janweinreich / geometric-geniuses

Contribution for 24' LLM Hackathon for Applications in Materials and Chemistry

Chemical feature vectors for LLMs

Team "geometric-geniuses" Contribution for 24' LLM Hackathon for Applications in Materials and Chemistry

Video explanation

https://www.youtube.com/watch?v=WZz1pVRS4RA&t=5s

Setup

Create a new conda environment. Then install all requiered dependencies with the following command: pip install .

Running the code

Tutorial

Check out the jupyter notebook file tutorial.ipynb.

Create input data from MD17 dataset of small molecule MD trajectories

First change to the main directory

cd Feat2LLM

then

python load_data.py --do_small --n_components 10

Afterwards you will get files in the data folder with the following names:

rep_aspirin.pkl
rep_benzene.pkl
rep_ethanol.pkl

Fine-tune the model roberta-base

python roberta_finetuning.py --small True --data ethanol --rep cMBDF

Evaluate the model's performance

python eval_roberta.py --small True --data ethanol --rep cMBDF