pcastle 1.0.0
Pipeline for causal structure learning
License: Apache License 2.0
Requires Python: >=3.6

# gCastle

[中文版本](./README.cn.md)

Version 1.0.0 released.

## Introduction

`gCastle` is a causal structure learning toolchain developed by [Huawei Noah's Ark Lab](https://www.noahlab.com.hk/#/home). The package contains various functionality related to causal learning and evaluation, including: 
* Data generation and processing: data simulation, data reading operators, and data pre-processing operators（such as prior injection and variable selection).
* Causal structure learning: causal structure learning methods, including both classic and recently developed methods, especially gradient-based ones that can handle large problems.
* Evaluation metrics: various commonly used metrics for causal structure learning, including F1, SHD, FDR, TPR, FDR, NNZ, etc.

## Algorithm List

| Algorithm | Category (based on data) | Description | Status |
| :--: | :-- | :-- | :-- |
| [PC](https://arxiv.org/abs/math/0510436) | IID | A classic causal discovery algorithm based on conditional independence tests | v1.0.0 |
| [DirectLiNGAM](https://arxiv.org/abs/1101.2489) | IID | A direct learning algorithm for linear non-Gaussian acyclic model (LiNGAM) | v1.0.0 |
| [ICALiNGAM](https://dl.acm.org/doi/10.5555/1248547.1248619) | IID | An ICA-based learning algorithm for linear non-Gaussian acyclic model (LiNGAM) | v1.0.0 |
| [NOTEARS](https://arxiv.org/abs/1803.01422) | IID | A gradient-based algorithm for linear data models (typically with least-squares loss) | v1.0.0 |
| [NOTEARS-MLP](https://arxiv.org/abs/1909.13189) | IID | A gradient-based algorithm using neural network modeling for non-linear causal relationships | v1.0.0 |
| [NOTEARS-SOB](https://arxiv.org/abs/1909.13189) | IID | A gradient-based algorithm using Sobolev space modeling for non-linear causal relationships | v1.0.0 |
| [NOTEARS-lOW-RANK](https://arxiv.org/abs/2006.05691) | IID | Adapting NOTEARS for large problems with low-rank causal graphs | v1.0.0 |
| [GOLEM](https://arxiv.org/abs/2006.10201) | IID | A more efficient version of NOTEARS that can reduce number of optimization iterations | v1.0.0 |
| [GraN_DAG](https://arxiv.org/abs/1906.02226) | IID | A gradient-based algorithm using neural network modeling for non-linear additive noise data  | v1.0.0 |
| [MCSL](https://arxiv.org/abs/1910.08527) | IID | A gradient-based algorithm for non-linear additive noise data by learning the binary adjacency matrix| v1.0.0 |
| [GAE](https://arxiv.org/abs/1911.07420) | IID | A gradient-based algorithm using graph autoencoder to model non-linear causal relationships| v1.0.0 |
| [RL](https://arxiv.org/abs/1906.04477) | IID | A RL-based algorithm that can work with flexible score functions (including non-smooth ones) | v1.0.0 |
| CORL1 | IID | A RL- and order-based algorithm that improves the efficiency and scalability of previous RL-based approach | v1.0.0 |
| CORL2 | IID | A RL- and order-based algorithm that improves the efficiency and scalability of previous RL-based approach | v1.0.0 |
| TTPM | EVENT SEQUENCE | A causal structure learning algorithm based on Topological Hawkes process for spatio-temporal event sequences | under development. |
| HPCI | EVENT SEQUENCE | A causal structure learning algorithm based on Hawkes process and CI tests for event sequences | under development. |
| PCTS | TS | A causal structure learning algorithm based on CI tests for time series data (time series version of the PC algorithm) | under development. |


## Installation

### Dependencies
gCastle requires:
- python (>= 3.6)
- tqdm (>= 4.48.2)
- numpy (>= 1.19.2)
- pandas (>= 0.22.0)
- scipy (>= 1.4.1)
- scikit-learn (>= 0.21.1)
- matplotlib (>=2.1.2)
- python-igraph (>= 0.8.2)
- loguru (>= 0.5.3)
- networkx (>= 2.5)
- torch (>= 1.4.0)
- tensorflow (== 1.15.0)


### Obtain the installation package (installing from source code)
Download：[castle-1.0.0-py3-none-any.whl](./packages/gcastle-1.0.0-py3-none-any.whl)

### PIP installation
```
pip install gcastle-1.0.0-py3-none-any.whl
```

## Usage Example (PC algorithm)
```python
from castle.common import GraphDAG
from castle.metrics import MetricsDAG
from castle.datasets import IIDSimulation, DAG
from castle.algorithms import PC

# data simulation, simulate true causal dag and train_data.
weighted_random_dag = DAG.erdos_renyi(n_nodes=10, n_edges=10, 
                                      weight_range=(0.5, 2.0), seed=1)
dataset = IIDSimulation(W=weighted_random_dag, n=2000, method='linear', 
                        sem_type='gauss')
true_causal_matrix, X = dataset.B, dataset.X

# structure learning
pc = PC()
pc.learn(X)

# plot predict_dag and true_dag
GraphDAG(pc.causal_matrix, true_causal_matrix, 'result')

# calculate metrics
mt = MetricsDAG(pc.causal_matrix, true_causal_matrix)
print(mt.metrics)
```
You can visit [examples](./castle/example) to find more examples.


## Next Up & Contributing
This is the first released version of `gCastle`, we'll be continuously complementing and optimizing the code and documentation. The following items are the main additions planned to be released in the next version (~late April 2021): 
* A more sound documentation: including introductions to each algorithm, a guide on how to quickly design an experiment/test using the 'gCastle' tools, more easily readable APIs, etc.
* Extension of the algorithm library: add new algorithms including `GES`, `HPCI`, and `TTPM`, and easily configurable scripts to help learn causal structures using the corresponding algorithms.
* Real-world datasets: add a couple of interesting time series and event sequences datasets collected from AIOPS scenarios where the true graphs are obtained based on expertise.

We welcome new contributors of all experience levels. If you have any questions or suggestions (such as, contributing new algorithms, optimizing code, improving documentation), please submit an issue here. We will reply as soon as possible.