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b/src/utils/training.py |
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""" |
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Contains functions for running hyperparameter sweep and |
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Continual Learning model-training and evaluation. |
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""" |
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import json |
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import warnings |
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from pathlib import Path |
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from functools import partial |
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# import random |
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# import numpy as np |
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import torch |
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from ray import tune |
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from torch import nn, optim |
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from avalanche.logging import InteractiveLogger, TensorboardLogger |
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from avalanche.training.plugins import EvaluationPlugin |
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from avalanche.training.plugins.early_stopping import EarlyStoppingPlugin |
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from avalanche.evaluation.metrics import ( |
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accuracy_metrics, |
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loss_metrics, |
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StreamConfusionMatrix, |
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) |
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# Local imports |
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from utils import models, plotting, data_processing, cl_strategies |
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from utils.metrics import ( |
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balancedaccuracy_metrics, |
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sensitivity_metrics, |
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specificity_metrics, |
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precision_metrics, |
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rocauc_metrics, |
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auprc_metrics, |
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) |
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# Suppressing erroneous MaxPool1d named tensors warning |
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warnings.filterwarnings("once", category=UserWarning) |
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# GLOBALS |
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RESULTS_DIR = Path(__file__).parents[1] / "results" |
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CONFIG_DIR = Path(__file__).parents[1] / "config" |
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CUDA = torch.cuda.is_available() |
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DEVICE = "cuda" if CUDA else "cpu" |
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# Reproducibility |
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SEED = 12345 |
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# random.seed(SEED) |
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# np.random.seed(SEED) |
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torch.manual_seed(SEED) |
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def save_params(data, domain, outcome, model, strategy, best_params): |
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"""Save hyper-param config to json.""" |
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file_loc = CONFIG_DIR / data / outcome / domain |
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file_loc.mkdir(parents=True, exist_ok=True) |
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with open( |
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file_loc / f"config_{model}_{strategy}.json", "w", encoding="utf-8" |
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) as json_file: |
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json.dump(best_params, json_file) |
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def load_params(data, domain, outcome, model, strategy): |
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"""Load hyper-param config from json.""" |
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file_loc = CONFIG_DIR / data / outcome / domain |
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with open( |
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file_loc / f"config_{model}_{strategy}.json", encoding="utf-8" |
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) as json_file: |
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best_params = json.load(json_file) |
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return best_params |
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def save_results(data, outcome, domain, res): |
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"""Saves results to .json (excluding tensor confusion matrix).""" |
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with open( |
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RESULTS_DIR / f"results_{data}_{outcome}_{domain}.json", "w", encoding="utf-8" |
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) as handle: |
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res_no_tensors = { |
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m: { |
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s: [ |
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{ |
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metric: value |
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for metric, value in run.items() |
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if "Confusion" not in metric |
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} |
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for run in runs |
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] |
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for s, runs in strats.items() |
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} |
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for m, strats in res.items() |
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} |
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json.dump(res_no_tensors, handle) |
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def load_strategy( |
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model, |
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model_name, |
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strategy_name, |
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data="", |
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domain="", |
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n_tasks=0, |
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weight=None, |
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validate=False, |
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config=None, |
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benchmark=None, |
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early_stopping=False, |
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): |
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""" |
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- `stream` Avg accuracy over all experiences (may rely on tasks being roughly same size?) |
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- `experience` Accuracy for each experience |
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""" |
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strategy = cl_strategies.STRATEGIES[strategy_name] |
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criterion = nn.CrossEntropyLoss(weight=weight) |
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if config["generic"]["optimizer"] == "SGD": |
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optimizer = optim.SGD( |
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model.parameters(), lr=config["generic"]["lr"], momentum=0.9 |
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) |
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elif config["generic"]["optimizer"] == "Adam": |
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optimizer = optim.Adam(model.parameters(), lr=config["generic"]["lr"]) |
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if validate: |
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loggers = [] |
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else: |
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timestamp = plotting.get_timestamp() |
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log_dir = ( |
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RESULTS_DIR |
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/ "log" |
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/ "tensorboard" |
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/ f"{data}_{domain}_{timestamp}" |
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/ model_name |
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/ strategy_name |
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) |
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interactive_logger = InteractiveLogger() |
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tb_logger = TensorboardLogger(tb_log_dir=log_dir) |
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loggers = [interactive_logger, tb_logger] |
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eval_plugin = EvaluationPlugin( |
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StreamConfusionMatrix(save_image=False), |
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loss_metrics(stream=True, experience=not validate), |
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accuracy_metrics(trained_experience=True, stream=True, experience=not validate), |
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balancedaccuracy_metrics( |
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trained_experience=True, stream=True, experience=not validate |
