From 518f12cdbd09a37674f1301836b4ccfb03de9abe Mon Sep 17 00:00:00 2001
From: MilanShao <99186862+MilanShao@users.noreply.github.com>
Date: Fri, 30 Jun 2023 16:28:03 +0200
Subject: [PATCH] Add files via upload
---
.gitignore | 6 +++
README.md | 95 ++++++++++++++++++++++++++++++++++++++++-
eval.py | 76 +++++++++++++++++++++++++++++++++
requirements.txt | 12 ++++++
train.py | 108 +++++++++++++++++++++++++++++++++++++++++++++++
5 files changed, 295 insertions(+), 2 deletions(-)
create mode 100644 .gitignore
create mode 100644 eval.py
create mode 100644 requirements.txt
create mode 100644 train.py
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..6ee9c9a
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,6 @@
+ModeConvModel/results
+processed_lux
+processed_simulated_smart_bridge
+lightning_logs
+
+*.ckpt
\ No newline at end of file
diff --git a/README.md b/README.md
index 4be52e9..5190b81 100644
--- a/README.md
+++ b/README.md
@@ -1,2 +1,93 @@
-# ModeConv
-Official repository to the paper "ModeConv: A novel convolution for distinguishing anomalous and normal structural behavior"
+# ModeConv: A novel convolution for distinguishing anomalous and normal Structural Behavior
+
+
+
+## Installation
+
+Dependencies:
+
+```
+pip install torch --index-url https://download.pytorch.org/whl/cu117
+pip install -r requirements.txt
+```
+
+## How to use
+
+### Training and evaluating a model
+```
+python train.py
+
+optional arguments:
+ -h, --help show this help message and exit
+ --model MODEL options: 'ModeConvFast', 'ModeConvLaplace', 'ChebConv', 'AGCRN', 'MtGNN' (default: 'ModeConvFast')
+ --dataset DATASET options: 'simulated_smart_bridge', 'luxemburg' (default: 'luxemburg')
+ --epochs N (default: 50)
+ --batch-size N (default: 256)
+ --lr lr initial learning rate for optimizer e.g.: 1e-4 | 'auto' (default: 'auto')
+ --num-layer N (default: 3)
+ --decoder DECODER options: 'linear' for linear layer only decoder, 'custom': to use ModeConv/ChebConv/etc. layers in decoder (default: 'custom')
+ --hidden-dim N (default: 8)
+ --bottleneck N (default: 2)
+ --no-maha-threshold mahalanobis threshold calculation/evaluation is very slow; disabling saves 30min-2h in val and test on luxemburg dataset (default: True)
+ --seed N (default: 3407)
+ --no-cuda (default: False)
+
+```
+
+### Evaluating a model
+```
+python eval.py Path
+
+positional arguments:
+ Path path to pretrained weights, e.g. data/pretrained/luxemburg/ModeConvFast/GNN.statedict
+
+optional arguments:
+ -h, --help show this help message and exit
+ --model MODEL options: 'ModeConvFast', 'ModeConvLaplace', 'ChebConv', 'AGCRN', 'MtGNN' (default: 'ModeConvFast')
+ --dataset DATASET options: 'simulated_smart_bridge', 'luxemburg' (default: 'luxemburg')
+ --batch-size N (default: 256)
+ --num-layer N (default: 3)
+ --decoder DECODER options: 'linear' for linear layer only decoder, 'custom': to use ModeConv/ChebConv/etc. layers in decoder (default: 'custom')
+ --hidden-dim N (default: 8)
+ --bottleneck N (default: 2)
+ --no-maha-threshold mahalanobis threshold calculation/evaluation is very slow; disabling saves 30min-2h in val and test on luxemburg dataset (default: True)
+ --seed N (default: 3407)
+ --no-cuda (default: False)
+
+```
+
+## Datasets
+
+The csv files for the luxemburg dataset only contain about 5% of the full data used.
+
+The csv files for the simulated_smart_bridge dataset only contain about 6% of the full data.
