Detecting Encrypted TOR Traffic with Boosting and Topological Data Analysis¶
HJ van Veen  MLWave
Last run 20211008 with kmapper version 2.0.1
We establish strong baselines for both supervised and unsupervised detection of encrypted TOR traffic.
Introduction¶
Gradient Boosted Decision Trees (GBDT) is a very powerful learning algorithm for supervised learning on tabular data [1]. Modern implementations include XGBoost [2], Catboost [3], LightGBM [4] and scikitlearn’s GradientBoostingClassifier [5]. Of these, especially XGBoost has seen tremendous successes in machine learning competitions [6], starting with its introduction during the Higgs Boson Detection challenge in 2014 [7]. The success of XGBoost can be explained on multiple dimensions: It is a robust implementation of the original algorithms, it is very fast – allowing data scientists to quickly find better parameters [8], it does not suffer much from overfit, is scaleinvariant, and it has an active community providing constant improvements, such as early stopping [9] and GPU support [10].
Anomaly detection algorithms automatically find samples that are different from regular samples. Many methods exist. We use the Isolation Forest in combination with nearest neighbor distances. The Isolation Forest works by randomly splitting up the data [11]. Outliers, on average, are easier to isolate through splitting. Nearest neighbor distance looks at the summed distances for a sample and its five nearest neighbors. Outliers, on average, have a larger distance between their nearest neighbors than regular samples [12].
Topological Data Analysis (TDA) is concerned with the meaning, shape, and connectedness of data [13]. Benefits of TDA include: Unsupervised data exploration / automatic hypothesis generation, ability to deal with noise and missing values, invariance, and the generation of meaningful compressed summaries. TDA has shown efficient applications in a number of diverse fields: healthcare [14], computational biology [15], control theory [16], community detection [17], machine learning [18], sports analysis [19], and information security [20]. One tool from TDA is the \(MAPPER\) algorithm. \(MAPPER\) turns data and data projections into a graph by covering it with overlapping intervals and clustering [21]. To guide exploration, the nodes of the graph may be colored with a function of interest [22]. There are an increasing number of implementations of \(MAPPER\). We use the open source implementation KeplerMapper from scikitTDA [23].
The TOR network allows users to communicate and host content while preserving privacy and anonimity [24]. As such, it can be used by dissidents and other people who prefer not to be tracked by commercial companies or governments. But these strong privacy and anonimity features are also attractive to criminals. A 2016 study in ‘Survival  Global Politics and Strategy’ found at least 57% of TOR websites are involved in illicit behavior, ranging from the trade in illegal arms, counterfeit ID documents, pornography, and drugs, money laundering & credit card fraud, and the sharing of violent material, such as bomb making tutorials and terrorist propaganda [25].
Network Intrusion Detection Systems are a first line of defense for governments and companies [26]. An undetected hacker will try to elevate their priviledges, moving from the weakest link to more hardened systemcritical network nodes [27]. If the hacker’s goal is to get access to sensitive data (for instance: for resale , industrial espionage , or extortion purposes) then any stolen data needs to be exfiltrated. Similarly, cryptolockers often need to communicate with a command & control server outside the network. Depending on the level of sophistication of the malware or hackers, exfiltration may be open and visible, run encrypted through the TOR network in an effort to hide the destination, or use advanced DNS tunneling techniques.
Motivation¶
Current Network Intrusion Detection Systems, much like the old spam detectors, rely mostly on rules, signatures, and anomaly detection. Labeled data is scarce. Writing rules is a very costly task requiring domain expertise. Signatures may fail to catch new types of attacks until they are updated. Anomalous/unusual behavior is not necessarily suspicous/adversarial behavior.
Machine Learning for Information Security suffers a lot from poor false positive rates. False positives lead to alarm fatigue and can swamp an intelligence analyst with irrelevant work.
Despite the possibility of false positives, it is often better to be safe than sorry. Suspicious network behavior, such as outgoing connections to the TOR network, require immediate attention. A network node can be shut down remotely, after which a security engineer can investigate the machine. The best practice of a multilayered security makes this possible [28]: Instead of a single firewall to rule them all, hackers can be detected in various stages of their network intrusion, up to the final step of data exfilitration.
Data¶
We use a dataset written for the paper “Characterization of Tor Traffic Using Time Based Features” (Lashkari et al.) [29], graciously provided by the Canadian Institute for Cybersecurity [30]. This dataset combines older research on nonTOR network traffic with more recently captured TOR traffic (both were created on the same network) [31]. The data includes features that are more specific to the network used, such as the source and destination IP/Port, and a range of timebased features with a 10 second lag.
Feature 
Type 
Description 
Timebased 

‘Source IP’ 
Object 
Source IP4 Address. String with dots. 
No 
‘ Source Port’ 
Float 
Source Port sending packets. 
No 
‘ Destination IP’ 
Object 
Destination IP4 Address. 
No 
‘ Destination Port’ 
Float 
Destination Port receiving packets. 
No 
‘ Protocol’ 
Float 
Integer [517] denoting protocol used. 
No 
‘ Flow Duration’ 
Float 
Length of connection in seconds 
Yes 
‘ Flow Bytes/s’ 
Float 
Bytes per seconds send 
Yes 
‘ Flow Packets/s’ 
Object 
Packets per second send.
Contains 
Yes 
‘ Flow IAT Mean’ 
Float 
Flow Inter Arrival Time. 
Yes 
‘ Flow IAT Std’ 
Float 
Yes 

‘ Flow IAT Max’ 
Float 
Yes 

‘ Flow IAT Min’ 
Float 
Yes 

‘Fwd IAT Mean’ 
Float 
Forward Inter Arrival Time. 
Yes 
‘ Fwd IAT Std’ 
Float 
Yes 

‘ Fwd IAT Max’ 
Float 
Yes 

‘ Fwd IAT Min’ 
Float 
Yes 

‘Bwd IAT Mean’ 
Float 
Backwards Inter Arrival Time. 
Yes 
‘ Bwd IAT Std’ 
Float 
Yes 

‘ Bwd IAT Max’ 
Float 
Yes 

‘ Bwd IAT Min’ 
Float 
Yes 

‘Active Mean’ 
Float 
Average amount of time in seconds before connection went idle. 
Yes 
‘ Active Std’ 
Float 
Yes 

