Predicting AP-MALDI response using Machine Learning

The trained models and predictions can be found in the training_results/paper_results folder.

How to Install

• conda create --name apMALDIresponseEnv python=3.8
• conda activate apMALDIresponseEnv
• pip install -r requirements.txt
• python setup.py install

Predicting AP-MALDI response for custom molecules

Follow the instructions in the notebook predict_intensities.ipynb to predict AP-MALDI response on your custom set of molecules.

Reproducing paper results

To reproduce the paper results, follow these steps:

• Retrain the models by running python train_models.py --exp_name <YOUR_NEW_EXPERIMENT_NAME>
• After training is done, models and predictions can be found in the training_results/YOUR_NEW_EXPERIMENT_NAME folder
• To compute scores and make plots, use the evaluate_trained_models.ipynb notebook