+
+## Results
+
+### Luxemburg
+
+```
+python train.py --model {Model} --dataset luxemburg
+```
+
+| Model | AUC | F1 |
+|----------------- |-------|-------|
+| ModeConvFast | 99.99 | 93.09 |
+| ModeConvLaplace | 92.16 | 73.74 |
+| ChebConv | 92.07 | 74.53 |
+| AGCRN | 98.18 | 86.67 |
+| MtGNN | 99.99 | 82.00 |
+
+### Simulated Smart Bridge
+
+```
+python train.py --model {Model} --dataset simulated_smart_bridge
+```
+
+| Model | AUC | F1 |
+|----------------- |-------|-------|
+| ModeConvFast | 92.23 | 87.93 |
+| ModeConvLaplace | 92.43 | 88.07 |
+| ChebConv | 82.15 | 83.89 |
+| AGCRN | 92.26 | 87.76 |
+| MtGNN | 91.19 | 86.78 |
\ No newline at end of file
diff --git a/eval.py b/eval.py
new file mode 100644
index 0000000..3ad59d2
--- /dev/null
+++ b/eval.py
@@ -0,0 +1,76 @@
+import datetime
+import json
+import sys
+import os
+import torch
+import torch_geometric as pyg
+import pytorch_lightning as pl
+from torch_geometric.loader import DataLoader
+
+from ModeConvModel.models.select_model import select_model
+from ModeConvModel.dataset import SimulatedSmartBridgeDataset, LuxemburgDataset
+import argparse
+
+
+def getArgs(argv=None):
+ parser = argparse.ArgumentParser(description="ModeConv")
+ parser.add_argument("weights", metavar="Path",
+ help="path to pretrained weights, e.g. data/pretrained/luxemburg/ModeConvFast/GNN.statedict")
+ parser.add_argument("--model", default="ModeConvFast", help="options: 'ModeConvFast', 'ModeConvLaplace', 'ChebConv', 'AGCRN', 'MtGNN'")
+ parser.add_argument("--dataset", default="luxemburg", help="options: 'simulated_smart_bridge', 'luxemburg'")
+ parser.add_argument('--batch-size', type=int, default=256, metavar="N")
+ parser.add_argument('--num-layer', type=int, default=3, metavar="N")
+ parser.add_argument('--decoder', default="custom", help="options: 'linear' for linear layer decoder;"
+ "'custom': to use ModeConv/ChebConv/etc. layers in decoder")
+ parser.add_argument('--hidden-dim', type=int, default=8, metavar="N")
+ parser.add_argument('--bottleneck', type=int, default=2, metavar="N")
+ parser.add_argument("--no-maha-threshold", action="store_true", default=True,
+ help="mahalanobis threshold calculation/evaluation is very slow; disabling saves 30min+ in val and test on luxemburg dataset")
+ parser.add_argument('--seed', type=int, default=3407, metavar="N")
+ parser.add_argument("--no-cuda", action="store_true", default=False)
+
+ args = parser.parse_args(argv)
+ args.__dict__["lr"] = 0
+
+ return args
+
+
+if __name__ == "__main__":
+ args = getArgs(sys.argv[1:])
+ pl.seed_everything(args.seed)
+
+ starttime = datetime.datetime.now()
+ starttime = starttime.strftime("%H:%M:%S")
+
+ model = select_model(args)
+ model.load_state_dict(torch.load(args.weights))
+
+ trainer = pl.Trainer(
+ logger=True,
+ enable_checkpointing=False,
+ max_epochs=0,
+ gpus=0 if args.no_cuda else 1,
+ )
+
+ if args.dataset == "simulated_smart_bridge":
+ val_ds = SimulatedSmartBridgeDataset("./processed_simulated_smart_bridge/", mode="val")
+ elif args.dataset == "luxemburg":
+ val_ds = LuxemburgDataset("./processed_lux", mode="val")
+ val_dl = DataLoader(val_ds, batch_size=args.batch_size, shuffle=False)
+ trainer.validate(model, val_dl)
+ del val_ds, val_dl
+
+ if args.dataset == "simulated_smart_bridge":
+ test_ds = SimulatedSmartBridgeDataset("./processed_simulated_smart_bridge/", mode="test")
+ elif args.dataset == "luxemburg":
+ test_ds = LuxemburgDataset("./processed_lux", mode="test")
+
+ test_dl = DataLoader(test_ds, batch_size=args.batch_size, shuffle=False)
+ trainer.test(model, test_dl)
+
+ endtime = datetime.datetime.now()
+ endtime = endtime.strftime("%H:%M:%S")
+ out = {"args": vars(args), "Start time": starttime, "End time": endtime,
+ "Last epoch duration": model.epoch_duration}
+ with open(model.prefix + "/args.json", "w") as outfile:
+ json.dump(out, outfile, indent=4, sort_keys=False)
\ No newline at end of file
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 0000000..b8e7a02
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,12 @@
+torch-geometric==2.2.0
+torch-cluster -f https://data.pyg.org/whl/torch-2.0.0+cu117.html
+torch-scatter -f https://data.pyg.org/whl/torch-2.0.0+cu117.html
+torch-sparse -f https://data.pyg.org/whl/torch-2.0.0+cu117.html
+torch-spline-conv -f https://data.pyg.org/whl/torch-2.0.0+cu117.html
+numpy==1.23.5
+scipy==1.10.1
+scikit-learn==1.2.1
+pandas==1.5.3
+networkx==3.0
+tqdm==4.64.1
+pytorch-lightning==1.9.2
\ No newline at end of file
