diff --git a/README.md b/README.md index 6aeda20..05e08ef 100644 --- a/README.md +++ b/README.md @@ -31,7 +31,7 @@ docker build -t gcae/genocae:build -f docker/build.dockerfile . #### CLI -``` Shell +``` $ docker run -it --rm -v ${PWD}:/workspace gcae/genocae:build python3 run_gcae.py --help GenoCAE. @@ -62,7 +62,7 @@ Options: ``` If you have a Docker with GPU support. -``` Shell +``` $ docker run -it --gpus=all --rm -v ${PWD}:/workspace gcae/genocae:build python3 run_gcae.py --help GenoCAE. @@ -164,13 +164,13 @@ A small example data set **HumanOrigins249_tiny** is in [example_tiny/](example These options affect how data is input to the model. Passed to the CLI with option **--data_opts**, specifying a json file in the directory [data_opts/](data_opts/) -Example: ([data_opts/b.json](data_opts/b_0_1.json)) +Example: ([data_opts/b_0_4.json](data_opts/b_0_4.json)) { "norm_mode" : "genotypewise01", "norm_opts" : {"flip": false, "missing_val":-1.0}, "impute_missing" : true, "validation_split" : 0.2, - "sparsifies" : [0.0, 0.1] + "sparsifies" : [0.0, 0.1, 0.2, 0.3, 0.4] } @@ -333,7 +333,7 @@ Example with categorical cross-entropy loss and a learning rate scheme: ([train_ optional: -* **lr_scheme:** scheme to apply to learning rate. the example above is to use exponential decay, see [tf documentation](https://www.tensorflow.org/versions/r1.12/api_docs/python/tf/train/exponential_decay). +* **lr_scheme:** scheme to apply to learning rate. the example above is to use exponential decay, see [tf documentation](https://www.tensorflow.org/api_docs/python/tf/keras/optimizers/schedules/ExponentialDecay). > if the loss is sigmoid_cross_entropy_with_logits, the normalized genotypes should be in range (0,1) - so normalized using e.g. genotypewise01