Command Line Interface (CLI)

There are two modes: oracle (review) and simulation (benchmark) mode.

Oracle mode

Start a review process in the CMD.exe or shell.

asreview oracle YOUR_DATA.csv

The available parameters are shown with the command asreview oracle --help:

usage: asreview oracle [-h] [-m MODEL] [-q QUERY_STRATEGY]
                       [-b BALANCE_STRATEGY] [--n_instances N_INSTANCES]
                       [--n_queries N_QUERIES] [-n N_PAPERS]
                       [--embedding EMBEDDING_FP] [--config_file CONFIG_FILE]
                       [-s SRC_LOG_FP]
                       [--prior_included [PRIOR_INCLUDED [PRIOR_INCLUDED ...]]]
                       [--prior_excluded [PRIOR_EXCLUDED [PRIOR_EXCLUDED ...]]]
                       [--log_file LOG_FILE] [--save_model SAVE_MODEL_FP]
                       [--verbose VERBOSE]
                       X

Automated Systematic Review (ASReview) with interaction with oracle.

The oracle modus is used to perform a systematic review with
interaction by the reviewer (the ‘oracle’ in literature on active
learning). The software presents papers to the reviewer, whereafter
the reviewer classifies them.

positional arguments:
  X                     File path to the dataset or one of the built-in datasets.

optional arguments:
  -h, --help            show this help message and exit
  -m MODEL, --model MODEL
                        The prediction model for Active Learning. Default 'lstm_pool'.
  -q QUERY_STRATEGY, --query_strategy QUERY_STRATEGY
                        The query strategy for Active Learning. Default 'rand_max'.
  -b BALANCE_STRATEGY, --balance_strategy BALANCE_STRATEGY
                        Data rebalancing strategy mainly for RNN methods. Helps against imbalanced dataset with few inclusions and many exclusions. Default 'triple_balance'
  --n_instances N_INSTANCES
                        Number of papers queried each query.Default 20.
  --n_queries N_QUERIES
                        The number of queries. By default, the program stops after all documents are reviewed or is interrupted by the user.
  -n N_PAPERS, --n_papers N_PAPERS
                        The number of papers to be reviewed. By default, the program stops after all documents are reviewed or is interrupted by the user.
  --embedding EMBEDDING_FP
                        File path of embedding matrix. Required for LSTM models.
  --config_file CONFIG_FILE
                        Configuration file with model parameters
  -s SRC_LOG_FP, --session-from-log SRC_LOG_FP
                        Continue session starting from previous log file.
  --prior_included [PRIOR_INCLUDED [PRIOR_INCLUDED ...]]
                        A list of included papers.
  --prior_excluded [PRIOR_EXCLUDED [PRIOR_EXCLUDED ...]]
                        A list of excluded papers. Optional.
  --log_file LOG_FILE, -l LOG_FILE
                        Location to store the log results.
  --save_model SAVE_MODEL_FP
                        Location to store the model and weights. Only works for Keras/RNN models. End file extension with '.json'.
  --verbose VERBOSE, -v VERBOSE
                        Verbosity

Simulation mode

The CLI for the ASR software in simulation modus is similar to the CLI of the oracle modus. Instead of asreview oracle, use asreview simulate.

asreview simulate YOUR_DATA.csv

The available parameters are:

usage: asreview simulate [-h] [-m MODEL] [-q QUERY_STRATEGY]
                         [-b BALANCE_STRATEGY] [--n_instances N_INSTANCES]
                         [--n_queries N_QUERIES] [-n N_PAPERS]
                         [--embedding EMBEDDING_FP]
                         [--config_file CONFIG_FILE] [-s SRC_LOG_FP]
                         [--prior_included [PRIOR_INCLUDED [PRIOR_INCLUDED ...]]]
                         [--prior_excluded [PRIOR_EXCLUDED [PRIOR_EXCLUDED ...]]]
                         [--n_prior_included N_PRIOR_INCLUDED]
                         [--n_prior_excluded N_PRIOR_EXCLUDED]
                         [--log_file LOG_FILE] [--save_model SAVE_MODEL_FP]
                         [--verbose VERBOSE]
                         X

Automated Systematic Review (ASReview) for simulation runs.

The simulation modus is used to measure the performance of our
software on existing systematic reviews. The software shows how many
papers you could have potentially skipped during the systematic
review.

positional arguments:
  X                     File path to the dataset or one of the built-in datasets.

optional arguments:
  -h, --help            show this help message and exit
  -m MODEL, --model MODEL
                        The prediction model for Active Learning. Default 'lstm_pool'.
  -q QUERY_STRATEGY, --query_strategy QUERY_STRATEGY
                        The query strategy for Active Learning. Default 'rand_max'.
  -b BALANCE_STRATEGY, --balance_strategy BALANCE_STRATEGY
                        Data rebalancing strategy mainly for RNN methods. Helps against imbalanced dataset with few inclusions and many exclusions. Default 'triple_balance'
  --n_instances N_INSTANCES
                        Number of papers queried each query.Default 20.
  --n_queries N_QUERIES
                        The number of queries. By default, the program stops after all documents are reviewed or is interrupted by the user.
  -n N_PAPERS, --n_papers N_PAPERS
                        The number of papers to be reviewed. By default, the program stops after all documents are reviewed or is interrupted by the user.
  --embedding EMBEDDING_FP
                        File path of embedding matrix. Required for LSTM models.
  --config_file CONFIG_FILE
                        Configuration file with model parameters
  -s SRC_LOG_FP, --session-from-log SRC_LOG_FP
                        Continue session starting from previous log file.
  --prior_included [PRIOR_INCLUDED [PRIOR_INCLUDED ...]]
                        A list of included papers.
  --prior_excluded [PRIOR_EXCLUDED [PRIOR_EXCLUDED ...]]
                        A list of excluded papers. Optional.
  --n_prior_included N_PRIOR_INCLUDED
                        Sample n prior included papers. Only used when --prior_included is not given. Default 10
  --n_prior_excluded N_PRIOR_EXCLUDED
                        Sample n prior excluded papers. Only used when --prior_excluded is not given. Default 10
  --log_file LOG_FILE, -l LOG_FILE
                        Location to store the log results.
  --save_model SAVE_MODEL_FP
                        Location to store the model and weights. Only works for Keras/RNN models. End file extension with '.json'.
  --verbose VERBOSE, -v VERBOSE
                        Verbosity