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stringlengths 407
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stringlengths 2.6k
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seaborn | 6 | seaborn/_base.py | def iter_data(
self, grouping_vars=None, *,
reverse=False, from_comp_data=False,
by_facet=True, allow_empty=False, dropna=True,
):
"""Generator for getting subsets of data defined by semantic variables.
Also injects "col" and "row" into grouping semantics.
Parameters
----------
grouping_vars : string or list of strings
Semantic variables that define the subsets of data.
reverse : bool
If True, reverse the order of iteration.
from_comp_data : bool
If True, use self.comp_data rather than self.plot_data
by_facet : bool
If True, add faceting variables to the set of grouping variables.
allow_empty : bool
If True, yield an empty dataframe when no observations exist for
combinations of grouping variables.
dropna : bool
If True, remove rows with missing data.
Yields
------
sub_vars : dict
Keys are semantic names, values are the level of that semantic.
sub_data : :class:`pandas.DataFrame`
Subset of ``plot_data`` for this combination of semantic values.
"""
| /usr/src/app/target_test_cases/failed_tests_VectorPlotter.iter_data.txt | def iter_data(
self, grouping_vars=None, *,
reverse=False, from_comp_data=False,
by_facet=True, allow_empty=False, dropna=True,
):
"""Generator for getting subsets of data defined by semantic variables.
Also injects "col" and "row" into grouping semantics.
Parameters
----------
grouping_vars : string or list of strings
Semantic variables that define the subsets of data.
reverse : bool
If True, reverse the order of iteration.
from_comp_data : bool
If True, use self.comp_data rather than self.plot_data
by_facet : bool
If True, add faceting variables to the set of grouping variables.
allow_empty : bool
If True, yield an empty dataframe when no observations exist for
combinations of grouping variables.
dropna : bool
If True, remove rows with missing data.
Yields
------
sub_vars : dict
Keys are semantic names, values are the level of that semantic.
sub_data : :class:`pandas.DataFrame`
Subset of ``plot_data`` for this combination of semantic values.
"""
# TODO should this default to using all (non x/y?) semantics?
# or define grouping vars somewhere?
if grouping_vars is None:
grouping_vars = []
elif isinstance(grouping_vars, str):
grouping_vars = [grouping_vars]
elif isinstance(grouping_vars, tuple):
grouping_vars = list(grouping_vars)
# Always insert faceting variables
if by_facet:
facet_vars = {"col", "row"}
grouping_vars.extend(
facet_vars & set(self.variables) - set(grouping_vars)
)
# Reduce to the semantics used in this plot
grouping_vars = [var for var in grouping_vars if var in self.variables]
if from_comp_data:
data = self.comp_data
else:
data = self.plot_data
if dropna:
data = data.dropna()
levels = self.var_levels.copy()
if from_comp_data:
for axis in {"x", "y"} & set(grouping_vars):
converter = self.converters[axis].iloc[0]
if self.var_types[axis] == "categorical":
if self._var_ordered[axis]:
# If the axis is ordered, then the axes in a possible
# facet grid are by definition "shared", or there is a
# single axis with a unique cat -> idx mapping.
# So we can just take the first converter object.
levels[axis] = converter.convert_units(levels[axis])
else:
# Otherwise, the mappings may not be unique, but we can
# use the unique set of index values in comp_data.
levels[axis] = np.sort(data[axis].unique())
else:
transform = converter.get_transform().transform
levels[axis] = transform(converter.convert_units(levels[axis]))
if grouping_vars:
grouped_data = data.groupby(
grouping_vars, sort=False, as_index=False, observed=False,
)
grouping_keys = []
for var in grouping_vars:
key = levels.get(var)
grouping_keys.append([] if key is None else key)
iter_keys = itertools.product(*grouping_keys)
if reverse:
iter_keys = reversed(list(iter_keys))
for key in iter_keys:
pd_key = (
key[0] if len(key) == 1 and _version_predates(pd, "2.2.0") else key
)
try:
data_subset = grouped_data.get_group(pd_key)
except KeyError:
# XXX we are adding this to allow backwards compatibility
# with the empty artists that old categorical plots would
# add (before 0.12), which we may decide to break, in which
# case this option could be removed
data_subset = data.loc[[]]
if data_subset.empty and not allow_empty:
continue
sub_vars = dict(zip(grouping_vars, key))
yield sub_vars, data_subset.copy()
else:
yield {}, data.copy()
| VectorPlotter.iter_data | Self-Contained |
seaborn | 21 | seaborn/axisgrid.py | def add_legend(self, legend_data=None, title=None, label_order=None,
adjust_subtitles=False, **kwargs):
"""Draw a legend, maybe placing it outside axes and resizing the figure.
Parameters
----------
legend_data : dict
Dictionary mapping label names (or two-element tuples where the
second element is a label name) to matplotlib artist handles. The
default reads from ``self._legend_data``.
title : string
Title for the legend. The default reads from ``self._hue_var``.
label_order : list of labels
The order that the legend entries should appear in. The default
reads from ``self.hue_names``.
adjust_subtitles : bool
If True, modify entries with invisible artists to left-align
the labels and set the font size to that of a title.
kwargs : key, value pairings
Other keyword arguments are passed to the underlying legend methods
on the Figure or Axes object.
Returns
-------
self : Grid instance
Returns self for easy chaining.
"""
| /usr/src/app/target_test_cases/failed_tests_axisgrid.Grid.add_legend.txt | def add_legend(self, legend_data=None, title=None, label_order=None,
adjust_subtitles=False, **kwargs):
"""Draw a legend, maybe placing it outside axes and resizing the figure.
Parameters
----------
legend_data : dict
Dictionary mapping label names (or two-element tuples where the
second element is a label name) to matplotlib artist handles. The
default reads from ``self._legend_data``.
title : string
Title for the legend. The default reads from ``self._hue_var``.
label_order : list of labels
The order that the legend entries should appear in. The default
reads from ``self.hue_names``.
adjust_subtitles : bool
If True, modify entries with invisible artists to left-align
the labels and set the font size to that of a title.
kwargs : key, value pairings
Other keyword arguments are passed to the underlying legend methods
on the Figure or Axes object.
Returns
-------
self : Grid instance
Returns self for easy chaining.
"""
# Find the data for the legend
if legend_data is None:
legend_data = self._legend_data
if label_order is None:
if self.hue_names is None:
label_order = list(legend_data.keys())
else:
label_order = list(map(utils.to_utf8, self.hue_names))
blank_handle = mpl.patches.Patch(alpha=0, linewidth=0)
handles = [legend_data.get(lab, blank_handle) for lab in label_order]
title = self._hue_var if title is None else title
title_size = mpl.rcParams["legend.title_fontsize"]
# Unpack nested labels from a hierarchical legend
labels = []
for entry in label_order:
if isinstance(entry, tuple):
_, label = entry
else:
label = entry
labels.append(label)
# Set default legend kwargs
kwargs.setdefault("scatterpoints", 1)
if self._legend_out:
kwargs.setdefault("frameon", False)
kwargs.setdefault("loc", "center right")
# Draw a full-figure legend outside the grid
figlegend = self._figure.legend(handles, labels, **kwargs)
self._legend = figlegend
figlegend.set_title(title, prop={"size": title_size})
if adjust_subtitles:
adjust_legend_subtitles(figlegend)
# Draw the plot to set the bounding boxes correctly
_draw_figure(self._figure)
# Calculate and set the new width of the figure so the legend fits
legend_width = figlegend.get_window_extent().width / self._figure.dpi
fig_width, fig_height = self._figure.get_size_inches()
self._figure.set_size_inches(fig_width + legend_width, fig_height)
# Draw the plot again to get the new transformations
_draw_figure(self._figure)
# Now calculate how much space we need on the right side
legend_width = figlegend.get_window_extent().width / self._figure.dpi
space_needed = legend_width / (fig_width + legend_width)
margin = .04 if self._margin_titles else .01
self._space_needed = margin + space_needed
right = 1 - self._space_needed
# Place the subplot axes to give space for the legend
self._figure.subplots_adjust(right=right)
self._tight_layout_rect[2] = right
else:
# Draw a legend in the first axis
ax = self.axes.flat[0]
kwargs.setdefault("loc", "best")
leg = ax.legend(handles, labels, **kwargs)
leg.set_title(title, prop={"size": title_size})
self._legend = leg
if adjust_subtitles:
adjust_legend_subtitles(leg)
return self
| axisgrid.Grid.add_legend | Repo-Level |
seaborn | 28 | seaborn/axisgrid.py | def __init__(
self, data, *, hue=None, vars=None, x_vars=None, y_vars=None,
hue_order=None, palette=None, hue_kws=None, corner=False, diag_sharey=True,
height=2.5, aspect=1, layout_pad=.5, despine=True, dropna=False,
):
"""Initialize the plot figure and PairGrid object.
Parameters
----------
data : DataFrame
Tidy (long-form) dataframe where each column is a variable and
each row is an observation.
hue : string (variable name)
Variable in ``data`` to map plot aspects to different colors. This
variable will be excluded from the default x and y variables.
vars : list of variable names
Variables within ``data`` to use, otherwise use every column with
a numeric datatype.