‘ Active Max’ 
Float 
Yes 

‘ Active Min’ 
Float 
Yes 

‘Idle Mean’ 
Float 
Average amount of time in seconds before connection became active. 
Yes 
‘ Idle Std’ 
Float 
Zero variance feature. 
Yes 
‘ Idle Max’ 
Float 
Yes 

‘ Idle Min’ 
Float 
Yes 

‘label’ 
Object 
Either 
Experimental setup¶
Supervised ML. We establish a strong baseline with XGBoost on the full data and on a subset (only timebased features, which generalize better to new domains). We follow the dataset standard of creating a 20% holdout validation set, and use 5fold stratified crossvalidation for parameter tuning [32]. For tuning we use random search on sane parameter ranges, as random search is easy to implement and given enough time, will equal or beat more sophisticated methods [33]. We do not use feature selection, but opt to let our learning algorithm deal with those. Missing values are also handled by XGBoost and not manually imputed or hardcoded.
Unsupervised ML. We use \(MAPPER\) in combination with the Isolation Forest and the summed distances to the five nearest neighbors. We use an overlap percentage of 50% and 40 intervals per dimension for a total of 1600 hypercubes. Clustering is done with agglomerative clustering using the euclidean distance metric and 3 clusters per interval. For these experiments we use only the timebased features. We don’t scale the data, despite only Isolation Forest being scaleinvariant.
[1]:
import numpy as np
import pandas as pd
import xgboost
from sklearn import model_selection, metrics
Data Prep¶
The last 39 records in are
SelectedFeatures10sTORNonTOR.csv
look like datacollection artifacts – we drop them.There are string values
"Infinity"
inside the data, causing mixed types.We need to labelencode the target column.
We turn the IP addresses into floats by removing the dots.
We also create a subset of features by removing
Source Port
,Source IP
,Destination Port
,Destination IP
, andProtocol
. This to avoid overfitting/improve future generalization and focus only on the timebased features, like most other researchers have done.
[2]:
def load_and_prep_data():
# download `SelectedFeatures10sTORNonTOR.csv` dataset from here:
# * https://www.unb.ca/cic/datasets/tor.html
# * http://205.174.165.80/CICDataset/ISCXTorNonTor2017/
# * https://github.com/rambasnet/DeepLearningTorTraffic
df = pd.read_csv("input/SelectedFeatures10sTORNonTOR.csv")
df.drop(df.index[39:], inplace=True)
df.replace('Infinity', 1, inplace=True)
df["label"] = df["label"].map({"nonTOR": 0, "TOR": 1})
df["Source IP"] = df["Source IP"].apply(lambda x: float(x.replace(".", "")))
df[" Destination IP"] = df[" Destination IP"].apply(lambda x: float(x.replace(".", "")))
return df
[3]:
df = load_and_prep_data()
[4]:
features_all = [c for c in df.columns if c not in
['label']]
features = [c for c in df.columns if c not in
['Source IP',
' Source Port',
' Destination IP',
' Destination Port',
' Protocol',
'label']]
X = np.array(df[features])
X_all = np.array(df[features_all])
y = np.array(df.label)
print(X.shape, np.mean(y))
(67795, 23) 0.11865181798067705
Local evaluation setup¶
We create a stratified holdout set of 20%. Any modeling choices (such as parameter tuning) are guided by 5fold stratified crossvalidation on the remaining dataset.
[5]:
splitter = model_selection.StratifiedShuffleSplit(
n_splits=1,
test_size=0.2,
random_state=0)
for train_index, test_index in splitter.split(X, y):
X_train, X_holdout = X[train_index], X[test_index]
X_train_all, X_holdout_all = X_all[train_index], X_all[test_index]
y_train, y_holdout = y[train_index], y[test_index]
print(X_train.shape, X_holdout.shape)
(54236, 23) (13559, 23)
5fold nontuned XGBoost¶
[6]:
model = xgboost.XGBClassifier(seed=0)
print(model)
skf = model_selection.StratifiedKFold(
n_splits=5,
shuffle=True,
random_state=0)
for i, (train_index, test_index) in enumerate(skf.split(X_train, y_train)):
X_train_fold, X_test_fold = X_train[train_index], X_train[test_index]
y_train_fold, y_test_fold = y_train[train_index], y_train[test_index]
model.fit(X_train_fold, y_train_fold)
probas = model.predict_proba(X_test_fold)[:,1]
preds = (probas > 0.5).astype(int)
print(""*60)
print("Fold: %d (%s/%s)" %(i, X_train_fold.shape, X_test_fold.shape))
print(metrics.classification_report(y_test_fold, preds, target_names=["nonTOR", "TOR"]))
print("Confusion Matrix: \n%s\n"%metrics.confusion_matrix(y_test_fold, preds))
print("Log loss : %f" % (metrics.log_loss(y_test_fold, probas)))
print("AUC : %f" % (metrics.roc_auc_score(y_test_fold, probas)))
print("Accuracy : %f" % (metrics.accuracy_score(y_test_fold, preds)))
print("Precision: %f" % (metrics.precision_score(y_test_fold, preds)))
print("Recall : %f" % (metrics.recall_score(y_test_fold, preds)))
print("F1score : %f" % (metrics.f1_score(y_test_fold, preds)))
XGBClassifier(base_score=None, booster=None, colsample_bylevel=None,
colsample_bynode=None, colsample_bytree=None, gamma=None,
gpu_id=None, importance_type='gain', interaction_constraints=None,
learning_rate=None, max_delta_step=None, max_depth=None,
min_child_weight=None, missing=nan, monotone_constraints=None,
n_estimators=100, n_jobs=None, num_parallel_tree=None,
random_state=None, reg_alpha=None, reg_lambda=None,
scale_pos_weight=None, seed=0, subsample=None, tree_method=None,
validate_parameters=None, verbosity=None)
/mnt/c/Users/deargle/projects/keplermapper/.venv/lib/python3.6/sitepackages/xgboost/sklearn.py:1146: UserWarning: The use of label encoder in XGBClassifier is deprecated and will be removed in a future release. To remove this warning, do the following: 1) Pass option use_label_encoder=False when constructing XGBClassifier object; and 2) Encode your labels (y) as integers starting with 0, i.e. 0, 1, 2, ..., [num_class  1].
warnings.warn(label_encoder_deprecation_msg, UserWarning)
[11:54:35] WARNING: ../src/learner.cc:1095: Starting in XGBoost 1.3.0, the default evaluation metric used with the objective 'binary:logistic' was changed from 'error' to 'logloss'. Explicitly set eval_metric if you'd like to restore the old behavior.

