--- a/README.md +++ b/README.md @@ -1,60 +1,60 @@ -# About DeepDTA: deep drug-target binding affinity prediction - -The approach used in this work is the modeling of protein sequences and compound 1D representations (SMILES) with convolutional neural networks (CNNs) to predict the binding affinity value of drug-target pairs. - - -# Installation - -## Data - -Please see the [README](https://github.com/hkmztrk/DeepDTA/blob/master/data/README.md) for detailed explanation. - -## Requirements - -You'll need to install following in order to run the codes. Refer to [deepdta.yml](https://github.com/hkmztrk/DeepDTA/blob/master/deepdta.yml) for a conda environment tested in Linux. - -* [Python 3.4 <=](https://www.python.org/downloads/) -* [Keras 2.x](https://pypi.org/project/Keras/) -* [Tensorflow 1.x](https://www.tensorflow.org/install/) -* numpy -* matplotlib -* scikit-learn - - - -You have to place "data" folder under "source" directory. - -# Usage -``` -python run_experiments.py --num_windows 32 \ - --seq_window_lengths 8 12 \ - --smi_window_lengths 4 8 \ - --batch_size 256 \ - --num_epoch 100 \ - --max_seq_len 1000 \ - --max_smi_len 100 \ - --dataset_path 'data/kiba/' \ - --problem_type 1 \ - --log_dir 'logs/' - - -``` - - - - - -**For citation:** - -``` -@article{ozturk2018deepdta, - title={DeepDTA: deep drug--target binding affinity prediction}, - author={{\"O}zt{\"u}rk, Hakime and {\"O}zg{\"u}r, Arzucan and Ozkirimli, Elif}, - journal={Bioinformatics}, - volume={34}, - number={17}, - pages={i821--i829}, - year={2018}, - publisher={Oxford University Press} -} -``` +# About DeepDTA: deep drug-target binding affinity prediction + +The approach used in this work is the modeling of protein sequences and compound 1D representations (SMILES) with convolutional neural networks (CNNs) to predict the binding affinity value of drug-target pairs. + + +# Installation + +## Data + +Please see the [README](https://github.com/hkmztrk/DeepDTA/blob/master/data/README.md) for detailed explanation. + +## Requirements + +You'll need to install following in order to run the codes. Refer to [deepdta.yml](https://github.com/hkmztrk/DeepDTA/blob/master/deepdta.yml) for a conda environment tested in Linux. + +* [Python 3.4 <=](https://www.python.org/downloads/) +* [Keras 2.x](https://pypi.org/project/Keras/) +* [Tensorflow 1.x](https://www.tensorflow.org/install/) +* numpy +* matplotlib +* scikit-learn + + + +You have to place "data" folder under "source" directory. + +# Usage +``` +python run_experiments.py --num_windows 32 \ + --seq_window_lengths 8 12 \ + --smi_window_lengths 4 8 \ + --batch_size 256 \ + --num_epoch 100 \ + --max_seq_len 1000 \ + --max_smi_len 100 \ + --dataset_path 'data/kiba/' \ + --problem_type 1 \ + --log_dir 'logs/' + + +``` + + + + + +**For citation:** + +``` +@article{ozturk2018deepdta, + title={DeepDTA: deep drug--target binding affinity prediction}, + author={{\"O}zt{\"u}rk, Hakime and {\"O}zg{\"u}r, Arzucan and Ozkirimli, Elif}, + journal={Bioinformatics}, + volume={34}, + number={17}, + pages={i821--i829}, + year={2018}, + publisher={Oxford University Press} +} +```