{x, y}_vars : lists of variable names
Variables within ``data`` to use separately for the rows and
columns of the figure; i.e. to make a non-square plot.
hue_order : list of strings
Order for the levels of the hue variable in the palette
palette : dict or seaborn color palette
Set of colors for mapping the ``hue`` variable. If a dict, keys
should be values in the ``hue`` variable.
hue_kws : dictionary of param -> list of values mapping
Other keyword arguments to insert into the plotting call to let
other plot attributes vary across levels of the hue variable (e.g.
the markers in a scatterplot).
corner : bool
If True, don't add axes to the upper (off-diagonal) triangle of the
grid, making this a "corner" plot.
height : scalar
Height (in inches) of each facet.
aspect : scalar
Aspect * height gives the width (in inches) of each facet.
layout_pad : scalar
Padding between axes; passed to ``fig.tight_layout``.
despine : boolean
Remove the top and right spines from the plots.
dropna : boolean
Drop missing values from the data before plotting.
See Also
--------
pairplot : Easily drawing common uses of :class:`PairGrid`.
FacetGrid : Subplot grid for plotting conditional relationships.
Examples
--------
.. include:: ../docstrings/PairGrid.rst
"""
| /usr/src/app/target_test_cases/failed_tests_axisgrid.PairGrid.__init__.txt | def __init__(
self, data, *, hue=None, vars=None, x_vars=None, y_vars=None,
hue_order=None, palette=None, hue_kws=None, corner=False, diag_sharey=True,
height=2.5, aspect=1, layout_pad=.5, despine=True, dropna=False,
):
"""Initialize the plot figure and PairGrid object.
Parameters
----------
data : DataFrame
Tidy (long-form) dataframe where each column is a variable and
each row is an observation.
hue : string (variable name)
Variable in ``data`` to map plot aspects to different colors. This
variable will be excluded from the default x and y variables.
vars : list of variable names
Variables within ``data`` to use, otherwise use every column with
a numeric datatype.
{x, y}_vars : lists of variable names
Variables within ``data`` to use separately for the rows and
columns of the figure; i.e. to make a non-square plot.
hue_order : list of strings
Order for the levels of the hue variable in the palette
palette : dict or seaborn color palette
Set of colors for mapping the ``hue`` variable. If a dict, keys
should be values in the ``hue`` variable.
hue_kws : dictionary of param -> list of values mapping
Other keyword arguments to insert into the plotting call to let
other plot attributes vary across levels of the hue variable (e.g.
the markers in a scatterplot).
corner : bool
If True, don't add axes to the upper (off-diagonal) triangle of the
grid, making this a "corner" plot.
height : scalar
Height (in inches) of each facet.
aspect : scalar
Aspect * height gives the width (in inches) of each facet.
layout_pad : scalar
Padding between axes; passed to ``fig.tight_layout``.
despine : boolean
Remove the top and right spines from the plots.
dropna : boolean
Drop missing values from the data before plotting.
See Also
--------
pairplot : Easily drawing common uses of :class:`PairGrid`.
FacetGrid : Subplot grid for plotting conditional relationships.
Examples
--------
.. include:: ../docstrings/PairGrid.rst
"""
super().__init__()
data = handle_data_source(data)
# Sort out the variables that define the grid
numeric_cols = self._find_numeric_cols(data)
if hue in numeric_cols:
numeric_cols.remove(hue)
if vars is not None:
x_vars = list(vars)
y_vars = list(vars)
if x_vars is None:
x_vars = numeric_cols
if y_vars is None:
y_vars = numeric_cols
if np.isscalar(x_vars):
x_vars = [x_vars]
if np.isscalar(y_vars):
y_vars = [y_vars]
self.x_vars = x_vars = list(x_vars)
self.y_vars = y_vars = list(y_vars)
self.square_grid = self.x_vars == self.y_vars
if not x_vars:
raise ValueError("No variables found for grid columns.")
if not y_vars:
raise ValueError("No variables found for grid rows.")
# Create the figure and the array of subplots
figsize = len(x_vars) * height * aspect, len(y_vars) * height
with _disable_autolayout():
fig = plt.figure(figsize=figsize)
axes = fig.subplots(len(y_vars), len(x_vars),
sharex="col", sharey="row",
squeeze=False)
# Possibly remove upper axes to make a corner grid
# Note: setting up the axes is usually the most time-intensive part
# of using the PairGrid. We are foregoing the speed improvement that
# we would get by just not setting up the hidden axes so that we can
# avoid implementing fig.subplots ourselves. But worth thinking about.
self._corner = corner
if corner:
hide_indices = np.triu_indices_from(axes, 1)
for i, j in zip(*hide_indices):
axes[i, j].remove()
axes[i, j] = None
self._figure = fig
self.axes = axes
self.data = data
# Save what we are going to do with the diagonal
self.diag_sharey = diag_sharey
self.diag_vars = None
self.diag_axes = None
self._dropna = dropna
# Label the axes
self._add_axis_labels()
# Sort out the hue variable
self._hue_var = hue
if hue is None:
self.hue_names = hue_order = ["_nolegend_"]
self.hue_vals = pd.Series(["_nolegend_"] * len(data),
index=data.index)
else:
# We need hue_order and hue_names because the former is used to control
# the order of drawing and the latter is used to control the order of
# the legend. hue_names can become string-typed while hue_order must
# retain the type of the input data. This is messy but results from
# the fact that PairGrid can implement the hue-mapping logic itself
# (and was originally written exclusively that way) but now can delegate
# to the axes-level functions, while always handling legend creation.
# See GH2307
hue_names = hue_order = categorical_order(data[hue], hue_order)
if dropna:
# Filter NA from the list of unique hue names
hue_names = list(filter(pd.notnull, hue_names))
self.hue_names = hue_names
self.hue_vals = data[hue]
# Additional dict of kwarg -> list of values for mapping the hue var
self.hue_kws = hue_kws if hue_kws is not None else {}
self._orig_palette = palette
self._hue_order = hue_order
self.palette = self._get_palette(data, hue, hue_order, palette)
self._legend_data = {}
# Make the plot look nice
for ax in axes[:-1, :].flat:
if ax is None:
continue
for label in ax.get_xticklabels():
label.set_visible(False)
ax.xaxis.offsetText.set_visible(False)
ax.xaxis.label.set_visible(False)
for ax in axes[:, 1:].flat:
if ax is None:
continue
for label in ax.get_yticklabels():
label.set_visible(False)
ax.yaxis.offsetText.set_visible(False)
ax.yaxis.label.set_visible(False)
self._tight_layout_rect = [.01, .01, .99, .99]
self._tight_layout_pad = layout_pad
self._despine = despine
if despine:
utils.despine(fig=fig)
self.tight_layout(pad=layout_pad)
| axisgrid.PairGrid.__init__ | Repo-Level |
seaborn | 29 | seaborn/axisgrid.py | def pairplot(
data, *,
hue=None, hue_order=None, palette=None,
vars=None, x_vars=None, y_vars=None,
kind="scatter", diag_kind="auto", markers=None,
height=2.5, aspect=1, corner=False, dropna=False,
plot_kws=None, diag_kws=None, grid_kws=None, size=None,
):
"""Plot pairwise relationships in a dataset.
By default, this function will create a grid of Axes such that each numeric
variable in ``data`` will by shared across the y-axes across a single row and
the x-axes across a single column. The diagonal plots are treated
differently: a univariate distribution plot is drawn to show the marginal
distribution of the data in each column.
It is also possible to show a subset of variables or plot different
variables on the rows and columns.
This is a high-level interface for :class:`PairGrid` that is intended to
make it easy to draw a few common styles. You should use :class:`PairGrid`
directly if you need more flexibility.
Parameters
----------
data : `pandas.DataFrame`
Tidy (long-form) dataframe where each column is a variable and
each row is an observation.
hue : name of variable in ``data``
Variable in ``data`` to map plot aspects to different colors.
hue_order : list of strings
Order for the levels of the hue variable in the palette
palette : dict or seaborn color palette
Set of colors for mapping the ``hue`` variable. If a dict, keys
should be values in the ``hue`` variable.
vars : list of variable names
Variables within ``data`` to use, otherwise use every column with
a numeric datatype.
{x, y}_vars : lists of variable names
Variables within ``data`` to use separately for the rows and
columns of the figure; i.e. to make a non-square plot.
kind : {'scatter', 'kde', 'hist', 'reg'}
Kind of plot to make.
diag_kind : {'auto', 'hist', 'kde', None}
Kind of plot for the diagonal subplots. If 'auto', choose based on
whether or not ``hue`` is used.
markers : single matplotlib marker code or list
Either the marker to use for all scatterplot points or a list of markers
with a length the same as the number of levels in the hue variable so that
differently colored points will also have different scatterplot
markers.
height : scalar
Height (in inches) of each facet.
aspect : scalar
Aspect * height gives the width (in inches) of each facet.
corner : bool
If True, don't add axes to the upper (off-diagonal) triangle of the
grid, making this a "corner" plot.
dropna : boolean
Drop missing values from the data before plotting.
{plot, diag, grid}_kws : dicts
Dictionaries of keyword arguments. ``plot_kws`` are passed to the
bivariate plotting function, ``diag_kws`` are passed to the univariate
plotting function, and ``grid_kws`` are passed to the :class:`PairGrid`
constructor.
Returns
-------
grid : :class:`PairGrid`
Returns the underlying :class:`PairGrid` instance for further tweaking.
See Also
--------
PairGrid : Subplot grid for more flexible plotting of pairwise relationships.
JointGrid : Grid for plotting joint and marginal distributions of two variables.
