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Fix links in README.
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kausmees committed Jun 16, 2021
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10 changes: 5 additions & 5 deletions README.md
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Expand Up @@ -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.
Expand Down Expand Up @@ -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.
Expand Down Expand Up @@ -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]
}


Expand Down Expand Up @@ -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
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