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tigerlily

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TigerLily: Finding drug interactions in silico with the Graph.

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- - main.yaml
- edges.csv
- pagerank_scores.csv
- pagerank_toy_scores.csv
- target.csv
- - conf.py
  - index.rst
- index.html
- Makefile
- requirements_1.txt
- pair_scoring.jpg
- pair_scoring_A.jpg
- pair_scoring_B.jpg
- pair_scoring_C.jpg
- pair_scoring_D.jpg
- tigerlily_logo.jpg
- personalized_pagerank.gqsl
- test_tigerlily.py
- __init__.py
- dataset.py
- embedding.py
- operator.py
- pagerank.py
- version.py
.coveragerc
.gitignore
CONTRIBUTING.md
example_notebook.ipynb
LICENSE
MANIFEST.in
pyproject.toml
README.md
readthedocs.yaml
setup.cfg
setup.py
TigerLilyReport.pdf
tox.ini

# Installation Guide

1. Get the code

git clone https://github.com/benedekrozemberczki/tigerlily

Downloads the entire project code from GitHub to your computer.

cd tigerlily

Moves into the project folder you just downloaded.

2. Official Install Script

Easy Recommended

Prerequisites

Python 3 Python is required to use pip.

pip install tigerlily

Installs the package published on PyPI directly — no need to clone the source.

✅ After installing, open a new terminal and run the program's version command (e.g. --version) to confirm it worked.

Pulled directly from this repo's README.

3. Python

Easy

Prerequisites

Git Needed to download the project code from GitHub.
Python 3 On Windows, be sure to check 'Add Python to PATH' during installation.

pip install tigerlily

Installs the package published on PyPI directly — no need to clone the source.

✅ If it runs without errors and prints output in the terminal, it worked.

Pulled directly from this repo's README.

// repository documentation

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[pypi-image]: https://badge.fury.io/py/tigerlily.svg
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[build-image]: https://github.com/benedekrozemberczki/tigerlily/workflows/CI/badge.svg
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[coverage-image]: https://codecov.io/gh/benedekrozemberczki/tigerlily/branch/main/graph/badge.svg?token=30XLVBUIEH
[coverage-url]: https://codecov.io/github/benedekrozemberczki/tigerlily?branch=main

[![PyPI Version][pypi-image]][pypi-url]
[![Docs Status][docs-image]][docs-url]
[![Code Coverage][coverage-image]][coverage-url]
[![Build Status][build-image]][build-url]
[![Arxiv](https://img.shields.io/badge/ArXiv-2204.08206-orange.svg)](https://arxiv.org/abs/2204.08206)

<p align="center">
  <img width="100%" src="https://github.com/benedekrozemberczki/tigerlily/blob/main/images/tigerlily_logo.jpg?sanitize=true" />
</p>

----------------------------------------------------------------------

### **Drug Interaction Prediction with Tigerlily**

**[Documentation](https://tigerlily.readthedocs.io)** | **[Example Notebook](https://github.com/benedekrozemberczki/tigerlily/blob/main/example_notebook.ipynb)** |  **[Youtube Video](https://www.youtube.com/watch?v=fEWcor96tt8)** |  **[Project Report](http://arxiv.org/abs/2204.08206)**

**Tigerlily** is a [TigerGraph](https://www.tigergraph.com/) based system designed to solve the [drug interaction prediction task](https://arxiv.org/abs/2111.02916). In this machine learning task, we want to predict whether two drugs have an adverse interaction. Our framework allows us to solve this **[highly relevant real-world problem](https://www.newscientist.com/article/2143486-side-effects-kill-thousands-but-our-data-on-them-is-flawed/)** using graph mining techniques in these steps:

- **(a)** Using [PyTigergraph](https://github.com/pyTigerGraph/pyTigerGraph) we create a heterogeneous biological graph of drugs and proteins.
- **(b)** We calculate the [personalized PageRank](https://github.com/tigergraph/gsql-graph-algorithms/blob/master/algorithms/Centrality/pagerank/personalized/multi_source/tg_pagerank_pers.gsql) scores of drug nodes in the [TigerGraph Cloud](https://tgcloud.io/).
- **(c)** We embed the nodes using [sparse non-negative matrix factorization](https://scikit-learn.org/stable/modules/generated/sklearn.decomposition.NMF.html) of the personalized PageRank matrix.
- **(d)** Using the node embeddings we train a [gradient boosting](https://lightgbm.readthedocs.io/en/latest/) based drug interaction predictor.