Examples
--------
.. include:: ../docstrings/pairplot.rst
"""
| /usr/src/app/target_test_cases/failed_tests_axisgrid.pairplot.txt | def pairplot(
data, *,
hue=None, hue_order=None, palette=None,
vars=None, x_vars=None, y_vars=None,
kind="scatter", diag_kind="auto", markers=None,
height=2.5, aspect=1, corner=False, dropna=False,
plot_kws=None, diag_kws=None, grid_kws=None, size=None,
):
"""Plot pairwise relationships in a dataset.
By default, this function will create a grid of Axes such that each numeric
variable in ``data`` will by shared across the y-axes across a single row and
the x-axes across a single column. The diagonal plots are treated
differently: a univariate distribution plot is drawn to show the marginal
distribution of the data in each column.
It is also possible to show a subset of variables or plot different
variables on the rows and columns.
This is a high-level interface for :class:`PairGrid` that is intended to
make it easy to draw a few common styles. You should use :class:`PairGrid`
directly if you need more flexibility.
Parameters
----------
data : `pandas.DataFrame`
Tidy (long-form) dataframe where each column is a variable and
each row is an observation.
hue : name of variable in ``data``
Variable in ``data`` to map plot aspects to different colors.
hue_order : list of strings
Order for the levels of the hue variable in the palette
palette : dict or seaborn color palette
Set of colors for mapping the ``hue`` variable. If a dict, keys
should be values in the ``hue`` variable.
vars : list of variable names
Variables within ``data`` to use, otherwise use every column with
a numeric datatype.
{x, y}_vars : lists of variable names
Variables within ``data`` to use separately for the rows and
columns of the figure; i.e. to make a non-square plot.
kind : {'scatter', 'kde', 'hist', 'reg'}
Kind of plot to make.
diag_kind : {'auto', 'hist', 'kde', None}
Kind of plot for the diagonal subplots. If 'auto', choose based on
whether or not ``hue`` is used.
markers : single matplotlib marker code or list
Either the marker to use for all scatterplot points or a list of markers
with a length the same as the number of levels in the hue variable so that
differently colored points will also have different scatterplot
markers.
height : scalar
Height (in inches) of each facet.
aspect : scalar
Aspect * height gives the width (in inches) of each facet.
corner : bool
If True, don't add axes to the upper (off-diagonal) triangle of the
grid, making this a "corner" plot.
dropna : boolean
Drop missing values from the data before plotting.
{plot, diag, grid}_kws : dicts
Dictionaries of keyword arguments. ``plot_kws`` are passed to the
bivariate plotting function, ``diag_kws`` are passed to the univariate
plotting function, and ``grid_kws`` are passed to the :class:`PairGrid`
constructor.
Returns
-------
grid : :class:`PairGrid`
Returns the underlying :class:`PairGrid` instance for further tweaking.
See Also
--------
PairGrid : Subplot grid for more flexible plotting of pairwise relationships.
JointGrid : Grid for plotting joint and marginal distributions of two variables.
Examples
--------
.. include:: ../docstrings/pairplot.rst
"""
# Avoid circular import
from .distributions import histplot, kdeplot
# Handle deprecations
if size is not None:
height = size
msg = ("The `size` parameter has been renamed to `height`; "
"please update your code.")
warnings.warn(msg, UserWarning)
if not isinstance(data, pd.DataFrame):
raise TypeError(
f"'data' must be pandas DataFrame object, not: {type(data)}")
plot_kws = {} if plot_kws is None else plot_kws.copy()
diag_kws = {} if diag_kws is None else diag_kws.copy()
grid_kws = {} if grid_kws is None else grid_kws.copy()
# Resolve "auto" diag kind
if diag_kind == "auto":
if hue is None:
diag_kind = "kde" if kind == "kde" else "hist"
else:
diag_kind = "hist" if kind == "hist" else "kde"
# Set up the PairGrid
grid_kws.setdefault("diag_sharey", diag_kind == "hist")
grid = PairGrid(data, vars=vars, x_vars=x_vars, y_vars=y_vars, hue=hue,
hue_order=hue_order, palette=palette, corner=corner,
height=height, aspect=aspect, dropna=dropna, **grid_kws)
# Add the markers here as PairGrid has figured out how many levels of the
# hue variable are needed and we don't want to duplicate that process
if markers is not None:
if kind == "reg":
# Needed until regplot supports style
if grid.hue_names is None:
n_markers = 1
else:
n_markers = len(grid.hue_names)
if not isinstance(markers, list):
markers = [markers] * n_markers
if len(markers) != n_markers:
raise ValueError("markers must be a singleton or a list of "
"markers for each level of the hue variable")
grid.hue_kws = {"marker": markers}
elif kind == "scatter":
if isinstance(markers, str):
plot_kws["marker"] = markers
elif hue is not None:
plot_kws["style"] = data[hue]
plot_kws["markers"] = markers
# Draw the marginal plots on the diagonal
diag_kws = diag_kws.copy()
diag_kws.setdefault("legend", False)
if diag_kind == "hist":
grid.map_diag(histplot, **diag_kws)
elif diag_kind == "kde":
diag_kws.setdefault("fill", True)
diag_kws.setdefault("warn_singular", False)
grid.map_diag(kdeplot, **diag_kws)
# Maybe plot on the off-diagonals
if diag_kind is not None:
plotter = grid.map_offdiag
else:
plotter = grid.map
if kind == "scatter":
from .relational import scatterplot # Avoid circular import
plotter(scatterplot, **plot_kws)
elif kind == "reg":
from .regression import regplot # Avoid circular import
plotter(regplot, **plot_kws)
elif kind == "kde":
from .distributions import kdeplot # Avoid circular import
plot_kws.setdefault("warn_singular", False)
plotter(kdeplot, **plot_kws)
elif kind == "hist":
from .distributions import histplot # Avoid circular import
plotter(histplot, **plot_kws)
# Add a legend
if hue is not None:
grid.add_legend()
grid.tight_layout()
return grid
| axisgrid.pairplot | Self-Contained |
seaborn | 33 | seaborn/palettes.py | def color_palette(palette=None, n_colors=None, desat=None, as_cmap=False):
"""Return a list of colors or continuous colormap defining a palette.
Possible ``palette`` values include:
- Name of a seaborn palette (deep, muted, bright, pastel, dark, colorblind)
- Name of matplotlib colormap
- 'husl' or 'hls'
- 'ch:<cubehelix arguments>'
- 'light:<color>', 'dark:<color>', 'blend:<color>,<color>',
- A sequence of colors in any format matplotlib accepts
Calling this function with ``palette=None`` will return the current
matplotlib color cycle.
This function can also be used in a ``with`` statement to temporarily
set the color cycle for a plot or set of plots.
See the :ref:`tutorial <palette_tutorial>` for more information.
Parameters
----------
palette : None, string, or sequence, optional
Name of palette or None to return current palette. If a sequence, input
colors are used but possibly cycled and desaturated.
n_colors : int, optional
Number of colors in the palette. If ``None``, the default will depend
on how ``palette`` is specified. Named palettes default to 6 colors,
but grabbing the current palette or passing in a list of colors will
not change the number of colors unless this is specified. Asking for
more colors than exist in the palette will cause it to cycle. Ignored
when ``as_cmap`` is True.
desat : float, optional
Proportion to desaturate each color by.
as_cmap : bool
If True, return a :class:`matplotlib.colors.ListedColormap`.
Returns
-------
list of RGB tuples or :class:`matplotlib.colors.ListedColormap`
See Also
--------
set_palette : Set the default color cycle for all plots.
set_color_codes : Reassign color codes like ``"b"``, ``"g"``, etc. to
colors from one of the seaborn palettes.
Examples
--------
.. include:: ../docstrings/color_palette.rst
"""
| /usr/src/app/target_test_cases/failed_tests_color_palette.txt | def color_palette(palette=None, n_colors=None, desat=None, as_cmap=False):
"""Return a list of colors or continuous colormap defining a palette.
Possible ``palette`` values include:
- Name of a seaborn palette (deep, muted, bright, pastel, dark, colorblind)
- Name of matplotlib colormap
- 'husl' or 'hls'
- 'ch:<cubehelix arguments>'
- 'light:<color>', 'dark:<color>', 'blend:<color>,<color>',
- A sequence of colors in any format matplotlib accepts
Calling this function with ``palette=None`` will return the current
matplotlib color cycle.
This function can also be used in a ``with`` statement to temporarily
set the color cycle for a plot or set of plots.
See the :ref:`tutorial <palette_tutorial>` for more information.
Parameters
----------
palette : None, string, or sequence, optional
Name of palette or None to return current palette. If a sequence, input
colors are used but possibly cycled and desaturated.
n_colors : int, optional
Number of colors in the palette. If ``None``, the default will depend
on how ``palette`` is specified. Named palettes default to 6 colors,
but grabbing the current palette or passing in a list of colors will
not change the number of colors unless this is specified. Asking for
more colors than exist in the palette will cause it to cycle. Ignored
when ``as_cmap`` is True.
desat : float, optional
Proportion to desaturate each color by.
as_cmap : bool
If True, return a :class:`matplotlib.colors.ListedColormap`.
Returns
-------
list of RGB tuples or :class:`matplotlib.colors.ListedColormap`
See Also
--------
set_palette : Set the default color cycle for all plots.
set_color_codes : Reassign color codes like ``"b"``, ``"g"``, etc. to
colors from one of the seaborn palettes.
