diff --git a/.gitattributes b/.gitattributes
index 7afc87cb5..0be747b84 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -14,3 +14,4 @@
 *.npz filter=lfs diff=lfs merge=lfs -text
 *.dcm filter=lfs diff=lfs merge=lfs -text
 *.zip filter=lfs diff=lfs merge=lfs -text
+*.jpg filter=lfs diff=lfs merge=lfs -text
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 95c36bcd0..54cd6aa6b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,6 +13,8 @@ created.
 ## Upcoming
 
 ### Added
+- ([#492](https://github.com/microsoft/InnerEye-DeepLearning/pull/492)) Adding capability for regression tests for test
+jobs that run in AzureML.
 
 ### Changed
 
diff --git a/InnerEye/ML/baselines_util.py b/InnerEye/ML/baselines_util.py
index 1196bad9e..11fc65780 100755
--- a/InnerEye/ML/baselines_util.py
+++ b/InnerEye/ML/baselines_util.py
@@ -3,15 +3,20 @@
 #  Licensed under the MIT License (MIT). See LICENSE in the repo root for license information.
 #  ------------------------------------------------------------------------------------------
 import logging
+import os
+import shutil
+import tempfile
 from dataclasses import dataclass
 from pathlib import Path
-from typing import Dict, List, Tuple
+from typing import Dict, List, Optional, Tuple
 
 import matplotlib.pyplot as plt
 import pandas as pd
+from azureml.core import Run
 
 from InnerEye.Azure.azure_config import AzureConfig
-from InnerEye.Azure.azure_util import AZUREML_RUN_FOLDER_PREFIX, get_comparison_baseline_paths, strip_prefix
+from InnerEye.Azure.azure_util import AZUREML_RUN_FOLDER_PREFIX, PARENT_RUN_CONTEXT, RUN_CONTEXT, \
+    get_comparison_baseline_paths, is_offline_run_context, strip_prefix
 from InnerEye.Common import common_util
 from InnerEye.Common.Statistics import wilcoxon_signed_rank_test
 from InnerEye.Common.Statistics.wilcoxon_signed_rank_test import WilcoxonTestConfig
@@ -24,6 +29,12 @@
 from InnerEye.ML.visualizers.metrics_scatterplot import write_to_scatterplot_directory
 from InnerEye.ML.visualizers.plot_cross_validation import convert_rows_for_comparisons, may_write_lines_to_file
 
+REGRESSION_TEST_AZUREML_FOLDER = "AZUREML_OUTPUT"
+REGRESSION_TEST_AZUREML_PARENT_FOLDER = "AZUREML_PARENT_OUTPUT"
+CONTENTS_MISMATCH = "Contents mismatch"
+MISSING_FILE = "Missing file"
+TEXT_FILE_SUFFIXES = [".txt", ".csv", ".json", ".html", ".md"]
+
 
 @dataclass
 class DiceScoreComparisonResult:
@@ -173,3 +184,119 @@ def get_comparison_baselines(outputs_folder: Path, azure_config: AzureConfig,
         else:
             raise ValueError(f"could not find comparison data for run {run_rec_id}")
     return comparison_baselines
+
+
+def compare_files(expected: Path, actual: Path) -> str:
+    """
+    Compares two individual files for regression testing. It returns an empty string if the two files appear identical.
+    If the files are not identical, an error message with details is return. This handles known text file formats,
+    where it ignores differences in line breaks. All other files are treated as binary, and compared on a byte-by-byte
+    basis.
+    :param expected: A file that contains the expected contents. The type of comparison (text or binary) is chosen
+    based on the extension of this file.
+    :param actual: A file that contains the actual contents.
+    :return: An empty string if the files appear identical, or otherwise an error message with details.
+    """
+
+    def print_lines(prefix: str, lines: List[str]) -> None:
+        count = 5
+        logging.debug(f"{prefix} {len(lines)} lines, first {count} of those:")
+        logging.debug(os.linesep.join(lines[:count]))
+
+    if expected.suffix in TEXT_FILE_SUFFIXES:
+        # Compare line-by-line to avoid issues with line separators
+        expected_lines = expected.read_text().splitlines()
+        actual_lines = actual.read_text().splitlines()
+        if expected_lines != actual_lines:
+            print_lines("Expected", expected_lines)
+            print_lines("Actual", actual_lines)
+            return CONTENTS_MISMATCH
+    else:
+        expected_binary = expected.read_bytes()
+        actual_binary = actual.read_bytes()
+        if expected_binary != actual_binary:
+            logging.debug(f"Expected {len(expected_binary)} bytes, actual {len(actual_binary)} bytes")
+            return CONTENTS_MISMATCH
+    return ""
+
+
+def compare_folder_contents(expected_folder: Path,
+                            actual_folder: Optional[Path] = None,
+                            run: Optional[Run] = None) -> None:
+    """
+    Compares a set of files in a folder, against files in either the other folder or files stored in the given
+    AzureML run. Each file that is present in the "expected" folder must be also present in the "actual" folder
+    (or the AzureML run), with exactly the same contents, in the same folder structure.
+    For example, if there is a file "<expected>/foo/bar/contents.txt", then there must also be a file
+    "<actual>/foo/bar/contents.txt"
+    If a file is missing, or does not have the expected contents, an exception is raised.
+    :param expected_folder: A folder with files that are expected to be present.
+    :param actual_folder: The output folder with the actually produced files.
+    :param run: An AzureML run
+    """
+    logging.debug(f"Checking job output against expected files in folder {expected_folder}")
+    logging.debug(f"Current working directory: {Path.cwd()}")
+    messages = []
+    if not expected_folder.is_dir():
+        raise ValueError(f"Folder with expected files does not exist: {expected_folder}")
+    if run and is_offline_run_context(run):
+        logging.warning("Skipping file comparison because the given run context is an AzureML offline run.")
+        return
+    files_in_run: List[str] = run.get_file_names() if run else []
+    temp_folder = Path(tempfile.mkdtemp()) if run else None
+    for file in expected_folder.rglob("*"):
+        # rglob also returns folders, skip those
+        if file.is_dir():
+            continue
+        logging.debug(f"Checking file {file}")
+        # All files stored in AzureML runs use Linux-style path
+        file_relative = file.relative_to(expected_folder).as_posix()
+        if str(file_relative).startswith(REGRESSION_TEST_AZUREML_FOLDER) or \
+                str(file_relative).startswith(REGRESSION_TEST_AZUREML_PARENT_FOLDER):
+            continue
+        actual_file: Optional[Path] = None
+        if actual_folder:
+            actual_file = actual_folder / file_relative
+            if not actual_file.is_file():
+                actual_file = None
+        elif temp_folder is not None and run is not None:
+            if file_relative in files_in_run:
+                actual_file = temp_folder / file_relative
+                run.download_file(name=str(file_relative), output_file_path=str(actual_file))
+        message = compare_files(expected=file, actual=actual_file) if actual_file else "Missing file"
+        if message:
+            logging.debug(f"Error: {message}")
+            messages.append(f"{message}: {file_relative}")
+    if temp_folder:
+        shutil.rmtree(temp_folder)
+    if messages:
+        raise ValueError(f"Some expected files were missing or did not have the expected contents:{os.linesep}"
+                         f"{os.linesep.join(messages)}")
+
+
+def compare_folders_and_run_outputs(expected: Path, actual: Path) -> None:
+    """
+    Compares the actual set of run outputs in the `actual` folder against an expected set of files in the `expected`
+    folder. The `expected` folder can have two special subfolders AZUREML_OUTPUT and AZUREML_PARENT_OUTPUT, that
+    contain files that are expected to be present in the AzureML run context of the present run (AZUREML_OUTPUT)
+    or the run context of the parent run (AZUREML_PARENT_OUTPUT).
+    If a file is missing, or does not have the expected contents, an exception is raised.
+    :param expected: A folder with files that are expected to be present.
+    :param actual: The output folder with the actually produced files.
