neighbors.models.Mean
The Mean algorithm simply uses the mean of other users to make predictions about items. It's primarily useful as a good baseline model.
Source code in neighbors/models.py
class Mean(Base):
"""
The Mean algorithm simply uses the mean of other users to make predictions about items. It's primarily useful as a good baseline model.
"""
def __init__(
self, data, mask=None, n_mask_items=None, verbose=True, random_state=None
):
"""
Args:
data (pd.DataFrame): users x items dataframe
mask (pd.DataFrame, optional): A boolean dataframe used to split the data into 'observed' and 'missing' datasets. Defaults to None.
n_mask_items (int/float, optional): number of items to mask out, while the rest are treated as observed; Defaults to None.
data_range (int/float, optional): max - min of the data; Default computed from the input data. This is useful to set manually in case the input data do not span the full range of possible values
random_state (None, int, RandomState): a seed or random state used for all internal random operations (e.g. randomly mask half the data given n_mask_item = .05). Passing None will generate a new random seed. Default None.
verbose (bool; optional): print any initialization warnings; Default True
"""
super().__init__(
data, mask, n_mask_items, random_state=random_state, verbose=verbose
)
self.mean = None
def fit(self, dilate_by_nsamples=None, axis=0, **kwargs):
"""Fit model to train data. Simply learns item-wise mean using observed (non-missing) values.
Args:
dilate_ts_n_samples (int): will dilate masked samples by n_samples to leverage auto-correlation in estimating time-series data
axis (int): dimension along which to compute mean, 0 = mean across users separately by item, 1 = mean across items separately by user; Default 0
"""
# Call parent fit which acts as a guard for non-masked data
super().fit()
self.dilate_mask(n_samples=dilate_by_nsamples)
self.mean = self.masked_data.mean(skipna=True, axis=axis)
self._predict()
self.is_fit = True
def _predict(self):
"""Predict missing items using other subject's item means."""
# Always predict mean (learned on observed values) for observed and missing values
self.predictions = pd.concat([self.mean] * self.data.shape[0], axis=1).T
self.predictions.index = self.data.index
self.predictions.columns = self.data.columns
__init__(self, data, mask=None, n_mask_items=None, verbose=True, random_state=None)
special
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
data |
pd.DataFrame |
users x items dataframe |
required |
mask |
pd.DataFrame |
A boolean dataframe used to split the data into 'observed' and 'missing' datasets. Defaults to None. |
None |
n_mask_items |
int/float |
number of items to mask out, while the rest are treated as observed; Defaults to None. |
None |
data_range |
int/float |
max - min of the data; Default computed from the input data. This is useful to set manually in case the input data do not span the full range of possible values |
required |
random_state |
None, int, RandomState |
a seed or random state used for all internal random operations (e.g. randomly mask half the data given n_mask_item = .05). Passing None will generate a new random seed. Default None. |
None |
verbose |
bool; optional |
print any initialization warnings; Default True |
True |
Source code in neighbors/models.py
def __init__(
self, data, mask=None, n_mask_items=None, verbose=True, random_state=None
):
"""
Args:
data (pd.DataFrame): users x items dataframe
mask (pd.DataFrame, optional): A boolean dataframe used to split the data into 'observed' and 'missing' datasets. Defaults to None.
n_mask_items (int/float, optional): number of items to mask out, while the rest are treated as observed; Defaults to None.
data_range (int/float, optional): max - min of the data; Default computed from the input data. This is useful to set manually in case the input data do not span the full range of possible values
random_state (None, int, RandomState): a seed or random state used for all internal random operations (e.g. randomly mask half the data given n_mask_item = .05). Passing None will generate a new random seed. Default None.