Examples
--------
.. include:: ../docstrings/color_palette.rst
"""
if palette is None:
palette = get_color_cycle()
if n_colors is None:
n_colors = len(palette)
elif not isinstance(palette, str):
palette = palette
if n_colors is None:
n_colors = len(palette)
else:
if n_colors is None:
# Use all colors in a qualitative palette or 6 of another kind
n_colors = QUAL_PALETTE_SIZES.get(palette, 6)
if palette in SEABORN_PALETTES:
# Named "seaborn variant" of matplotlib default color cycle
palette = SEABORN_PALETTES[palette]
elif palette == "hls":
# Evenly spaced colors in cylindrical RGB space
palette = hls_palette(n_colors, as_cmap=as_cmap)
elif palette == "husl":
# Evenly spaced colors in cylindrical Lab space
palette = husl_palette(n_colors, as_cmap=as_cmap)
elif palette.lower() == "jet":
# Paternalism
raise ValueError("No.")
elif palette.startswith("ch:"):
# Cubehelix palette with params specified in string
args, kwargs = _parse_cubehelix_args(palette)
palette = cubehelix_palette(n_colors, *args, **kwargs, as_cmap=as_cmap)
elif palette.startswith("light:"):
# light palette to color specified in string
_, color = palette.split(":")
reverse = color.endswith("_r")
if reverse:
color = color[:-2]
palette = light_palette(color, n_colors, reverse=reverse, as_cmap=as_cmap)
elif palette.startswith("dark:"):
# light palette to color specified in string
_, color = palette.split(":")
reverse = color.endswith("_r")
if reverse:
color = color[:-2]
palette = dark_palette(color, n_colors, reverse=reverse, as_cmap=as_cmap)
elif palette.startswith("blend:"):
# blend palette between colors specified in string
_, colors = palette.split(":")
colors = colors.split(",")
palette = blend_palette(colors, n_colors, as_cmap=as_cmap)
else:
try:
# Perhaps a named matplotlib colormap?
palette = mpl_palette(palette, n_colors, as_cmap=as_cmap)
except (ValueError, KeyError): # Error class changed in mpl36
raise ValueError(f"{palette!r} is not a valid palette name")
if desat is not None:
palette = [desaturate(c, desat) for c in palette]
if not as_cmap:
# Always return as many colors as we asked for
pal_cycle = cycle(palette)
palette = [next(pal_cycle) for _ in range(n_colors)]
# Always return in r, g, b tuple format
try:
palette = map(mpl.colors.colorConverter.to_rgb, palette)
palette = _ColorPalette(palette)
except ValueError:
raise ValueError(f"Could not generate a palette for {palette}")
return palette
| color_palette | Repo-Level |
seaborn | 71 | seaborn/utils.py | def despine(fig=None, ax=None, top=True, right=True, left=False,
bottom=False, offset=None, trim=False):
"""Remove the top and right spines from plot(s).
fig : matplotlib figure, optional
Figure to despine all axes of, defaults to the current figure.
ax : matplotlib axes, optional
Specific axes object to despine. Ignored if fig is provided.
top, right, left, bottom : boolean, optional
If True, remove that spine.
offset : int or dict, optional
Absolute distance, in points, spines should be moved away
from the axes (negative values move spines inward). A single value
applies to all spines; a dict can be used to set offset values per
side.
trim : bool, optional
If True, limit spines to the smallest and largest major tick
on each non-despined axis.
Returns
-------
None
"""
| /usr/src/app/target_test_cases/failed_tests_utils.despine.txt | def despine(fig=None, ax=None, top=True, right=True, left=False,
bottom=False, offset=None, trim=False):
"""Remove the top and right spines from plot(s).
fig : matplotlib figure, optional
Figure to despine all axes of, defaults to the current figure.
ax : matplotlib axes, optional
Specific axes object to despine. Ignored if fig is provided.
top, right, left, bottom : boolean, optional
If True, remove that spine.
offset : int or dict, optional
Absolute distance, in points, spines should be moved away
from the axes (negative values move spines inward). A single value
applies to all spines; a dict can be used to set offset values per
side.
trim : bool, optional
If True, limit spines to the smallest and largest major tick
on each non-despined axis.
Returns
-------
None
"""
# Get references to the axes we want
if fig is None and ax is None:
axes = plt.gcf().axes
elif fig is not None:
axes = fig.axes
elif ax is not None:
axes = [ax]
for ax_i in axes:
for side in ["top", "right", "left", "bottom"]:
# Toggle the spine objects
is_visible = not locals()[side]
ax_i.spines[side].set_visible(is_visible)
if offset is not None and is_visible:
try:
val = offset.get(side, 0)
except AttributeError:
val = offset
ax_i.spines[side].set_position(('outward', val))
# Potentially move the ticks
if left and not right:
maj_on = any(
t.tick1line.get_visible()
for t in ax_i.yaxis.majorTicks
)
min_on = any(
t.tick1line.get_visible()
for t in ax_i.yaxis.minorTicks
)
ax_i.yaxis.set_ticks_position("right")
for t in ax_i.yaxis.majorTicks:
t.tick2line.set_visible(maj_on)
for t in ax_i.yaxis.minorTicks:
t.tick2line.set_visible(min_on)
if bottom and not top:
maj_on = any(
t.tick1line.get_visible()
for t in ax_i.xaxis.majorTicks
)
min_on = any(
t.tick1line.get_visible()
for t in ax_i.xaxis.minorTicks
)
ax_i.xaxis.set_ticks_position("top")
for t in ax_i.xaxis.majorTicks:
t.tick2line.set_visible(maj_on)
for t in ax_i.xaxis.minorTicks:
t.tick2line.set_visible(min_on)
if trim:
# clip off the parts of the spines that extend past major ticks
xticks = np.asarray(ax_i.get_xticks())
if xticks.size:
firsttick = np.compress(xticks >= min(ax_i.get_xlim()),
xticks)[0]
lasttick = np.compress(xticks <= max(ax_i.get_xlim()),
xticks)[-1]
ax_i.spines['bottom'].set_bounds(firsttick, lasttick)
ax_i.spines['top'].set_bounds(firsttick, lasttick)
newticks = xticks.compress(xticks <= lasttick)
newticks = newticks.compress(newticks >= firsttick)
ax_i.set_xticks(newticks)
yticks = np.asarray(ax_i.get_yticks())
if yticks.size:
firsttick = np.compress(yticks >= min(ax_i.get_ylim()),
yticks)[0]
lasttick = np.compress(yticks <= max(ax_i.get_ylim()),
yticks)[-1]
ax_i.spines['left'].set_bounds(firsttick, lasttick)
ax_i.spines['right'].set_bounds(firsttick, lasttick)
newticks = yticks.compress(yticks <= lasttick)
newticks = newticks.compress(newticks >= firsttick)
ax_i.set_yticks(newticks)
| utils.despine | Self-Contained |
seaborn | 73 | seaborn/utils.py | def move_legend(obj, loc, **kwargs):
"""
Recreate a plot's legend at a new location.
The name is a slight misnomer. Matplotlib legends do not expose public
control over their position parameters. So this function creates a new legend,
copying over the data from the original object, which is then removed.
Parameters
----------
obj : the object with the plot
This argument can be either a seaborn or matplotlib object:
- :class:`seaborn.FacetGrid` or :class:`seaborn.PairGrid`
- :class:`matplotlib.axes.Axes` or :class:`matplotlib.figure.Figure`
loc : str or int
Location argument, as in :meth:`matplotlib.axes.Axes.legend`.
kwargs
Other keyword arguments are passed to :meth:`matplotlib.axes.Axes.legend`.
Examples
--------
.. include:: ../docstrings/move_legend.rst
"""
| /usr/src/app/target_test_cases/failed_tests_utils.move_legend.txt | def move_legend(obj, loc, **kwargs):
"""
Recreate a plot's legend at a new location.
The name is a slight misnomer. Matplotlib legends do not expose public
control over their position parameters. So this function creates a new legend,
copying over the data from the original object, which is then removed.
Parameters
----------
obj : the object with the plot
This argument can be either a seaborn or matplotlib object:
- :class:`seaborn.FacetGrid` or :class:`seaborn.PairGrid`
- :class:`matplotlib.axes.Axes` or :class:`matplotlib.figure.Figure`
loc : str or int
Location argument, as in :meth:`matplotlib.axes.Axes.legend`.
kwargs
Other keyword arguments are passed to :meth:`matplotlib.axes.Axes.legend`.