+    """
+    if not expected.is_dir():
+        raise ValueError(f"Folder with expected files does not exist: {expected}")
+    # First compare the normal output files that the run produces
+    compare_folder_contents(expected, actual)
+    # Compare the set of files in the magic folder with the outputs stored in the run context
+    azureml_folder = expected / REGRESSION_TEST_AZUREML_FOLDER
+    if azureml_folder.is_dir():
+        compare_folder_contents(azureml_folder, run=RUN_CONTEXT)
+    # Compare the set of files in the magic folder with the outputs stored in the run context of the parent run
+    azureml_parent_folder = expected / REGRESSION_TEST_AZUREML_PARENT_FOLDER
+    if azureml_parent_folder.is_dir():
+        if PARENT_RUN_CONTEXT is None:
+            raise ValueError(f"The set of expected test results in {expected} contains a folder "
+                             f"{REGRESSION_TEST_AZUREML_PARENT_FOLDER}, but the present run is not a cross-validation "
+                             "child run")
+        compare_folder_contents(azureml_parent_folder, run=PARENT_RUN_CONTEXT)
diff --git a/InnerEye/ML/configs/reports/CovidHierarchicalModelReport.ipynb b/InnerEye/ML/configs/reports/CovidHierarchicalModelReport.ipynb
index 07afe2543..6e87854d9 100644
--- a/InnerEye/ML/configs/reports/CovidHierarchicalModelReport.ipynb
+++ b/InnerEye/ML/configs/reports/CovidHierarchicalModelReport.ipynb
@@ -48,7 +48,6 @@
    "source": [
     "import sys\n",
     "\n",
-    "print(f\"Adding to path: {innereye_path}\")\n",
     "if str(innereye_path) not in sys.path:\n",
     "    sys.path.append(str(innereye_path))\n",
     "\n",
diff --git a/InnerEye/ML/deep_learning_config.py b/InnerEye/ML/deep_learning_config.py
index ed1840205..1c35926d4 100644
--- a/InnerEye/ML/deep_learning_config.py
+++ b/InnerEye/ML/deep_learning_config.py
@@ -230,6 +230,13 @@ class WorkflowParams(param.Parameterized):
     monitoring_interval_seconds: int = param.Integer(0, doc="Seconds delay between logging GPU/CPU resource "
                                                             "statistics. If 0 or less, do not log any resource "
                                                             "statistics.")
+    regression_test_folder: Optional[Path] = \
+        param.ClassSelector(class_=Path, default=None, allow_None=True,
+                            doc="A path to a folder that contains a set of files. At the end of training and "
+                                "model evaluation, all files given in that folder must be present in the job's output "
+                                "folder, and their contents must match exactly. When running in AzureML, you need to "
+                                "ensure that this folder is part of the snapshot that gets uploaded. The path should "
+                                "be relative to the repository root directory.")
 
     def validate(self) -> None:
         if self.weights_url and self.local_weights_path:
diff --git a/InnerEye/ML/reports/classification_crossval_report.ipynb b/InnerEye/ML/reports/classification_crossval_report.ipynb
index 547a58714..3cf022762 100644
--- a/InnerEye/ML/reports/classification_crossval_report.ipynb
+++ b/InnerEye/ML/reports/classification_crossval_report.ipynb
@@ -48,7 +48,6 @@
    "outputs": [],
    "source": [
     "import sys\n",
-    "print(f\"Adding to path: {innereye_path}\")\n",
     "if str(innereye_path) not in sys.path:\n",
     "    sys.path.append(str(innereye_path))\n",
     "\n",
diff --git a/InnerEye/ML/reports/classification_multilabel_report.ipynb b/InnerEye/ML/reports/classification_multilabel_report.ipynb
index 39a0e71f4..91e453611 100644
--- a/InnerEye/ML/reports/classification_multilabel_report.ipynb
+++ b/InnerEye/ML/reports/classification_multilabel_report.ipynb
@@ -54,7 +54,6 @@
    "outputs": [],
    "source": [
     "import sys\n",
-    "print(f\"Adding to path: {innereye_path}\")\n",
     "if str(innereye_path) not in sys.path:\n",
     "    sys.path.append(str(innereye_path))\n",
     "\n",
diff --git a/InnerEye/ML/reports/segmentation_report.ipynb b/InnerEye/ML/reports/segmentation_report.ipynb
index 026db5483..b9344b8c4 100644
--- a/InnerEye/ML/reports/segmentation_report.ipynb
+++ b/InnerEye/ML/reports/segmentation_report.ipynb
@@ -43,7 +43,6 @@
     "import matplotlib.pyplot as plt\n",
     "import sys\n",
     "\n",
-    "print(f\"Adding to path: {innereye_path}\")\n",
     "if str(innereye_path) not in sys.path:\n",
     "    sys.path.append(str(innereye_path))\n",
     "from InnerEye.ML.reports.segmentation_report import plot_scores_for_csv\n",
diff --git a/InnerEye/ML/reports/segmentation_report.py b/InnerEye/ML/reports/segmentation_report.py
index db41836e9..44959571a 100644
--- a/InnerEye/ML/reports/segmentation_report.py
+++ b/InnerEye/ML/reports/segmentation_report.py
@@ -2,12 +2,14 @@
 #  Copyright (c) Microsoft Corporation. All rights reserved.
 #  Licensed under the MIT License (MIT). See LICENSE in the repo root for license information.
 #  ------------------------------------------------------------------------------------------
+from pathlib import Path
 
 import matplotlib.pyplot as plt
 import pandas as pd
 from IPython.display import HTML, display
 from pandas import DataFrame
 
+from InnerEye.Common.fixed_paths import DEFAULT_AML_UPLOAD_DIR
 from InnerEye.Common.metrics_constants import MetricsFileColumns
 from InnerEye.ML.reports.notebook_report import print_header
 from InnerEye.ML.utils.csv_util import mark_outliers
@@ -18,7 +20,14 @@ def plot_scores_for_csv(path_csv: str, outlier_range: float, max_row_count: int)
     Displays all the tables and figures given a csv file with segmentation metrics
     Columns expected: Patient,Structure,Dice,HausdorffDistance_mm,MeanDistance_mm
     """
-    print(f"Reading raw metrics data from: {path_csv}")
+    # For diagnostics, it is nice to see whether the metrics were read from the correct file. In AzureML,
+    # those paths contain the run ID, meaning that the output is different for each run, and hence can't have
+    # HTML files in regression tests. Try to be smart and print as much information as possible up to the "outputs"
+    # folder
+    path = Path(path_csv)
+    outputs_folder = [p for p in path.parents if p.name == DEFAULT_AML_UPLOAD_DIR]
+    path_to_print = path.relative_to(outputs_folder[0]) if len(outputs_folder) == 1 else path
+    print(f"Reading raw metrics data from: {path_to_print}")
     df = pd.read_csv(path_csv)
     with pd.option_context('display.max_rows', None, 'display.max_columns', None, 'display.width', 150):
         display_metric(df, MetricsFileColumns.Dice.value, outlier_range, max_row_count, high_values_are_good=True)
diff --git a/InnerEye/ML/run_ml.py b/InnerEye/ML/run_ml.py
index f423dd5f0..f9a9a49d6 100644
--- a/InnerEye/ML/run_ml.py
+++ b/InnerEye/ML/run_ml.py
@@ -34,6 +34,7 @@
     change_working_directory, get_best_epoch_results_path, is_windows, logging_section, logging_to_file, \
     print_exception, remove_file_or_directory
 from InnerEye.Common.fixed_paths import INNEREYE_PACKAGE_NAME, LOG_FILE_NAME, PYTHON_ENVIRONMENT_NAME
+from InnerEye.ML.baselines_util import compare_folder_contents
 from InnerEye.ML.common import ModelExecutionMode
 from InnerEye.ML.config import SegmentationModelBase
 from InnerEye.ML.deep_learning_config import CHECKPOINT_FOLDER, DeepLearningConfig, FINAL_ENSEMBLE_MODEL_FOLDER, \
@@ -404,6 +405,25 @@ def run(self) -> None:
                 with change_working_directory(self.container.outputs_folder):
                     self.container.create_report()
 
+        if self.container.regression_test_folder:
+            # Comparison with stored results for cross-validation runs only operates on child run 0. This run
+            # has usually already downloaded the results for the other runs, and uploaded files to the parent
+            # run context.
+            logging.info("Comparing the current results against stored results")
+            if self.is_normal_run_or_crossval_child_0():
+                compare_folder_contents(expected_folder=self.container.regression_test_folder,
+                                        actual_folder=self.container.outputs_folder)
+            else:
+                logging.info("Skipping because this is not cross-validation child run 0.")
+
+    def is_normal_run_or_crossval_child_0(self) -> bool:
+        """
+        Returns True if the present run is a non-crossvalidation run, or child run 0 of a crossvalidation run.
