scholar-inbox ask "question"	Ask NotebookLM paper library a question
/scholar-inbox like 1,3,5	Upvote papers by report index

Prerequisites

Dependency	Purpose	Install
playwright-cli	Scholar Inbox browser login	npm install -g @anthropic-ai/playwright-cli
notebooklm-py	NotebookLM API (notebooks, sources, chat)	pipx install "notebooklm-py[browser]"

• Basic Mode only requires playwright-cli (for Scholar Inbox login)
• Enhanced Mode additionally requires notebooklm-py with Google auth completed (notebooklm login)

Why notebooklm-py?

Scholar Agent 的深度阅读功能通过 notebooklm CLI 实现：自动创建笔记本、批量添加 arXiv 论文为 source、查询 Gemini 获取 source-grounded 回答。notebooklm-py 使用 Google 内部 RPC API（非浏览器自动化），稳定性远高于 DOM 操作。

安装 notebooklm-py 后，你也可以独立使用它管理任意 NotebookLM 笔记本（不限于论文）：

notebooklm list                                    # 列出所有笔记本
notebooklm use <id>                                # 选择笔记本
notebooklm source add "https://arxiv.org/abs/..."  # 添加 source
notebooklm ask "summarize the key findings"        # 提问

Setup

One-click environment check and login:

PYTHONPATH=<skill-path> python3 -m scholar_inbox setup

Checks: Python → playwright-cli → Scholar Inbox login → notebooklm CLI

Manual install steps:

# 1. Scholar Inbox browser login (required)
npm install -g @anthropic-ai/playwright-cli

# 2. NotebookLM API (required for Enhanced Mode)
pipx install "notebooklm-py[browser]"

# 3. NotebookLM Google login (first time only — opens browser)
notebooklm login

Filtering Configuration

Config files at ~/.config/scholar-inbox/:

File	Purpose
context.md	Global preferences (research interests, institution tiers, daily limit, etc.)
<project>.md	Project-level config (keyword filters + NotebookLM classification rules)

When /scholar-inbox is invoked, the corresponding project config is loaded based on the current working directory name. If a project config exists, papers are filtered by keywords and institution tiers, and classified into NotebookLM notebooks according to the rules.

First-Time Setup

On first /scholar-inbox invocation, check if ~/.config/scholar-inbox/context.md exists:

• Exists → Load config, proceed to normal flow
• Missing → Interactively collect preferences via AskUserQuestion, then generate config

Round 1: Research Preferences (ask 3 questions simultaneously)

1. Research Interests

   • header: "Research interest keywords"
   • options: "RL, VLM, visual reasoning" / "NLP, LLM, alignment" / Other (custom)
   • preview: Used for relevance ranking during paper filtering\nExample: "reinforcement learning, vision-language model, tool use"

2. Institution Preference

   • header: "Institution tiering"
   • options: "Tier-aware (top > well-known > other)" / "No preference"
   • preview: When enabled: OpenAI/DeepMind/META etc. shown first

3. Daily Paper Count

   • header: "Papers per day"
   • options: "5" / "10" / "15"

Round 2: Classification + Project (ask 2 questions simultaneously)

4. NotebookLM Classification

   • header: "Notebook classification dimension"
   • options: "Auto-classify by research topic" / "By method type (RL / SFT / Data / Eval)" / "All in one notebook"

5. Project-Level Config

   • header: "Enable project-level filtering?"
   • options: "Yes (only show project-relevant papers in specific project directories)" / "No"
   • If "Yes", follow up with the current project's core keywords

Config Generation

Based on user answers, generate ~/.config/scholar-inbox/context.md:

# Scholar Inbox Global Config

## Research Interests
keywords: RL, VLM, visual reasoning, tool use

## Filtering Preferences
daily_limit: 10
institution_tier: true  # whether to tier institutions

## NotebookLM Classification
mode: auto_topic  # auto_topic / method_type / single_notebook

If project-level config is enabled, also generate ~/.config/scholar-inbox/<project>.md:

# <project> Project Config

## Project Keywords
keywords: agentic reasoning, image editing, multi-turn tool use

## Filtering Rules
Only show papers matching project keywords; demote others but don't hide them.

Config files can be manually edited afterwards.