Examples
--------
.. include:: ../docstrings/move_legend.rst
"""
# This is a somewhat hackish solution that will hopefully be obviated by
# upstream improvements to matplotlib legends that make them easier to
# modify after creation.
from seaborn.axisgrid import Grid # Avoid circular import
# Locate the legend object and a method to recreate the legend
if isinstance(obj, Grid):
old_legend = obj.legend
legend_func = obj.figure.legend
elif isinstance(obj, mpl.axes.Axes):
old_legend = obj.legend_
legend_func = obj.legend
elif isinstance(obj, mpl.figure.Figure):
if obj.legends:
old_legend = obj.legends[-1]
else:
old_legend = None
legend_func = obj.legend
else:
err = "`obj` must be a seaborn Grid or matplotlib Axes or Figure instance."
raise TypeError(err)
if old_legend is None:
err = f"{obj} has no legend attached."
raise ValueError(err)
# Extract the components of the legend we need to reuse
# Import here to avoid a circular import
from seaborn._compat import get_legend_handles
handles = get_legend_handles(old_legend)
labels = [t.get_text() for t in old_legend.get_texts()]
# Handle the case where the user is trying to override the labels
if (new_labels := kwargs.pop("labels", None)) is not None:
if len(new_labels) != len(labels):
err = "Length of new labels does not match existing legend."
raise ValueError(err)
labels = new_labels
# Extract legend properties that can be passed to the recreation method
# (Vexingly, these don't all round-trip)
legend_kws = inspect.signature(mpl.legend.Legend).parameters
props = {k: v for k, v in old_legend.properties().items() if k in legend_kws}
# Delegate default bbox_to_anchor rules to matplotlib
props.pop("bbox_to_anchor")
# Try to propagate the existing title and font properties; respect new ones too
title = props.pop("title")
if "title" in kwargs:
title.set_text(kwargs.pop("title"))
title_kwargs = {k: v for k, v in kwargs.items() if k.startswith("title_")}
for key, val in title_kwargs.items():
title.set(**{key[6:]: val})
kwargs.pop(key)
# Try to respect the frame visibility
kwargs.setdefault("frameon", old_legend.legendPatch.get_visible())
# Remove the old legend and create the new one
props.update(kwargs)
old_legend.remove()
new_legend = legend_func(handles, labels, loc=loc, **props)
new_legend.set_title(title.get_text(), title.get_fontproperties())
# Let the Grid object continue to track the correct legend object
if isinstance(obj, Grid):
obj._legend = new_legend
| utils.move_legend | Self-Contained |
scikit-learn | 0 | sklearn/linear_model/_bayes.py | def fit(self, X, y):
"""Fit the model according to the given training data and parameters.
Iterative procedure to maximize the evidence
Parameters
----------
X : array-like of shape (n_samples, n_features)
Training vector, where `n_samples` is the number of samples and
`n_features` is the number of features.
y : array-like of shape (n_samples,)
Target values (integers). Will be cast to X's dtype if necessary.
Returns
-------
self : object
Fitted estimator.
"""
| /usr/src/app/target_test_cases/failed_tests_ARDRegression.fit.txt | def fit(self, X, y):
"""Fit the model according to the given training data and parameters.
Iterative procedure to maximize the evidence
Parameters
----------
X : array-like of shape (n_samples, n_features)
Training vector, where `n_samples` is the number of samples and
`n_features` is the number of features.
y : array-like of shape (n_samples,)
Target values (integers). Will be cast to X's dtype if necessary.
Returns
-------
self : object
Fitted estimator.
"""
X, y = validate_data(
self,
X,
y,
dtype=[np.float64, np.float32],
force_writeable=True,
y_numeric=True,
ensure_min_samples=2,
)
dtype = X.dtype
n_samples, n_features = X.shape
coef_ = np.zeros(n_features, dtype=dtype)
X, y, X_offset_, y_offset_, X_scale_ = _preprocess_data(
X, y, fit_intercept=self.fit_intercept, copy=self.copy_X
)
self.X_offset_ = X_offset_
self.X_scale_ = X_scale_
# Launch the convergence loop
keep_lambda = np.ones(n_features, dtype=bool)
lambda_1 = self.lambda_1
lambda_2 = self.lambda_2
alpha_1 = self.alpha_1
alpha_2 = self.alpha_2
verbose = self.verbose
# Initialization of the values of the parameters
eps = np.finfo(np.float64).eps
# Add `eps` in the denominator to omit division by zero if `np.var(y)`
# is zero.
# Explicitly set dtype to avoid unintended type promotion with numpy 2.
alpha_ = np.asarray(1.0 / (np.var(y) + eps), dtype=dtype)
lambda_ = np.ones(n_features, dtype=dtype)
self.scores_ = list()
coef_old_ = None
def update_coeff(X, y, coef_, alpha_, keep_lambda, sigma_):
coef_[keep_lambda] = alpha_ * np.linalg.multi_dot(
[sigma_, X[:, keep_lambda].T, y]
)
return coef_
update_sigma = (
self._update_sigma
if n_samples >= n_features
else self._update_sigma_woodbury
)
# Iterative procedure of ARDRegression
for iter_ in range(self.max_iter):
sigma_ = update_sigma(X, alpha_, lambda_, keep_lambda)
coef_ = update_coeff(X, y, coef_, alpha_, keep_lambda, sigma_)
# Update alpha and lambda
rmse_ = np.sum((y - np.dot(X, coef_)) ** 2)
gamma_ = 1.0 - lambda_[keep_lambda] * np.diag(sigma_)
lambda_[keep_lambda] = (gamma_ + 2.0 * lambda_1) / (
(coef_[keep_lambda]) ** 2 + 2.0 * lambda_2
)
alpha_ = (n_samples - gamma_.sum() + 2.0 * alpha_1) / (
rmse_ + 2.0 * alpha_2
)
# Prune the weights with a precision over a threshold
keep_lambda = lambda_ < self.threshold_lambda
coef_[~keep_lambda] = 0
# Compute the objective function
if self.compute_score:
s = (lambda_1 * np.log(lambda_) - lambda_2 * lambda_).sum()
s += alpha_1 * log(alpha_) - alpha_2 * alpha_
s += 0.5 * (
fast_logdet(sigma_)
+ n_samples * log(alpha_)
+ np.sum(np.log(lambda_))
)
s -= 0.5 * (alpha_ * rmse_ + (lambda_ * coef_**2).sum())
self.scores_.append(s)
# Check for convergence
if iter_ > 0 and np.sum(np.abs(coef_old_ - coef_)) < self.tol:
if verbose:
print("Converged after %s iterations" % iter_)
break
coef_old_ = np.copy(coef_)
if not keep_lambda.any():
break
self.n_iter_ = iter_ + 1
if keep_lambda.any():
# update sigma and mu using updated params from the last iteration
sigma_ = update_sigma(X, alpha_, lambda_, keep_lambda)
coef_ = update_coeff(X, y, coef_, alpha_, keep_lambda, sigma_)
else:
sigma_ = np.array([]).reshape(0, 0)
self.coef_ = coef_
self.alpha_ = alpha_
self.sigma_ = sigma_
self.lambda_ = lambda_
self._set_intercept(X_offset_, y_offset_, X_scale_)
return self
| ARDRegression.fit | Repo-Level |
scikit-learn | 9 | sklearn/linear_model/_bayes.py | def fit(self, X, y, sample_weight=None):
"""Fit the model.
Parameters
----------
X : ndarray of shape (n_samples, n_features)
Training data.
y : ndarray of shape (n_samples,)
Target values. Will be cast to X's dtype if necessary.
sample_weight : ndarray of shape (n_samples,), default=None
Individual weights for each sample.
.. versionadded:: 0.20
parameter *sample_weight* support to BayesianRidge.
Returns
-------
self : object
Returns the instance itself.
"""
| /usr/src/app/target_test_cases/failed_tests_BayesianRidge.fit.txt | def fit(self, X, y, sample_weight=None):
"""Fit the model.
Parameters
----------
X : ndarray of shape (n_samples, n_features)
Training data.
y : ndarray of shape (n_samples,)
Target values. Will be cast to X's dtype if necessary.
sample_weight : ndarray of shape (n_samples,), default=None
Individual weights for each sample.
.. versionadded:: 0.20
parameter *sample_weight* support to BayesianRidge.
Returns
-------
self : object
Returns the instance itself.
"""
X, y = validate_data(
self,
X,
y,
dtype=[np.float64, np.float32],
force_writeable=True,
y_numeric=True,
)
dtype = X.dtype
if sample_weight is not None:
sample_weight = _check_sample_weight(sample_weight, X, dtype=dtype)
X, y, X_offset_, y_offset_, X_scale_ = _preprocess_data(
X,
y,
fit_intercept=self.fit_intercept,
copy=self.copy_X,
sample_weight=sample_weight,
)
if sample_weight is not None:
# Sample weight can be implemented via a simple rescaling.
X, y, _ = _rescale_data(X, y, sample_weight)
self.X_offset_ = X_offset_
self.X_scale_ = X_scale_
n_samples, n_features = X.shape
# Initialization of the values of the parameters
eps = np.finfo(np.float64).eps
# Add `eps` in the denominator to omit division by zero if `np.var(y)`
# is zero
alpha_ = self.alpha_init
lambda_ = self.lambda_init
if alpha_ is None:
alpha_ = 1.0 / (np.var(y) + eps)
if lambda_ is None:
lambda_ = 1.0
# Avoid unintended type promotion to float64 with numpy 2
alpha_ = np.asarray(alpha_, dtype=dtype)
lambda_ = np.asarray(lambda_, dtype=dtype)
verbose = self.verbose
lambda_1 = self.lambda_1
lambda_2 = self.lambda_2
alpha_1 = self.alpha_1
alpha_2 = self.alpha_2
self.scores_ = list()
coef_old_ = None
XT_y = np.dot(X.T, y)
U, S, Vh = linalg.svd(X, full_matrices=False)
eigen_vals_ = S**2
# Convergence loop of the bayesian ridge regression
for iter_ in range(self.max_iter):
# update posterior mean coef_ based on alpha_ and lambda_ and
# compute corresponding rmse
coef_, rmse_ = self._update_coef_(
X, y, n_samples, n_features, XT_y, U, Vh, eigen_vals_, alpha_, lambda_
)
if self.compute_score:
# compute the log marginal likelihood
s = self._log_marginal_likelihood(
n_samples, n_features, eigen_vals_, alpha_, lambda_, coef_, rmse_
)
self.scores_.append(s)
# Update alpha and lambda according to (MacKay, 1992)
gamma_ = np.sum((alpha_ * eigen_vals_) / (lambda_ + alpha_ * eigen_vals_))
lambda_ = (gamma_ + 2 * lambda_1) / (np.sum(coef_**2) + 2 * lambda_2)
alpha_ = (n_samples - gamma_ + 2 * alpha_1) / (rmse_ + 2 * alpha_2)
# Check for convergence
if iter_ != 0 and np.sum(np.abs(coef_old_ - coef_)) < self.tol:
if verbose:
print("Convergence after ", str(iter_), " iterations")
break
coef_old_ = np.copy(coef_)
self.n_iter_ = iter_ + 1
# return regularization parameters and corresponding posterior mean,
# log marginal likelihood and posterior covariance
self.alpha_ = alpha_
self.lambda_ = lambda_
self.coef_, rmse_ = self._update_coef_(
X, y, n_samples, n_features, XT_y, U, Vh, eigen_vals_, alpha_, lambda_
)
if self.compute_score:
# compute the log marginal likelihood
s = self._log_marginal_likelihood(
n_samples, n_features, eigen_vals_, alpha_, lambda_, coef_, rmse_
)
self.scores_.append(s)
self.scores_ = np.array(self.scores_)
# posterior covariance is given by 1/alpha_ * scaled_sigma_
scaled_sigma_ = np.dot(
Vh.T, Vh / (eigen_vals_ + lambda_ / alpha_)[:, np.newaxis]
)
self.sigma_ = (1.0 / alpha_) * scaled_sigma_
self._set_intercept(X_offset_, y_offset_, X_scale_)
return self
| BayesianRidge.fit | Repo-Level |
scikit-learn | 14 | sklearn/cluster/_bisect_k_means.py | def fit(self, X, y=None, sample_weight=None):
"""Compute bisecting k-means clustering.
Parameters
----------
X : {array-like, sparse matrix} of shape (n_samples, n_features)
Training instances to cluster.
.. note:: The data will be converted to C ordering,
which will cause a memory copy
if the given data is not C-contiguous.
y : Ignored
Not used, present here for API consistency by convention.
sample_weight : array-like of shape (n_samples,), default=None
The weights for each observation in X. If None, all observations
are assigned equal weight. `sample_weight` is not used during
initialization if `init` is a callable.
Returns
-------
self
Fitted estimator.
"""
| /usr/src/app/target_test_cases/failed_tests_BisectingKMeans.fit.txt | def fit(self, X, y=None, sample_weight=None):
"""Compute bisecting k-means clustering.
Parameters
----------
X : {array-like, sparse matrix} of shape (n_samples, n_features)
Training instances to cluster.
.. note:: The data will be converted to C ordering,
which will cause a memory copy
if the given data is not C-contiguous.
y : Ignored
Not used, present here for API consistency by convention.
sample_weight : array-like of shape (n_samples,), default=None
The weights for each observation in X. If None, all observations
are assigned equal weight. `sample_weight` is not used during
initialization if `init` is a callable.
Returns
-------
self
Fitted estimator.
"""
X = validate_data(
self,
X,
accept_sparse="csr",
dtype=[np.float64, np.float32],
order="C",
copy=self.copy_x,
accept_large_sparse=False,
)
self._check_params_vs_input(X)
self._random_state = check_random_state(self.random_state)
sample_weight = _check_sample_weight(sample_weight, X, dtype=X.dtype)
self._n_threads = _openmp_effective_n_threads()
if self.algorithm == "lloyd" or self.n_clusters == 1:
self._kmeans_single = _kmeans_single_lloyd
self._check_mkl_vcomp(X, X.shape[0])
else:
self._kmeans_single = _kmeans_single_elkan
# Subtract of mean of X for more accurate distance computations
if not sp.issparse(X):
self._X_mean = X.mean(axis=0)
X -= self._X_mean
# Initialize the hierarchical clusters tree
self._bisecting_tree = _BisectingTree(
indices=np.arange(X.shape[0]),
center=X.mean(axis=0),
score=0,
)
x_squared_norms = row_norms(X, squared=True)
for _ in range(self.n_clusters - 1):
# Chose cluster to bisect
cluster_to_bisect = self._bisecting_tree.get_cluster_to_bisect()
# Split this cluster into 2 subclusters
self._bisect(X, x_squared_norms, sample_weight, cluster_to_bisect)
# Aggregate final labels and centers from the bisecting tree
self.labels_ = np.full(X.shape[0], -1, dtype=np.int32)
self.cluster_centers_ = np.empty((self.n_clusters, X.shape[1]), dtype=X.dtype)
for i, cluster_node in enumerate(self._bisecting_tree.iter_leaves()):
self.labels_[cluster_node.indices] = i
self.cluster_centers_[i] = cluster_node.center
cluster_node.label = i # label final clusters for future prediction
cluster_node.indices = None # release memory
# Restore original data
if not sp.issparse(X):
X += self._X_mean
self.cluster_centers_ += self._X_mean
_inertia = _inertia_sparse if sp.issparse(X) else _inertia_dense
self.inertia_ = _inertia(
X, sample_weight, self.cluster_centers_, self.labels_, self._n_threads
)
self._n_features_out = self.cluster_centers_.shape[0]
return self
| BisectingKMeans.fit | Repo-Level |
scikit-learn | 15 | sklearn/calibration.py | def fit(self, X, y, sample_weight=None, **fit_params):
"""Fit the calibrated model.
Parameters
----------
X : array-like of shape (n_samples, n_features)
Training data.
y : array-like of shape (n_samples,)
Target values.
sample_weight : array-like of shape (n_samples,), default=None
Sample weights. If None, then samples are equally weighted.
**fit_params : dict
Parameters to pass to the `fit` method of the underlying
classifier.
Returns
-------
self : object
Returns an instance of self.
"""
| /usr/src/app/target_test_cases/failed_tests_CalibratedClassifierCV.fit.txt | def fit(self, X, y, sample_weight=None, **fit_params):
"""Fit the calibrated model.
Parameters
----------
X : array-like of shape (n_samples, n_features)
Training data.
y : array-like of shape (n_samples,)
Target values.
sample_weight : array-like of shape (n_samples,), default=None
Sample weights. If None, then samples are equally weighted.
**fit_params : dict
Parameters to pass to the `fit` method of the underlying
classifier.
Returns
-------
self : object
Returns an instance of self.
"""
check_classification_targets(y)
X, y = indexable(X, y)
if sample_weight is not None:
sample_weight = _check_sample_weight(sample_weight, X)
estimator = self._get_estimator()
self.calibrated_classifiers_ = []
if self.cv == "prefit":
# `classes_` should be consistent with that of estimator
check_is_fitted(self.estimator, attributes=["classes_"])
self.classes_ = self.estimator.classes_
predictions, _ = _get_response_values(
estimator,
X,
response_method=["decision_function", "predict_proba"],
)
if predictions.ndim == 1:
# Reshape binary output from `(n_samples,)` to `(n_samples, 1)`
predictions = predictions.reshape(-1, 1)
calibrated_classifier = _fit_calibrator(
estimator,
predictions,
y,
self.classes_,
self.method,
sample_weight,
)
self.calibrated_classifiers_.append(calibrated_classifier)
else:
# Set `classes_` using all `y`
label_encoder_ = LabelEncoder().fit(y)
self.classes_ = label_encoder_.classes_
if _routing_enabled():
routed_params = process_routing(
self,
"fit",
sample_weight=sample_weight,
**fit_params,
)
else:
# sample_weight checks
fit_parameters = signature(estimator.fit).parameters
supports_sw = "sample_weight" in fit_parameters
if sample_weight is not None and not supports_sw:
estimator_name = type(estimator).__name__
warnings.warn(
f"Since {estimator_name} does not appear to accept"
" sample_weight, sample weights will only be used for the"
" calibration itself. This can be caused by a limitation of"
" the current scikit-learn API. See the following issue for"
" more details:"
" https://github.com/scikit-learn/scikit-learn/issues/21134."
" Be warned that the result of the calibration is likely to be"
" incorrect."
)
routed_params = Bunch()
routed_params.splitter = Bunch(split={}) # no routing for splitter
routed_params.estimator = Bunch(fit=fit_params)
if sample_weight is not None and supports_sw:
routed_params.estimator.fit["sample_weight"] = sample_weight
# Check that each cross-validation fold can have at least one
# example per class
if isinstance(self.cv, int):
n_folds = self.cv
elif hasattr(self.cv, "n_splits"):
n_folds = self.cv.n_splits
else:
n_folds = None
if n_folds and np.any(np.unique(y, return_counts=True)[1] < n_folds):
raise ValueError(
f"Requesting {n_folds}-fold "
"cross-validation but provided less than "
f"{n_folds} examples for at least one class."
)
if isinstance(self.cv, LeaveOneOut):
raise ValueError(
"LeaveOneOut cross-validation does not allow"
"all classes to be present in test splits. "
"Please use a cross-validation generator that allows "
"all classes to appear in every test and train split."