+        """
+        if self.container.number_of_cross_validation_splits > 0:
+            return self.container.cross_validation_split_index == 0
+        return True
+
     def run_inference_for_lightning_models(self, checkpoint_paths: List[Path]) -> None:
         """
         Run inference on the test set for all models that are specified via a LightningContainer.
diff --git a/RegressionTestResults/PR_BasicModel2Epochs/AZUREML_OUTPUT/final_model/model_inference_config.json b/RegressionTestResults/PR_BasicModel2Epochs/AZUREML_OUTPUT/final_model/model_inference_config.json
new file mode 100644
index 000000000..54359101d
--- /dev/null
+++ b/RegressionTestResults/PR_BasicModel2Epochs/AZUREML_OUTPUT/final_model/model_inference_config.json
@@ -0,0 +1 @@
+{"model_name": "BasicModel2Epochs", "checkpoint_paths": ["checkpoints/best_checkpoint.ckpt"], "model_configs_namespace": "InnerEye.ML.configs.segmentation.BasicModel2Epochs"}
\ No newline at end of file
diff --git a/RegressionTestResults/PR_BasicModel2Epochs/Train/epoch_metrics.csv b/RegressionTestResults/PR_BasicModel2Epochs/Train/epoch_metrics.csv
new file mode 100644
index 000000000..9b8f039c6
--- /dev/null
+++ b/RegressionTestResults/PR_BasicModel2Epochs/Train/epoch_metrics.csv
@@ -0,0 +1,3 @@
+subject_count,loss,learning_rate,Dice/AverageAcrossStructures,Dice/spinalcord,Dice/lung_r,Dice/lung_l,VoxelCount/spinalcord,VoxelCount/lung_r,VoxelCount/lung_l,epoch,cross_validation_split_index
+2.000000,0.718717,0.000100,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,126273.000000,0,-1
+2.000000,0.775691,0.000090,0.000000,0.000000,0.000000,0.000000,0.000000,84030.000000,0.000000,1,-1
diff --git a/RegressionTestResults/PR_BasicModel2Epochs/Val/epoch_metrics.csv b/RegressionTestResults/PR_BasicModel2Epochs/Val/epoch_metrics.csv
new file mode 100644
index 000000000..72b267213
--- /dev/null
+++ b/RegressionTestResults/PR_BasicModel2Epochs/Val/epoch_metrics.csv
@@ -0,0 +1,3 @@
+subject_count,loss,Dice/AverageAcrossStructures,Dice/spinalcord,Dice/lung_r,Dice/lung_l,VoxelCount/spinalcord,VoxelCount/lung_r,VoxelCount/lung_l,epoch,cross_validation_split_index
+2.000000,0.716739,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,84282.000000,0,-1
+2.000000,0.716731,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,84282.000000,1,-1
diff --git a/RegressionTestResults/PR_BasicModel2Epochs/best_validation_epoch/Test/005/background.nii.gz b/RegressionTestResults/PR_BasicModel2Epochs/best_validation_epoch/Test/005/background.nii.gz
new file mode 100644
index 000000000..d43a233dd
--- /dev/null
+++ b/RegressionTestResults/PR_BasicModel2Epochs/best_validation_epoch/Test/005/background.nii.gz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:1cf48e384762c4304b6b3cfedd50ad4a13024f7e9e9d1f40515b6c9af4d25f3c
+size 31943
diff --git a/RegressionTestResults/PR_BasicModel2Epochs/best_validation_epoch/Test/005/posterior_lung_l.nii.gz b/RegressionTestResults/PR_BasicModel2Epochs/best_validation_epoch/Test/005/posterior_lung_l.nii.gz
new file mode 100644
index 000000000..f379ade17
--- /dev/null
+++ b/RegressionTestResults/PR_BasicModel2Epochs/best_validation_epoch/Test/005/posterior_lung_l.nii.gz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:92c64089d4d4ddebc2ef79a2486574fcedde44c796ae9118ec86193c983cdc7a
+size 41162
diff --git a/RegressionTestResults/PR_BasicModel2Epochs/best_validation_epoch/Test/005/uncertainty.nii.gz b/RegressionTestResults/PR_BasicModel2Epochs/best_validation_epoch/Test/005/uncertainty.nii.gz
new file mode 100644
index 000000000..178f30897
--- /dev/null
+++ b/RegressionTestResults/PR_BasicModel2Epochs/best_validation_epoch/Test/005/uncertainty.nii.gz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:9027ce6164d9dbc666a19b9406bbde3f1a966b7049597dea76ac0348b46d439c
+size 41162
diff --git a/RegressionTestResults/PR_BasicModel2Epochs/best_validation_epoch/Test/dataset_id.txt b/RegressionTestResults/PR_BasicModel2Epochs/best_validation_epoch/Test/dataset_id.txt
new file mode 100644
index 000000000..54c6bb305
--- /dev/null
+++ b/RegressionTestResults/PR_BasicModel2Epochs/best_validation_epoch/Test/dataset_id.txt
@@ -0,0 +1 @@
+2339eba2-8ec5-4ccb-86ff-c170470ac6e2_geonorm_with_train_test_split_2020_05_26
diff --git a/RegressionTestResults/PR_BasicModel2Epochs/best_validation_epoch/Test/ground_truth_ids.txt b/RegressionTestResults/PR_BasicModel2Epochs/best_validation_epoch/Test/ground_truth_ids.txt
new file mode 100644
index 000000000..31e5b9204
--- /dev/null
+++ b/RegressionTestResults/PR_BasicModel2Epochs/best_validation_epoch/Test/ground_truth_ids.txt
@@ -0,0 +1,3 @@
+spinalcord
+lung_r
+lung_l
diff --git a/RegressionTestResults/PR_BasicModel2Epochs/best_validation_epoch/Test/image_channel_ids.txt b/RegressionTestResults/PR_BasicModel2Epochs/best_validation_epoch/Test/image_channel_ids.txt
new file mode 100644
index 000000000..d8e29fa97
--- /dev/null
+++ b/RegressionTestResults/PR_BasicModel2Epochs/best_validation_epoch/Test/image_channel_ids.txt
@@ -0,0 +1,2 @@
+ct
+heart
diff --git a/RegressionTestResults/PR_BasicModel2Epochs/best_validation_epoch/Test/metrics.csv b/RegressionTestResults/PR_BasicModel2Epochs/best_validation_epoch/Test/metrics.csv
new file mode 100644
index 000000000..18c70f2a0
--- /dev/null
+++ b/RegressionTestResults/PR_BasicModel2Epochs/best_validation_epoch/Test/metrics.csv
@@ -0,0 +1,4 @@
+Patient,Structure,Dice,HausdorffDistance_mm,MeanDistance_mm
+5,lung_l,0.000,inf,inf
+5,lung_r,0.000,inf,inf
+5,spinalcord,0.000,inf,inf
diff --git a/RegressionTestResults/PR_BasicModel2Epochs/best_validation_epoch/Test/metrics_aggregates.csv b/RegressionTestResults/PR_BasicModel2Epochs/best_validation_epoch/Test/metrics_aggregates.csv
new file mode 100644
index 000000000..bd43149b2
--- /dev/null
+++ b/RegressionTestResults/PR_BasicModel2Epochs/best_validation_epoch/Test/metrics_aggregates.csv
@@ -0,0 +1,2 @@
+Structure,count,DiceNumeric_mean,DiceNumeric_std,DiceNumeric_min,DiceNumeric_max,HausdorffDistance_mm_mean,HausdorffDistance_mm_std,HausdorffDistance_mm_min,HausdorffDistance_mm_max,MeanDistance_mm_mean,MeanDistance_mm_std,MeanDistance_mm_min,MeanDistance_mm_max
+lung_l,1.000,0.000,,0.000,0.000,inf,,inf,inf,inf,,inf,inf
diff --git a/RegressionTestResults/PR_BasicModel2Epochs/best_validation_epoch/Test/metrics_boxplot.png b/RegressionTestResults/PR_BasicModel2Epochs/best_validation_epoch/Test/metrics_boxplot.png
new file mode 100644
index 000000000..d3940aacf
--- /dev/null
+++ b/RegressionTestResults/PR_BasicModel2Epochs/best_validation_epoch/Test/metrics_boxplot.png
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:251cce95dc7361a4b4d750f3709d321dcf0a6cb70ec51b1b6ae40c0d54533006
+size 3324
diff --git a/RegressionTestResults/PR_BasicModel2Epochs/best_validation_epoch/Test/thumbnails/005_lung_l_slice_053.png b/RegressionTestResults/PR_BasicModel2Epochs/best_validation_epoch/Test/thumbnails/005_lung_l_slice_053.png
new file mode 100644
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diff --git a/RegressionTestResults/PR_GlaucomaCV/AZUREML_PARENT_OUTPUT/CrossValResults/0/Val/metrics.csv b/RegressionTestResults/PR_GlaucomaCV/AZUREML_PARENT_OUTPUT/CrossValResults/0/Val/metrics.csv
new file mode 100644
index 000000000..d9f6d5bfb
--- /dev/null