verbose (bool; optional): print any initialization warnings; Default True
"""
super().__init__(
data, mask, n_mask_items, random_state=random_state, verbose=verbose
)
self.mean = None
create_masked_data(self, n_mask_items=0.2)
inherited
Create a mask and apply it to data using number of items or % of items
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
n_items |
int/float |
if an integer is passed its raw value is used. Otherwise if a float is passed its taken to be a (rounded) percentage of the total items; Default 0.1 (10% of the data) |
required |
Source code in neighbors/models.py
def create_masked_data(self, n_mask_items=0.2):
"""
Create a mask and apply it to data using number of items or % of items
Args:
n_items (int/float, optional): if an integer is passed its raw value is used. Otherwise if a float is passed its taken to be a (rounded) percentage of the total items; Default 0.1 (10% of the data)
"""
if (
isinstance(n_mask_items, np.floating)
and (n_mask_items >= 1.0 or n_mask_items <= 0.0)
) or (
isinstance(n_mask_items, int)
and (n_mask_items >= self.data.shape[1] or n_mask_items <= 0)
):
raise TypeError(
"n_items should a float between 0-1 or an integer < the number of items"
)
self.mask = create_sparse_mask(
self.data, n_mask_items, random_state=self.random_state
)
self.masked_data = self.data[self.mask]
self.is_masked = True
self.n_mask_items = n_mask_items
dilate_mask(self, n_samples=None)
inherited
Dilate sparse time-series data by n_samples.
Overlapping data will be averaged. This method computes and stores the dilated mask in .dilated_mask and internally updates the .masked_data. Repeated calls to this method on the same model instance do not stack, but rather perform a new dilation on the original masked data. Called this method with None will undo any dilation.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
nsamples |
int |
Number of samples to dilate data |
required |
Source code in neighbors/models.py
def dilate_mask(self, n_samples=None):
"""Dilate sparse time-series data by n_samples.
Overlapping data will be averaged. This method computes and stores the dilated mask in `.dilated_mask` and internally updates the `.masked_data`. Repeated calls to this method on the same model instance **do not** stack, but rather perform a new dilation on the original masked data. Called this method with `None` will undo any dilation.
Args:
nsamples (int): Number of samples to dilate data
"""
if self.mask is None:
raise ValueError("Model has no mask and requires one to perform dilation")
if not self.is_masked and n_samples is not None:
raise ValueError("Make sure model instance has been masked.")
if isinstance(n_samples, np.floating) or (
n_samples is not None and n_samples >= self.data.shape[1]
):
raise TypeError("nsamples should be an integer < the number of items")
# Always reset to the undilated mask first
self.masked_data = self.data[self.mask]
if n_samples is not None:
# After masking, perform dilation and save as the new masked data
self.masked_data = self.masked_data.apply(
lambda x: self._conv_ts_mean_overlap(x, n_samples=n_samples),
axis=1,
result_type="broadcast",
)
# Calculate and save dilated mask
self.dilated_mask = ~self.masked_data.isnull()
self.is_mask_dilated = True
self.dilated_by_nsamples = n_samples
else:
self.dilated_mask = None
self.is_mask_dilated = False
self.dilated_by_nsamples = None
downsample(self, n_samples, sampling_freq=None, target_type='samples')
inherited
Downsample a model's rating matrix to a new target frequency or number of samples using averaging. Also downsamples a model's mask and dilated mask if they exist as well as a model's predictions if it's already been fit.
If target_type = 'samples' and sampling_freq is None, the new user x item matrix will have shape users x items * (1 / n_samples).
If target_type = 'seconds', the new user x item matrix will have shape users x items * (1 / n_samples * sampling_freq).
If target_type = 'hz', the new user x item matrix will have shape users x items * (1 / sampling_freq / n_samples).
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
n_samples |
int |
number of samples |
required |
sampling_freq |
int/float |
Sampling frequency of data; Default None |
None |
target_type |
str |
how to downsample; must be one of "samples", "seconds" or "hz". Defaults to "samples". |
'samples' |
Source code in neighbors/models.py
def downsample(self, n_samples, sampling_freq=None, target_type="samples"):
"""
Downsample a model's rating matrix to a new target frequency or number of samples using averaging. Also downsamples a model's mask and dilated mask if they exist as well as a model's predictions if it's already been fit.
If target_type = 'samples' and sampling_freq is None, the new user x item matrix will have shape users x items * (1 / n_samples).
If target_type = 'seconds', the new user x item matrix will have shape users x items * (1 / n_samples * sampling_freq).
If target_type = 'hz', the new user x item matrix will have shape users x items * (1 / sampling_freq / n_samples).