Fold: 0 ((43388, 23)/(10848, 23))
precision recall f1score support
nonTOR 0.99 0.99 0.99 9561
TOR 0.96 0.96 0.96 1287
accuracy 0.99 10848
macro avg 0.98 0.98 0.98 10848
weighted avg 0.99 0.99 0.99 10848
Confusion Matrix:
[[9513 48]
[ 54 1233]]
Log loss : 0.026506
AUC : 0.998835
Accuracy : 0.990597
Precision: 0.962529
Recall : 0.958042
F1score : 0.960280
[11:54:41] WARNING: ../src/learner.cc:1095: Starting in XGBoost 1.3.0, the default evaluation metric used with the objective 'binary:logistic' was changed from 'error' to 'logloss'. Explicitly set eval_metric if you'd like to restore the old behavior.
/mnt/c/Users/deargle/projects/keplermapper/.venv/lib/python3.6/sitepackages/xgboost/sklearn.py:1146: UserWarning: The use of label encoder in XGBClassifier is deprecated and will be removed in a future release. To remove this warning, do the following: 1) Pass option use_label_encoder=False when constructing XGBClassifier object; and 2) Encode your labels (y) as integers starting with 0, i.e. 0, 1, 2, ..., [num_class  1].
warnings.warn(label_encoder_deprecation_msg, UserWarning)

Fold: 1 ((43389, 23)/(10847, 23))
precision recall f1score support
nonTOR 0.99 1.00 0.99 9560
TOR 0.97 0.95 0.96 1287
accuracy 0.99 10847
macro avg 0.98 0.97 0.98 10847
weighted avg 0.99 0.99 0.99 10847
Confusion Matrix:
[[9521 39]
[ 67 1220]]
Log loss : 0.027315
AUC : 0.998858
Accuracy : 0.990228
Precision: 0.969023
Recall : 0.947941
F1score : 0.958366
[11:54:47] WARNING: ../src/learner.cc:1095: Starting in XGBoost 1.3.0, the default evaluation metric used with the objective 'binary:logistic' was changed from 'error' to 'logloss'. Explicitly set eval_metric if you'd like to restore the old behavior.
/mnt/c/Users/deargle/projects/keplermapper/.venv/lib/python3.6/sitepackages/xgboost/sklearn.py:1146: UserWarning: The use of label encoder in XGBClassifier is deprecated and will be removed in a future release. To remove this warning, do the following: 1) Pass option use_label_encoder=False when constructing XGBClassifier object; and 2) Encode your labels (y) as integers starting with 0, i.e. 0, 1, 2, ..., [num_class  1].
warnings.warn(label_encoder_deprecation_msg, UserWarning)

Fold: 2 ((43389, 23)/(10847, 23))
precision recall f1score support
nonTOR 0.99 0.99 0.99 9560
TOR 0.96 0.95 0.95 1287
accuracy 0.99 10847
macro avg 0.98 0.97 0.97 10847
weighted avg 0.99 0.99 0.99 10847
Confusion Matrix:
[[9508 52]
[ 65 1222]]
Log loss : 0.032290
AUC : 0.997622
Accuracy : 0.989214
Precision: 0.959184
Recall : 0.949495
F1score : 0.954315
[11:54:53] WARNING: ../src/learner.cc:1095: Starting in XGBoost 1.3.0, the default evaluation metric used with the objective 'binary:logistic' was changed from 'error' to 'logloss'. Explicitly set eval_metric if you'd like to restore the old behavior.
/mnt/c/Users/deargle/projects/keplermapper/.venv/lib/python3.6/sitepackages/xgboost/sklearn.py:1146: UserWarning: The use of label encoder in XGBClassifier is deprecated and will be removed in a future release. To remove this warning, do the following: 1) Pass option use_label_encoder=False when constructing XGBClassifier object; and 2) Encode your labels (y) as integers starting with 0, i.e. 0, 1, 2, ..., [num_class  1].
warnings.warn(label_encoder_deprecation_msg, UserWarning)

Fold: 3 ((43389, 23)/(10847, 23))
precision recall f1score support
nonTOR 0.99 0.99 0.99 9560
TOR 0.95 0.96 0.96 1287
accuracy 0.99 10847
macro avg 0.97 0.98 0.97 10847
weighted avg 0.99 0.99 0.99 10847
Confusion Matrix:
[[9500 60]
[ 54 1233]]
Log loss : 0.027810
AUC : 0.998797
Accuracy : 0.989490
Precision: 0.953596
Recall : 0.958042
F1score : 0.955814
[11:54:59] WARNING: ../src/learner.cc:1095: Starting in XGBoost 1.3.0, the default evaluation metric used with the objective 'binary:logistic' was changed from 'error' to 'logloss'. Explicitly set eval_metric if you'd like to restore the old behavior.
/mnt/c/Users/deargle/projects/keplermapper/.venv/lib/python3.6/sitepackages/xgboost/sklearn.py:1146: UserWarning: The use of label encoder in XGBClassifier is deprecated and will be removed in a future release. To remove this warning, do the following: 1) Pass option use_label_encoder=False when constructing XGBClassifier object; and 2) Encode your labels (y) as integers starting with 0, i.e. 0, 1, 2, ..., [num_class  1].
warnings.warn(label_encoder_deprecation_msg, UserWarning)