CLI Quick Reference

Running the CLI: If scholar-inbox is not on PATH:

PYTHONPATH=<skill-path> python3 -m scholar_inbox <command>

Command	Description
scholar-inbox setup	One-click environment check + login
scholar-inbox doctor	Diagnose NotebookLM/auth/profile/script issues
scholar-inbox doctor --online	Open Scholar Inbox / NotebookLM pages and verify live page state
scholar-inbox status	Check login status
scholar-inbox login [--browser] [--cookie VAL]	Authenticate
scholar-inbox digest [--limit N] [--min-score F] [--json]	Today's papers
scholar-inbox paper ID	Paper details + AI summaries
scholar-inbox rate ID up/down/reset	Rate a paper
scholar-inbox rate-batch RATING ID...	Batch rate
scholar-inbox trending [--category CAT --days N]	Trending papers
scholar-inbox collections	List collections
scholar-inbox collect ID COLLECTION	Add to collection
scholar-inbox config set interests "RL, VLM, ..."	Set research interests

Authentication

Session cookie stored at ~/.config/scholar-inbox/session.json (~7 day expiry).

scholar-inbox login              # auto-extract from Playwright profile
scholar-inbox login --browser    # open browser, auto-extract cookie on login
scholar-inbox login --cookie VAL # manual paste from DevTools
scholar-inbox status             # check if session is valid

Execution Flow

Mode 1: /scholar-inbox (Daily Paper Filtering + Reading)

Phase A: Collect + Filter + Ingest [Dispatch Subagent in Background]

Dispatch a subagent with incremental output — subagent must write results to a temp file after each step, so partial work survives if killed.

Subagent prompt must include:

将每一步的结果增量写入 /tmp/scholar_inbox_results.json。
每处理完一篇论文就更新文件，确保文件随时是有效 JSON。
格式：{"papers": [...], "status": "in_progress|done", "last_updated": "ISO8601"}

Step A1: Fetch Papers from Scholar Inbox (REST API)

scholar-inbox digest --json --limit 20
scholar-inbox config  # get user's research interests

Step A2: AI Filtering

Filter top 5-10 most relevant papers based on user's research interests. Skip already-rated/read papers. If interests are not configured, sort by score and take top 10.

Step A3: Dynamic Classification

Auto-classify papers into NotebookLM notebooks based on title and keywords. Category names are dynamically generated from paper content — no hardcoded categories.

Each category maps to a NotebookLM notebook. Search for existing notebooks:

notebooklm list  # list all notebooks, find matching one by title

If no matching notebook exists, auto-create one:

notebooklm create "<topic>"
# Note the notebook ID from output, then set as active:
notebooklm use <notebook_id>

Step A4: Batch Add Sources to NotebookLM

Add arXiv URLs as sources to the target notebook:

notebooklm use <notebook_id>
notebooklm source add "https://arxiv.org/abs/XXXX.XXXXX"
notebooklm source add "https://arxiv.org/abs/YYYY.YYYYY"
# ... repeat for each paper

Check source status before querying (ensure status is "ready"):

notebooklm source list  # check all sources are "ready" before asking questions

Subagent returns: filtered paper list + classifications + ingestion status

If subagent is killed: Read /tmp/scholar_inbox_results.json for partial results. Continue from where it stopped — don't restart from scratch.

Phase B: Deep Reading [Main Context]

After receiving the paper list from the subagent, query NotebookLM:

notebooklm use <notebook_id>

# Overview
notebooklm ask "Summarize each paper's core contribution (2-3 sentences), label with paper title"

# Method comparison
notebooklm ask "Compare the methodological innovations, technical approaches, and baselines across papers"

# Relevance to user's research
notebooklm ask "How do these papers relate to [user interests]? Which findings are most actionable?"

Follow-up is important: Each notebooklm ask continues the conversation by default. If the answer is incomplete or raises new questions, keep asking. Use --new to start a fresh conversation.

