AI for Scientific Discovery 2026 Starter Package

Important

(4/28/2026) - Instructional accounts on Grace will be deleted after Monday 5/4/2026. Please make sure to offload any data you might have stored on these accounts as you will not have access after this date. For instructions on how to download your files, see this guide from YCRC. You will want to access FileBrowser from the special link we used to access OOD.

Additionally, API keys for OpenRouter as well as enterprise access to Anthropic will be discontinued after Friday 5/22/2026.

If you would like to use ShinkaEvolve, please see instructions found in Setting up ShinkaEvolve locally. You will need to provision your own OpenRouter API key to use the notebooks in this repository. See also the ShinkaEvolve Getting Started Guide.

This repository contains tutorial material used during the Yale FDS Workshop on AI for Scientific Discovery. You will find a collection of Jupyter notebooks which use ShinkaEvolve for various tasks, as well as a collection of markdown guides that walk through various work flows involving ShinkaEvolve.

• recipes/ - This directory contains a collection of markdown guides which illustrate different ways to use ShinkaEvolve. It also contains guides on how to use ShinkaEvolve through Claude Code and how to access provisioned resources on Grace, the high performance computing cluster managed by the Yale Center for Research Computing.

• circle_packing/ - This directory contains all files related to using ShinkaEvolve to solve Circle Packing.

• komlos/ - This directory contains all files related to using ShinkaEvolve to validate a lower bound to the Komlos conjecture

• qml_unitary_learning/ - This directory contains all files related to using ShinkaEvolve to find a quantum circuit which approximates a hidden 4-qubit unitary transformation subject to connectivity constraints.

• stellar_evo/ - This directory contains all files related to using ShinkaEvolve for finding a neural network architecture which interpolates evolutionary tracks of stars.

References

References for ShinkaEvolve

• ShinkaEvolve Github repository

• ShinkaEvolve getting started instructions

• ShinkaEvolve paper

• ShinkaEvolve talk video

Stellar Evolution references

• (Hon, Li & Ong, 2024) Flow Based Generative Emulation of Grids of Stellar Evolutionary Models

• (Ying et. al., 2025) Dartmouth Stellar Evolution Emulator (DSEE) 1: Generative Stellar Evolution Model Database

• (Christensen-Dalsgaard, 2007) ASTEC -- the Aarhus STellar Evolution Code

• Official MESA Documentation

References to YCRC resources

• YCRC's Grace HPC cluster overview guide