Fold: 4 ((43389, 23)/(10847, 23))
precision recall f1score support
nonTOR 0.99 0.99 0.99 9560
TOR 0.96 0.95 0.96 1287
accuracy 0.99 10847
macro avg 0.98 0.97 0.97 10847
weighted avg 0.99 0.99 0.99 10847
Confusion Matrix:
[[9508 52]
[ 62 1225]]
Log loss : 0.027349
AUC : 0.998739
Accuracy : 0.989490
Precision: 0.959280
Recall : 0.951826
F1score : 0.955538
Hyper parameter tuning¶
We found the below parameters by running a random gridsearch on the first fold in ~50 iterations (minimizing log loss). We use an AWS distributed closedsource autotuning library called “Cher” with the following parameter ranges:
"XGBClassifier": {
"max_depth": (2,12),
"n_estimators": (20, 2500),
"objective": ["binary:logistic"],
"missing": np.nan,
"gamma": [0, 0, 0, 0, 0, 0.01, 0.1, 0.2, 0.3, 0.5, 1., 10., 100.],
"learning_rate": [0.01, 0.02, 0.03, 0.04, 0.05, 0.06, 0.07, 0.08, 0.09, 0.1, 0.15, 0.2, 0.1 ,0.1],
"min_child_weight": [1, 1, 1, 1, 2, 3, 4, 5, 1, 6, 7, 8, 9, 10, 11, 15, 30, 60, 100, 1, 1, 1],
"max_delta_step": [0, 0, 0, 0, 0, 1, 2, 5, 8],
"nthread": 1,
"subsample": [i/100. for i in range(20,100)],
"colsample_bytree": [i/100. for i in range(20,100)],
"colsample_bylevel": [i/100. for i in range(20,100)],
"reg_alpha": [0, 0, 0, 0, 0, 0.00000001, 0.00000005, 0.0000005, 0.000005],
"reg_lambda": [1, 1, 1, 1, 2, 3, 4, 5, 1],
"scale_pos_weight": 1,
"base_score": 0.5,
"seed": (0,999999)
}
[7]:
model = xgboost.XGBClassifier(base_score=0.5, colsample_bylevel=0.68, colsample_bytree=0.84,
gamma=0.1, learning_rate=0.1, max_delta_step=0, max_depth=11,
min_child_weight=1, missing=np.nan, n_estimators=1122, nthread=1,
objective='binary:logistic', reg_alpha=0.0, reg_lambda=4,
scale_pos_weight=1, seed=189548, silent=True, subsample=0.98)
5fold tuned XGBoost¶
[8]:
print(model)
for i, (train_index, test_index) in enumerate(skf.split(X_train, y_train)):
X_train_fold, X_test_fold = X_train[train_index], X_train[test_index]
y_train_fold, y_test_fold = y_train[train_index], y_train[test_index]
model.fit(X_train_fold, y_train_fold)
probas = model.predict_proba(X_test_fold)[:,1]
preds = (probas > 0.5).astype(int)
print(""*60)
print("Fold: %d (%s/%s)" %(i, X_train_fold.shape, X_test_fold.shape))
print(metrics.classification_report(y_test_fold, preds, target_names=["nonTOR", "TOR"]))
print("Confusion Matrix: \n%s\n"%metrics.confusion_matrix(y_test_fold, preds))
print("Log loss : %f" % (metrics.log_loss(y_test_fold, probas)))
print("AUC : %f" % (metrics.roc_auc_score(y_test_fold, probas)))
print("Accuracy : %f" % (metrics.accuracy_score(y_test_fold, preds)))
print("Precision: %f" % (metrics.precision_score(y_test_fold, preds)))
print("Recall : %f" % (metrics.recall_score(y_test_fold, preds)))
print("F1score : %f" % (metrics.f1_score(y_test_fold, preds)))
XGBClassifier(base_score=0.5, booster=None, colsample_bylevel=0.68,
colsample_bynode=None, colsample_bytree=0.84, gamma=0.1,
gpu_id=None, importance_type='gain', interaction_constraints=None,
learning_rate=0.1, max_delta_step=0, max_depth=11,
min_child_weight=1, missing=nan, monotone_constraints=None,
n_estimators=1122, n_jobs=None, nthread=1,
num_parallel_tree=None, random_state=None, reg_alpha=0.0,
reg_lambda=4, scale_pos_weight=1, seed=189548, silent=True,
subsample=0.98, tree_method=None, validate_parameters=None,
verbosity=None)
[11:55:05] WARNING: ../src/learner.cc:573:
Parameters: { "silent" } might not be used.
This may not be accurate due to some parameters are only used in language bindings but
passed down to XGBoost core. Or some parameters are not used but slip through this
verification. Please open an issue if you find above cases.
[11:55:05] WARNING: ../src/learner.cc:1095: Starting in XGBoost 1.3.0, the default evaluation metric used with the objective 'binary:logistic' was changed from 'error' to 'logloss'. Explicitly set eval_metric if you'd like to restore the old behavior.
/mnt/c/Users/deargle/projects/keplermapper/.venv/lib/python3.6/sitepackages/xgboost/sklearn.py:1146: UserWarning: The use of label encoder in XGBClassifier is deprecated and will be removed in a future release. To remove this warning, do the following: 1) Pass option use_label_encoder=False when constructing XGBClassifier object; and 2) Encode your labels (y) as integers starting with 0, i.e. 0, 1, 2, ..., [num_class  1].
warnings.warn(label_encoder_deprecation_msg, UserWarning)

Fold: 0 ((43388, 23)/(10848, 23))
precision recall f1score support
nonTOR 1.00 0.99 1.00 9561
TOR 0.96 0.96 0.96 1287
accuracy 0.99 10848
macro avg 0.98 0.98 0.98 10848
weighted avg 0.99 0.99 0.99 10848
Confusion Matrix:
[[9512 49]
[ 46 1241]]
Log loss : 0.027303
AUC : 0.998891
Accuracy : 0.991243
Precision: 0.962016
Recall : 0.964258
F1score : 0.963135
[11:56:21] WARNING: ../src/learner.cc:573:
Parameters: { "silent" } might not be used.
This may not be accurate due to some parameters are only used in language bindings but
passed down to XGBoost core. Or some parameters are not used but slip through this
verification. Please open an issue if you find above cases.
[11:56:21] WARNING: ../src/learner.cc:1095: Starting in XGBoost 1.3.0, the default evaluation metric used with the objective 'binary:logistic' was changed from 'error' to 'logloss'. Explicitly set eval_metric if you'd like to restore the old behavior.
/mnt/c/Users/deargle/projects/keplermapper/.venv/lib/python3.6/sitepackages/xgboost/sklearn.py:1146: UserWarning: The use of label encoder in XGBClassifier is deprecated and will be removed in a future release. To remove this warning, do the following: 1) Pass option use_label_encoder=False when constructing XGBClassifier object; and 2) Encode your labels (y) as integers starting with 0, i.e. 0, 1, 2, ..., [num_class  1].
warnings.warn(label_encoder_deprecation_msg, UserWarning)

