Added documentation for the polling detection module (#601)

* added g test

* Finished polling detector

* finished unit tests for periodogram polling detector

* removed unused variables

* removed unused import

* added additional test for multiple observations at each timestep

* reformatted files and added tutorial notebook

* reformatted to meet black, pylint, mypy and prospector requirements

* Added further analysis to the documentation notebook

* reformatted code to conform with linting requirements

* Finished polling docs

* reformatted with black

* Removed junit xml file

* Added tests and functionality to accept a dataframe

* reformatted files to conform to linting requirements

---------

Co-authored-by: Pete Bryan <[email protected]>
Co-authored-by: Ian Hellen <[email protected]>

msticpy/analysis/polling_detection.py

@@ -0,0 +1,229 @@
+# -------------------------------------------------------------------------
+# Copyright (c) Microsoft Corporation. All rights reserved.
+# Licensed under the MIT License. See License.txt in the project root for
+# license information.
+# --------------------------------------------------------------------------
+"""
+Polling detection module.
+
+This module is used to highlight edges that are highly periodic and likely to be
+generated automatically. The periodic edges could be software polling a server for
+updates or malware beaconing and checking for instructions.
+
+There is currently only one technique available for filtering polling data which is
+the class PeriodogramPollingDetector.
+"""
+from collections import Counter
+from typing import Optional, Tuple, Union, List
+
+import numpy as np
+import numpy.typing as npt
+import pandas as pd
+
+from scipy import signal, special
+
+from ..common.utility import export
+
+
+@export
+class PeriodogramPollingDetector:
+    """
+    Polling detector using the Periodogram to detect strong frequencies.
+
+    Attributes
+    ----------
+    data: DataFrame
+        Dataframe containing the data to be analysed. Must contain a
+        column of edges and a column of timestamps
+
+    Methods
+    -------
+    detect_polling(timestamps, process_start, process_end, interval)
+        Detect strong periodic frequencies
+
+    """
+
+    def __init__(self, data: pd.DataFrame, copy: bool = False) -> None:
+        """
+        Create periodogram polling detector.
+
+        Parameters
+        ----------
+        data: DataFrame
+            Dataframe containing the data to be analysed. Must contain a
+            column of edges and a column of timestamps
+
+        copy: bool
+            A bool to indicate whether to copy the dataframe supplied to data
+        """
+        if copy:
+            self.data = data.copy()
+        else:
+            self.data = data
+
+    def _g_test(self, pxx: npt.NDArray, exclude_pi: bool) -> Tuple[float, float]:
+        """
+        Carry out fishers g test for periodicity.
+
+        Fisher's g test tests the null hypothesis that the time series is gaussian white noise
+        against the alternative that there is a deterministic periodic component[1]
+
+        If the length of the time series is even then the intensity at pi should be excluded
+
+        If the length of the power spectral density estimate is larger than 700 then an approximate
+        p value is calculated otherwise the exact p value is calculate.
+
+        This implementation was taken from the R package GeneCycle[2]
+
+        Parameters
+        ----------
+        pxx: ArrayLike
+            Estimate of the power spectral density
+
+        exclude_pi: bool
+            A bool to indicate whether the frequnecy located at pi should be removed.
+
+        Returns
+        -------
+        Tuple[float, float]
+            G test test statistic
+            G test P value
+
+        References
+        ----------
+        [1] M. Ahdesmaki, H. Lahdesmaki and O. Yli-Harja, "Robust Fisher's Test for Periodicity
+        Detection in Noisy Biological Time Series," 2007 IEEE International Workshop on Genomic
+        Signal Processing and Statistics, 2007, pp. 1-4, doi: 10.1109/GENSIPS.2007.4365817.
+        [2] https://github.com/cran/GeneCycle/blob/master/R/fisher.g.test.R
+
+        """
+        if exclude_pi:
+            pxx = pxx[:-1]
+
+        pxx_length = len(pxx)
+        test_statistic = np.max(pxx) / sum(pxx)
+        upper = np.floor(1 / test_statistic).astype("int")
+
+        if pxx_length > 700:
+            p_value = 1 - (1 - np.exp(-pxx_length * test_statistic)) ** pxx_length
+        else:
+            compose = []
+            for j in range(1, upper):
+                compose.append(
+                    (-1) ** (j - 1)
+                    * np.exp(
+                        np.log(special.binom(pxx_length, j))
+                        + (pxx_length - 1) * np.log(1 - j * test_statistic)
+                    )
+                )
+
+            p_value = sum(compose)
+
+        p_value = min(p_value, 1)
+
+        return test_statistic, p_value
+
+    def _detect_polling_arr(
+        self,
+        timestamps: npt.NDArray,
+        process_start: int,
+        process_end: int,
+        interval: int = 1,
+    ) -> Tuple[float, float, float]:
+        """
+        Carry out periodogram polling detecton on an array of timestamps.
+
+        Carries out the the procedure outlined in [1] to detect if the arrival times have a strong
+        periodic component.
+        The procedure estimates the periodogram for the data and passes the results to fishers G
+        test.
+
+        For more information run PeriodogramPollingDetector._g_test.__doc__
+
+        This code was adapted from [2].
+
+        Parameters
+        ----------
+        timestamps: ArrayLike
+            An array like object containing connection arrival times as timestamps
+        process_start: int
+            The timestamp representing the start of the counting process
+        process_end: int
+            The timestamp representing the end of the counting process
+        interval: int
+            The interval in seconds between observations
+
+        Returns
+        -------
+        p_val: float
+            The p value from fishers G test
+
+        References
+        ----------
+          [1] Heard, N. A. and Rubin-Delanchy, P. T. G. and Lawson, D. J. (2014) Filtering
+          automated polling traffic in computer network flow data. In proceedings of IEEE
+          Joint Intelligence and Security Informatics Conference 2014
+          [2] https://github.com/fraspass/human_activity/blob/master/fourier.py
+
+        """
+        time_steps = np.arange(process_start, process_end, step=interval)
+        counting_process = Counter(timestamps)
+
+        dn_ = np.array([counting_process[t] for t in time_steps])
+        dn_star = dn_ - len(timestamps) / len(time_steps)
+
+        freq, pxx = signal.periodogram(dn_star)
+
+        max_pxx_freq = freq[np.argmax(pxx)]
+
+        if len(dn_star) % 2 == 0:
+            _, p_val = self._g_test(pxx, True)
+        else:
+            _, p_val = self._g_test(pxx, False)
+
+        return p_val, max_pxx_freq, 1 / max_pxx_freq
+
+    def detect_polling(
+        self, time_column: str, groupby: Optional[Union[List[str], str]] = None
+    ) -> None:
+        """
+        Detect the time interval which is highly periodic.
+
+        Runs PeriodogramPollingDetector._detect_polling_arr on the time_column and populates a
+        p_value column, dominant_frequency column and dominant_interval column.
+
+        If groupby column(s) are given then PeriodogramPollingDetector._detect_polling_arr is ran on
+        each group.
+
+        Parameters
+        ----------
+        time_column: str
+            The name of the column that contains timestamps
+        groupby: str or list[str], optional
+            Column(s) to group by
+        """
+        ts_col = self.data[time_column]
+
+        start = min(ts_col)
+        end = max(ts_col)
+
+        if not groupby:
+            p_value, freq, interval = self._detect_polling_arr(ts_col, start, end)
+
+            self.data["p_value"] = p_value
+            self.data["dominant_frequency"] = freq
+            self.data["dominant_interval"] = interval
+        else:
+            grouped_results = self.data.groupby(groupby).apply(
+                lambda x: self._detect_polling_arr(
+                    x[time_column], min(x[time_column]), max(x[time_column])
+                )
+            )
+
+            grouped_results_df = pd.DataFrame(
+                grouped_results.tolist(),
+                columns=["p_value", "dominant_frequency", "dominant_interval"],
+                index=grouped_results.index,
+            ).reset_index()
+
+            self.data = self.data.merge(grouped_results_df)