Args:
n_samples (int): number of samples
sampling_freq (int/float): Sampling frequency of data; Default None
target_type (str, optional): how to downsample; must be one of "samples", "seconds" or "hz". Defaults to "samples".
"""
self.data = downsample_dataframe(
self.data,
sampling_freq=sampling_freq,
n_samples=n_samples,
target_type=target_type,
)
if self.is_masked:
# Also downsample mask
self.mask = downsample_dataframe(
self.mask,
sampling_freq=sampling_freq,
n_samples=n_samples,
target_type=target_type,
)
# Ensure mask stays boolean
self.mask.loc[:, :] = self.mask > 0
# Masked data
self.masked_data = downsample_dataframe(
self.masked_data,
sampling_freq=sampling_freq,
n_samples=n_samples,
target_type=target_type,
)
# Dilated mask
if self.is_mask_dilated:
self.dilated_mask = downsample_dataframe(
self.dilated_mask,
sampling_freq=sampling_freq,
n_samples=n_samples,
target_type=target_type,
)
# Ensure mask stays boolean
self.dilated_mask.loc[:, :] = self.dilated_mask > 0
if self.is_fit:
self.predictions = downsample_dataframe(
self.predictions,
sampling_freq=sampling_freq,
n_samples=n_samples,
target_type=target_type,
)
fit(self, dilate_by_nsamples=None, axis=0, **kwargs)
Fit model to train data. Simply learns item-wise mean using observed (non-missing) values.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
dilate_ts_n_samples |
int |
will dilate masked samples by n_samples to leverage auto-correlation in estimating time-series data |
required |
axis |
int |
dimension along which to compute mean, 0 = mean across users separately by item, 1 = mean across items separately by user; Default 0 |
0 |
Source code in neighbors/models.py
def fit(self, dilate_by_nsamples=None, axis=0, **kwargs):
"""Fit model to train data. Simply learns item-wise mean using observed (non-missing) values.
Args:
dilate_ts_n_samples (int): will dilate masked samples by n_samples to leverage auto-correlation in estimating time-series data
axis (int): dimension along which to compute mean, 0 = mean across users separately by item, 1 = mean across items separately by user; Default 0
"""
# Call parent fit which acts as a guard for non-masked data
super().fit()
self.dilate_mask(n_samples=dilate_by_nsamples)
self.mean = self.masked_data.mean(skipna=True, axis=axis)
self._predict()
self.is_fit = True
plot_predictions(self, dataset='missing', figsize=(16, 8), label_fontsize=16, hide_title=False, heatmap_kwargs={})
inherited
Create plot of actual vs predicted values.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
dataset |
str; optional |
one of 'full', 'observed', or 'missing'. Default 'missing'. |
'missing' |
figsize |
tuple; optional |
matplotlib figure size; Default (16,8) |
(16, 8) |
label_fontsize |
int; optional |
fontsize for all axis labels and titles; Default 16 |
16 |
hide_title |
bool; optional |
hide title containing RMSE and correlation performance if available; Default False |
False |
heatmap_kwargs |
dict |
addition arguments to seaborn.heatmap. |
{} |
Returns:
| Type | Description |
|---|---|
tuple |
(figure handle, axis handle) |
Source code in neighbors/models.py
def plot_predictions(
self,
dataset="missing",
figsize=(16, 8),
label_fontsize=16,
hide_title=False,
heatmap_kwargs={},
):
"""Create plot of actual vs predicted values.
Args:
dataset (str; optional): one of 'full', 'observed', or 'missing'. Default 'missing'.
figsize (tuple; optional): matplotlib figure size; Default (16,8)
label_fontsize (int; optional): fontsize for all axis labels and titles; Default 16
hide_title (bool; optional): hide title containing RMSE and correlation performance if available; Default False
heatmap_kwargs (dict, optional): addition arguments to seaborn.heatmap.
Returns:
tuple: (figure handle, axis handle)
"""
if not self.is_fit:
raise ValueError("Model has not been fit")
vmax = max(self.data.max().max(), self.data.max().max())
vmin = min(self.data.min().min(), self.data.min().min())
actual, pred = self._retrieve_predictions(dataset)
if actual is None:
ncols = 2
warnings.warn(
"Cannot score predictions on missing data because true values were never observed!"