)
cv = check_cv(self.cv, y, classifier=True)
if self.ensemble:
parallel = Parallel(n_jobs=self.n_jobs)
self.calibrated_classifiers_ = parallel(
delayed(_fit_classifier_calibrator_pair)(
clone(estimator),
X,
y,
train=train,
test=test,
method=self.method,
classes=self.classes_,
sample_weight=sample_weight,
fit_params=routed_params.estimator.fit,
)
for train, test in cv.split(X, y, **routed_params.splitter.split)
)
else:
this_estimator = clone(estimator)
method_name = _check_response_method(
this_estimator,
["decision_function", "predict_proba"],
).__name__
predictions = cross_val_predict(
estimator=this_estimator,
X=X,
y=y,
cv=cv,
method=method_name,
n_jobs=self.n_jobs,
params=routed_params.estimator.fit,
)
if len(self.classes_) == 2:
# Ensure shape (n_samples, 1) in the binary case
if method_name == "predict_proba":
# Select the probability column of the postive class
predictions = _process_predict_proba(
y_pred=predictions,
target_type="binary",
classes=self.classes_,
pos_label=self.classes_[1],
)
predictions = predictions.reshape(-1, 1)
this_estimator.fit(X, y, **routed_params.estimator.fit)
# Note: Here we don't pass on fit_params because the supported
# calibrators don't support fit_params anyway
calibrated_classifier = _fit_calibrator(
this_estimator,
predictions,
y,
self.classes_,
self.method,
sample_weight,
)
self.calibrated_classifiers_.append(calibrated_classifier)
first_clf = self.calibrated_classifiers_[0].estimator
if hasattr(first_clf, "n_features_in_"):
self.n_features_in_ = first_clf.n_features_in_
if hasattr(first_clf, "feature_names_in_"):
self.feature_names_in_ = first_clf.feature_names_in_
return self
| CalibratedClassifierCV.fit | Repo-Level |
scikit-learn | 38 | sklearn/linear_model/_coordinate_descent.py | def fit(self, X, y, sample_weight=None, check_input=True):
"""Fit model with coordinate descent.
Parameters
----------
X : {ndarray, sparse matrix, sparse array} of (n_samples, n_features)
Data.
Note that large sparse matrices and arrays requiring `int64`
indices are not accepted.
y : ndarray of shape (n_samples,) or (n_samples, n_targets)
Target. Will be cast to X's dtype if necessary.
sample_weight : float or array-like of shape (n_samples,), default=None
Sample weights. Internally, the `sample_weight` vector will be
rescaled to sum to `n_samples`.
.. versionadded:: 0.23
check_input : bool, default=True
Allow to bypass several input checking.
Don't use this parameter unless you know what you do.
Returns
-------
self : object
Fitted estimator.
Notes
-----
Coordinate descent is an algorithm that considers each column of
data at a time hence it will automatically convert the X input
as a Fortran-contiguous numpy array if necessary.
To avoid memory re-allocation it is advised to allocate the
initial data in memory directly using that format.
"""
| /usr/src/app/target_test_cases/failed_tests_ElasticNet.fit.txt | def fit(self, X, y, sample_weight=None, check_input=True):
"""Fit model with coordinate descent.
Parameters
----------
X : {ndarray, sparse matrix, sparse array} of (n_samples, n_features)
Data.
Note that large sparse matrices and arrays requiring `int64`
indices are not accepted.
y : ndarray of shape (n_samples,) or (n_samples, n_targets)
Target. Will be cast to X's dtype if necessary.
sample_weight : float or array-like of shape (n_samples,), default=None
Sample weights. Internally, the `sample_weight` vector will be
rescaled to sum to `n_samples`.
.. versionadded:: 0.23
check_input : bool, default=True
Allow to bypass several input checking.
Don't use this parameter unless you know what you do.
Returns
-------
self : object
Fitted estimator.
Notes
-----
Coordinate descent is an algorithm that considers each column of
data at a time hence it will automatically convert the X input
as a Fortran-contiguous numpy array if necessary.
To avoid memory re-allocation it is advised to allocate the
initial data in memory directly using that format.
"""
if self.alpha == 0:
warnings.warn(
(
"With alpha=0, this algorithm does not converge "
"well. You are advised to use the LinearRegression "
"estimator"
),
stacklevel=2,
)
# Remember if X is copied
X_copied = False
# We expect X and y to be float64 or float32 Fortran ordered arrays
# when bypassing checks
if check_input:
X_copied = self.copy_X and self.fit_intercept
X, y = validate_data(
self,
X,
y,
accept_sparse="csc",
order="F",
dtype=[np.float64, np.float32],
force_writeable=True,
accept_large_sparse=False,
copy=X_copied,
multi_output=True,
y_numeric=True,
)
y = check_array(
y, order="F", copy=False, dtype=X.dtype.type, ensure_2d=False
)
n_samples, n_features = X.shape
alpha = self.alpha
if isinstance(sample_weight, numbers.Number):
sample_weight = None
if sample_weight is not None:
if check_input:
sample_weight = _check_sample_weight(sample_weight, X, dtype=X.dtype)
# TLDR: Rescale sw to sum up to n_samples.
# Long: The objective function of Enet
#
# 1/2 * np.average(squared error, weights=sw)
# + alpha * penalty (1)
#
# is invariant under rescaling of sw.
# But enet_path coordinate descent minimizes
#
# 1/2 * sum(squared error) + alpha' * penalty (2)
#
# and therefore sets
#
# alpha' = n_samples * alpha (3)
#
# inside its function body, which results in objective (2) being
# equivalent to (1) in case of no sw.
# With sw, however, enet_path should set
#
# alpha' = sum(sw) * alpha (4)
#
# Therefore, we use the freedom of Eq. (1) to rescale sw before
# calling enet_path, i.e.
#
# sw *= n_samples / sum(sw)
#
# such that sum(sw) = n_samples. This way, (3) and (4) are the same.
sample_weight = sample_weight * (n_samples / np.sum(sample_weight))
# Note: Alternatively, we could also have rescaled alpha instead
# of sample_weight:
#
# alpha *= np.sum(sample_weight) / n_samples
# Ensure copying happens only once, don't do it again if done above.
# X and y will be rescaled if sample_weight is not None, order='F'
# ensures that the returned X and y are still F-contiguous.
should_copy = self.copy_X and not X_copied
X, y, X_offset, y_offset, X_scale, precompute, Xy = _pre_fit(
X,
y,
None,
self.precompute,
fit_intercept=self.fit_intercept,
copy=should_copy,
check_input=check_input,
sample_weight=sample_weight,
)
# coordinate descent needs F-ordered arrays and _pre_fit might have
# called _rescale_data
if check_input or sample_weight is not None:
X, y = _set_order(X, y, order="F")
if y.ndim == 1:
y = y[:, np.newaxis]
if Xy is not None and Xy.ndim == 1:
Xy = Xy[:, np.newaxis]
n_targets = y.shape[1]
if not self.warm_start or not hasattr(self, "coef_"):
coef_ = np.zeros((n_targets, n_features), dtype=X.dtype, order="F")
else:
coef_ = self.coef_
if coef_.ndim == 1:
coef_ = coef_[np.newaxis, :]
dual_gaps_ = np.zeros(n_targets, dtype=X.dtype)
self.n_iter_ = []
for k in range(n_targets):
if Xy is not None:
this_Xy = Xy[:, k]
else:
this_Xy = None
_, this_coef, this_dual_gap, this_iter = self.path(
X,
y[:, k],
l1_ratio=self.l1_ratio,
eps=None,
n_alphas=None,
alphas=[alpha],
precompute=precompute,
Xy=this_Xy,
copy_X=True,
coef_init=coef_[k],
verbose=False,
return_n_iter=True,
positive=self.positive,
check_input=False,
# from here on **params
tol=self.tol,
X_offset=X_offset,
X_scale=X_scale,
max_iter=self.max_iter,
random_state=self.random_state,
selection=self.selection,
sample_weight=sample_weight,
)
coef_[k] = this_coef[:, 0]
dual_gaps_[k] = this_dual_gap[0]
self.n_iter_.append(this_iter[0])
if n_targets == 1:
self.n_iter_ = self.n_iter_[0]
self.coef_ = coef_[0]
self.dual_gap_ = dual_gaps_[0]
else:
self.coef_ = coef_
self.dual_gap_ = dual_gaps_
self._set_intercept(X_offset, y_offset, X_scale)
# check for finiteness of coefficients
if not all(np.isfinite(w).all() for w in [self.coef_, self.intercept_]):
raise ValueError(
"Coordinate descent iterations resulted in non-finite parameter"
" values. The input data may contain large values and need to"
" be preprocessed."
)
# return self for chaining fit and predict calls
return self
| ElasticNet.fit | Repo-Level |
scikit-learn | 55 | sklearn/gaussian_process/_gpc.py | def log_marginal_likelihood(
self, theta=None, eval_gradient=False, clone_kernel=True
):
"""Return log-marginal likelihood of theta for training data.
In the case of multi-class classification, the mean log-marginal
likelihood of the one-versus-rest classifiers are returned.
Parameters
----------
theta : array-like of shape (n_kernel_params,), default=None
Kernel hyperparameters for which the log-marginal likelihood is
evaluated. In the case of multi-class classification, theta may
be the hyperparameters of the compound kernel or of an individual
kernel. In the latter case, all individual kernel get assigned the
same theta values. If None, the precomputed log_marginal_likelihood
of ``self.kernel_.theta`` is returned.
eval_gradient : bool, default=False
If True, the gradient of the log-marginal likelihood with respect
to the kernel hyperparameters at position theta is returned
additionally. Note that gradient computation is not supported
for non-binary classification. If True, theta must not be None.
clone_kernel : bool, default=True
If True, the kernel attribute is copied. If False, the kernel
attribute is modified, but may result in a performance improvement.