+++ b/RegressionTestResults/PR_GlaucomaCV/AZUREML_PARENT_OUTPUT/CrossValResults/0/Val/metrics.csv
@@ -0,0 +1,1001 @@
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diff --git a/RegressionTestResults/PR_GlaucomaCV/AZUREML_PARENT_OUTPUT/CrossValResults/0/dataset.csv b/RegressionTestResults/PR_GlaucomaCV/AZUREML_PARENT_OUTPUT/CrossValResults/0/dataset.csv
new file mode 100644
index 000000000..d44250183
--- /dev/null
+++ b/RegressionTestResults/PR_GlaucomaCV/AZUREML_PARENT_OUTPUT/CrossValResults/0/dataset.csv
@@ -0,0 +1,1111 @@
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diff --git a/RegressionTestResults/PR_GlaucomaCV/AZUREML_PARENT_OUTPUT/CrossValResults/1/Test/metrics.csv b/RegressionTestResults/PR_GlaucomaCV/AZUREML_PARENT_OUTPUT/CrossValResults/1/Test/metrics.csv
new file mode 100644
index 000000000..f8e1f62cc
--- /dev/null
+++ b/RegressionTestResults/PR_GlaucomaCV/AZUREML_PARENT_OUTPUT/CrossValResults/1/Test/metrics.csv
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diff --git a/RegressionTestResults/PR_GlaucomaCV/AZUREML_PARENT_OUTPUT/CrossValResults/1/Train/metrics.csv b/RegressionTestResults/PR_GlaucomaCV/AZUREML_PARENT_OUTPUT/CrossValResults/1/Train/metrics.csv
new file mode 100644
index 000000000..77fe28f8f
--- /dev/null
+++ b/RegressionTestResults/PR_GlaucomaCV/AZUREML_PARENT_OUTPUT/CrossValResults/1/Train/metrics.csv
@@ -0,0 +1,1001 @@
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diff --git a/RegressionTestResults/PR_GlaucomaCV/AZUREML_PARENT_OUTPUT/CrossValResults/1/Val/metrics.csv b/RegressionTestResults/PR_GlaucomaCV/AZUREML_PARENT_OUTPUT/CrossValResults/1/Val/metrics.csv
new file mode 100644
index 000000000..554fbfbab
--- /dev/null
+++ b/RegressionTestResults/PR_GlaucomaCV/AZUREML_PARENT_OUTPUT/CrossValResults/1/Val/metrics.csv
@@ -0,0 +1,1001 @@
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diff --git a/RegressionTestResults/PR_GlaucomaCV/AZUREML_PARENT_OUTPUT/CrossValResults/1/dataset.csv b/RegressionTestResults/PR_GlaucomaCV/AZUREML_PARENT_OUTPUT/CrossValResults/1/dataset.csv
new file mode 100644
index 000000000..d44250183
--- /dev/null
+++ b/RegressionTestResults/PR_GlaucomaCV/AZUREML_PARENT_OUTPUT/CrossValResults/1/dataset.csv
@@ -0,0 +1,1111 @@
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diff --git a/RegressionTestResults/PR_GlaucomaCV/AZUREML_PARENT_OUTPUT/CrossValResults/MetricsAcrossAllRuns.csv b/RegressionTestResults/PR_GlaucomaCV/AZUREML_PARENT_OUTPUT/CrossValResults/MetricsAcrossAllRuns.csv
new file mode 100644
index 000000000..53f7a4225
--- /dev/null
+++ b/RegressionTestResults/PR_GlaucomaCV/AZUREML_PARENT_OUTPUT/CrossValResults/MetricsAcrossAllRuns.csv
@@ -0,0 +1,2221 @@
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diff --git a/RegressionTestResults/PR_GlaucomaCV/AZUREML_PARENT_OUTPUT/CrossValResults/dataset.csv b/RegressionTestResults/PR_GlaucomaCV/AZUREML_PARENT_OUTPUT/CrossValResults/dataset.csv
new file mode 100644
index 000000000..d44250183
--- /dev/null
+++ b/RegressionTestResults/PR_GlaucomaCV/AZUREML_PARENT_OUTPUT/CrossValResults/dataset.csv
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diff --git a/RegressionTestResults/PR_GlaucomaCV/AZUREML_PARENT_OUTPUT/CrossValResults/metrics_aggregates.csv b/RegressionTestResults/PR_GlaucomaCV/AZUREML_PARENT_OUTPUT/CrossValResults/metrics_aggregates.csv
new file mode 100644
index 000000000..2ac53c8cf
--- /dev/null
+++ b/RegressionTestResults/PR_GlaucomaCV/AZUREML_PARENT_OUTPUT/CrossValResults/metrics_aggregates.csv
@@ -0,0 +1,6 @@
+prediction_target,area_under_roc_curve,area_under_pr_curve,accuracy_at_optimal_threshold,false_positive_rate_at_optimal_threshold,false_negative_rate_at_optimal_threshold,optimal_threshold,cross_entropy,accuracy_at_threshold_05,subject_count,data_split,epoch
+Default,0.60030,0.78831,0.49554,0.14706,0.65385,0.39453,0.85501,0.30357,224.00000,Test,best_validation_epoch
+Default,0.54386,0.82674,0.41784,0.19651,0.65540,0.53906,0.68702,0.50501,998.00000,Train,0
+Default,0.63757,0.85404,0.76253,0.68122,0.10013,0.47534,0.67850,0.50501,998.00000,Train,1
+Default,0.61292,0.84750,0.45691,0.16157,0.65150,0.39356,0.84968,0.22946,998.00000,Val,0
+Default,0.61088,0.84921,0.46994,0.15721,0.63589,0.38892,0.89472,0.22946,998.00000,Val,1
diff --git a/RegressionTestResults/PR_GlaucomaCV/AZUREML_PARENT_OUTPUT/final_ensemble_model/model_inference_config.json b/RegressionTestResults/PR_GlaucomaCV/AZUREML_PARENT_OUTPUT/final_ensemble_model/model_inference_config.json
new file mode 100644
index 000000000..04b475ca2
--- /dev/null
+++ b/RegressionTestResults/PR_GlaucomaCV/AZUREML_PARENT_OUTPUT/final_ensemble_model/model_inference_config.json
@@ -0,0 +1 @@
+{"model_name": "GlaucomaPublic", "checkpoint_paths": ["checkpoints/OTHER_RUNS/1/best_checkpoint.ckpt", "checkpoints/best_checkpoint.ckpt"], "model_configs_namespace": "InnerEye.ML.configs.classification.GlaucomaPublic"}
\ No newline at end of file
diff --git a/RegressionTestResults/PR_HelloContainer/AZUREML_OUTPUT/model_inference_config.json b/RegressionTestResults/PR_HelloContainer/AZUREML_OUTPUT/model_inference_config.json
new file mode 100644
index 000000000..247a6a337
--- /dev/null
+++ b/RegressionTestResults/PR_HelloContainer/AZUREML_OUTPUT/model_inference_config.json
@@ -0,0 +1 @@
+{"model_name": "HelloContainer", "checkpoint_paths": ["checkpoints/best_checkpoint.ckpt"], "model_configs_namespace": "InnerEye.ML.configs.other.HelloContainer"}
\ No newline at end of file
diff --git a/RegressionTestResults/PR_HelloContainer/test_mse.txt b/RegressionTestResults/PR_HelloContainer/test_mse.txt
new file mode 100644
index 000000000..5ccc7afeb
--- /dev/null
+++ b/RegressionTestResults/PR_HelloContainer/test_mse.txt
@@ -0,0 +1 @@
+0.011612942442297935
\ No newline at end of file
diff --git a/RegressionTestResults/PR_Train2Nodes/Train/epoch_metrics.csv b/RegressionTestResults/PR_Train2Nodes/Train/epoch_metrics.csv
new file mode 100644
index 000000000..ef43fba9c
--- /dev/null
+++ b/RegressionTestResults/PR_Train2Nodes/Train/epoch_metrics.csv
@@ -0,0 +1,3 @@
+subject_count,loss,learning_rate,Dice/AverageAcrossStructures,Dice/spinalcord,Dice/lung_r,Dice/lung_l,VoxelCount/spinalcord,VoxelCount/lung_r,VoxelCount/lung_l,epoch,cross_validation_split_index
+4.000000,0.716913,0.000100,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,99342.000000,0,-1
+4.000000,0.773825,0.000090,0.000000,0.000000,0.000000,0.000000,181.250000,83803.250000,122.250000,1,-1
diff --git a/RegressionTestResults/PR_Train2Nodes/Val/epoch_metrics.csv b/RegressionTestResults/PR_Train2Nodes/Val/epoch_metrics.csv
new file mode 100644
index 000000000..51a3b2dba
--- /dev/null
+++ b/RegressionTestResults/PR_Train2Nodes/Val/epoch_metrics.csv
@@ -0,0 +1,3 @@
+subject_count,loss,Dice/AverageAcrossStructures,Dice/spinalcord,Dice/lung_r,Dice/lung_l,VoxelCount/spinalcord,VoxelCount/lung_r,VoxelCount/lung_l,epoch,cross_validation_split_index
+4.000000,0.729041,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,65335.000000,0,-1
+4.000000,0.729027,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,65335.000000,1,-1
diff --git a/RegressionTestResults/PR_Train2Nodes/best_validation_epoch/Test/metrics.csv b/RegressionTestResults/PR_Train2Nodes/best_validation_epoch/Test/metrics.csv