)
else:
ncols = 3
heatmap_kwargs.setdefault("square", False)
heatmap_kwargs.setdefault("xticklabels", False)
heatmap_kwargs.setdefault("yticklabels", False)
heatmap_kwargs.setdefault("vmax", vmax)
heatmap_kwargs.setdefault("vmin", vmin)
f, ax = plt.subplots(nrows=1, ncols=ncols, figsize=figsize)
# The original data matrix (potentially masked)
sns.heatmap(self.masked_data, ax=ax[0], **heatmap_kwargs)
ax[0].set_title("Actual User/Item Ratings", fontsize=label_fontsize)
ax[0].set_xlabel("Items", fontsize=label_fontsize)
ax[0].set_ylabel("Users", fontsize=label_fontsize)
# The predicted data matrix
sns.heatmap(self.predictions, ax=ax[1], **heatmap_kwargs)
ax[1].set_title("Predicted User/Item Ratings", fontsize=label_fontsize)
ax[1].set_xlabel("Items", fontsize=label_fontsize)
ax[1].set_ylabel("Users", fontsize=label_fontsize)
f.tight_layout()
# Scatter plot if we can calculate it
if actual is not None:
nans = np.logical_or(np.isnan(actual), np.isnan(pred))
ax[2].scatter(
actual[~nans],
pred[~nans],
)
ax[2].set_xlabel("Actual", fontsize=label_fontsize)
ax[2].set_ylabel("Predicted", fontsize=label_fontsize)
ax[2].set_title("Ratings", fontsize=label_fontsize)
sns.despine()
r = self.score(dataset=dataset, by_user=True, metric="correlation")
rmse = self.score(dataset=dataset, by_user=True, metric="rmse")
if not hide_title:
plt.suptitle(
f"Mean RMSE: {np.round(rmse.mean(),3)} +/- {np.round(rmse.std(), 3)}\nMean Correlation: {np.round(r.mean(), 3)} +/- {np.round(r.std(), 3)}",
y=1.07,
fontsize=label_fontsize + 2,
)
plt.subplots_adjust(wspace=0.2)
return f, ax
score(self, metric='rmse', dataset='missing', by_user=True, actual=None)
inherited
Get the performance of a fitted model by comparing observed and predicted data. This method is primarily useful if you want to calculate a single metric. Otherwise you should prefer the .summary() method instead, which scores all metrics.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
metric |
str; optional |
what metric to compute, one of 'rmse', 'mse', 'mae' or 'correlation'; Default 'rmse'. |
'rmse' |
dataset |
str; optional |
how to compute scoring, either using 'observed', 'missing' or 'full'. Default 'missing'. |
'missing' |
by_user |
bool; optional |
whether to return a single score over all data points or a pandas Series of scores per user. Default True. |
True |
actual |
pd.DataFrame, None; optional |
a dataframe to score against; Default is None which uses the data provided when the model was initialized |
None |
Returns:
| Type | Description |
|---|---|
float/pd.Series |
score |
Source code in neighbors/models.py
def score(
self,
metric="rmse",
dataset="missing",
by_user=True,
actual=None,
):
"""Get the performance of a fitted model by comparing observed and predicted data. This method is primarily useful if you want to calculate a single metric. Otherwise you should prefer the `.summary()` method instead, which scores all metrics.
Args:
metric (str; optional): what metric to compute, one of 'rmse', 'mse', 'mae' or 'correlation'; Default 'rmse'.
dataset (str; optional): how to compute scoring, either using 'observed', 'missing' or 'full'. Default 'missing'.
by_user (bool; optional): whether to return a single score over all data points or a pandas Series of scores per user. Default True.
actual (pd.DataFrame, None; optional): a dataframe to score against; Default is None which uses the data provided when the model was initialized
Returns:
float/pd.Series: score
"""
if not self.is_fit:
raise ValueError("You must fit() model first before using this method.")
if metric not in ["rmse", "mse", "mae", "correlation"]:
raise ValueError(
"metric must be one of 'rmse', 'mse', 'mae', or 'correlation'"
)
# Get dataframes of observed and predicted values
# This will be a dense or sparse matrix the same shape as the input data
model_actual, pred = self._retrieve_predictions(dataset)
if actual is None:
actual = model_actual
else:
if actual.shape != self.data.shape:
raise ValueError(
"actual values dataframe supplied but shape does not match original data"
)
if actual is None:
warnings.warn(
"Cannot score predictions on missing data because true values were never observed!"
