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Thesis: NetSurfP 3.0 Protein secondary structure and relative solvent accessibility

The repository contains the source code for the updated version of NetSurfP, which replaces HMM profiles with embeddings, from the pretrained model ESM-1b. The previous version of NetSurfP 2.0 is written with the Keras framework. Wheras the updated version works with the PyTorch framework.

Table of Contents

Folder Structure

nsp3/
│
├── nsp3/
│    │
│    ├── logging.yml - logging configuration
│    ├── cli.py - command line interface
│    ├── main.py - main script to start train/test
│    │
│    ├── base/ - abstract base classes
│    │
│    ├── data_loader/ - anything about data loading goes here
│    │
│    ├── embeddings/ - folder containing the ESM1b model
│    │
│    ├── models/ - models, losses, and metrics
│    │
│    ├── experiments/ - directory for storing configuration files
│    │
│    ├── trainer/ - trainers
│    │
│    ├── eval/ - evaluators
│    │
│    ├── predict/ - predictors
│    │
│    └── utils/ - utilities for logging and tensorboard visualization
│
├── nsp2/* - Previous version of netsurfp (Keras framework)
│
├── data/ - directory for storing input data
│
├── study/ - directory for storing optuna studies
│
├── models/ - directory for storing pre-trained models
│
├── notebooks/ - directory for storing notebooks used for prototyping
│
├── saved/ - directory for checkpoints and logs
│
├── biolib/ - directory for deploying to biolib
│
├── sh/ - directory for running code on computerome
│
└── tests/ - tests folder

Usage

Start by creating an enviroment to install the project requirements .. code-block:

$ conda env create --file environment.yml
$ conda activate nsp3

Now you can either use the package out of the box

$ cd nsp3
$ python setup.py install

Or develop further the project. This will create a symbolic link to the package. Changes to the source code will be automatically applied.

$ python setup.py develop

Training a model based on a experiment configuration (includes evaluating in the end with best model)

$ nsp3 train -c experiments/config.yml

Predicting, which uses a model, its configuration and a predictor class .. code-block:

$ nsp3 predict -c config.yml -d model.pth -p "SecondaryFeatures" -i example_input.txt

Config file format

Config files are in .yml format:

name: CNNbLSTM
save_dir: saved/nsp3/CNNbLSTM/
seed: 1234
target_devices: [0]

arch:
  type: CNNbLSTM_ESM1b_Complete
  args:
    init_n_channels: 1280
    out_channels: 32
    cnn_layers: 2
    kernel_size: [129, 257]
    padding: [64, 128]
    n_hidden: 1024
    dropout: 0.5
    lstm_layers: 2
    embedding_args:
      arch: roberta_large
      dropout: 0.0
      attention_dropout: 0.0
      activation_dropout: 0.0
      ffn_embed_dim: 5120
      layers: 33
      attention_heads: 20
      embed_dim: 1280
      max_positions: 1024
      learned_pos: true
      activation_fn: gelu
      use_bert_init: true
      normalize_before: true
      preact_normalize: true
      normalize_after: true
      token_dropout: true
      no_seed_provided: false
      pooler_activation_fn: 'tanh'
      pooler_dropout: 0.0
      checkpoint_transformer_block: false
      untie_weights_roberta: false
    embedding_pretrained: "../models/esm1b_t33_650M_UR50S.pt"

data_loader:
  type: NSPDataLoader
  args:
    train_path: [../data/nsp2/training_data/Train_HHblits_small.npz]
    test_path: [../data/nsp2/training_data/CASP12_HHblits.npz,
                ../data/nsp2/training_data/CB513_HHblits.npz,
                ../data/nsp2/training_data/TS115_HHblits.npz]
    dataset_loader: NSPDataOnlyEncoding
    batch_size: 15
    nworkers: 2
    shuffle: true
    validation_split: 0.05

loss: multi_task_loss

metrics:
  metric_ss8: 0
  metric_ss3: 1
  metric_dis_mcc: 2
  metric_dis_fpr: 2
  metric_rsa: 3
  metric_asa: 3
  metric_phi: 4
  metric_psi: 5

optimizer:
  type: Adam
  args:
    lr: 0.0005
    weight_decay: 0

lr_scheduler:
  type: null

training:
  early_stop: 3
  epochs: 100
  monitor: min val_loss
  save_period: 1
  tensorboard: true

Add addional configurations if you need.

Using config files

Modify the configurations in .yml config files, then run:

$ nsp3 train -c experiments/<config>.yml

Resuming from checkpoints

You can resume from a previously saved checkpoint by:

nsp3 train -c experiments/<config>.yml -r path/to/checkpoint

Checkpoints

You can specify the name of the training session in config files:

"name": "CNNbLSTM"

The checkpoints will be saved in save_dir/name/timestamp/checkpoint_epoch_n, with timestamp in mmdd_HHMMSS format.

A copy of config file will be saved in the same folder.

Note: checkpoints contain:

checkpoint = {
  'arch': arch,
  'epoch': epoch,
  'state_dict': self.model.state_dict(),
  'optimizer': self.optimizer.state_dict(),
  'monitor_best': self.mnt_best,
  'config': self.config
}

Tensorboard Visualization

This template supports https://pytorch.org/docs/stable/tensorboard.html visualization.

  1. Run training

    Set tensorboard option in config file true.

  2. Open tensorboard server

    Type tensorboard --logdir saved/runs/ at the project root, then server will open at http://localhost:6006

By default, values of loss and metrics specified in config file, input images, and histogram of model parameters will be logged. If you need more visualizations, use add_scalar('tag', data), add_image('tag', image), etc in the trainer._train_epoch method. add_something() methods in this template are basically wrappers for those of tensorboard.SummaryWriter module.

Note: You don't have to specify current steps, since TensorboardWriter class defined at logger/visualization.py will track current steps.