Inspecting SVM models.

This example uses the ‘fmri’ dataset, performs simple binary classification using a Support Vector Machine classifier and analyse the model.

References

Waskom, M.L., Frank, M.C., Wagner, A.D. (2016). Adaptive engagement of cognitive control in context-dependent decision-making. Cerebral Cortex.

# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
#          Shammi More <s.more@fz-juelich.de>
#
# License: AGPL

import numpy as np
import pandas as pd

from sklearn.model_selection import GroupShuffleSplit

import matplotlib.pyplot as plt
import seaborn as sns
from seaborn import load_dataset

from julearn import run_cross_validation
from julearn.utils import configure_logging
from julearn.inspect import preprocess

Set the logging level to info to see extra information

configure_logging(level="INFO")

2023-07-19 12:41:55,485 - julearn - INFO - ===== Lib Versions =====
2023-07-19 12:41:55,486 - julearn - INFO - numpy: 1.25.1
2023-07-19 12:41:55,486 - julearn - INFO - scipy: 1.11.1
2023-07-19 12:41:55,486 - julearn - INFO - sklearn: 1.3.0
2023-07-19 12:41:55,486 - julearn - INFO - pandas: 2.0.3
2023-07-19 12:41:55,486 - julearn - INFO - julearn: 0.3.1.dev1
2023-07-19 12:41:55,486 - julearn - INFO - ========================

Dealing with Cross-Validation techniques

df_fmri = load_dataset("fmri")

First, lets get some information on what the dataset has:

print(df_fmri.head())

  subject  timepoint event    region    signal
0     s13         18  stim  parietal -0.017552
1      s5         14  stim  parietal -0.080883
2     s12         18  stim  parietal -0.081033
3     s11         18  stim  parietal -0.046134
4     s10         18  stim  parietal -0.037970

From this information, we can infer that it is an fMRI study in which there were several subjects, timepoints, events and signal extracted from several brain regions.

Lets check how many kinds of each we have.

print(df_fmri["event"].unique())
print(df_fmri["region"].unique())
print(sorted(df_fmri["timepoint"].unique()))
print(df_fmri["subject"].unique())

['stim' 'cue']
['parietal' 'frontal']
[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18]
['s13' 's5' 's12' 's11' 's10' 's9' 's8' 's7' 's6' 's4' 's3' 's2' 's1' 's0']

We have data from parietal and frontal regions during 2 types of events (cue and stim) during 18 timepoints and for 14 subjects. Lets see how many samples we have for each condition

print(df_fmri.groupby(["subject", "timepoint", "event", "region"]).count())
print(
    np.unique(
        df_fmri.groupby(["subject", "timepoint", "event", "region"])
        .count()
        .values
    )
)

                                  signal
subject timepoint event region
s0      0         cue   frontal        1
                        parietal       1
                  stim  frontal        1
                        parietal       1
        1         cue   frontal        1
...                                  ...
s9      17        stim  parietal       1
        18        cue   frontal        1
                        parietal       1
                  stim  frontal        1
                        parietal       1

[1064 rows x 1 columns]
[1]

We have exactly one value per condition.

Lets try to build a model, that uses parietal and frontal signal to predicts whether the event was a cue or a stim.

First we define our X and y variables.

X = ["parietal", "frontal"]
y = "event"

In order for this to work, both parietal and frontal must be columns. We need to pivot the table.

The values of region will be the columns. The column signal will be the values. And the columns subject, timepoint and event will be the index

df_fmri = df_fmri.pivot(
    index=["subject", "timepoint", "event"], columns="region", values="signal"
)

df_fmri = df_fmri.reset_index()

Here we want to zscore all the features and then train a Support Vector Machine classifier.

scores = run_cross_validation(
    X=X,
    y=y,
    data=df_fmri,
    preprocess="zscore",
    model="svm",
    problem_type="classification",
)

print(scores["test_score"].mean())