Fold: 1 ((43389, 23)/(10847, 23))
precision recall f1score support
nonTOR 0.99 1.00 1.00 9560
TOR 0.97 0.95 0.96 1287
accuracy 0.99 10847
macro avg 0.98 0.97 0.98 10847
weighted avg 0.99 0.99 0.99 10847
Confusion Matrix:
[[9528 32]
[ 63 1224]]
Log loss : 0.025370
AUC : 0.999025
Accuracy : 0.991242
Precision: 0.974522
Recall : 0.951049
F1score : 0.962643
[11:57:36] WARNING: ../src/learner.cc:573:
Parameters: { "silent" } might not be used.
This may not be accurate due to some parameters are only used in language bindings but
passed down to XGBoost core. Or some parameters are not used but slip through this
verification. Please open an issue if you find above cases.
[11:57:36] WARNING: ../src/learner.cc:1095: Starting in XGBoost 1.3.0, the default evaluation metric used with the objective 'binary:logistic' was changed from 'error' to 'logloss'. Explicitly set eval_metric if you'd like to restore the old behavior.
/mnt/c/Users/deargle/projects/keplermapper/.venv/lib/python3.6/sitepackages/xgboost/sklearn.py:1146: UserWarning: The use of label encoder in XGBClassifier is deprecated and will be removed in a future release. To remove this warning, do the following: 1) Pass option use_label_encoder=False when constructing XGBClassifier object; and 2) Encode your labels (y) as integers starting with 0, i.e. 0, 1, 2, ..., [num_class  1].
warnings.warn(label_encoder_deprecation_msg, UserWarning)

Fold: 2 ((43389, 23)/(10847, 23))
precision recall f1score support
nonTOR 0.99 0.99 0.99 9560
TOR 0.96 0.95 0.96 1287
accuracy 0.99 10847
macro avg 0.98 0.97 0.97 10847
weighted avg 0.99 0.99 0.99 10847
Confusion Matrix:
[[9512 48]
[ 66 1221]]
Log loss : 0.031088
AUC : 0.998214
Accuracy : 0.989490
Precision: 0.962175
Recall : 0.948718
F1score : 0.955399
[11:58:48] WARNING: ../src/learner.cc:573:
Parameters: { "silent" } might not be used.
This may not be accurate due to some parameters are only used in language bindings but
passed down to XGBoost core. Or some parameters are not used but slip through this
verification. Please open an issue if you find above cases.
[11:58:48] WARNING: ../src/learner.cc:1095: Starting in XGBoost 1.3.0, the default evaluation metric used with the objective 'binary:logistic' was changed from 'error' to 'logloss'. Explicitly set eval_metric if you'd like to restore the old behavior.
/mnt/c/Users/deargle/projects/keplermapper/.venv/lib/python3.6/sitepackages/xgboost/sklearn.py:1146: UserWarning: The use of label encoder in XGBClassifier is deprecated and will be removed in a future release. To remove this warning, do the following: 1) Pass option use_label_encoder=False when constructing XGBClassifier object; and 2) Encode your labels (y) as integers starting with 0, i.e. 0, 1, 2, ..., [num_class  1].
warnings.warn(label_encoder_deprecation_msg, UserWarning)

Fold: 3 ((43389, 23)/(10847, 23))
precision recall f1score support
nonTOR 0.99 0.99 0.99 9560
TOR 0.96 0.96 0.96 1287
accuracy 0.99 10847
macro avg 0.98 0.98 0.98 10847
weighted avg 0.99 0.99 0.99 10847
Confusion Matrix:
[[9512 48]
[ 55 1232]]
Log loss : 0.025460
AUC : 0.999137
Accuracy : 0.990504
Precision: 0.962500
Recall : 0.957265
F1score : 0.959875
[11:59:59] WARNING: ../src/learner.cc:573:
Parameters: { "silent" } might not be used.
This may not be accurate due to some parameters are only used in language bindings but
passed down to XGBoost core. Or some parameters are not used but slip through this
verification. Please open an issue if you find above cases.
[11:59:59] WARNING: ../src/learner.cc:1095: Starting in XGBoost 1.3.0, the default evaluation metric used with the objective 'binary:logistic' was changed from 'error' to 'logloss'. Explicitly set eval_metric if you'd like to restore the old behavior.
/mnt/c/Users/deargle/projects/keplermapper/.venv/lib/python3.6/sitepackages/xgboost/sklearn.py:1146: UserWarning: The use of label encoder in XGBClassifier is deprecated and will be removed in a future release. To remove this warning, do the following: 1) Pass option use_label_encoder=False when constructing XGBClassifier object; and 2) Encode your labels (y) as integers starting with 0, i.e. 0, 1, 2, ..., [num_class  1].
warnings.warn(label_encoder_deprecation_msg, UserWarning)

