| Usage | |
| ===== | |
| Quick Start | |
| ~~~~~~~~~~~ | |
| Predict a new network using a trained model | |
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| Pre-trained models can be downloaded from [TBD]. | |
| Candidate pairs should be in tab-separated (``.tsv``) format with no header, and columns for [protein name 1], [protein name 2]. | |
| Optionally, a third column with [label] can be provided, so predictions can be made using training or test data files (but the label will not affect the predictions). | |
| .. code-block:: bash | |
| dscript predict --pairs [input data] --seqs [sequences, .fasta format] --model [model file] | |
| Embed sequences with language model | |
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| Sequences should be in ``.fasta`` format. | |
| .. code-block:: bash | |
| dscript embed --seqs [sequences] --outfile [embedding file] | |
| Train and save a model | |
| ^^^^^^^^^^^^^^^^^^^^^^ | |
| Training and validation data should be in tab-separated (``.tsv``) format with no header, and columns for [protein name 1], [protein name 2], [label]. | |
| .. code-block:: bash | |
| dscript train --train [training data] --val [validation data] --embedding [embedding file] --save-prefix [prefix] | |
| Evaluate a trained model | |
| ^^^^^^^^^^^^^^^^^^^^^^^^ | |
| .. code-block:: bash | |
| dscript eval --model [model file] --test [test data] --embedding [embedding file] --outfile [result file] | |
| Prediction | |
| ~~~~~~~~~~ | |
| .. code-block:: bash | |
| usage: dscript predict [-h] --pairs PAIRS --model MODEL [--seqs SEQS] | |
| [--embeddings EMBEDDINGS] [-o OUTFILE] [-d DEVICE] | |
| [--thresh THRESH] | |
| Make new predictions with a pre-trained model. One of --seqs and --embeddings is required. | |
| optional arguments: | |
| -h, --help show this help message and exit | |
| --pairs PAIRS Candidate protein pairs to predict | |
| --model MODEL Pretrained Model | |
| --seqs SEQS Protein sequences in .fasta format | |
| --embeddings EMBEDDINGS | |
| h5 file with embedded sequences | |
| -o OUTFILE, --outfile OUTFILE | |
| File for predictions | |
| -d DEVICE, --device DEVICE | |
| Compute device to use | |
| --thresh THRESH Positive prediction threshold - used to store contact | |
| maps and predictions in a separate file. [default: | |
| 0.5] | |
| Embedding | |
| ~~~~~~~~~ | |
| .. code-block:: bash | |
| usage: dscript embed [-h] --seqs SEQS --outfile OUTFILE [-d DEVICE] | |
| Generate new embeddings using pre-trained language model | |
| optional arguments: | |
| -h, --help show this help message and exit | |
| --seqs SEQS Sequences to be embedded | |
| --outfile OUTFILE h5 file to write results | |
| -d DEVICE, --device DEVICE | |
| Compute device to use | |
| Training | |
| ~~~~~~~~ | |
| .. code-block:: bash | |
| usage: dscript train [-h] --train TRAIN --val VAL --embedding EMBEDDING | |
| [--augment] [--projection-dim PROJECTION_DIM] | |
| [--dropout-p DROPOUT_P] [--hidden-dim HIDDEN_DIM] | |
| [--kernel-width KERNEL_WIDTH] [--use-w] | |
| [--pool-width POOL_WIDTH] | |
| [--negative-ratio NEGATIVE_RATIO] | |
| [--epoch-scale EPOCH_SCALE] [--num-epochs NUM_EPOCHS] | |
| [--batch-size BATCH_SIZE] [--weight-decay WEIGHT_DECAY] | |
| [--lr LR] [--lambda LAMBDA_] [-o OUTFILE] | |
| [--save-prefix SAVE_PREFIX] [-d DEVICE] | |
| [--checkpoint CHECKPOINT] | |
| Train a new model | |
| optional arguments: | |
| -h, --help show this help message and exit | |
| Data: | |
| --train TRAIN Training data | |
| --val VAL Validation data | |
| --embedding EMBEDDING | |
| h5 file with embedded sequences | |
| --augment Set flag to augment data by adding (B A) for all pairs | |
| (A B) | |
| Projection Module: | |
| --projection-dim PROJECTION_DIM | |
| Dimension of embedding projection layer (default: 100) | |
| --dropout-p DROPOUT_P | |
| Parameter p for embedding dropout layer (default: 0.5) | |
| Contact Module: | |
| --hidden-dim HIDDEN_DIM | |
| Number of hidden units for comparison layer in contact | |
| prediction (default: 50) | |
| --kernel-width KERNEL_WIDTH | |
| Width of convolutional filter for contact prediction | |
| (default: 7) | |
| Interaction Module: | |
| --use-w Use weight matrix in interaction prediction model | |
| --pool-width POOL_WIDTH | |
| Size of max-pool in interaction model (default: 9) | |
| Training: | |
| --negative-ratio NEGATIVE_RATIO | |
| Number of negative training samples for each positive | |
| training sample (default: 10) | |
| --epoch-scale EPOCH_SCALE | |
| Report heldout performance every this many epochs | |
| (default: 5) | |
| --num-epochs NUM_EPOCHS | |
| Number of epochs (default: 100) | |
| --batch-size BATCH_SIZE | |
| Minibatch size (default: 25) | |
| --weight-decay WEIGHT_DECAY | |
| L2 regularization (default: 0) | |
| --lr LR Learning rate (default: 0.001) | |
| --lambda LAMBDA_ Weight on the similarity objective (default: 0.35) | |
| Output and Device: | |
| -o OUTPUT, --output OUTPUT | |
| Output file path (default: stdout) | |
| --save-prefix SAVE_PREFIX | |
| Path prefix for saving models | |
| -d DEVICE, --device DEVICE | |
| Compute device to use | |
| --checkpoint CHECKPOINT | |
| Checkpoint model to start training from`` | |
| Evaluation | |
| ~~~~~~~~~~ | |
| .. code-block:: bash | |
| usage: dscript eval [-h] --model MODEL --test TEST --embedding EMBEDDING | |
| [-o OUTFILE] [-d DEVICE] | |
| Evaluate a trained model | |
| optional arguments: | |
| -h, --help show this help message and exit | |
| --model MODEL Trained prediction model | |
| --test TEST Test Data | |
| --embedding EMBEDDING | |
| h5 file with embedded sequences | |
| -o OUTFILE, --outfile OUTFILE | |
| Output file to write results | |
| -d DEVICE, --device DEVICE | |
| Compute device to use | |