2023-07-19 12:41:55,513 - julearn - INFO - ==== Input Data ====
2023-07-19 12:41:55,513 - julearn - INFO - Using dataframe as input
2023-07-19 12:41:55,513 - julearn - INFO -      Features: ['parietal', 'frontal']
2023-07-19 12:41:55,513 - julearn - INFO -      Target: event
2023-07-19 12:41:55,513 - julearn - INFO -      Expanded features: ['parietal', 'frontal']
2023-07-19 12:41:55,513 - julearn - INFO -      X_types:{}
2023-07-19 12:41:55,513 - julearn - WARNING - The following columns are not defined in X_types: ['parietal', 'frontal']. They will be treated as continuous.
/home/runner/work/julearn/julearn/julearn/utils/logging.py:238: RuntimeWarning: The following columns are not defined in X_types: ['parietal', 'frontal']. They will be treated as continuous.
  warn(msg, category=category)
2023-07-19 12:41:55,515 - julearn - INFO - ====================
2023-07-19 12:41:55,515 - julearn - INFO -
2023-07-19 12:41:55,515 - julearn - INFO - Adding step zscore that applies to ColumnTypes<types={'continuous'}; pattern=(?:__:type:__continuous)>
2023-07-19 12:41:55,516 - julearn - INFO - Step added
2023-07-19 12:41:55,516 - julearn - INFO - Adding step svm that applies to ColumnTypes<types={'continuous'}; pattern=(?:__:type:__continuous)>
2023-07-19 12:41:55,516 - julearn - INFO - Step added
2023-07-19 12:41:55,517 - julearn - INFO - = Model Parameters =
2023-07-19 12:41:55,517 - julearn - INFO - ====================
2023-07-19 12:41:55,517 - julearn - INFO -
2023-07-19 12:41:55,517 - julearn - INFO - = Data Information =
2023-07-19 12:41:55,517 - julearn - INFO -      Problem type: classification
2023-07-19 12:41:55,517 - julearn - INFO -      Number of samples: 532
2023-07-19 12:41:55,518 - julearn - INFO -      Number of features: 2
2023-07-19 12:41:55,518 - julearn - INFO - ====================
2023-07-19 12:41:55,518 - julearn - INFO -
2023-07-19 12:41:55,518 - julearn - INFO -      Number of classes: 2
2023-07-19 12:41:55,518 - julearn - INFO -      Target type: object
2023-07-19 12:41:55,519 - julearn - INFO -      Class distributions: event
cue     266
stim    266
Name: count, dtype: int64
2023-07-19 12:41:55,520 - julearn - INFO - Using outer CV scheme KFold(n_splits=5, random_state=None, shuffle=False)
2023-07-19 12:41:55,520 - julearn - INFO - Binary classification problem detected.
0.7218303650149884

This results indicate that we can decode the kind of event by looking at the parietal and frontal signal. However, that claim is true only if we have some data from the same subject already acquired.

The problem is that we split the data randomly into 5 folds (default, see run_cross_validation()). This means that data from one subject could be both in the training and the testing set. If this is the case, then the model can learn the subjects’ specific characteristics and apply it to the testing set. Thus, it is not true that we can decode it for an unseen subject, but for an unseen timepoint for a subject that for whom we already have data.

To test for unseen subject, we need to make sure that all the data from each subject is either on the training or the testing set, but not in both.

We can use scikit-learn’s sklearn.model_selection.GroupShuffleSplit. And specify which is the grouping column using the group parameter.

By setting return_estimator=’final’, the run_cross_validation() function return the estimator fitted with all the data. We will use this later to do some analysis.

cv = GroupShuffleSplit(n_splits=5, test_size=0.5, random_state=42)

scores, model = run_cross_validation(
    X=X,
    y=y,
    data=df_fmri,
    preprocess="zscore",
    model="svm",
    cv=cv,
    groups="subject",
    problem_type="classification",
    return_estimator="final",
)

print(scores["test_score"].mean())

