Merge branch 'main' into hypergraphs

.dockerignore

@@ -0,0 +1,139 @@
+/data_validation/
+.DS_Store
+/venv/
+/.idea/
+/.git/
+/docker-compose.yml
+*.ipynb_checkpoints
+__pycache__
+/cache/
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/

.gitignore

@@ -1,11 +1,13 @@
 data_validation
 .DS_Store
-venv
-.idea
-.git
+/venv/
+/.idea/
+/.git/
+/docker-compose.yml
 *.ipynb_checkpoints
 __pycache__
 .gitignore
+/cache/
 
 # Byte-compiled / optimized / DLL files
 __pycache__/
@@ -135,4 +137,4 @@ venv.bak/
 dmypy.json
 
 # Pyre type checker
-.pyre/
+.pyre/

Dockerfile

@@ -0,0 +1,50 @@
+FROM nvidia/cuda:11.6.2-devel-ubuntu20.04
+ENV DEBIAN_FRONTEND=noninteractive
+WORKDIR /app
+
+# Install required packages
+RUN set -xe \
+ && apt-get -y update \
+ && apt-get install -fyqq software-properties-common curl build-essential git libaio-dev llvm-10 clang wget \
+ && apt-get -y update \
+ && add-apt-repository universe \
+ && apt-get -y update \
+ && apt-get -fyqq install python3.9-full python3.9-dev python3-pip \
+ && apt-get clean
+
+# Let's upgrade pip first
+RUN set -xe \
+ && python3.9 -m pip install --upgrade pip
+
+# Install python packages
+RUN set -xe \
+    # PyTorch MUST BE installed first
+ && python3.9 -m pip install \
+      'torch==1.12.1+cu116' \
+      -f https://download.pytorch.org/whl/torch_stable.html \
+    # And only then all other dependencies
+ && python3.9 -m pip install \
+      'torch-geometric==2.0.4' \
+      'torch-sparse==0.6.15+pt112cu116' \
+      'torch-scatter==2.1.0+pt112cu116' \
+      -f https://data.pyg.org/whl/torch-1.12.1+cu116.html
+
+# Install Jupyter
+EXPOSE 8080
+RUN set -xe \
+ && python3.9 -m pip install jupyter \
+ && jupyter notebook --generate-config \
+ && echo "c.ServerApp.allow_origin = '*'" >> /root/.jupyter/jupyter_notebook_config.py \
+ && echo "c.ServerApp.allow_remote_access = True" >> /root/.jupyter/jupyter_notebook_config.py \
+    # passwd('admin','sha1')
+ && echo "c.NotebookApp.password = u'sha1:fd40b23609dd:882af6cdf722657245be6f4abd9b641a84ef9c2a'" >> /root/.jupyter/jupyter_notebook_config.py
+
+# Install requirements
+COPY requirements.txt ./
+RUN set -xe \
+ && python3.9 -m pip install --no-cache-dir -r requirements.txt
+
+# Copy project files
+COPY . .
+
+ENTRYPOINT ["/app/entrypoint.sh"]

README_DOCKER.md

@@ -0,0 +1,53 @@
+# Docker Devbox
+
+Requirements:
+
+* Docker
+* Docker Compose
+* Docker Nvidia Runtime
+
+## How to run
+
+Copy docker-compose from example:
+
+```shell
+cp docker-compose.dist.yml docker-compose.yml
+```
+
+Build an image:
+
+```shell
+docker-compose build
+```
+
+Start a container:
+
+```shell
+docker-compose up -d
+```
+
+## How to use inside a container
+
+Login into a container:
+
+```shell
+docker-compose exec app bash
+```
+
+Use python3.9 interpreter for running all your tasks, e.g. tutorials:
+
+```shell
+# Prepare environment
+cd tutorials
+ln -s ../stable_gnn
+
+# Run graph classification task
+python3.9 graph_classification.py
+
+# Run node classification task
+python3.9 node_classification.py
+```
+
+## How to use from IDE like PyCharm
+
+You need to `Add New Interpreter` via menu of PyCharn, then select `Docker Compose`

docker-compose.dist.yml

@@ -0,0 +1,19 @@
+version: "3.9"
+
+services:
+
+  app:
+    restart: "unless-stopped"
+    build:
+      context: .
+    volumes:
+      - ./:/app
+    ports:
+      - "127.0.0.1:8888:8888"
+    deploy:
+      resources:
+        reservations:
+          devices:
+            - driver: nvidia
+              count: 1
+              capabilities: [ gpu ]

entrypoint.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+
+JN_PORT=${PORT:-8888}
+if [ -z "$JN_IP" ]; then
+    JN_IP=$(hostname -I | awk '{print $1}')
+fi
+
+jupyter notebook --allow-root --ip="$JN_IP" --port="$JN_PORT" --no-browser

requirements.txt

@@ -1,4 +1,4 @@
-bamt
-optuna
-pgmpy
-pandas
+bamt==1.1.44
+optuna==2.10.1
+pgmpy==0.1.20
+pandas==1.5.2

stable_gnn/embedding/model_train_embeddings.py

@@ -123,7 +123,7 @@ def _objective(self, trial: Trial) -> Tensor:
 
         loss_to_train = {}
         for name in self.loss:
-            if type(self.loss[name]) == list:
+            if isinstance(self.loss[name], list):
                 if len(self.loss[name]) == 3:
                     var = trial.suggest_int(
                         name,
@@ -141,7 +141,7 @@ def _objective(self, trial: Trial) -> Tensor:
             else:
                 loss_to_train[name] = self.loss[name]
 
-            if name == "q" and type(self.loss[name]) == list:
+            if name == "q" and isinstance(self.loss[name], list):
                 var_5 = trial.suggest_categorical("p", self.loss["p"])
                 var_4 = trial.suggest_categorical("q", self.loss[name])
                 if var_4 > 1:

stable_gnn/model_gc.py

@@ -1,11 +1,11 @@
 from typing import List, Optional, Tuple
 
-import bamt.Networks as Nets
+import bamt.networks as Nets
 import numpy as np
 import pandas as pd
 import torch
 import torch.nn.functional as F
-from bamt.Preprocessors import Preprocessor
+from bamt.preprocessors import Preprocessor
 from pgmpy.estimators import K2Score
 from sklearn import preprocessing
 from torch import device
@@ -215,7 +215,7 @@ def _data_eigen_exctractor(self, dataset: List[Graph]) -> pd.DataFrame:
 
         return data_bamt
 
-    def _bayesian_network_build(self, data_bamt: pd.DataFrame) -> Nets.HybridBN:
+    def _bayesian_network_build(self, data_bamt: pd.DataFrame):
         # поиск весов для bamt
         for col in data_bamt.columns[: len(data_bamt.columns)]:
             data_bamt[col] = data_bamt[col].astype(float)

stable_gnn/pipelines/graph_classification_pipeline.py

@@ -111,7 +111,7 @@ def test(self, model: Module, loader: DataLoader) -> Tuple[float, float]:
 
             y_true_list = y_true.cpu().tolist()
             y_pred_list = y_pred.squeeze().tolist()
-            if type(y_pred_list) != list:
+            if not isinstance(y_pred_list, list):
                 y_pred_list = [y_pred_list]
             accs_micro.append(f1_score(y_true_list, y_pred_list, average="micro"))
             accs_macro.append(f1_score(y_true_list, y_pred_list, average="macro"))