new file mode 100644
index 000000000..b543319b2
--- /dev/null
+++ b/RegressionTestResults/PR_Train2Nodes/best_validation_epoch/Test/metrics.csv
@@ -0,0 +1,13 @@
+Patient,Structure,Dice,HausdorffDistance_mm,MeanDistance_mm
+4,lung_l,0.000,inf,inf
+5,lung_l,0.000,inf,inf
+6,lung_l,0.000,inf,inf
+7,lung_l,0.000,inf,inf
+4,lung_r,0.000,inf,inf
+5,lung_r,0.000,inf,inf
+6,lung_r,0.000,inf,inf
+7,lung_r,0.000,inf,inf
+4,spinalcord,0.000,inf,inf
+5,spinalcord,0.000,inf,inf
+6,spinalcord,0.000,inf,inf
+7,spinalcord,0.000,inf,inf
diff --git a/RegressionTestResults/PR_Train2Nodes/best_validation_epoch/Val/metrics.csv b/RegressionTestResults/PR_Train2Nodes/best_validation_epoch/Val/metrics.csv
new file mode 100644
index 000000000..4ec56b6be
--- /dev/null
+++ b/RegressionTestResults/PR_Train2Nodes/best_validation_epoch/Val/metrics.csv
@@ -0,0 +1,7 @@
+Patient,Structure,Dice,HausdorffDistance_mm,MeanDistance_mm
+8,lung_l,0.000,inf,inf
+9,lung_l,0.000,inf,inf
+8,lung_r,0.000,inf,inf
+9,lung_r,0.000,inf,inf
+8,spinalcord,0.000,inf,inf
+9,spinalcord,0.000,inf,inf
diff --git a/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/CrossValResults/0/Test/metrics.csv b/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/CrossValResults/0/Test/metrics.csv
new file mode 100644
index 000000000..18c70f2a0
--- /dev/null
+++ b/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/CrossValResults/0/Test/metrics.csv
@@ -0,0 +1,4 @@
+Patient,Structure,Dice,HausdorffDistance_mm,MeanDistance_mm
+5,lung_l,0.000,inf,inf
+5,lung_r,0.000,inf,inf
+5,spinalcord,0.000,inf,inf
diff --git a/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/CrossValResults/0/Val/metrics.csv b/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/CrossValResults/0/Val/metrics.csv
new file mode 100644
index 000000000..a7ebff144
--- /dev/null
+++ b/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/CrossValResults/0/Val/metrics.csv
@@ -0,0 +1,7 @@
+Patient,Structure,Dice,HausdorffDistance_mm,MeanDistance_mm
+1,lung_l,0.000,inf,inf
+2,lung_l,0.000,inf,inf
+1,lung_r,0.000,inf,inf
+2,lung_r,0.000,inf,inf
+1,spinalcord,0.000,inf,inf
+2,spinalcord,0.000,inf,inf
diff --git a/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/CrossValResults/0/dataset.csv b/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/CrossValResults/0/dataset.csv
new file mode 100644
index 000000000..c6e178882
--- /dev/null
+++ b/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/CrossValResults/0/dataset.csv
@@ -0,0 +1,361 @@
+subject,filePath,channel,seriesId,institutionId,imageFilePathInPortal,groundTruthFilePathInPortal,tags,DIM_X,DIM_Y,DIM_Z
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+23,23/lung_r.nii.gz,lung_r,0e9d570979bcec7d101350b6c9fad3ff99599058617974b550c32abfdb29809e,b7f757fb-12e0-489e-a6da-f64895cdd229,LungChallenge/d4711d76e9b6a277319bf217c8764ee61965defd95d04e1e1cd83755d9fbac4d/b1b672b99836d7f12cb4238cffa4821de0c67b4de9d26423ef5dbe91871963cd/CT_0e9d570979bcec7d101350b6c9fad3ff99599058617974b550c32abfdb29809e_20200512173023.zip,LungChallenge/d4711d76e9b6a277319bf217c8764ee61965defd95d04e1e1cd83755d9fbac4d/b1b672b99836d7f12cb4238cffa4821de0c67b4de9d26423ef5dbe91871963cd/StructureSet_655e403fea2dd33587bfb599feb2d7b6a9e18e46857a8288a70b20c59bfc22c1_20200512172750.zip,[LungChallenge;LungChallenge_S3_LiveTest],152,500,500
+23,23/lung_l.nii.gz,lung_l,0e9d570979bcec7d101350b6c9fad3ff99599058617974b550c32abfdb29809e,b7f757fb-12e0-489e-a6da-f64895cdd229,LungChallenge/d4711d76e9b6a277319bf217c8764ee61965defd95d04e1e1cd83755d9fbac4d/b1b672b99836d7f12cb4238cffa4821de0c67b4de9d26423ef5dbe91871963cd/CT_0e9d570979bcec7d101350b6c9fad3ff99599058617974b550c32abfdb29809e_20200512173023.zip,LungChallenge/d4711d76e9b6a277319bf217c8764ee61965defd95d04e1e1cd83755d9fbac4d/b1b672b99836d7f12cb4238cffa4821de0c67b4de9d26423ef5dbe91871963cd/StructureSet_655e403fea2dd33587bfb599feb2d7b6a9e18e46857a8288a70b20c59bfc22c1_20200512172750.zip,[LungChallenge;LungChallenge_S3_LiveTest],152,500,500
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+3,3/spinalcord.nii.gz,spinalcord,9810bb101b20c58f2dd16ed9b7d3109e0749d31b4e827721b68b512130754e76,b7f757fb-12e0-489e-a6da-f64895cdd229,LungChallenge/7881bc5e58ae849cab8efe7f4fe8a6c1ffcf15fa76c083a96f2aabc4a122c44b/3dc79a4fdca733c3ca23a2af7b255f6ffe3d1cc3dbb5b63c49d3470d532fe97f/CT_9810bb101b20c58f2dd16ed9b7d3109e0749d31b4e827721b68b512130754e76_20200512163604.zip,LungChallenge/7881bc5e58ae849cab8efe7f4fe8a6c1ffcf15fa76c083a96f2aabc4a122c44b/3dc79a4fdca733c3ca23a2af7b255f6ffe3d1cc3dbb5b63c49d3470d532fe97f/StructureSet_396004673c52802640405fa141f0bf13bab6673a4070923ea29b56b8dbaf8d97_20200512163219.zip,[LungChallenge;LungChallenge_S1_OffsiteTest],131,500,500
+3,3/lung_r.nii.gz,lung_r,9810bb101b20c58f2dd16ed9b7d3109e0749d31b4e827721b68b512130754e76,b7f757fb-12e0-489e-a6da-f64895cdd229,LungChallenge/7881bc5e58ae849cab8efe7f4fe8a6c1ffcf15fa76c083a96f2aabc4a122c44b/3dc79a4fdca733c3ca23a2af7b255f6ffe3d1cc3dbb5b63c49d3470d532fe97f/CT_9810bb101b20c58f2dd16ed9b7d3109e0749d31b4e827721b68b512130754e76_20200512163604.zip,LungChallenge/7881bc5e58ae849cab8efe7f4fe8a6c1ffcf15fa76c083a96f2aabc4a122c44b/3dc79a4fdca733c3ca23a2af7b255f6ffe3d1cc3dbb5b63c49d3470d532fe97f/StructureSet_396004673c52802640405fa141f0bf13bab6673a4070923ea29b56b8dbaf8d97_20200512163219.zip,[LungChallenge;LungChallenge_S1_OffsiteTest],131,500,500
+3,3/lung_l.nii.gz,lung_l,9810bb101b20c58f2dd16ed9b7d3109e0749d31b4e827721b68b512130754e76,b7f757fb-12e0-489e-a6da-f64895cdd229,LungChallenge/7881bc5e58ae849cab8efe7f4fe8a6c1ffcf15fa76c083a96f2aabc4a122c44b/3dc79a4fdca733c3ca23a2af7b255f6ffe3d1cc3dbb5b63c49d3470d532fe97f/CT_9810bb101b20c58f2dd16ed9b7d3109e0749d31b4e827721b68b512130754e76_20200512163604.zip,LungChallenge/7881bc5e58ae849cab8efe7f4fe8a6c1ffcf15fa76c083a96f2aabc4a122c44b/3dc79a4fdca733c3ca23a2af7b255f6ffe3d1cc3dbb5b63c49d3470d532fe97f/StructureSet_396004673c52802640405fa141f0bf13bab6673a4070923ea29b56b8dbaf8d97_20200512163219.zip,[LungChallenge;LungChallenge_S1_OffsiteTest],131,500,500
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+11,11/lung_r.nii.gz,lung_r,c82cbd49e15f3088fb35a3c0c2808c6cacd6f1bea71ceaa089e8c7fa0cdc510b,b7f757fb-12e0-489e-a6da-f64895cdd229,LungChallenge/5606712ee1aa438a707d77fdea68a4070af557dd647705ebf7bb7b1dfab7ce87/7806d66600379e58701786f26530bcb1259b7ac96ada8bc281b0c22384729bad/CT_c82cbd49e15f3088fb35a3c0c2808c6cacd6f1bea71ceaa089e8c7fa0cdc510b_20200512165447.zip,LungChallenge/5606712ee1aa438a707d77fdea68a4070af557dd647705ebf7bb7b1dfab7ce87/7806d66600379e58701786f26530bcb1259b7ac96ada8bc281b0c22384729bad/StructureSet_805e8382da741748266348415384774f8494f8f6251d9ed9d06321d5248bb55a_20200512165049.zip,[LungChallenge;LungChallenge_S2_OffsiteTest],120,500,500
+11,11/lung_l.nii.gz,lung_l,c82cbd49e15f3088fb35a3c0c2808c6cacd6f1bea71ceaa089e8c7fa0cdc510b,b7f757fb-12e0-489e-a6da-f64895cdd229,LungChallenge/5606712ee1aa438a707d77fdea68a4070af557dd647705ebf7bb7b1dfab7ce87/7806d66600379e58701786f26530bcb1259b7ac96ada8bc281b0c22384729bad/CT_c82cbd49e15f3088fb35a3c0c2808c6cacd6f1bea71ceaa089e8c7fa0cdc510b_20200512165447.zip,LungChallenge/5606712ee1aa438a707d77fdea68a4070af557dd647705ebf7bb7b1dfab7ce87/7806d66600379e58701786f26530bcb1259b7ac96ada8bc281b0c22384729bad/StructureSet_805e8382da741748266348415384774f8494f8f6251d9ed9d06321d5248bb55a_20200512165049.zip,[LungChallenge;LungChallenge_S2_OffsiteTest],120,500,500
