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Jamaludin Mohd Yusof
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Updated README to match CANDLE version output.
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‎Pilot1/UnoMT/README.md‎

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# UnoMT in Pytorch
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Multi-tasking (drug response, cell line classification, etc.) Uno Implemented in PyTorch.
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https://github.com/xduan7/UnoPytorch
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## Todos
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* More labels for the network like drug labels;
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* Dataloader hanging problem when num_workers set to more than 0;
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* Better pre-processing for drug descriptor integer features;
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* Network regularization with weight decay and/or dropout;
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* Hyper-parameter searching;
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## Prerequisites
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```
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Python 3.6.4
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PyTorch 0.4.1
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SciPy 1.1.0
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pandas 0.23.4
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Scikit-Learn 0.19.1
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urllib3 1.23
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joblib 0.12.2
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```
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The default network structure is shown below:
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<img src="https://github.com/xduan7/UnoPytorch/blob/master/images/default_network.jpg" width="100%">
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An example of the program output for training on NCI60 and valdiation on all other data sources is shown below:
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```
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python unoMT_baseline_pytorch.py --resp_val_start_epoch 2 --epochs 5
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Importing candle utils for pytorch
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Created unoMT benchmark
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Configuration file: ./unoMT_default_model.txt
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{'autoencoder_init': True,
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'cl_clf_layer_dim': 256,
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'cl_clf_lr': 0.008,
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'cl_clf_num_layers': 2,
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'cl_clf_opt': 'SGD',
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'disjoint_cells': True,
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'disjoint_drugs': False,
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'drop': 0.1,
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'drug_feature_usage': 'both',
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'drug_latent_dim': 1024,
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'drug_layer_dim': 4096,
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'drug_num_layers': 2,
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'drug_qed_activation': 'sigmoid',
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'drug_qed_layer_dim': 1024,
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'drug_qed_loss_func': 'mse',
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'drug_qed_lr': 0.01,
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'drug_qed_num_layers': 2,
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'drug_qed_opt': 'SGD',
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'drug_target_layer_dim': 1024,
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'drug_target_lr': 0.002,
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'drug_target_num_layers': 2,
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'drug_target_opt': 'SGD',
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'dscptr_nan_threshold': 0.0,
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'dscptr_scaling': 'std',
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'early_stop_patience': 5,
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'epochs': 1000,
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'gene_latent_dim': 512,
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'gene_layer_dim': 1024,
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'gene_num_layers': 2,
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'grth_scaling': 'none',
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'l2_regularization': 1e-05,
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'lr_decay_factor': 0.98,
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'max_num_batches': 1000,
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'qed_scaling': 'none',
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'resp_activation': 'none',
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'resp_layer_dim': 2048,
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'resp_loss_func': 'mse',
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'resp_lr': 1e-05,
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'resp_num_blocks': 4,
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'resp_num_layers': 2,
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'resp_num_layers_per_block': 2,
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'resp_opt': 'SGD',
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'resp_val_start_epoch': 0,
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'rnaseq_feature_usage': 'combat',
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'rnaseq_scaling': 'std',
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'rng_seed': 0,
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'save_path': 'save/unoMT',
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'solr_root': '',
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'timeout': 3600,
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'train_sources': 'NCI60',
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'trn_batch_size': 32,
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'val_batch_size': 256,
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'val_sources': ['NCI60', 'CTRP', 'GDSC', 'CCLE', 'gCSI'],
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'val_split': 0.2}
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Params:
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{'autoencoder_init': True,
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'cl_clf_layer_dim': 256,
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'cl_clf_lr': 0.008,
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'cl_clf_num_layers': 2,
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'cl_clf_opt': 'SGD',
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'datatype': <class 'numpy.float32'>,
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'disjoint_cells': True,
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'disjoint_drugs': False,
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'drop': 0.1,
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'drug_feature_usage': 'both',
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'drug_latent_dim': 1024,
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'drug_layer_dim': 4096,
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'drug_num_layers': 2,
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'drug_qed_activation': 'sigmoid',
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'drug_qed_layer_dim': 1024,
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'drug_qed_loss_func': 'mse',
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'drug_qed_lr': 0.01,
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'drug_qed_num_layers': 2,
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'drug_qed_opt': 'SGD',
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'drug_target_layer_dim': 1024,
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'drug_target_lr': 0.002,
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'drug_target_num_layers': 2,
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'drug_target_opt': 'SGD',
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'dscptr_nan_threshold': 0.0,
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'dscptr_scaling': 'std',
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'early_stop_patience': 5,
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'epochs': 5,
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'experiment_id': 'EXP000',
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'gene_latent_dim': 512,
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'gene_layer_dim': 1024,
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'gene_num_layers': 2,
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'gpus': [],
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'grth_scaling': 'none',
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'l2_regularization': 1e-05,
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'logfile': None,
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'lr_decay_factor': 0.98,
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'max_num_batches': 1000,
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'multi_gpu': False,
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'no_cuda': False,
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'output_dir': '/home/jamal/Code/ECP/CANDLE/Benchmarks/Pilot1/UnoMT/Output/EXP000/RUN000',
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'qed_scaling': 'none',
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'resp_activation': 'none',
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'resp_layer_dim': 2048,
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'resp_loss_func': 'mse',
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'resp_lr': 1e-05,
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'resp_num_blocks': 4,
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'resp_num_layers': 2,
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'resp_num_layers_per_block': 2,
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'resp_opt': 'SGD',
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'resp_val_start_epoch': 2,
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'rnaseq_feature_usage': 'combat',
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'rnaseq_scaling': 'std',
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'rng_seed': 0,
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'run_id': 'RUN000',
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'save_path': 'save/unoMT',
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'shuffle': False,
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'solr_root': '',
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'timeout': 3600,
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'train_bool': True,
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'train_sources': 'NCI60',
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'trn_batch_size': 32,
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'val_batch_size': 256,
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'val_sources': ['NCI60', 'CTRP', 'GDSC', 'CCLE', 'gCSI'],
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'val_split': 0.2,
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'verbose': None}
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Parameters initialized
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Failed to split NCI60 cells in stratified way. Splitting randomly ...