Fold: 4 ((43389, 23)/(10847, 23))
precision recall f1score support
nonTOR 0.99 1.00 1.00 9560
TOR 0.97 0.96 0.97 1287
accuracy 0.99 10847
macro avg 0.98 0.98 0.98 10847
weighted avg 0.99 0.99 0.99 10847
Confusion Matrix:
[[9522 38]
[ 48 1239]]
Log loss : 0.026125
AUC : 0.998922
Accuracy : 0.992072
Precision: 0.970243
Recall : 0.962704
F1score : 0.966459
Holdout set evaluation¶
[9]:
model.fit(X_train, y_train)
probas = model.predict_proba(X_holdout)[:,1]
preds = (probas > 0.5).astype(int)
print(metrics.classification_report(y_holdout, preds, target_names=["nonTOR", "TOR"]))
print("Confusion Matrix: \n%s\n"%metrics.confusion_matrix(y_holdout, preds))
print("Log loss : %f" % (metrics.log_loss(y_holdout, probas)))
print("AUC : %f" % (metrics.roc_auc_score(y_holdout, probas)))
print("Accuracy : %f" % (metrics.accuracy_score(y_holdout, preds)))
print("Precision: %f" % (metrics.precision_score(y_holdout, preds)))
print("Recall : %f" % (metrics.recall_score(y_holdout, preds)))
print("F1score : %f" % (metrics.f1_score(y_holdout, preds)))
[12:01:12] WARNING: ../src/learner.cc:573:
Parameters: { "silent" } might not be used.
This may not be accurate due to some parameters are only used in language bindings but
passed down to XGBoost core. Or some parameters are not used but slip through this
verification. Please open an issue if you find above cases.
[12:01:12] WARNING: ../src/learner.cc:1095: Starting in XGBoost 1.3.0, the default evaluation metric used with the objective 'binary:logistic' was changed from 'error' to 'logloss'. Explicitly set eval_metric if you'd like to restore the old behavior.
/mnt/c/Users/deargle/projects/keplermapper/.venv/lib/python3.6/sitepackages/xgboost/sklearn.py:1146: UserWarning: The use of label encoder in XGBClassifier is deprecated and will be removed in a future release. To remove this warning, do the following: 1) Pass option use_label_encoder=False when constructing XGBClassifier object; and 2) Encode your labels (y) as integers starting with 0, i.e. 0, 1, 2, ..., [num_class  1].
warnings.warn(label_encoder_deprecation_msg, UserWarning)
precision recall f1score support
nonTOR 1.00 1.00 1.00 11950
TOR 0.97 0.97 0.97 1609
accuracy 0.99 13559
macro avg 0.98 0.98 0.98 13559
weighted avg 0.99 0.99 0.99 13559
Confusion Matrix:
[[11909 41]
[ 55 1554]]
Log loss : 0.021121
AUC : 0.999294
Accuracy : 0.992920
Precision: 0.974295
Recall : 0.965817
F1score : 0.970037
Results¶
Model 
Precision 
Recall 
F1Score 

Logistic Regression (Singh et al., 2018) [34] 
0.87 
0.87 
0.87 
SVM (Singh et al., 2018) 
0.9 
0.9 
0.9 
Naïve Bayes (Singh et al., 2018) 
0.91 
0.6 
0.7 
C4.5 Decision Tree + Feature Selection (Lashkari et al., 2017) [29] 
0.948 
0.934 

Deep Learning (Singh et al., 2018) 
0.95 
0.95 
0.95 
Random Forest (Singh et al., 2018) 
0.96 
0.96 
0.96 
XGBoost + Tuning 
0.974 
0.977 
0.976 
Holdout evaluation with all the available features¶
Using all the features results in near perfect performance, suggesting “leaky” features (These features are not to be used for predictive modeling, but are there for completeness). Nevertheless we show how using all features also results in a strong baseline over previous research.
[10]:
model.fit(X_train_all, y_train)
probas = model.predict_proba(X_holdout_all)[:,1]
preds = (probas > 0.5).astype(int)
print(metrics.classification_report(y_holdout, preds, target_names=["nonTOR", "TOR"]))
print("Confusion Matrix: \n%s\n"%metrics.confusion_matrix(y_holdout, preds))
print("Log loss : %f" % (metrics.log_loss(y_holdout, probas)))
print("AUC : %f" % (metrics.roc_auc_score(y_holdout, probas)))
print("Accuracy : %f" % (metrics.accuracy_score(y_holdout, preds)))
print("Precision: %f" % (metrics.precision_score(y_holdout, preds)))
print("Recall : %f" % (metrics.recall_score(y_holdout, preds)))
[12:02:43] WARNING: ../src/learner.cc:573:
Parameters: { "silent" } might not be used.
This may not be accurate due to some parameters are only used in language bindings but
passed down to XGBoost core. Or some parameters are not used but slip through this
verification. Please open an issue if you find above cases.
[12:02:43] WARNING: ../src/learner.cc:1095: Starting in XGBoost 1.3.0, the default evaluation metric used with the objective 'binary:logistic' was changed from 'error' to 'logloss'. Explicitly set eval_metric if you'd like to restore the old behavior.
/mnt/c/Users/deargle/projects/keplermapper/.venv/lib/python3.6/sitepackages/xgboost/sklearn.py:1146: UserWarning: The use of label encoder in XGBClassifier is deprecated and will be removed in a future release. To remove this warning, do the following: 1) Pass option use_label_encoder=False when constructing XGBClassifier object; and 2) Encode your labels (y) as integers starting with 0, i.e. 0, 1, 2, ..., [num_class  1].
warnings.warn(label_encoder_deprecation_msg, UserWarning)
precision recall f1score support
nonTOR 1.00 1.00 1.00 11950
TOR 1.00 1.00 1.00 1609
accuracy 1.00 13559
macro avg 1.00 1.00 1.00 13559
weighted avg 1.00 1.00 1.00 13559
Confusion Matrix:
[[11946 4]
[ 0 1609]]
Log loss : 0.000963
AUC : 0.999999
Accuracy : 0.999705
Precision: 0.997520
Recall : 1.000000
Results¶
Model 
Precision 
Recall 
Accuracy 