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), |
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specificity_metrics( |
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trained_experience=True, stream=True, experience=not validate |
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), |
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sensitivity_metrics( |
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trained_experience=True, stream=True, experience=not validate |
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), |
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precision_metrics( |
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trained_experience=True, stream=True, experience=not validate |
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), |
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# rocauc_metrics(trained_experience=True, stream=True, experience=not validate), |
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# auprc_metrics(trained_experience=True, stream=True, experience=not validate), |
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loggers=loggers, |
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benchmark=benchmark, |
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) |
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if early_stopping: |
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early_stopping = EarlyStoppingPlugin( |
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patience=5, |
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val_stream_name="train_stream/Task000", |
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metric_name="BalancedAccuracy_On_Trained_Experiences", |
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) |
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plugins = [early_stopping] |
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else: |
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plugins = None |
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if strategy_name == "Joint": |
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eval_every = None |
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cl_strategy = strategy( |
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model, |
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optimizer=optimizer, |
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device=DEVICE, |
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criterion=criterion, |
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eval_mb_size=1024, |
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eval_every=0, # if validate or n_tasks > 5 else 1, |
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evaluator=eval_plugin, |
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train_epochs=15, |
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train_mb_size=config["generic"]["train_mb_size"], |
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plugins=plugins, |
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**config["strategy"], |
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) |
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return cl_strategy |
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def train_cl_method(cl_strategy, scenario, strategy_name, validate=False): |
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""" |
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Avalanche Cl training loop. For each 'experience' in scenario's train_stream: |
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- Trains method on experience |
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- evaluates model on train_stream and test_stream |
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""" |
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if not validate: |
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print("Starting experiment...") |
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if strategy_name == "Joint": |
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if not validate: |
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print(f"Joint training:") |
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cl_strategy.train( |
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scenario.train_stream, |
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eval_streams=[scenario.train_stream, scenario.test_stream], |
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) |
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if not validate: |
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print("Training completed", "\n\n") |
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else: |
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for experience in scenario.train_stream: |
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if not validate: |
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print( |
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f"{strategy_name} - Start of experience: {experience.current_experience}" |
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) |
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cl_strategy.train( |
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experience, eval_streams=[scenario.train_stream, scenario.test_stream] |
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) |
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if not validate: |
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print("Training completed", "\n\n") |
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if validate: |
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return cl_strategy.evaluator.get_last_metrics() |
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else: |
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return cl_strategy.evaluator.get_all_metrics() |
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def training_loop( |
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config, |
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data, |
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domain, |
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outcome, |
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model_name, |
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strategy_name, |
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validate=False, |
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checkpoint_dir=None, |
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): |
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""" |
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Training wrapper: |
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- loads data |
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- instantiates model |
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- equips model with CL strategy |
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- trains and evaluates method |
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- returns either results or hyperparam optimisation if `validate` |
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""" |
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# Loading data into 'stream' of 'experiences' (tasks) |
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if not validate: |
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print("Loading data...") |
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scenario, n_tasks, n_timesteps, n_channels, weight = data_processing.load_data( |
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data, domain, outcome, validate |
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) |
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if weight is not None: |
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weight = weight.to(DEVICE) |
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if not validate: |
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print("Data loaded.\n") |
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if not validate: |
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print(f"N timesteps: {n_timesteps}\nN features: {n_channels}") |
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265 |
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model = models.MODELS[model_name](n_channels, n_timesteps, **config["model"]) |
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cl_strategy = load_strategy( |
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model, |
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model_name, |
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strategy_name, |
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data, |
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domain, |
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n_tasks=n_tasks, |
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weight=weight, |
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validate=validate, |
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config=config, |
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benchmark=scenario, |
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) |
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results = train_cl_method(cl_strategy, scenario, strategy_name, validate=validate) |
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if validate: |
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loss = results["Loss_Stream/eval_phase/test_stream/Task000"] |
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accuracy = results[ |
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"Accuracy_On_Trained_Experiences/eval_phase/test_stream/Task000" |
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] |
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balancedaccuracy = results[ |
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"BalancedAccuracy_On_Trained_Experiences/eval_phase/test_stream/Task000" |
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] |
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# sensitivity = results['Sens_Stream/eval_phase/test_stream/Task000'] |
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# specificity = results['Spec_Stream/eval_phase/test_stream/Task000'] |