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Failed to split NCI60 cells in stratified way. Splitting randomly ...
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Failed to split CCLE cells in stratified way. Splitting randomly ...
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Failed to split CCLE drugs stratified on growth and correlation. Splitting solely on avg growth ...
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Failed to split gCSI drugs stratified on growth and correlation. Splitting solely on avg growth ...
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RespNet(
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(_RespNet__gene_encoder): Sequential(
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(dense_0): Linear(in_features=942, out_features=1024, bias=True)
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(relu_0): ReLU()
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(dense_1): Linear(in_features=1024, out_features=1024, bias=True)
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(relu_1): ReLU()
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(dense_2): Linear(in_features=1024, out_features=512, bias=True)
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)
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(_RespNet__drug_encoder): Sequential(
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(dense_0): Linear(in_features=4688, out_features=4096, bias=True)
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(relu_0): ReLU()
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(dense_1): Linear(in_features=4096, out_features=4096, bias=True)
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(relu_1): ReLU()
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(dense_2): Linear(in_features=4096, out_features=1024, bias=True)
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)
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(_RespNet__resp_net): Sequential(
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(dense_0): Linear(in_features=1537, out_features=2048, bias=True)
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(activation_0): ReLU()
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(residual_block_0): ResBlock(
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(block): Sequential(
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(res_dense_0): Linear(in_features=2048, out_features=2048, bias=True)
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(res_dropout_0): Dropout(p=0.1)
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(res_relu_0): ReLU()
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(res_dense_1): Linear(in_features=2048, out_features=2048, bias=True)
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(res_dropout_1): Dropout(p=0.1)
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)
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(activation): ReLU()
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)
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(residual_block_1): ResBlock(
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(block): Sequential(
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(res_dense_0): Linear(in_features=2048, out_features=2048, bias=True)
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(res_dropout_0): Dropout(p=0.1)
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(res_relu_0): ReLU()
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(res_dense_1): Linear(in_features=2048, out_features=2048, bias=True)
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(res_dropout_1): Dropout(p=0.1)
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)
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(activation): ReLU()
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)
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(residual_block_2): ResBlock(
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(block): Sequential(
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(res_dense_0): Linear(in_features=2048, out_features=2048, bias=True)
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(res_dropout_0): Dropout(p=0.1)
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(res_relu_0): ReLU()
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(res_dense_1): Linear(in_features=2048, out_features=2048, bias=True)
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(res_dropout_1): Dropout(p=0.1)
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)
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(activation): ReLU()
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)
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(residual_block_3): ResBlock(
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(block): Sequential(
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(res_dense_0): Linear(in_features=2048, out_features=2048, bias=True)
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(res_dropout_0): Dropout(p=0.1)
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(res_relu_0): ReLU()
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(res_dense_1): Linear(in_features=2048, out_features=2048, bias=True)
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(res_dropout_1): Dropout(p=0.1)
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)
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(activation): ReLU()
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)
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(dense_1): Linear(in_features=2048, out_features=2048, bias=True)
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(dropout_1): Dropout(p=0.1)
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(res_relu_1): ReLU()
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(dense_2): Linear(in_features=2048, out_features=2048, bias=True)
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(dropout_2): Dropout(p=0.1)
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(res_relu_2): ReLU()
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(dense_out): Linear(in_features=2048, out_features=1, bias=True)
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)
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)
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Data sizes:
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Train:
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Data set: NCI60 Size: 882873
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Validation:
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Data set: NCI60 Size: 260286
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Data set: CTRP Size: 1040021
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Data set: GDSC Size: 235812
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Data set: CCLE Size: 17510
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Data set: gCSI Size: 10323
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================================================================================
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Training Epoch 1:
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Drug Weighted QED Regression Loss: 0.022274
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Drug Response Regression Loss: 1881.89
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Epoch Running Time: 13.2 Seconds.
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================================================================================
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Training Epoch 2:
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Drug Weighted QED Regression Loss: 0.019416
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Drug Response Regression Loss: 1348.13
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Epoch Running Time: 12.9 Seconds.