tests/analysis/polling_detection/conftest.py

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+# -------------------------------------------------------------------------
+# Copyright (c) Microsoft Corporation. All rights reserved.
+# Licensed under the MIT License. See License.txt in the project root for
+# license information.
+# --------------------------------------------------------------------------
+"""Polling detection module test fixtures"""
+import numpy as np
+import pandas as pd
+import pytest
+
+np.random.seed(10)
+
+
+@pytest.fixture()
+def periodic_data():
+    np.random.seed(10)
+
+    N = 86400
+    start_ts = 1669852800
+    end_ts = start_ts + N
+
+    homo_pois = np.random.poisson(1.5, N)
+    freq = 0.01666666666666
+    periodic = (10 * np.sin(2 * np.pi * freq * np.arange(0, N))).astype("int")
+    periodic[periodic < 0] = 0
+    x = (periodic + homo_pois).astype("bool")
+    ts = np.arange(start_ts, end_ts)[x]
+
+    return pd.DataFrame({"edges": "periodic_edge", "timestamps": ts})
+
+
+@pytest.fixture()
+def non_periodic_data():
+    np.random.seed(10)
+
+    N = 86400
+    start_ts = 1669852800
+    end_ts = start_ts + N
+
+    homo_pois = np.random.poisson(1.5, N)
+    x = homo_pois.astype("bool")
+    ts = np.arange(start_ts, end_ts)[x]
+
+    return pd.DataFrame({"edges": "non_periodic_edge", "timestamps": ts})