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+13,13/lung_r.nii.gz,lung_r,8ab073836e79b38adc53bc391ed6f47e294a4c547aea29888ad142f154f98f18,b7f757fb-12e0-489e-a6da-f64895cdd229,LungChallenge/068a3128b217295820f9d4fabb61177b0fa3d533fa643944e978c1c03dc1c477/ed3dcbff143717a7a878181811feebedb0beb687f9d0b92a940766e5c2e7e4f4/CT_8ab073836e79b38adc53bc391ed6f47e294a4c547aea29888ad142f154f98f18_20200512170635.zip,LungChallenge/068a3128b217295820f9d4fabb61177b0fa3d533fa643944e978c1c03dc1c477/ed3dcbff143717a7a878181811feebedb0beb687f9d0b92a940766e5c2e7e4f4/StructureSet_a1877c5277d8ef3b3e4be01eab805419222f6c4b04d067deb1f45de8167e5785_20200512170259.zip,[LungChallenge;LungChallenge_S2_LiveTest],118,500,500
+13,13/lung_l.nii.gz,lung_l,8ab073836e79b38adc53bc391ed6f47e294a4c547aea29888ad142f154f98f18,b7f757fb-12e0-489e-a6da-f64895cdd229,LungChallenge/068a3128b217295820f9d4fabb61177b0fa3d533fa643944e978c1c03dc1c477/ed3dcbff143717a7a878181811feebedb0beb687f9d0b92a940766e5c2e7e4f4/CT_8ab073836e79b38adc53bc391ed6f47e294a4c547aea29888ad142f154f98f18_20200512170635.zip,LungChallenge/068a3128b217295820f9d4fabb61177b0fa3d533fa643944e978c1c03dc1c477/ed3dcbff143717a7a878181811feebedb0beb687f9d0b92a940766e5c2e7e4f4/StructureSet_a1877c5277d8ef3b3e4be01eab805419222f6c4b04d067deb1f45de8167e5785_20200512170259.zip,[LungChallenge;LungChallenge_S2_LiveTest],118,500,500
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diff --git a/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/CrossValResults/1/Test/metrics.csv b/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/CrossValResults/1/Test/metrics.csv
new file mode 100644
index 000000000..c344a2e52
--- /dev/null
+++ b/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/CrossValResults/1/Test/metrics.csv
@@ -0,0 +1,4 @@
+Patient,Structure,Dice,HausdorffDistance_mm,MeanDistance_mm
+5,lung_l,0.000,inf,inf
+5,lung_r,0.000,inf,inf
+5,spinalcord,0.000,169.770,108.318
diff --git a/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/CrossValResults/1/Val/metrics.csv b/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/CrossValResults/1/Val/metrics.csv
new file mode 100644
index 000000000..1c6b5ff82
--- /dev/null
+++ b/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/CrossValResults/1/Val/metrics.csv
@@ -0,0 +1,4 @@
+Patient,Structure,Dice,HausdorffDistance_mm,MeanDistance_mm
+0,lung_l,0.000,inf,inf
+0,lung_r,0.000,inf,inf
+0,spinalcord,0.000,160.223,98.037
diff --git a/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/CrossValResults/1/dataset.csv b/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/CrossValResults/1/dataset.csv
new file mode 100644
index 000000000..c6e178882
--- /dev/null
+++ b/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/CrossValResults/1/dataset.csv
@@ -0,0 +1,361 @@
+subject,filePath,channel,seriesId,institutionId,imageFilePathInPortal,groundTruthFilePathInPortal,tags,DIM_X,DIM_Y,DIM_Z
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+10,10/lung_r.nii.gz,lung_r,d7799ced245c36e4543eaf5747f6dcf46c88142ef20e66f6c73e6d246d3cac28,b7f757fb-12e0-489e-a6da-f64895cdd229,LungChallenge/3c52c047a3e667169be6d0bd3b6183badbf63e161760d1199076656fd423fc0a/9e9ccb93caf016620e1c8bfdc0d8c75ee09085b3a47a743e70b50594d1597791/CT_d7799ced245c36e4543eaf5747f6dcf46c88142ef20e66f6c73e6d246d3cac28_20200512165329.zip,LungChallenge/3c52c047a3e667169be6d0bd3b6183badbf63e161760d1199076656fd423fc0a/9e9ccb93caf016620e1c8bfdc0d8c75ee09085b3a47a743e70b50594d1597791/StructureSet_9351f4624611f2c186396990ead2c63d8f88a315dc21d01c429f4562f4bb75c3_20200512165031.zip,[LungChallenge;LungChallenge_S2_OffsiteTest],100,500,500
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+11,11/lung_l.nii.gz,lung_l,c82cbd49e15f3088fb35a3c0c2808c6cacd6f1bea71ceaa089e8c7fa0cdc510b,b7f757fb-12e0-489e-a6da-f64895cdd229,LungChallenge/5606712ee1aa438a707d77fdea68a4070af557dd647705ebf7bb7b1dfab7ce87/7806d66600379e58701786f26530bcb1259b7ac96ada8bc281b0c22384729bad/CT_c82cbd49e15f3088fb35a3c0c2808c6cacd6f1bea71ceaa089e8c7fa0cdc510b_20200512165447.zip,LungChallenge/5606712ee1aa438a707d77fdea68a4070af557dd647705ebf7bb7b1dfab7ce87/7806d66600379e58701786f26530bcb1259b7ac96ada8bc281b0c22384729bad/StructureSet_805e8382da741748266348415384774f8494f8f6251d9ed9d06321d5248bb55a_20200512165049.zip,[LungChallenge;LungChallenge_S2_OffsiteTest],120,500,500
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diff --git a/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/CrossValResults/Test_outliers.txt b/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/CrossValResults/Test_outliers.txt
new file mode 100644
index 000000000..b1ac6c222
--- /dev/null
+++ b/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/CrossValResults/Test_outliers.txt
@@ -0,0 +1,9 @@
+
+
+=== METRIC: Dice ===
+
+No outliers found
+
+=== METRIC: HausdorffDistance_mm ===
+
+No outliers found
\ No newline at end of file
diff --git a/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/CrossValResults/Val_outliers.txt b/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/CrossValResults/Val_outliers.txt
new file mode 100644
index 000000000..b1ac6c222
--- /dev/null
+++ b/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/CrossValResults/Val_outliers.txt
@@ -0,0 +1,9 @@
+
+
+=== METRIC: Dice ===
+
+No outliers found
+
+=== METRIC: HausdorffDistance_mm ===
+
+No outliers found
\ No newline at end of file
diff --git a/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/best_validation_epoch/Test/005/posterior_lung_r.nii.gz b/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/best_validation_epoch/Test/005/posterior_lung_r.nii.gz
new file mode 100644
index 000000000..49939bb38
--- /dev/null
+++ b/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/best_validation_epoch/Test/005/posterior_lung_r.nii.gz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:750a36ad0a16e6b61df51a30a658925d73b44f73fd8be065dce9f81ca228296b
+size 41162
diff --git a/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/best_validation_epoch/Test/005/uncertainty.nii.gz b/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/best_validation_epoch/Test/005/uncertainty.nii.gz
new file mode 100644
index 000000000..178f30897
--- /dev/null
+++ b/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/best_validation_epoch/Test/005/uncertainty.nii.gz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:9027ce6164d9dbc666a19b9406bbde3f1a966b7049597dea76ac0348b46d439c
+size 41162
diff --git a/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/best_validation_epoch/Test/metrics.csv b/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/best_validation_epoch/Test/metrics.csv
new file mode 100644
index 000000000..6879d67ec
--- /dev/null
+++ b/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/best_validation_epoch/Test/metrics.csv
@@ -0,0 +1,4 @@
+Patient,Structure,Dice,HausdorffDistance_mm,MeanDistance_mm
+5,lung_l,0.000,103.189,38.122
+5,lung_r,0.000,inf,inf
+5,spinalcord,0.000,inf,inf
diff --git a/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/best_validation_epoch/Test/thumbnails/005_spinalcord_slice_088.png b/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/best_validation_epoch/Test/thumbnails/005_spinalcord_slice_088.png