ANN (Hodo et al., 2017) [35] 
0.983 
0.937 
0.991 
SVM (Hodo et al., 2017) 
0.79 
0.67 
0.94 
ANN + Feature Selection (Hodo et al., 2017) 
0.998 
0.988 
0.998 
SVM + Feature Selection (Hodo et al., 2017) 
0.8 
0.984 
0.881 
XGBoost + Tuning 
0.999 
1. 
0.999 
Topological Data Analysis¶
[11]:
import kmapper as km
import pandas as pd
import numpy as np
from sklearn import ensemble, cluster
df = load_and_prep_data()
features = [c for c in df.columns if c not in
['Source IP',
' Source Port',
' Destination IP',
' Destination Port',
' Protocol',
'label']]
X = np.array(df[features])
y = np.array(df.label)
projector = ensemble.IsolationForest(random_state=0, n_jobs=1)
projector.fit(X)
lens1 = projector.decision_function(X)
mapper = km.KeplerMapper(verbose=3)
lens2 = mapper.fit_transform(X, projection="knn_distance_5")
lens = np.c_[lens1, lens2]
KeplerMapper(verbose=3)
..Composing projection pipeline of length 1:
Projections: knn_distance_5
Distance matrices: False
Scalers: MinMaxScaler()
..Projecting on data shaped (67795, 23)
..Projecting data using: knn_distance_5
..Scaling with: MinMaxScaler()
[12]:
G = mapper.map(
lens,
X,
cover = km.Cover(n_cubes=20,
perc_overlap=.15),
clusterer=cluster.AgglomerativeClustering(3))
print(f"num nodes: {len(G['nodes'])}")
print(f"num edges: {sum([len(values) for key, values in G['links'].items()])}")
Mapping on data shaped (67795, 23) using lens shaped (67795, 2)
Minimal points in hypercube before clustering: 3
Creating 400 hypercubes.
> Found 3 clusters in hypercube 0.
> Found 3 clusters in hypercube 1.
> Found 3 clusters in hypercube 2.
Cube_3 is empty.
Cube_4 is empty.
> Found 3 clusters in hypercube 5.
Cube_6 is empty.
> Found 3 clusters in hypercube 7.
> Found 3 clusters in hypercube 8.
> Found 3 clusters in hypercube 9.
> Found 3 clusters in hypercube 10.
> Found 3 clusters in hypercube 11.
> Found 3 clusters in hypercube 12.
Cube_13 is empty.
> Found 3 clusters in hypercube 14.
> Found 3 clusters in hypercube 15.
> Found 3 clusters in hypercube 16.
> Found 3 clusters in hypercube 17.
> Found 3 clusters in hypercube 18.
> Found 3 clusters in hypercube 19.
Cube_20 is empty.
Cube_21 is empty.
> Found 3 clusters in hypercube 22.
> Found 3 clusters in hypercube 23.
> Found 3 clusters in hypercube 24.
> Found 3 clusters in hypercube 25.
> Found 3 clusters in hypercube 26.
> Found 3 clusters in hypercube 27.
Cube_28 is empty.
Cube_29 is empty.
> Found 3 clusters in hypercube 30.
> Found 3 clusters in hypercube 31.
> Found 3 clusters in hypercube 32.
> Found 3 clusters in hypercube 33.
Cube_34 is empty.
Cube_35 is empty.
Cube_36 is empty.
Cube_37 is empty.
Cube_38 is empty.
> Found 3 clusters in hypercube 39.
> Found 3 clusters in hypercube 40.
> Found 3 clusters in hypercube 41.
> Found 3 clusters in hypercube 42.
> Found 3 clusters in hypercube 43.
Cube_44 is empty.
Cube_45 is empty.
Cube_46 is empty.
Cube_47 is empty.
> Found 3 clusters in hypercube 48.
> Found 3 clusters in hypercube 49.
> Found 3 clusters in hypercube 50.
> Found 3 clusters in hypercube 51.
Cube_52 is empty.
Cube_53 is empty.
Cube_54 is empty.
Cube_55 is empty.
> Found 3 clusters in hypercube 56.
> Found 3 clusters in hypercube 57.
> Found 3 clusters in hypercube 58.
> Found 3 clusters in hypercube 59.
Cube_60 is empty.
> Found 3 clusters in hypercube 61.
> Found 3 clusters in hypercube 62.
> Found 3 clusters in hypercube 63.
> Found 3 clusters in hypercube 64.
> Found 3 clusters in hypercube 65.
> Found 3 clusters in hypercube 66.
> Found 3 clusters in hypercube 67.
Cube_68 is empty.
Cube_69 is empty.
Cube_70 is empty.
Cube_71 is empty.
> Found 3 clusters in hypercube 72.
> Found 3 clusters in hypercube 73.
> Found 3 clusters in hypercube 74.
> Found 3 clusters in hypercube 75.
> Found 3 clusters in hypercube 76.
Cube_77 is empty.
> Found 3 clusters in hypercube 78.
> Found 3 clusters in hypercube 79.
> Found 3 clusters in hypercube 80.
Cube_81 is empty.
> Found 3 clusters in hypercube 82.
> Found 3 clusters in hypercube 83.
> Found 3 clusters in hypercube 84.
Cube_85 is empty.
> Found 3 clusters in hypercube 86.
> Found 3 clusters in hypercube 87.
Cube_88 is empty.
Cube_89 is empty.
> Found 3 clusters in hypercube 90.
> Found 3 clusters in hypercube 91.
> Found 3 clusters in hypercube 92.
> Found 3 clusters in hypercube 93.
Cube_94 is empty.
> Found 3 clusters in hypercube 95.
> Found 3 clusters in hypercube 96.
> Found 3 clusters in hypercube 97.
Cube_98 is empty.
> Found 3 clusters in hypercube 99.
> Found 3 clusters in hypercube 100.
Cube_101 is empty.
> Found 3 clusters in hypercube 102.
> Found 3 clusters in hypercube 103.
> Found 3 clusters in hypercube 104.
> Found 3 clusters in hypercube 105.
Created 352 edges and 216 nodes in 0:02:01.070359.
num nodes: 216
num edges: 352
[13]:
_ = mapper.visualize(
G,
custom_tooltips=y,
color_values=y,
color_function_name="target",
path_html="output/tortda.html",
X=X,
X_names=list(df[features].columns),
lens=lens,
lens_names=["IsolationForest", "KNNdistance 5"],
title="Detecting encrypted Tor Traffic with Isolation Forest and Nearest Neighbor Distance"
)
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
/mnt/c/Users/deargle/projects/keplermapper/kmapper/visuals.py:413: RuntimeWarning: invalid value encountered in true_divide
std_m = np.sqrt((cluster_X_mean  X_mean) ** 2) / X_std
Wrote visualization to: tortda.html
[ ]:
from kmapper import jupyter
#jupyter.display("output/tortda.html")
Image of previous version of output¶
Link to previous version of output¶
Discussion¶
Both deep learning and unsupervised TDA may benefit from more data and rawer features. One strength of deep learning is its ability to automaticly generate useful features. A properly tuned and architected RNN/LSTM or ConvNet on more data will likely beat or equal gradient boosting [36]. Likewise for TDA: TDA is very good at extracting structure from raw timeseries data. Using the preprocessed 5 second lagfeatures turns the problem more into a classification problem, than a temporal /forecasting problem.