Phase C: Output Reading Report

## YYYY-MM-DD Paper Reading Report (N new papers)

### Category: RL Reward Design

#### 1. Paper Title | Author et al. (Institution)
- **Paper ID**: 4626954 | **Score**: 0.880
- **arXiv**: https://arxiv.org/abs/XXXX.XXXXX
- **Key Findings**: [from NotebookLM, with citation]
- **Method**: [key technical details]
- **Project Relevance**: [how it connects to user's work]

#### 2. ...

---
Upvote: `/scholar-inbox like 1,3`
Downvote: `scholar-inbox rate-batch down <id1> <id2>`

Mode 2: /scholar-inbox <arXiv ID>

1. Fetch paper info with scholar-inbox paper <id> (if paper_id)
2. Dynamically classify into the appropriate notebook by title keywords
3. Add arXiv URL: notebooklm use <notebook_id> && notebooklm source add "https://arxiv.org/abs/XXXX.XXXXX"
4. Wait for indexing: notebooklm source wait
5. Deep-read: notebooklm ask "Summarize this paper's core contribution, method, and key findings"
6. Output single-paper reading report

Mode 3: /scholar-inbox ask "question"

Directly query NotebookLM:

notebooklm ask "question"  # uses current notebook context
# or specify notebook:
notebooklm ask -n <notebook_id> "question"

If no notebook is active, use notebooklm use <id> first or pass -n.

Mode 4: /scholar-inbox like 1,3,5

Extract paper_ids from the most recent reading report by index, then batch upvote via REST API:

scholar-inbox rate-batch up <id1> <id2> <id3>

Basic Mode (No NotebookLM)

For quick browsing when deep reading isn't needed:

scholar-inbox digest --limit 10          # today's paper list
scholar-inbox digest --min-score 0.8     # high-score papers
scholar-inbox paper <id>                 # paper details (with Scholar Inbox AI summary)
scholar-inbox trending --days 7          # trending in past 7 days
scholar-inbox rate <id> up               # upvote
scholar-inbox rate-batch down 111 222    # batch downvote

When displaying papers: Show title, paper_id, score, keywords, one-line contribution, arXiv link.

Notebook Lifecycle

• Notebooks accumulate knowledge across sessions — papers added today can be queried tomorrow
• Source limit: 50/notebook. Check with notebooklm source list. At 40+, warn user; at 50, create "Topic v2"
• Process at most 10 new papers per run

Resilient Parallel Research

当需要多 agent 并行调研（如文献综述、领域调研）时，遵循以下模式防止全军覆没：

1. 最多 2-3 个并行 agent，不要 5+（越多越容易被 kill）
2. 每个 agent 必须增量写文件：/tmp/research_{agent_name}.md，每处理完一个 source 就更新
3. 文件随时可用：写入的 markdown 必须是完整的（不是半截 JSON），即使中断也能直接读
4. merge step 兼容 partial：最终合并时读所有 /tmp/research_*.md，有多少用多少
5. 记录缺口：如果某个 agent 没产出，在报告中标注"未覆盖：XXX 方向"

示例 agent prompt：

研究 [方向]。每分析完一篇论文，立即追加到 /tmp/research_[方向].md。
文件格式：每篇论文一个 ## 标题，包含要点和相关性评估。
确保文件随时是完整可读的 markdown。

Constraints

Rule	Reason
REST API over DOM scraping	More stable, no SPA dependency
Dynamic classification, no hardcoded categories	Hardcoded categories go stale
Use notebooklm CLI for all NotebookLM operations	RPC API is more stable than browser DOM automation
Follow up on NotebookLM answers	First answer is often incomplete

Verified Behaviors

The following have been verified in production:

• scholar-inbox status / digest / paper / rate / trending / collections
• scholar-inbox doctor --online
• notebooklm list / create / use / ask
• notebooklm source add <url> (single + batch)
• notebooklm auth check --test

Still recommended to test:

• scholar-inbox rate-batch
• scholar-inbox collect
• Larger batch NotebookLM source imports (10+ papers)
• NotebookLM multi-turn follow-up conversations

Error Handling

Error	Action
notebooklm not installed	pipx install "notebooklm-py[browser]" or fall back to Basic Mode
NotebookLM auth expired	notebooklm login (opens browser for Google login)
Source addition failed	Skip that paper, continue with the rest
NotebookLM rate limit	Fall back to Basic Mode
Scholar Inbox session expired	scholar-inbox login --browser to re-login

Run diagnostics:

scholar-inbox doctor              # Scholar Inbox login + basic checks
notebooklm auth check --test      # NotebookLM auth + cookie health

When to Use Browser Instead

• Scholar Maps — interactive visualization
• Full PDF inline — scholar-inbox.com's PDF viewer