bacteria-SANet

Source code and demos for "Scale-adaptive Deep Model for Bacterial Raman Spectra Identification"

Requirements

• Python 3.7.7
• Pytorch 1.7.0
• torchvision 0.8.1
• Numpy 1.18.5
• Scikit-learn 0.23.1
• Matplotlib 3.2.2
• Jupyter 6.2.0
• Seaborn 0.10.1
• tqdm 4.46.1

Model

The detail of the model can be found in model.py

Data

The data for the demos can be downloaded here and should be saved in the data directory.

• wavenumbers.npy : The wavenumbers of all spectra.
• X_reference.npy,y_refence.npy : reference spectra and their isolate-level labels.
• X_finetune.npy,y_finetune.npy : spectra used for finetuning and their isolate-level labels.
• X_test.npy,y_test.npy : spectra used for testing and their isolate-level labels.
• X_2018clinical.npy,y_2018clinical.npy,X_2019clinical.npy,y_2019clinical.npy : clinical spectra and their antibiotic-level labels.