doc(README.md): add Learner

Author: breakthewall

README.md

@@ -13,12 +13,15 @@ iCFree is a Python-based program designed to automate the process of generating
       - [Sampler](#sampler)
         - [Usage](#usage-1)
         - [Arguments](#arguments)
-      - [Plate Generator](#plate-generator)
+      - [Plate Designer](#plate-designer)
         - [Usage](#usage-2)
         - [Options](#options)
       - [Instructor](#instructor)
         - [Usage](#usage-3)
         - [Options](#options-1)
+      - [Learner](#learner)
+        - [Usage](#usage-4)
+        - [Options](#options-2)
     - [Example](#example)
   - [License](#license)
   - [Authors](#authors)
@@ -45,7 +48,7 @@ The main entry point of the program is the `__main__.py` file. You can run the p
 ### Basic Command
 
 ```bash
-python -m icfree --sampler_input_filename <input_file> --sampler_nb_samples <number_of_samples> --sampler_seed <seed> --sampler_output_filename <output_file> --plate_generator_input_filename <input_file> --plate_generator_sample_volume <volume> --plate_generator_default_dead_volume <dead_volume> --plate_generator_num_replicates <replicates> --plate_generator_well_capacity <capacity> --plate_generator_start_well_src_plt <start_well_src> --plate_generator_start_well_dst_plt <start_well_dst> --plate_generat...
+python -m icfree --sampler_input_filename <input_file> --sampler_nb_samples <number_of_samples> --sampler_seed <seed> --sampler_output_filename <output_file> --plate_designer_input_filename <input_file> --plate_designer_sample_volume <volume> --plate_designer_default_dead_volume <dead_volume> --plate_designer_num_replicates <replicates> --plate_designer_well_capacity <capacity> --plate_designer_start_well_src_plt <start_well_src> --plate_designer_start_well_dst_plt <start_well_dst> --plate_generat...
 ```
 
 ### Components
@@ -67,13 +70,13 @@ python icfree/sampler.py <input_file> <output_file> <num_samples> [--step <step_
 - --step: Step size for creating discrete ranges (default: 2.5).
 - --seed: Seed for random number generation for reproducibility (optional).
 
-#### Plate Generator
-The plate_generator.py script generates plates based on the sampled data.
+#### Plate Designer
+The plate_designer.py script generates plates based on the sampled data.
 
 ##### Usage
 
 ```bash
-python icfree/plate_generator.py <input_file> <sample_volume> [options]
+python icfree/plate_designer.py <input_file> <sample_volume> [options]
 ```
 
 ##### Options
@@ -102,12 +105,38 @@ python icfree/instructor.py <source_plate> <destination_plate> <output_instructi
 - --source_plate_type: Type of the source plate.
 - --split_components: Components to split.
 
+#### Learner
+The Learner module carries out an active learning process to both train the model and explore the space of possible cell-free combinations.
+
+##### Usage
+
+```bash
+python -m icfree.learner <data_folder> <parameter_file> <output_folder> [options]
+```
+
+##### Options
+
+  - --name_list: a comma-separated string of column names or identifiers, converted to a list of strings representing columns that contain labels (y). This separates y columns from the rest (X features). (Default: Yield1,Yield2,Yield3,Yield4,Yield5)
+  - --test: a flag for validating the model; not required to run inside the active learning loop. If not set, skip the validating step.
+  - --nb_rep NB_REP: the number of test repetitions for validating the model behavior. 80% of data is randomly separated for training, and 20% is used for testing. (Default: 100)
+  - --flatten: a flag to indicate whether to flatten Y data. If set, treats each repetition in the same experiment independently; multiple same X values with different y outputs are modeled. Else, calculates the average of y across repetitions and only model with y average.
+  - --seed SEED: the random seed value used for reproducibility in random operations. (Default: 85)
+  - --nb_new_data_predict: The number of new data points sampled from all possible cases. (Default: 1000)
+  - --nb_new_data: The number of new data points selected from the generated ones. These are the data points labeled after active learning loops. `nb_new_data_predict` must be greater than `nb_new_data` to be meaningful. (Default: 50)
+  - --parameter_step: The step size used to decrement the maximum predefined concentration sequentially. For example, if the maximum concentration is `max`, the sequence of concentrations is calculated as: `max - 1 * parameter_step`, `max - 2 * parameter_step`, `max - 3 * parameter_step`, and so on. Each concentration is a candidate for experimental testing. Smaller steps result in more possible combinations to sample. (Default: 10)
+  - --n_group: parameter for the cluster margin algorithm, specifying the number of groups into which generated data will be clustered. (Default: 15)
+  - --km: parameter for the cluster margin algorithm, specifying the number of data points for the first selection. Ensure `nb_new_data_predict > ks > km`. (Default: 50)
+  - --ks: parameter for the cluster margin algorithm, specifying the number of data points for the second selection. This is also similar to `nb_new_data`. (Default: 20)
+  - --plot: a flag to indicate whether to generate all plots for analysis visualization.
+  - --save_plot: a flag to indicate whether to save all generated plots.
+  - --verbose: flag to indicate whether to print all messages to the console.
+
 ### Example
 
 Here is an example of how to run the program with sample data:
 
 ```bash
-python -m icfree --sampler_input_filename data/components.csv --sampler_nb_samples 100 --sampler_seed 42 --sampler_output_filename results/samples.csv --plate_generator_input_filename results/samples.csv --plate_generator_sample_volume 10 --plate_generator_default_dead_volume 2 --plate_generator_num_replicates 3 --plate_generator_well_capacity 200 --plate_generator_start_well_src_plt A1 --plate_generator_start_well_dst_plt B1 --plate_generator_output_folder results/plates --instructor_max_transfer_volume...
+python -m icfree --sampler_input_filename data/components.csv --sampler_nb_samples 100 --sampler_seed 42 --sampler_output_filename results/samples.csv --plate_designer_input_filename results/samples.csv --plate_designer_sample_volume 10 --plate_designer_default_dead_volume 2 --plate_designer_num_replicates 3 --plate_designer_well_capacity 200 --plate_designer_start_well_src_plt A1 --plate_designer_start_well_dst_plt B1 --plate_designer_output_folder results/plates --instructor_max_transfer_volume...
 ```
 
 ## License