new file mode 100644
index 000000000..036fe34b5
--- /dev/null
+++ b/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/best_validation_epoch/Test/thumbnails/005_spinalcord_slice_088.png
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:0d0ec9d8c878f4472d10414907a6cfd589a03884214ef92412234410523fd56a
+size 102433
diff --git a/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/final_ensemble_model/model_inference_config.json b/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/final_ensemble_model/model_inference_config.json
new file mode 100644
index 000000000..05440a162
--- /dev/null
+++ b/RegressionTestResults/PR_TrainEnsemble/AZUREML_PARENT_OUTPUT/final_ensemble_model/model_inference_config.json
@@ -0,0 +1 @@
+{"model_name": "BasicModel2Epochs", "checkpoint_paths": ["checkpoints/best_checkpoint.ckpt", "checkpoints/OTHER_RUNS/1/best_checkpoint.ckpt"], "model_configs_namespace": "InnerEye.ML.configs.segmentation.BasicModel2Epochs"}
\ No newline at end of file
diff --git a/RegressionTestResults/PR_TrainEnsemble/Train/epoch_metrics.csv b/RegressionTestResults/PR_TrainEnsemble/Train/epoch_metrics.csv
new file mode 100644
index 000000000..e179b844d
--- /dev/null
+++ b/RegressionTestResults/PR_TrainEnsemble/Train/epoch_metrics.csv
@@ -0,0 +1,3 @@
+subject_count,loss,learning_rate,Dice/AverageAcrossStructures,Dice/spinalcord,Dice/lung_r,Dice/lung_l,VoxelCount/spinalcord,VoxelCount/lung_r,VoxelCount/lung_l,epoch,cross_validation_split_index
+2.000000,0.723947,0.000100,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,148093.000000,0,0
+2.000000,0.768603,0.000090,0.000000,0.000000,0.000000,0.000000,0.000000,86614.000000,0.000000,1,0
diff --git a/RegressionTestResults/PR_TrainEnsemble/Val/epoch_metrics.csv b/RegressionTestResults/PR_TrainEnsemble/Val/epoch_metrics.csv
new file mode 100644
index 000000000..5137305ea
--- /dev/null
+++ b/RegressionTestResults/PR_TrainEnsemble/Val/epoch_metrics.csv
@@ -0,0 +1,3 @@
+subject_count,loss,Dice/AverageAcrossStructures,Dice/spinalcord,Dice/lung_r,Dice/lung_l,VoxelCount/spinalcord,VoxelCount/lung_r,VoxelCount/lung_l,epoch,cross_validation_split_index
+2.000000,0.715168,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,94367.500000,0,0
+2.000000,0.715166,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,94367.500000,1,0
diff --git a/Tests/ML/test_regression_tests.py b/Tests/ML/test_regression_tests.py
new file mode 100644
index 000000000..89b963713
--- /dev/null
+++ b/Tests/ML/test_regression_tests.py
@@ -0,0 +1,205 @@
+#  ------------------------------------------------------------------------------------------
+#  Copyright (c) Microsoft Corporation. All rights reserved.
+#  Licensed under the MIT License (MIT). See LICENSE in the repo root for license information.
+#  ------------------------------------------------------------------------------------------
+import logging
+from pathlib import Path
+from unittest import mock
+
+import pytest
+
+from InnerEye.Common.common_util import CROSSVAL_RESULTS_FOLDER, logging_to_stdout
+from InnerEye.Common.fixed_paths import MODEL_INFERENCE_JSON_FILE_NAME
+from InnerEye.Common.output_directories import OutputFolderForTests
+from InnerEye.ML import baselines_util
+from InnerEye.ML.baselines_util import REGRESSION_TEST_AZUREML_FOLDER, REGRESSION_TEST_AZUREML_PARENT_FOLDER, \
+    compare_files, compare_folder_contents, compare_folders_and_run_outputs
+from InnerEye.ML.deep_learning_config import FINAL_MODEL_FOLDER
+from InnerEye.ML.run_ml import MLRunner
+from Tests.AfterTraining.test_after_training import FALLBACK_ENSEMBLE_RUN, FALLBACK_SINGLE_RUN, get_most_recent_run
+from Tests.ML.configs.lightning_test_containers import DummyContainerWithModel
+
+
+def create_folder_and_write_text(file: Path, text: str) -> None:
+    """
+    Writes the given text to a file. The folders in which the file lives are created too, unless they exist already.
+    Writing the text keeps the line separators as-is (no translation)
+    """
+    file.parent.mkdir(exist_ok=True, parents=True)
+    with file.open(mode="wt", newline="") as f:
+        f.write(text)
+
+
+def test_regression_test(test_output_dirs: OutputFolderForTests) -> None:
+    """
+    Test that the file comparison for regression tests is actually called in the workflow.
+    """
+    container = DummyContainerWithModel()
+    container.local_dataset = test_output_dirs.root_dir
+    container.regression_test_folder = Path("foo")
+    runner = MLRunner(container=container)
+    runner.setup(use_mount_or_download_dataset=False)
+    with pytest.raises(ValueError) as ex:
+        runner.run()
+    assert "Folder with expected files does not exist" in str(ex)
+
+
+def test_compare_folder_exists(test_output_dirs: OutputFolderForTests) -> None:
+    """
+    Test if the folder comparison method raises an exception on invalid input.
+    """
+    does_not_exist = test_output_dirs.root_dir / "foo"
+    with pytest.raises(ValueError) as ex:
+        compare_folder_contents(expected_folder=does_not_exist, actual_folder=test_output_dirs.root_dir)
+    assert "Folder with expected files does not exist" in str(ex)
+
+
+@pytest.mark.parametrize("file_extension", baselines_util.TEXT_FILE_SUFFIXES)
+def test_compare_files_text(test_output_dirs: OutputFolderForTests, file_extension: str) -> None:
+    """
+    Checks the basic code to compare the contents of two text files.
+    :param test_output_dirs:
+    :param file_extension: The extension of the file to create.
+    """
+    logging_to_stdout(log_level=logging.DEBUG)
+    expected = test_output_dirs.root_dir / f"expected{file_extension}"
+    actual = test_output_dirs.root_dir / "actual.does_not_matter"
+    # Make sure that we test different line endings - the files should still match
+    create_folder_and_write_text(expected, "Line1\r\nLine2")
+    create_folder_and_write_text(actual, "Line1\nLine2")
+    assert compare_files(expected=expected, actual=actual) == ""
+    actual.write_text("does_not_match")
+    assert compare_files(expected=expected, actual=actual) == baselines_util.CONTENTS_MISMATCH
+
+
+@pytest.mark.parametrize("file_extension", [".png", ".whatever"])
+def test_compare_files_binary(test_output_dirs: OutputFolderForTests, file_extension: str) -> None:
+    """
+    Checks the comparison of files that are not recognized as text files, for example images.
+    :param test_output_dirs:
+    :param file_extension: The extension of the file to create.
+    """
+    logging_to_stdout(log_level=logging.DEBUG)
+    expected = test_output_dirs.root_dir / f"expected{file_extension}"
+    actual = test_output_dirs.root_dir / "actual.does_not_matter"
+    data1 = bytes([1, 2, 3])
+    data2 = bytes([4, 5, 6])
+    expected.write_bytes(data1)
+    actual.write_bytes(data1)
+    assert compare_files(expected=expected, actual=actual) == ""
+    actual.write_bytes(data2)
+    assert compare_files(expected=expected, actual=actual) == baselines_util.CONTENTS_MISMATCH
+
+
+def test_compare_folder(test_output_dirs: OutputFolderForTests) -> None:
+    """
+    Test the comparison of folders that we use for regression tests.