)
return None
with warnings.catch_warnings():
# Catch 'Mean of empty slice' warnings from np.nanmean
warnings.simplefilter("ignore", category=RuntimeWarning)
if by_user:
scores = []
for userid in range(actual.shape[0]):
user_actual = actual.iloc[userid, :].values
user_pred = pred.iloc[userid, :].values
if metric == "rmse":
score = np.sqrt(np.nanmean((user_pred - user_actual) ** 2))
elif metric == "mse":
score = np.nanmean((user_pred - user_actual) ** 2)
elif metric == "mae":
score = np.nanmean(np.abs(user_pred - user_actual))
elif metric == "correlation":
nans = np.logical_or(np.isnan(user_actual), np.isnan(user_pred))
if len(user_actual[~nans]) < 2 or len(user_pred[~nans]) < 2:
score = np.nan
else:
score = pearsonr(user_actual[~nans], user_pred[~nans])[0]
scores.append(score)
return pd.Series(scores, index=actual.index, name=f"{metric}_{dataset}")
else:
actual, pred = actual.to_numpy().flatten(), pred.to_numpy().flatten()
if metric == "rmse":
return np.sqrt(np.nanmean((pred - actual) ** 2))
elif metric == "mse":
return np.nanmean((pred - actual) ** 2)
elif metric == "mae":
return np.nanmean(np.abs(pred - actual))
elif metric == "correlation":
nans = np.logical_or(np.isnan(actual), np.isnan(pred))
if len(actual[~nans]) < 2 or len(pred[~nans]) < 2:
return np.nan
else:
return pearsonr(actual[~nans], pred[~nans])[0]
summary(self, verbose=False, actual=None, dataset=None)
inherited
Calculate the performance of a model and return a dataframe of results. Computes performance across all, observed, and missing datasets. Scores using rmse, mse, mae, and correlation. Computes scores across all subjects (i.e. ignoring the fact that ratings are clustered by subject) and the mean performance for each metric after calculating per-subject performance.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
verbose |
bool |
Print warning messages during scoring. Defaults to False. |
False |
actual |
pd.DataFrame, None; optional |
a dataframe to score against; Default is None which uses the data provided when the model was initialized |
None |
dataset |
str/None |
dataset to score. Must be one of 'full', 'observed','missing' or None to score both 'observed' and 'missing'; Default None |
None |
Returns:
| Type | Description |
|---|---|
pd.DataFrame |
long-form dataframe of model performance |
Source code in neighbors/models.py
def summary(self, verbose=False, actual=None, dataset=None):
"""
Calculate the performance of a model and return a dataframe of results. Computes performance across all, observed, and missing datasets. Scores using rmse, mse, mae, and correlation. Computes scores across all subjects (i.e. ignoring the fact that ratings are clustered by subject) and the mean performance for each metric after calculating per-subject performance.
Args:
verbose (bool, optional): Print warning messages during scoring. Defaults to False.
actual (pd.DataFrame, None; optional): a dataframe to score against; Default is None which uses the data provided when the model was initialized
dataset (str/None): dataset to score. Must be one of 'full', 'observed','missing' or None to score both 'observed' and 'missing'; Default None
Returns:
pd.DataFrame: long-form dataframe of model performance
"""
if not self.is_fit:
raise ValueError("Model has not been fit!")