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# precision = results['Prec_Stream/eval_phase/test_stream/Task000'] |
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# rocauc = results['ROCAUC_Stream/eval_phase/test_stream/Task000'] |
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# auprc = results['AUPRC_Stream/eval_phase/test_stream/Task000'] |
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# WARNING: `return` overwrites raytune report |
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tune.report( |
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loss=loss, |
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accuracy=accuracy, |
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balancedaccuracy=balancedaccuracy, |
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# auprc=auprc, |
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# rocauc=rocauc |
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) |
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else: |
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return results |
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307 |
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def hyperparam_opt( |
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config, data, domain, outcome, model_name, strategy_name, num_samples |
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): |
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""" |
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Hyperparameter optimisation for the given model/strategy. |
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Runs over the validation data for the first 2 tasks. |
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""" |
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315 |
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reporter = tune.CLIReporter( |
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metric_columns=[ |
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"loss", |
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"accuracy", |
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"balancedaccuracy", |
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#'auprc', |
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#'rocauc' |
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] |
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) |
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resources = {"cpu": 4, "gpu": 0.5} if CUDA else {"cpu": 1} |
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326 |
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result = tune.run( |
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partial( |
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training_loop, |
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data=data, |
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domain=domain, |
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outcome=outcome, |
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model_name=model_name, |
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strategy_name=strategy_name, |
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validate=True, |
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), |
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config=config, |
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num_samples=num_samples, |
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progress_reporter=reporter, |
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raise_on_failed_trial=False, |
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resources_per_trial=resources, |
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name=f"{model_name}_{strategy_name}", |
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local_dir=RESULTS_DIR / "log" / "raytune" / f"{data}_{outcome}_{domain}", |
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trial_name_creator=lambda t: f"{model_name}_{strategy_name}_{t.trial_id}", |
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) |
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346 |
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best_trial = result.get_best_trial("balancedaccuracy", "max", "last") |
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print(f"Best trial config: {best_trial.config}") |
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print( |
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f"Best trial final validation loss: {best_trial.last_result['loss']}" |
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) |
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print( |
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f"Best trial final validation accuracy: {best_trial.last_result['accuracy']}" |
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) |
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print( |
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f"Best trial final validation balanced accuracy: {best_trial.last_result['balancedaccuracy']}" |
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) |
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358 |
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return best_trial.config |
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360 |
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361 |
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def main( |
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363 |
data, |
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domain, |
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365 |
outcome, |
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models, |
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strategies, |
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dropout=False, |
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config_generic={}, |
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config_model={}, |
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config_cl={}, |
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validate=False, |
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num_samples=50, |
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freeze_model_hp=False, |
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): |
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""" |
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377 |
Main training loop. Defines dataset given outcome/domain |
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and evaluates model/strategies over given hyperparams over this problem. |
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379 |
""" |
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380 |
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381 |
# Container for metrics results |
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382 |
res = {m: {s: [] for s in strategies} for m in models} |
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383 |
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384 |
for model in models: |
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for strategy in strategies: |
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386 |
# Garbage collection |
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387 |
torch.cuda.empty_cache() |
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388 |
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389 |
if validate: # Hyperparam opt over first 2 tasks |
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390 |
# Load generic tuned hyper-params |
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391 |
if strategy == "Naive" or not freeze_model_hp: |
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392 |
config = { |
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393 |
"generic": config_generic, |
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394 |
"model": config_model[model], |
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395 |
"strategy": config_cl.get(strategy, {}), |
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396 |
} |
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397 |
else: |
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398 |
naive_params = load_params(data, domain, outcome, model, "Naive") |
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399 |
config = { |
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400 |
"generic": naive_params["generic"], |
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401 |
"model": naive_params["model"], |
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402 |
"strategy": config_cl.get(strategy, {}), |
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403 |
} |
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404 |
|
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405 |
# JA: Investigate adding dropout to CNN (final FC layers only?) |
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406 |
if not dropout and model != "CNN": |
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407 |
config["model"]["dropout"] = 0 |
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408 |
|
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409 |
best_params = hyperparam_opt( |
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410 |
config, |
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411 |
data, |
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412 |
domain, |
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413 |
outcome, |
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414 |
model, |
|
|
415 |
strategy, |
|
|
416 |
num_samples=1 if strategy == "Naive" else num_samples, |
|
|
417 |
) |
|
|
418 |
save_params(data, domain, outcome, model, strategy, best_params) |
|
|
419 |
|
|
|
420 |
else: # Training loop over all tasks |
|
|
421 |
config = load_params(data, domain, outcome, model, strategy) |
|
|
422 |
|
|
|
423 |
# Multiple runs for Confidence Intervals |
|
|
424 |
n_repeats = 1 |
|
|
425 |
for _ in range(n_repeats): |
|
|
426 |
curr_results = training_loop( |
|
|
427 |
config, data, domain, outcome, model, strategy |
|
|
428 |
) |
|
|
429 |
res[model][strategy].append(curr_results) |
|
|
430 |
|
|
|
431 |
if not validate: |
|
|
432 |
save_results(data, outcome, domain, res) |
|
|
433 |
plotting.plot_all_figs(data, domain, outcome) |