--------------------------------------------------------------------------------

### (A) **Creating and populating a Graph**

<p align="center">
  <img width="90%" src="https://github.com/benedekrozemberczki/tigerlily/blob/main/images/pair_scoring_A.jpg?sanitize=true" />
</p>

As a first step, the basic **TigerLily** tools are imported, and we load the example dataset that integrated DrugBankDDI and the BioSNAP datasets. We create a ``PersonalizedPageRankMachine`` and connect to the host with the ``Graph``. The settings of this machine should be the appropriate user credentials and details; a secret is obtained in the **TigerGraph Graph Studio**. We install the default Personalized PageRank query and upload the edges of the example dataset used in our demonstrations. This graph has **drug** and **protein** nodes, **drug-protein** and **protein-protein** interactions. Our goal is to predict the **drug-drug** interactions.

```python
from tigerlily.dataset import ExampleDataset
from tigerlily.embedding import EmbeddingMachine
from tigerlily.operator import hadamard_operator
from tigerlily.pagerank import PersonalizedPageRankMachine

dataset = ExampleDataset()

edges = dataset.read_edges()
target = dataset.read_target()

machine = PersonalizedPageRankMachine(host="host_name",
                                      graphname="graph_name",
                                      username="username_value",
                                      secret="secret_value",
                                      password="password_value")
                           
machine.connect()
machine.install_query()

machine.upload_graph(new_graph=True, edges=edges)
```

### (B) **Computing the Approximate Personalized PageRank vectors**

<p align="center">
  <img width="90%" src="https://github.com/benedekrozemberczki/tigerlily/blob/main/images/pair_scoring_B.jpg?sanitize=true" />
</p>

We are only interested in describing the neighbourhood of drug nodes in the biological graph. Because of this, we only retrieve the neighbourhood of the drugs - for each drug we retrieve those nodes (top-k closest neighbors) which are the closest based on the Personalized PageRank scores. We are going to learn the drug embeddings based on these scores.

```python
drug_node_ids = machine.connection.getVertices("drug")

pagerank_scores = machine.get_personalized_pagerank(drug_node_ids)
```
### (C) Learning the Drug Embeddings and Drug Pair Feature Generation

<p align="center">
  <img width="90%" src="https://github.com/benedekrozemberczki/tigerlily/blob/main/images/pair_scoring_C.jpg?sanitize=true" />
</p>

We create an embedding machine that creates drug node representations. The embedding machine instance has a random seed, a dimensions hyperparameter (this sets the number of factors), and a maximal iteration count for the factorization. An embedding is learned from the Personalized PageRank scores and using the drug features we create drug pair features with the operator function.

```python
embedding_machine = EmbeddingMachine(seed=42,
                                     dimensions=32,
                                     max_iter=100)

embedding = embedding_machine.fit(pagerank_scores)

drug_pair_features = embedding_machine.create_features(target, hadamard_operator)
```
### (D) Predicting Drug Interactions and Inference

<p align="center">
  <img width="90%" src="https://github.com/benedekrozemberczki/tigerlily/blob/main/images/pair_scoring_D.jpg?sanitize=true" />
</p>

We load a gradient boosting-based classifier, an evaluation metric for binary classification, and a function to create train-test splits. We create a train and test portion of the drug pairs using 80% of the pairs for training. A gradient boosted tree model is trained, score the model on the test set. We compute an AUROC score on the test portion of the dataset and print it out.

```python
from lightgbm import LGBMClassifier
from sklearn.metrics import roc_auc_score
from sklearn.model_selection import train_test_split

X_train, X_test, y_train, y_test = train_test_split(drug_pair_features,
                                                    target,
                                                    train_size=0.8,
                                                    random_state=42)

model = LGBMClassifier(learning_rate=0.01,
                       n_estimators=100)

model.fit(X_train,y_train["label"])

predicted_label = model.predict_proba(X_test)

auroc_score_value = roc_auc_score(y_test["label"], predicted_label[:,1])

print(f'AUROC score: {auroc_score_value :.4f}')
```

Head over to the [documentation](https://tigerlily.readthedocs.io) to find out more about installation and a full API reference.
For a quick start, check out the [example notebook](https://github.com/benedekrozemberczki/tigerlily/blob/main/example_notebook.ipynb). If you notice anything unexpected, please open an [issue](github.com/benedekrozemberczki/tigerlily/issues).

--------------------------------------------------------------------------------

**Citing**

If you find *Tigerlily* useful in your research, please consider adding the following citation:

```bibtex
@misc{tigerlily2022,
  author = {Benedek Rozemberczki},
  title = {TigerLily: Finding drug interactions in silico with the Graph},
  year = {2022},
  publisher = {GitHub},
  journal = {GitHub repository},
  howpublished = {\url{https://github.com/benedekrozemberczki/tigerlily}},
}
```

--------------------------------------------------------------------------------

**Installation**

To install tigerlily, simply run:

```sh
pip install tigerlily
```

**Running tests**

Running tests requires that you run:

```
$ tox -e py
```
--------------------------------------------------------------------------------

**License**

- [Apache 2.0 License](https://github.com/benedekrozemberczki/tigerlily/blob/main/LICENSE)

--------------------------------------------------------------------------------

**Credit**

The **TigerLily** logo and the high level machine learning workflow image are based on:

- [Kubos Origami Font](https://www.fontspace.com/kubos-origami-font-f29538)
- [Noun Project Icons](https://thenounproject.com/)

Benedek Rozemberczki has a yearly subscription to the Noun Project that allows the customization and commercial use of the icons.