ai scientist - chunhualiao/public-docs GitHub Wiki

information retrieval

• GAIA benchmark
• https://github.com/bin123apple/InfantAgent

• idea generation:
• conduct experiments
• write the paper
  • related work section
  • manage citations: find related work papers, create/copy bibtext entries, then cite it in the text, BibTex Manager Extension of VS Code

https://www.futurehouse.org/research-announcements/launching-futurehouse-platform-ai-agents

The ai scientist: Towards fully automated open-ended scientific discovery. arXiv preprint arXiv:2408.06292, 2024a. The AI Scientist framework generates novel research ideas, writes code, conducts experiments, and creates a full scientific paper with an automated peer-review system to evaluate the work.

• The AI Scientist: Towards Fully Automated Open-Ended Scientific Discovery
  • https://github.com/SakanaAI/AI-Scientist or https://deepwiki.com/SakanaAI/AI-Scientist
• The AI Scientist-v2: Workshop-Level Automated Scientific Discovery via Agentic Tree Search
  • https://github.com/SakanaAI/AI-Scientist-v2

AI-Researcher: Fully-Automated Scientific Discovery with LLM Agents

• github.com/HKUDS/AI-Researcher

Agent Laboratory: Using LLM Agents as Research Assistants

Researchagent: Iterative research idea generation over scientific literature with large language models. arXiv preprint arXiv:2404.07738, 2024.

• automatically generates research ideas, methods, and experiment designs, iteratively refining them through feedback from multiple reviewing agents that mirror peer discussions and leverage human-aligned evaluation criteria to improve the outputs.

SCIAgents: automating scientific discovery through multi-agent intelligent graph reasoning, Sep, 2024

• Can llms generate novel research ideas? a large-scale human study with 100+ nlp researchers. arXiv preprint arXiv:2409.04109, 2024.

Five main categories, each with specific tools mentioned in the Nature article:

1. Literature Review Tools:

   • Gemini Deep Research - Conducts in-depth searches over 30 minutes with text, figures, and proper citations
   • OpenAI Deep Research - Advanced active learning for comprehensive literature exploration
   • SciSpace - "Chat with PDF" function for deep dives into specific papers
   • Other tools mentioned: Claude, NotebookLM, PDF.ai
   • check academic literature using either Semantic Scholar or OpenAlex APIs

2. Hypothesis Generation:

   • Research Rabbit - Visualization tool that generates interconnected webs of research by topic, author, or methodology
   • Allen Institute Tools - Upcoming hypothesis generation products combining ideas across papers into novel concepts
   • Elicit - Research assistant for generating experiments based on hypotheses

3. Experimental Assistants:

   • CRESt - Copilot for Real-world Experimental Scientist - helps craft and run experiments with robotic integration
   • Scite - AI research assistant for experiment planning and literature analysis
   • ChatGPT for Troubleshooting - Helps brainstorm explanations and debug experimental issues

4. Code & Statistics Tools:

   • GitHub Copilot - AI pair programmer for coding data analysis and visualizations
   • Amazon CodeWhisperer (Amazon Q Developer) - Code generation with security scanning capabilities
   • Cursor - Editor that makes data analysis easier with visualization capabilities
   • CatalyzeX - Locates and shares existing code from published papers

5. Scientific Writing Aids:

   • Paperpal - Checks academic manuscripts against journal submission guidelines
   • Thesify - Multi-stop platform for students with focus on grant writing and paper formatting
   • SciSpace - Templates for research proposals, literature reviews, and abstracts
   • Coral AI/Quillbot/Whisper - Translation capabilities covering dozens of languages

AI tools are spotting errors in research papers: inside a growing movement, Nature, 2025

• https://www.nature.com/articles/d41586-025-00648-5