2023-07-19 12:41:55,594 - julearn - INFO - ==== Input Data ====
2023-07-19 12:41:55,594 - julearn - INFO - Using dataframe as input
2023-07-19 12:41:55,594 - julearn - INFO -      Features: ['parietal', 'frontal']
2023-07-19 12:41:55,594 - julearn - INFO -      Target: event
2023-07-19 12:41:55,594 - julearn - INFO -      Expanded features: ['parietal', 'frontal']
2023-07-19 12:41:55,594 - julearn - INFO -      X_types:{}
2023-07-19 12:41:55,594 - julearn - WARNING - The following columns are not defined in X_types: ['parietal', 'frontal']. They will be treated as continuous.
/home/runner/work/julearn/julearn/julearn/utils/logging.py:238: RuntimeWarning: The following columns are not defined in X_types: ['parietal', 'frontal']. They will be treated as continuous.
  warn(msg, category=category)
2023-07-19 12:41:55,595 - julearn - INFO - Using subject as groups
2023-07-19 12:41:55,595 - julearn - INFO - ====================
2023-07-19 12:41:55,595 - julearn - INFO -
2023-07-19 12:41:55,595 - julearn - INFO - Adding step zscore that applies to ColumnTypes<types={'continuous'}; pattern=(?:__:type:__continuous)>
2023-07-19 12:41:55,595 - julearn - INFO - Step added
2023-07-19 12:41:55,595 - julearn - INFO - Adding step svm that applies to ColumnTypes<types={'continuous'}; pattern=(?:__:type:__continuous)>
2023-07-19 12:41:55,595 - julearn - INFO - Step added
2023-07-19 12:41:55,596 - julearn - INFO - = Model Parameters =
2023-07-19 12:41:55,596 - julearn - INFO - ====================
2023-07-19 12:41:55,596 - julearn - INFO -
2023-07-19 12:41:55,596 - julearn - INFO - = Data Information =
2023-07-19 12:41:55,596 - julearn - INFO -      Problem type: classification
2023-07-19 12:41:55,596 - julearn - INFO -      Number of samples: 532
2023-07-19 12:41:55,596 - julearn - INFO -      Number of features: 2
2023-07-19 12:41:55,596 - julearn - INFO - ====================
2023-07-19 12:41:55,596 - julearn - INFO -
2023-07-19 12:41:55,597 - julearn - INFO -      Number of classes: 2
2023-07-19 12:41:55,597 - julearn - INFO -      Target type: object
2023-07-19 12:41:55,597 - julearn - INFO -      Class distributions: event
cue     266
stim    266
Name: count, dtype: int64
2023-07-19 12:41:55,598 - julearn - INFO - Using outer CV scheme GroupShuffleSplit(n_splits=5, random_state=42, test_size=0.5, train_size=None)
2023-07-19 12:41:55,598 - julearn - INFO - Binary classification problem detected.
0.7210526315789474

After testing on independent subjects, we can now claim that given a new subject, we can predict the kind of event.

Lets do some visualization on how these two features interact and what the preprocessing part of the model does.

# Plot the raw features
fig, axes = plt.subplots(1, 2, figsize=(8, 4))
sns.scatterplot(
    x="parietal", y="frontal", hue="event", data=df_fmri, ax=axes[0], s=5
)
axes[0].set_title("Raw data")

# Plot the preprocessed features
pre_X = preprocess(
    model, X=X, data=df_fmri, until="zscore", with_column_types=True
)

pre_df = pre_X.join(df_fmri[y])

sns.scatterplot(
    x="parietal__:type:__continuous",
    y="frontal__:type:__continuous",
    hue="event",
    data=pre_df,
    ax=axes[1],
    s=5,
)

axes[1].set_title("Preprocessed data")

Text(0.5, 1.0, 'Preprocessed data')

In this case, the preprocessing is nothing more than a sklearn.preprocessing.StandardScaler.

It seems that the data is not quite linearly separable. Lets now visualize how the SVM does this complex task.

# get the model from the pipeline
clf = model[2]
fig = plt.figure()
ax = sns.scatterplot(
    x="parietal__:type:__continuous",
    y="frontal__:type:__continuous",
    hue="event",
    data=pre_df,
    s=5,
)

xlim = ax.get_xlim()
ylim = ax.get_ylim()

# create grid to evaluate model
xx = np.linspace(xlim[0], xlim[1], 30)
yy = np.linspace(ylim[0], ylim[1], 30)
YY, XX = np.meshgrid(yy, xx)
xy = np.vstack([XX.ravel(), YY.ravel()]).T

# Create pandas dataframe
xy_df = pd.DataFrame(
    data=xy,
    columns=["parietal__:type:__continuous", "frontal__:type:__continuous"],
)

Z = clf.decision_function(xy_df).reshape(XX.shape)
a = ax.contour(XX, YY, Z, colors="k", levels=[0], alpha=0.5, linestyles=["-"])
ax.set_title("Preprocessed data with SVM decision function boundaries")

Text(0.5, 1.0, 'Preprocessed data with SVM decision function boundaries')