if dataset is None:
if actual is None:
if self.is_dense:
dataset = ["missing", "observed"]
else:
dataset = ["observed"]
else:
dataset = ["missing", "observed"]
elif isinstance(dataset, str):
if actual is None and not self.is_dense and dataset in ["full", "missing"]:
raise ValueError(
"Cannot score predictions on missing values because no ground truth was observed"
)
dataset = [dataset]
# Compute results for all metrics, all datasets, separately for group and by subject
group_results = {
"algorithm": self.__class__.__name__,
}
subject_results = []
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
for metric in ["rmse", "mse", "mae", "correlation"]:
this_group_result = {}
this_subject_result = []
for dat in dataset:
this_group_result[dat] = self.score(
metric=metric, dataset=dat, actual=actual, by_user=False
)
this_subject_result.append(
self.score(
metric=metric,
dataset=dat,
by_user=True,
actual=actual,
)
)
# Dict of group results for this metric
group_results[metric] = this_group_result
# Dataframe of subject results for this metric
this_subject_result = pd.concat(this_subject_result, axis=1)
subject_results.append(this_subject_result)
group_results[f"{metric}_user"] = dict(
zip(
dataset,
this_subject_result.mean().values,
)
)
# Save final results to longform df
self.user_results = pd.concat(subject_results, axis=1)
group_results = pd.DataFrame(group_results)
group_results = (
group_results.reset_index()
.melt(
id_vars=["index", "algorithm"],
var_name="metric",
value_name="score",
)
.rename(columns={"index": "dataset"})
.sort_values(by=["dataset", "metric"])
.reset_index(drop=True)
.assign(
group=lambda df: df.metric.apply(
lambda x: "user" if "user" in x else "all"
),
metric=lambda df: df.metric.replace(
{
"correlation_user": "correlation",
"mse_user": "mse",
"rmse_user": "rmse",
"mae_user": "mae",
}
),
)
.sort_values(by=["dataset", "group", "metric"])
.reset_index(drop=True)[
["algorithm", "dataset", "group", "metric", "score"]
]
)
self.overall_results = group_results
if verbose:
if w:
print(w[-1].message)
print(
"User performance results (not returned) are accessible using .user_results"
)
print(
"Overall performance results (returned) are accesible using .overall_results"
)
return group_results
to_long_df(self)
inherited
Create a long format pandas dataframe with observed, predicted, and mask.
Source code in neighbors/models.py
def to_long_df(self):
"""Create a long format pandas dataframe with observed, predicted, and mask."""
observed = pd.DataFrame(columns=["User", "Item", "Rating", "Condition"])
for row in self.data.iterrows():
tmp = pd.DataFrame(columns=observed.columns)
tmp["Rating"] = row[1]
tmp["Item"] = self.data.columns
tmp["User"] = row[0]
tmp["Condition"] = "Observed"
if self.is_masked:
if self.is_mask_dilated:
tmp["Mask"] = self.dilated_mask.loc[row[0]]
else:
tmp["Mask"] = self.mask.loc[row[0]]
observed = observed.append(tmp)
if self.is_fit:
predicted = pd.DataFrame(columns=["User", "Item", "Rating", "Condition"])
for row in self.predictions.iterrows():
tmp = pd.DataFrame(columns=predicted.columns)
tmp["Rating"] = row[1]
tmp["Item"] = self.predictions.columns
tmp["User"] = row[0]
tmp["Condition"] = "Predicted"
if self.is_masked:
tmp["Mask"] = self.mask.loc[row[0]]
predicted = predicted.append(tmp)
observed = observed.append(predicted)
return observed
transform(self, return_only_predictions=False)
inherited
Return a user x item matrix of predictions after a model has been fit
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
return_only_predictions |
bool |
Returns both training and testing predictions rather than simply filling in missing values with predictions. Defaults to False. |
False |
Returns:
| Type | Description |
|---|---|
pd.DataFrame |
user x item ratings |
Source code in neighbors/models.py
def transform(self, return_only_predictions=False):
"""
Return a user x item matrix of predictions after a model has been fit
Args:
return_only_predictions (bool, optional): Returns both training and testing predictions rather than simply filling in missing values with predictions. Defaults to False.
Returns:
pd.DataFrame: user x item ratings
"""
if not self.is_fit:
raise ValueError("Model has not been fit!")
if return_only_predictions:
return self.predictions
else:
# Propagate observed values to return object
out = self.data[self.mask]
# Fill in missing values with predictions
out[~self.mask] = self.predictions[~self.mask]
return out