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================================================================================
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Training Epoch 3:
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Drug Weighted QED Regression Loss: 0.015868
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Drug Response Regression Loss: 1123.27
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Cell Line Classification:
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Category Accuracy: 99.01%;
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Site Accuracy: 94.11%;
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Type Accuracy: 94.18%
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Drug Target Family Classification Accuracy: 44.44%
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Drug Weighted QED Regression
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MSE: 0.018845 MAE: 0.111807 R2: +0.45
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Drug Response Regression:
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NCI60 MSE: 973.04 MAE: 22.18 R2: +0.69
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CTRP MSE: 2404.64 MAE: 34.04 R2: +0.32
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GDSC MSE: 2717.81 MAE: 36.53 R2: +0.19
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CCLE MSE: 2518.47 MAE: 36.60 R2: +0.38
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gCSI MSE: 2752.33 MAE: 36.97 R2: +0.35
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Epoch Running Time: 54.6 Seconds.
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================================================================================
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Training Epoch 4:
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Drug Weighted QED Regression Loss: 0.014096
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Drug Response Regression Loss: 933.27
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Cell Line Classification:
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Category Accuracy: 99.34%;
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Site Accuracy: 96.12%;
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Type Accuracy: 96.18%
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Drug Target Family Classification Accuracy: 44.44%
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Drug Weighted QED Regression
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MSE: 0.018467 MAE: 0.110287 R2: +0.46
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Drug Response Regression:
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NCI60 MSE: 844.51 MAE: 20.41 R2: +0.73
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CTRP MSE: 2314.19 MAE: 33.76 R2: +0.35
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GDSC MSE: 2747.73 MAE: 36.65 R2: +0.18
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CCLE MSE: 2482.03 MAE: 35.89 R2: +0.39
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gCSI MSE: 2665.35 MAE: 36.27 R2: +0.37
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Epoch Running Time: 54.9 Seconds.
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================================================================================
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Training Epoch 5:
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Drug Weighted QED Regression Loss: 0.013514
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Drug Response Regression Loss: 846.06
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Cell Line Classification:
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Category Accuracy: 99.38%;
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Site Accuracy: 95.89%;
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Type Accuracy: 95.30%
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Drug Target Family Classification Accuracy: 44.44%
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Drug Weighted QED Regression
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MSE: 0.017026 MAE: 0.106697 R2: +0.50
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Drug Response Regression:
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NCI60 MSE: 835.82 MAE: 21.33 R2: +0.74
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CTRP MSE: 2653.04 MAE: 37.98 R2: +0.25
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GDSC MSE: 2892.86 MAE: 39.76 R2: +0.13
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CCLE MSE: 2412.75 MAE: 36.82 R2: +0.41
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gCSI MSE: 2888.99 MAE: 38.70 R2: +0.32
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Epoch Running Time: 55.5 Seconds.
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Program Running Time: 191.1 Seconds.
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================================================================================
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Overall Validation Results:
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Best Results from Different Models (Epochs):
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Cell Line Categories Best Accuracy: 99.375% (Epoch = 5)
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Cell Line Sites Best Accuracy: 96.118% (Epoch = 4)
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Cell Line Types Best Accuracy: 96.184% (Epoch = 4)
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Drug Target Family Best Accuracy: 44.444% (Epoch = 3)
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Drug Weighted QED Best R2 Score: +0.5034 (Epoch = 5, MSE = 0.017026, MAE = 0.106697)
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NCI60 Best R2 Score: +0.7369 (Epoch = 5, MSE = 835.82, MAE = 21.33)
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CTRP Best R2 Score: +0.3469 (Epoch = 4, MSE = 2314.19, MAE = 33.76)
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GDSC Best R2 Score: +0.1852 (Epoch = 3, MSE = 2717.81, MAE = 36.53)
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CCLE Best R2 Score: +0.4094 (Epoch = 5, MSE = 2412.75, MAE = 36.82)
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gCSI Best R2 Score: +0.3693 (Epoch = 4, MSE = 2665.35, MAE = 36.27)
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Best Results from the Same Model (Epoch = 5):
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Cell Line Categories Accuracy: 99.375%
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Cell Line Sites Accuracy: 95.888%
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Cell Line Types Accuracy: 95.296%
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Drug Target Family Accuracy: 44.444%
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Drug Weighted QED R2 Score: +0.5034 (MSE = 0.017026, MAE = 0.106697)
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NCI60 R2 Score: +0.7369 (MSE = 835.82, MAE = 21.33)
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CTRP R2 Score: +0.2513 (MSE = 2653.04, MAE = 37.98)
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GDSC R2 Score: +0.1327 (MSE = 2892.86, MAE = 39.76)
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CCLE R2 Score: +0.4094 (MSE = 2412.75, MAE = 36.82)
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gCSI R2 Score: +0.3164 (MSE = 2888.99, MAE = 38.70)
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```
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For default hyper parameters, the transfer learning matrix results are shown below:
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<p align="center">
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<img src="https://github.com/xduan7/UnoPytorch/blob/master/images/default_results.jpg" width="80%">
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</p>
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Note that the green cells represents R2 score of higher than 0.1, red cells are R2 scores lower than -0.1 and yellows are for all the values in between.

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