Body-fluid proteins are very important because they are promising as biomarkers. This repository contains several prediction models for body-fluid protein discovery.
| Name | Description | Type | Script |
|---|---|---|---|
| SVM | Support Vector Machine | Supervised | svm.py |
| DT | Decision Tree | Supervised | dt.py |
| DNN | Deep Neural Network | Supervised | dnn.py |
| DeepSec | Deep Learning | Supervised | deepsec.py |
| MultiSec | Deep Learning + Multi-task learning | Supervised | multisec.py |
| PU-DT | DT + PU Bagging | Semi-supervised | pu-dt.py |
| PU-SVM | SVM + PU Bagging | Semi-supervised | pu-svm.py |
| MPUSec | Multi-task learning + PU Learning | Semi-supervised | mpusec.py |
Data can be downloaded from this link.
python script_name.py --folder data_dir
- Dan Shao, Lan Huang, et al. Computational Prediction of Human Body-Fluid Protein. BIBM 2019.
- Dan Shao, Lan Huang, et al. DeepSec: A Deep Learning Framework for Secreted Protein Discovery in Human Body Fluids. Bioinformatics 2021.
- Kai He, Yan Wang, et al. MultiSec: Multi-Task Deep Learning Improves Secreted Protein Discovery in Human Body Fluids. Mathematics 2022.
- Kai He, Yan Wang, et al. A Multi-task Positive-unlabeled Learning Framework to Predict Secreted Proteins in Human Body Fluids. Complex & Intelligent Systems 2023.
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