diff --git a/train.py b/train.py
new file mode 100644
index 0000000..c59c782
--- /dev/null
+++ b/train.py
@@ -0,0 +1,108 @@
+import datetime
+import json
+import sys
+import os
+import torch
+import torch_geometric as pyg
+import pytorch_lightning as pl
+from torch_geometric.loader import DataLoader
+
+from ModeConvModel.models.select_model import select_model
+from ModeConvModel.dataset import SimulatedSmartBridgeDataset, LuxemburgDataset
+import argparse
+
+
+def train(data_module, args):
+ starttime = datetime.datetime.now()
+ starttime = starttime.strftime("%H:%M:%S")
+
+ model = select_model(args)
+ auto_lr = True if args.lr == "auto" else False
+
+ trainer = pl.Trainer(
+ logger=True,
+ enable_checkpointing=False,
+ max_epochs=args.epochs,
+ gpus=0 if args.no_cuda else 1,
+ auto_lr_find=auto_lr # run learning rate finder, results override hparams.learning_rate
+ )
+
+ # call tune to find the batch_size and to optimize lr
+ trainer.tune(model, data_module)
+ data_module.kwargs["batch_size"] = model.batch_size
+ trainer.fit(model, data_module)
+ torch.save(model.state_dict(), model.prefix + "/GNN.statedict")
+ del data_module
+
+ trainendtime = datetime.datetime.now()
+ trainendtime = trainendtime.strftime("%H:%M:%S")
+ print("Current Time =", trainendtime)
+ print()
+
+ if args.dataset == "simulated_smart_bridge":
+ val_ds = SimulatedSmartBridgeDataset("./processed_simulated_smart_bridge/", mode="val")
+ elif args.dataset == "luxemburg":
+ val_ds = LuxemburgDataset("./processed_lux", mode="val")
+ val_dl = DataLoader(val_ds, batch_size=args.batch_size, shuffle=False)
+ trainer.validate(model, val_dl)
+ del val_ds, val_dl
+
+ if args.dataset == "simulated_smart_bridge":
+ test_ds = SimulatedSmartBridgeDataset("./processed_simulated_smart_bridge/", mode="test")
+ elif args.dataset == "luxemburg":
+ test_ds = LuxemburgDataset("./processed_lux", mode="test")
+
+ test_dl = DataLoader(test_ds, batch_size=args.batch_size, shuffle=False)
+ trainer.test(model, test_dl)
+
+ endtime = datetime.datetime.now()
+ endtime = endtime.strftime("%H:%M:%S")
+ out = {"args": vars(args), "Start time": starttime, "Train end time": trainendtime, "End time": endtime,
+ "Last epoch duration": model.epoch_duration}
+ with open(model.prefix + "/args.json", "w") as outfile:
+ json.dump(out, outfile, indent=4, sort_keys=False)
+
+
+def getArgs(argv=None):
+ parser = argparse.ArgumentParser(description="ModeConv")
+ parser.add_argument("--model", default="ModeConvFast", help="options: 'ModeConvFast', 'ModeConvLaplace', 'ChebConv', 'AGCRN', 'MtGNN'")
+ parser.add_argument("--dataset", default="luxemburg", help="options: 'simulated_smart_bridge', 'luxemburg'")
+ parser.add_argument("--epochs", type=int, default=50, metavar="N")
+ parser.add_argument('--batch-size', type=int, default=256, metavar="N")
+ parser.add_argument("--lr", default="auto", metavar="lr", # 1e-4
+ help="initial learning rate for optimizer e.g.: 1e-4 | 'auto'")
+ parser.add_argument('--num-layer', type=int, default=3, metavar="N")
+ parser.add_argument('--decoder', default="custom", help="options: 'linear' for linear layer decoder;"
+ "'custom': to use ModeConv/ChebConv/etc. layers in decoder")
+ parser.add_argument('--hidden-dim', type=int, default=8, metavar="N")
+ parser.add_argument('--bottleneck', type=int, default=2, metavar="N")
+ parser.add_argument("--no-maha-threshold", action="store_true", default=True,
+ help="mahalanobis threshold calculation/evaluation is very slow; disabling saves 30min+ in val and test on luxemburg dataset")
+ parser.add_argument('--seed', type=int, default=3407, metavar="N")
+ parser.add_argument("--no-cuda", action="store_true", default=False)
+
+ args = parser.parse_args(argv)
+
+ return args
+
+
+if __name__ == "__main__":
+ args = getArgs(sys.argv[1:])
+
+ pl.seed_everything(args.seed)
+ if args.dataset == "simulated_smart_bridge":
+ train_ds = SimulatedSmartBridgeDataset("./processed_simulated_smart_bridge/", mode="train")
+ elif args.dataset == "luxemburg":
+ train_ds = LuxemburgDataset("./processed_lux", mode="train")
+ else:
+ raise NotImplementedError(f"Dataset {args.dataset} not found; Choices: simulated_smart_bridge, luxemburg")
+
+ data_module = pyg.data.LightningDataset(
+ train_dataset=train_ds,
+ # val_dataset=val_ds,
+ # test_dataset=test_ds,
+ batch_size=args.batch_size,
+ num_workers=0
+ )
+
+ train(data_module=data_module, args=args)
--
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