The XGBoost baseline can be further improved: Other authors showed feature selection to be effective at discarding noise. Stacked generalization can improve many pure classification problems, at the cost of an increased complexity and latency. Likewise with feature expansion through feature interactions, the score can be improved a small bit [37].
The graph created with \(MAPPER\) shows a concentration of anomalous samples that are predominantly nonTor traffic. This confirms our earlier note that anomalous behavior is not necessarily suspicious behavior. The separation could be better, but it is already possible to identify different types of Tor traffic, and see how they differ (an above average or below average Flow Duration
can both signal Tor traffic.)
The large max_depth=11
found by XGBoost on this relatively small dataset signals that either the problem is very complex (and needs large complexity to be solved well), or that memorization of patterns is important for good performance on this dataset (larger max_depth
’s find more feature interactions and are better at memorization).
Thanks¶
Thanks to dr. Satnam Singh and Balamurali A R for the inspiring article. Thanks to my colleagues at Nubank InfoSec, especially Jonas Abreu, for helpful discussions and consulting on domain expertise. Thanks to the Canadian Institute for Cybersecurity (dr. Lashkari et al.) for creating and providing the data used [38], and writing the original paper with great clarity.
References¶
[1] Freund, Schapire (1999). A short introduction to boosting
[2] Chen, Tianqi and Guestrin, Carlos (2016) XGBoost: A Scalable Tree Boosting System
[3] Liudmila Prokhorenkova, Gleb Gusev, Aleksandr Vorobev, Anna Veronika Dorogush, Andrey Gulin (2017) CatBoost: unbiased boosting with categorical features
[4] Guolin Ke, Qi Meng, Thomas Finley, Taifeng Wang, Wei Chen, Weidong Ma, Qiwei Ye, and TieYan Liu. (2017) LightGBM: A Highly Efficient Gradient Boosting Decision Tree.
[5] Pedregosa, F. and Varoquaux, G. and Gramfort, A. and Michel, V. and Thirion, B. and Grisel, O. and Blondel, M. and Prettenhofer, P. and Weiss, R. and Dubourg, V. and Vanderplas, J. and Passos, A. and Cournapeau, D. and Brucher, M. and Perrot, M. and Duchesnay, E. (2011) Scikitlearn: Machine Learning in Python
[6] Community (2014). Awesome XGBoost
[7] CERN and Kaggle (2014) Higgs Boson Machine Learning Challenge
[8] Tianqi Chen on Quora (2015) What makes xgboost run much faster than many other implementations of gradient boosting?
[9] Zygmunt Zając (2015) Early stopping
[10] Rory Mitchell, Andrey Adinets, Thejaswi Rao, Eibe Frank (2018) XGBoost: Scalable GPU Accelerated Learning
[11] Fei Tony Liu, Kai Ming Ting, ZhiHua Zhou (2008) Isolation Forest
[12] Sridhar Ramaswamy, Rajeev Rastogi, and Kyuseok Shim. (2000) Efficient algorithms for mining outliers from large data sets
[13] Gunnar Carlsson (2008) Topology and Data
[14] Devi Ramanan (2015) Identification of Type 2 Diabetes Subgroups through Topological Data Analysis of Patient Similarity
[15] Pablo G. Cámara (2017) Topological methods for genomics: present and future directions
[16] Wei Guo, Ashis Gopal Banerjee (2017) Identification of Key Features Using Topological Data Analysis for Accurate Prediction of Manufacturing System Outputs
[17] Mustafa Hajij, Bei Wang, Paul Rosen (2018) MOG: Mapper on Graphs for Relationship Preserving Clustering
[18] Anthony Bak (2015) Topology and Machine Learning
[19] Muthu Alagappan (2012) From 5 to 13: Redefining the Positions in Basketball
[20] Marc Coudriau, Abdelkader Lahmadi, Jérôme François (2016) Topological analysis and visualisation of network monitoring data: Darknet case study
[21] Gurjeet Singh, Facundo Mémoli, and Gunnar Carlsson (2007) Topological Methods for the Analysis of High Dimensional Data Sets and 3D Object Recognition
[22] P. Y. Lum, G. Singh, A. Lehman, T. Ishkanov, M. VejdemoJohansson, M. Alagappan, J. Carlsson & G. Carlsson (2009) Extracting insights from the shape of complex data using topology
[23] Hendrik Jacob van Veen, and Nathaniel Saul (2017) KeplerMapper
[24] Karsten Loesing and Steven J. Murdoch and Roger Dingledine (2010) A Case Study on Measuring Statistical Data in the Tor Anonymity Network
[25] Daniel Moore, Thomas Rid (2016) Cryptopolitik and the Darknet
[26] Stephen Northcutt, Judy Novak (2002) Network Intrusion Detection, Third Edition
[27] Justin Grana, David Wolpert, Joshua Neil, Dongping Xie, Tanmoy Bhattacharya, Russell Bent (2016) A Likelihood Ratio Detector for Identifying WithinPerimeter Computer Network Attacks.
[28] Simon Denman (2012) Why multilayered security is still the best defence
[29] Arash Habibi Lashkari, Gerard Draper Gil, Mohammad Saiful Islam Mamun, Ali A. Ghorbani (2017) Characterization of Tor Traffic using Time based Features
[30] Canadian Institute for Cybersecurity (Retrieved: 2018) Canadian Institute for Cybersecurity
[31] DraperGil, G., Lashkari, A. H., Mamun, M. S. I., and Ghorbani, A. A. (2016). Characterization of encrypted and vpn traffic using timerelated features
[32] Trevor Hastie, Robert Tibshirani, Jerome H. Friedman (2001) The Elements of Statistical Learning
[33] James Bergstra, Yoshua Bengio (2012) Random Search for HyperParameter Optimization
[34] Satnam Singh, Balamurali A R (2018) Using Deep Learning for Information Security
[35] Elike Hodo, Xavier Bellekens, Ephraim Iorkyase, Andrew Hamilton, Christos Tachtatzis, Robert Atkinson (2017) Machine Learning Approach for Detection of nonTor Traffic
[36] Gábor Melis, Chris Dyer, Phil Blunsom (2017) On the State of the Art of Evaluation in Neural Language Models
[37] Marios Michailidis (2017) Investigating machine learning methods in recommender systems
[38] Canadian Institute for Cybersecurity (2016) TornonTor dataset (ISCXTor2016)
Changelog¶
2021.10.08 – Dave Eargle (@deargle)¶
Replace
merged_5s.csv
withSelectedFeatures10sTORNonTOR.csv
because I can’t find the former.n_cubes from
40
to20
and perc_overlap from1.5
=>0.15
because:the code bounds it from [0, 1]
trying to match the linked vis’ 192 nodes and ~500 links, and these settings lead to 216 nodes and 352 edges
my computer can’t handle any higher overlap