+    """
+    # Create a test of expected and actual files on the fly.
+    expected = test_output_dirs.root_dir / "expected"
+    actual = test_output_dirs.root_dir / "actual"
+    matching = "matching.txt"
+    missing = "missing.txt"
+    ignored = "ignored.txt"
+    # Comparison should cover at least .csv and .txt files
+    mismatch = "mismatch.csv"
+    extra = "extra.txt"
+    subfolder = Path("folder")
+    # This file exists in both expected and actual, should not raise any alerts because it contents matches
+    # apart from linebreaks
+    create_folder_and_write_text(expected / subfolder / matching, "Line1\r\nLine2")
+    create_folder_and_write_text(actual / subfolder / matching, "Line1\nLine2")
+    # This file only exists in the expected results, and should create an error
+    (expected / subfolder / missing).write_text("missing")
+    (actual / extra).write_text("extra")
+    # This file exists in both actual and expected, but has different contents, hence should create an error
+    (expected / subfolder / mismatch).write_text("contents1")
+    (actual / subfolder / mismatch).write_text("contents2")
+    # Create folders that hold the expected results in the AzureML run context. These should be ignored when doing
+    # the file-by-file comparison on the local output files.
+    for ignored_folder in [REGRESSION_TEST_AZUREML_FOLDER, REGRESSION_TEST_AZUREML_PARENT_FOLDER]:
+        azureml1 = expected / ignored_folder / ignored
+        azureml1.parent.mkdir()
+        azureml1.touch()
+
+    with pytest.raises(ValueError) as ex:
+        compare_folder_contents(expected_folder=expected, actual_folder=actual)
+    message = ex.value.args[0].splitlines()
+    # No message expected
+    assert matching not in str(ex)
+    assert extra not in str(ex)
+    assert ignored not in str(ex)
+    # Folders should be skipped in the comparison
+    assert f"{baselines_util.MISSING_FILE}: {subfolder}" not in message
+    assert f"{baselines_util.MISSING_FILE}: {subfolder}/{missing}" in message
+    assert f"{baselines_util.CONTENTS_MISMATCH}: {subfolder}/{mismatch}" in message
+
+
+@pytest.mark.after_training_single_run
+def test_compare_folder_against_run(test_output_dirs: OutputFolderForTests) -> None:
+    """
+    Test if we can compare that a set of files exists in an AML run.
+    """
+    logging_to_stdout(log_level=logging.DEBUG)
+    run = get_most_recent_run(fallback_run_id_for_local_execution=FALLBACK_SINGLE_RUN)
+    file1 = test_output_dirs.root_dir / REGRESSION_TEST_AZUREML_FOLDER / \
+            FINAL_MODEL_FOLDER / MODEL_INFERENCE_JSON_FILE_NAME
+    create_folder_and_write_text(file1,
+                                 '{"model_name": "BasicModel2Epochs", "checkpoint_paths": ['
+                                 '"checkpoints/best_checkpoint.ckpt"], '
+                                 '"model_configs_namespace": "InnerEye.ML.configs.segmentation.BasicModel2Epochs"}')
+    with mock.patch("InnerEye.ML.baselines_util.RUN_CONTEXT", run):
+        # First comparison only on the .json file should pass
+        compare_folders_and_run_outputs(expected=test_output_dirs.root_dir, actual=Path.cwd())
+        # Now add a file to the set of expected files that does not exist in the run: comparison should now fail
+        no_such_file = "no_such_file.txt"
+        file2 = test_output_dirs.root_dir / REGRESSION_TEST_AZUREML_FOLDER / no_such_file
+        create_folder_and_write_text(file2, "foo")
+        with pytest.raises(ValueError) as ex:
+            compare_folders_and_run_outputs(expected=test_output_dirs.root_dir, actual=Path.cwd())
+        message = ex.value.args[0].splitlines()
+        assert f"{baselines_util.MISSING_FILE}: {no_such_file}" in message
+    # Now run the same comparison that failed previously, without mocking the RUN_CONTEXT. This should now
+    # realize that the present run is an offline run, and skip the comparison
+    compare_folders_and_run_outputs(expected=test_output_dirs.root_dir, actual=Path.cwd())
+
+
+@pytest.mark.after_training_ensemble_run
+def test_compare_folder_against_parent_run(test_output_dirs: OutputFolderForTests) -> None:
+    """
+    Test if we can compare that a set of files exists in an AML run.
+    """
+    logging_to_stdout(log_level=logging.DEBUG)
+    parent_run = get_most_recent_run(fallback_run_id_for_local_execution=FALLBACK_ENSEMBLE_RUN)
+    file1 = test_output_dirs.root_dir / REGRESSION_TEST_AZUREML_PARENT_FOLDER / \
+            CROSSVAL_RESULTS_FOLDER / "Test_outliers.txt"
+    create_folder_and_write_text(file1, """
+
+=== METRIC: Dice ===
+
+No outliers found
+
+=== METRIC: HausdorffDistance_mm ===
+
+No outliers found""")
+    with mock.patch("InnerEye.ML.baselines_util.PARENT_RUN_CONTEXT", parent_run):
+        # No plain files to compare. The file Test_outliers.txt should be compared and found to match.
+        compare_folders_and_run_outputs(expected=test_output_dirs.root_dir, actual=Path.cwd())
+        create_folder_and_write_text(file1, "foo")
+        with pytest.raises(ValueError) as ex:
+            compare_folders_and_run_outputs(expected=test_output_dirs.root_dir, actual=Path.cwd())
+        message = ex.value.args[0].splitlines()
+        assert f"{baselines_util.CONTENTS_MISMATCH}: {CROSSVAL_RESULTS_FOLDER}/{file1.name}" in message
+        # Now add a file to the set of expected files that does not exist in the run: comparison should now fail
+        no_such_file = "no_such_file.txt"
+        file2 = test_output_dirs.root_dir / REGRESSION_TEST_AZUREML_PARENT_FOLDER / no_such_file
+        create_folder_and_write_text(file2, "foo")
+        with pytest.raises(ValueError) as ex:
+            compare_folders_and_run_outputs(expected=test_output_dirs.root_dir, actual=Path.cwd())
+        message = ex.value.args[0].splitlines()
+        assert f"{baselines_util.MISSING_FILE}: {no_such_file}" in message
+    # Now run the same comparison without mocking the PARENT_RUN_CONTEXT. This should now
+    # realize that the present run is a crossval child run
+    with pytest.raises(ValueError) as ex:
+        compare_folders_and_run_outputs(expected=test_output_dirs.root_dir, actual=Path.cwd())
+    assert "run is not a cross-validation child run" in str(ex)
diff --git a/azure-pipelines/build-pr.yml b/azure-pipelines/build-pr.yml
index fc62b07c9..935f009a4 100644
--- a/azure-pipelines/build-pr.yml
+++ b/azure-pipelines/build-pr.yml
@@ -34,7 +34,7 @@ jobs:
       - name: tag
         value: 'TrainBasicModel'
       - name: more_switches
-        value: '--log_level=DEBUG --use_dataset_mount=True'
+        value: '--log_level=DEBUG --use_dataset_mount=True --regression_test_folder=RegressionTestResults/PR_BasicModel2Epochs'
     pool:
       vmImage: 'ubuntu-18.04'
     steps:
@@ -97,6 +97,8 @@ jobs:
         value: 2
       - name: tag
         value: 'TrainEnsemble'
+      - name: more_switches
+        value: '--regression_test_folder=RegressionTestResults/PR_TrainEnsemble'
     pool:
       vmImage: 'ubuntu-18.04'
     steps:
@@ -118,7 +120,7 @@ jobs:
       - name: tag
         value: 'Train2Nodes'
       - name: more_switches
-        value: '--log_level=DEBUG --num_nodes=2'
+        value: '--log_level=DEBUG --num_nodes=2 --regression_test_folder=RegressionTestResults/PR_Train2Nodes'
     pool:
       vmImage: 'ubuntu-18.04'
     steps:
@@ -142,7 +144,7 @@ jobs:
       - name: number_of_cross_validation_splits
         value: 2
       - name: more_switches
-        value: '--num_epochs=2'
+        value: '--num_epochs=2 --regression_test_folder=RegressionTestResults/PR_GlaucomaCV'
     pool:
       vmImage: 'ubuntu-18.04'
     steps:
@@ -180,7 +182,7 @@ jobs:
       - name: tag
         value: 'HelloContainerPR'
       - name: more_switches
-        value: '--num_nodes=2'
+        value: '--num_nodes=2 --regression_test_folder=RegressionTestResults/PR_HelloContainer'
     pool:
       vmImage: 'ubuntu-18.04'
     steps: