From e2d6fa8d17ebcc7c0bd5143edf09249439dce109 Mon Sep 17 00:00:00 2001 From: xin-huang Date: Mon, 27 May 2024 23:37:01 +0200 Subject: [PATCH] Update --- docs/userguide/lr.md | 23 + .../results/inference/example.lr.predictions | 1001 +++++++++++++++++ gaia/utils/models/LRModel.py | 2 + 3 files changed, 1026 insertions(+) create mode 100644 examples/results/inference/example.lr.predictions diff --git a/docs/userguide/lr.md b/docs/userguide/lr.md index 5a6d72b..a7cc74c 100644 --- a/docs/userguide/lr.md +++ b/docs/userguide/lr.md @@ -245,8 +245,18 @@ This output feature file resembles the one generated by the `simulate` subcomman ## `train` +Once the training data is created using the `simulate` subcommand, users can use the `train` subcommand to train a logsitic regression model. + ### Example +An example command is below: + +``` +gaia lr train --training-data examples/results/data/training/examples.features --model-file examples/results/trained_model/example.lr.model --seed 12345 +``` + +The trained model, which is a binary file, can be found [here](https://github.com/xin-huang/gaia/blob/dev/examples/results/trained_model/example.lr.model). + ### Arguments | Argument | Description | @@ -261,8 +271,21 @@ This output feature file resembles the one generated by the `simulate` subcomman ## `infer` +Once a trained model is obtained, users can utilize the `infer` subcommand to make predicitions on the features processed by the `preprocess` subcommand. + ### Example +An example command is below: + +``` +gaia lr infer --inference-data examples/results/data/test/example.lr.features --model-file examples/results/trained_model/example.lr.model --output-file examples/results/inference/example.lr.predictions +``` + +The predictions are available [here](https://github.com/xin-huang/gaia/blob/dev/examples/results/inference/example.lr.predictions) and appears as follows: + +``` +``` + ### Arguments | Argument | Description | diff --git 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1.0 1.0307547692033626e-28 +1 960000 1010000 tsk_9_2 1.0 2.3825908402370597e-25 +1 970000 1020000 tsk_9_2 1.0 6.332565873656126e-26 +1 980000 1030000 tsk_9_2 1.0 1.2491759451991232e-19 +1 990000 1040000 tsk_9_2 0.9999999997869329 2.13067116306906e-10 diff --git a/gaia/utils/models/LRModel.py b/gaia/utils/models/LRModel.py index c0120fe..6b21514 100644 --- a/gaia/utils/models/LRModel.py +++ b/gaia/utils/models/LRModel.py @@ -117,6 +117,8 @@ def infer(inference_data: str, model_file: str, """ features = pd.read_csv(inference_data, sep="\t") + output_dir = os.path.dirname(output_file) + os.makedirs(output_dir, exist_ok=True) data = features.drop( columns=[