SAGED: Meta Learning-based Error Detection Method for Structured Data

In this repository, we introduce a novel method for automated error detection in structured data, referred to as SAGED (Software AG Error Detection). The core idea behind SAGED is to formulate the task of error detection as a classification problem. In this realm, we exploit the design-time artifacts while generating features required to train a detection classifier. To this end, meta-learning is utilized to transfer knowledge from a set of historical previously-repaired datasets to the new dirty datasets, i.e., the datasets to be cleaned. Specifically, SAGED consists of two phases, namely the knowledge extraction phase and the detection phase. In the former phase, we train a set of ML models to differentiate between erroneous and clean samples in the historical datasets. The latter phase begins with matching the new dirty dataset with a set of the historical datasets, before using the corresponding models to generate the feature vector for the meta-classifier. In this case, the features represent the predictions obtained from the base classifiers. To realize the adoption of meta learning in the proposed invention, two challenges, including the varying-length feature vector, and the irrelevant knowledge problem, have to be overcome. To this end, the invention implements a zero-padding mechanism and a clustering approach to group the base classifiers in the knowledge extraction phase.

Setup

Clone with submodules

git clone https://git.sagresearch.de/kompaki/cleanlearning/saged.git --recurse-submodules

Create a virtual environment and install requirements

Update All Packages On Ubuntu

sudo apt update && sudo apt upgrade -y

python3 -m venv venv 
source venv/bin/activate
pip3 install --upgrade setuptools
pip3 install --upgrade pip

Install error generator

cd baseline/setup/error_generator
python3 setup.py install

Install pyTorch

pip3 install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cpu

pip3 install -e .

Install error detection and repair methods

RAHA and BARAN

To install these methods, you can do so in two different ways:

Option 1: through pip3

pip3 install raha

Option 2: through the setup.py script which exists in the raha main directory

python3 setup.py install

Katara

For this method, we do not need to install packages, but we need to download the knowledge base: Download the knowledge base (link) and unzip the file. The files of the knowledge base should be placed in the following path.

cd detectors/katara/knowedge-base

FAHES

To install FAHES, navigate to the src directory and run make to compile the source code

cd FAHES/src/

make clean && make

HoloClean

To install HoloClean, read te installation part of its README file and make sure to active the Postgresql service.

Usage

To run SAGED, you need to have enough classifiers trained. To train MLP classifiers for every dataset in the datasets/ directory, run

python3 scripts/train_classifiers.py --datasets hospital --classifiers mlp_classifier

You can also specify datasets to train classifiers for with the --datasets argument and choose different classifiers.

Run SAGED

The following command runs the SAGED detector to find errors in a dirty dataset using the models trained on historical data. The options are as follows: - --dirty-dataset: String denoting the name of the input dirty dataset - --historical-datasets: String denoting the names of the historical datasts used for training the base models - --tags: String used to describe the experiment - --features: String denoting which features to use while training the detection classifier. It can take two values, either meta to run SAGED on the meta features or classic to run a No-meta-learning detector (similar to RAHA and ED2). - --verbose: print the logs

python3 scripts/run_saged.py 
        --dirty-dataset hospital 
        --historical-datasets adult beers airbnb flights movies_1 
        --tags "excluding rayyan and tax" 
        --verbose

To track the experiments and log the metrics, parameters, artifacts, and models

mlflow ui

Run baseline

The folloing command is used to detect errors in a dirty dataset using one of the baseline detectors.

python scripts/run_baseline.py --dirty-dataset nasa
                               --detection-method raha
                               --runs 10
                               --verbose

Test E2E pipelines using baseline detectors

The following command runs a ML pipeline consists of an error detection, a repair method, and a ML model building module.

python3 scripts/test_e2e_baseline.py 
        --dataset beers 
        --detection_method raha 
        --repair_method standardImputer

Test E2E pipelines using SAGED

The following command runs a ML pipeline which uses SAGED for detecting errors.

python3 scripts/test_e2e_saged.py 
        --dirty-dataset beers 
        --historical-datasets adult 
        --repair_method standardImputer
        --verbose

Components

Automatic featurization
Base models selection: clustering, cosine similarity
feature generation (serving base models)
Labeling (sampling): random, active learning, clustering, or heuristic
Label augmentation (sampling): none, random, active learning, prediction, knn-shapley

Performance evaluation

Experiments

Datasets

ToDos

Search for real datasets with real error profiles.
write scripts to run the various experiments and plotting the results
Setup a server to run the experiments

Follow-up Ideas

Recognizing the error type, e.g., outlier, rule violation, missing value, etc.
The current implementation of SAGED requires the availability of ground truth to label train data (y_train) of meta classifiers and to evaluate the performance (y_test). We need to modify this implementation to make it work even without ground truth. In this case, users will be asked to label the data directly.

mohamedyd/SAGED