Returns
-------
log_likelihood : float
Log-marginal likelihood of theta for training data.
log_likelihood_gradient : ndarray of shape (n_kernel_params,), optional
Gradient of the log-marginal likelihood with respect to the kernel
hyperparameters at position theta.
Only returned when `eval_gradient` is True.
"""
| /usr/src/app/target_test_cases/failed_tests_GaussianProcessClassifier.log_marginal_likelihood.txt | def log_marginal_likelihood(
self, theta=None, eval_gradient=False, clone_kernel=True
):
"""Return log-marginal likelihood of theta for training data.
In the case of multi-class classification, the mean log-marginal
likelihood of the one-versus-rest classifiers are returned.
Parameters
----------
theta : array-like of shape (n_kernel_params,), default=None
Kernel hyperparameters for which the log-marginal likelihood is
evaluated. In the case of multi-class classification, theta may
be the hyperparameters of the compound kernel or of an individual
kernel. In the latter case, all individual kernel get assigned the
same theta values. If None, the precomputed log_marginal_likelihood
of ``self.kernel_.theta`` is returned.
eval_gradient : bool, default=False
If True, the gradient of the log-marginal likelihood with respect
to the kernel hyperparameters at position theta is returned
additionally. Note that gradient computation is not supported
for non-binary classification. If True, theta must not be None.
clone_kernel : bool, default=True
If True, the kernel attribute is copied. If False, the kernel
attribute is modified, but may result in a performance improvement.
Returns
-------
log_likelihood : float
Log-marginal likelihood of theta for training data.
log_likelihood_gradient : ndarray of shape (n_kernel_params,), optional
Gradient of the log-marginal likelihood with respect to the kernel
hyperparameters at position theta.
Only returned when `eval_gradient` is True.
"""
check_is_fitted(self)
if theta is None:
if eval_gradient:
raise ValueError("Gradient can only be evaluated for theta!=None")
return self.log_marginal_likelihood_value_
theta = np.asarray(theta)
if self.n_classes_ == 2:
return self.base_estimator_.log_marginal_likelihood(
theta, eval_gradient, clone_kernel=clone_kernel
)
else:
if eval_gradient:
raise NotImplementedError(
"Gradient of log-marginal-likelihood not implemented for "
"multi-class GPC."
)
estimators = self.base_estimator_.estimators_
n_dims = estimators[0].kernel_.n_dims
if theta.shape[0] == n_dims: # use same theta for all sub-kernels
return np.mean(
[
estimator.log_marginal_likelihood(
theta, clone_kernel=clone_kernel
)
for i, estimator in enumerate(estimators)
]
)
elif theta.shape[0] == n_dims * self.classes_.shape[0]:
# theta for compound kernel
return np.mean(
[
estimator.log_marginal_likelihood(
theta[n_dims * i : n_dims * (i + 1)],
clone_kernel=clone_kernel,
)
for i, estimator in enumerate(estimators)
]
)
else:
raise ValueError(
"Shape of theta must be either %d or %d. "
"Obtained theta with shape %d."
% (n_dims, n_dims * self.classes_.shape[0], theta.shape[0])
)
| GaussianProcessClassifier.log_marginal_likelihood | Repo-Level |
scikit-learn | 57 | sklearn/gaussian_process/_gpr.py | def fit(self, X, y):
"""Fit Gaussian process regression model.
Parameters
----------
X : array-like of shape (n_samples, n_features) or list of object
Feature vectors or other representations of training data.
y : array-like of shape (n_samples,) or (n_samples, n_targets)
Target values.
Returns
-------
self : object
GaussianProcessRegressor class instance.
"""
| /usr/src/app/target_test_cases/failed_tests_GaussianProcessRegressor.fit.txt | def fit(self, X, y):
"""Fit Gaussian process regression model.
Parameters
----------
X : array-like of shape (n_samples, n_features) or list of object
Feature vectors or other representations of training data.
y : array-like of shape (n_samples,) or (n_samples, n_targets)
Target values.
Returns
-------
self : object
GaussianProcessRegressor class instance.
"""
if self.kernel is None: # Use an RBF kernel as default
self.kernel_ = C(1.0, constant_value_bounds="fixed") * RBF(
1.0, length_scale_bounds="fixed"
)
else:
self.kernel_ = clone(self.kernel)
self._rng = check_random_state(self.random_state)
if self.kernel_.requires_vector_input:
dtype, ensure_2d = "numeric", True
else:
dtype, ensure_2d = None, False
X, y = validate_data(
self,
X,
y,
multi_output=True,
y_numeric=True,
ensure_2d=ensure_2d,
dtype=dtype,
)
n_targets_seen = y.shape[1] if y.ndim > 1 else 1
if self.n_targets is not None and n_targets_seen != self.n_targets:
raise ValueError(
"The number of targets seen in `y` is different from the parameter "
f"`n_targets`. Got {n_targets_seen} != {self.n_targets}."
)
# Normalize target value
if self.normalize_y:
self._y_train_mean = np.mean(y, axis=0)
self._y_train_std = _handle_zeros_in_scale(np.std(y, axis=0), copy=False)
# Remove mean and make unit variance
y = (y - self._y_train_mean) / self._y_train_std
else:
shape_y_stats = (y.shape[1],) if y.ndim == 2 else 1
self._y_train_mean = np.zeros(shape=shape_y_stats)
self._y_train_std = np.ones(shape=shape_y_stats)
if np.iterable(self.alpha) and self.alpha.shape[0] != y.shape[0]:
if self.alpha.shape[0] == 1:
self.alpha = self.alpha[0]
else:
raise ValueError(
"alpha must be a scalar or an array with same number of "
f"entries as y. ({self.alpha.shape[0]} != {y.shape[0]})"
)
self.X_train_ = np.copy(X) if self.copy_X_train else X
self.y_train_ = np.copy(y) if self.copy_X_train else y
if self.optimizer is not None and self.kernel_.n_dims > 0:
# Choose hyperparameters based on maximizing the log-marginal
# likelihood (potentially starting from several initial values)
def obj_func(theta, eval_gradient=True):
if eval_gradient:
lml, grad = self.log_marginal_likelihood(
theta, eval_gradient=True, clone_kernel=False
)
return -lml, -grad
else:
return -self.log_marginal_likelihood(theta, clone_kernel=False)
# First optimize starting from theta specified in kernel
optima = [
(
self._constrained_optimization(
obj_func, self.kernel_.theta, self.kernel_.bounds
)
)
]
# Additional runs are performed from log-uniform chosen initial
# theta
if self.n_restarts_optimizer > 0:
if not np.isfinite(self.kernel_.bounds).all():
raise ValueError(
"Multiple optimizer restarts (n_restarts_optimizer>0) "
"requires that all bounds are finite."
)
bounds = self.kernel_.bounds
for iteration in range(self.n_restarts_optimizer):
theta_initial = self._rng.uniform(bounds[:, 0], bounds[:, 1])
optima.append(
self._constrained_optimization(obj_func, theta_initial, bounds)
)
# Select result from run with minimal (negative) log-marginal
# likelihood
lml_values = list(map(itemgetter(1), optima))
self.kernel_.theta = optima[np.argmin(lml_values)][0]
self.kernel_._check_bounds_params()
self.log_marginal_likelihood_value_ = -np.min(lml_values)
else:
self.log_marginal_likelihood_value_ = self.log_marginal_likelihood(
self.kernel_.theta, clone_kernel=False
)
# Precompute quantities required for predictions which are independent
# of actual query points
# Alg. 2.1, page 19, line 2 -> L = cholesky(K + sigma^2 I)
K = self.kernel_(self.X_train_)
K[np.diag_indices_from(K)] += self.alpha
try:
self.L_ = cholesky(K, lower=GPR_CHOLESKY_LOWER, check_finite=False)
except np.linalg.LinAlgError as exc:
exc.args = (
(
f"The kernel, {self.kernel_}, is not returning a positive "
"definite matrix. Try gradually increasing the 'alpha' "
"parameter of your GaussianProcessRegressor estimator."
),
) + exc.args
raise
# Alg 2.1, page 19, line 3 -> alpha = L^T \ (L \ y)
self.alpha_ = cho_solve(
(self.L_, GPR_CHOLESKY_LOWER),
self.y_train_,
check_finite=False,
)
return self
| GaussianProcessRegressor.fit | Repo-Level |
scikit-learn | 58 | sklearn/gaussian_process/_gpr.py | def log_marginal_likelihood(
self, theta=None, eval_gradient=False, clone_kernel=True
):
"""Return log-marginal likelihood of theta for training data.
Parameters
----------
theta : array-like of shape (n_kernel_params,) default=None
Kernel hyperparameters for which the log-marginal likelihood is
evaluated. If None, the precomputed log_marginal_likelihood
of ``self.kernel_.theta`` is returned.
eval_gradient : bool, default=False
If True, the gradient of the log-marginal likelihood with respect
to the kernel hyperparameters at position theta is returned
additionally. If True, theta must not be None.
clone_kernel : bool, default=True
If True, the kernel attribute is copied. If False, the kernel
attribute is modified, but may result in a performance improvement.
Returns
-------
log_likelihood : float
Log-marginal likelihood of theta for training data.
log_likelihood_gradient : ndarray of shape (n_kernel_params,), optional
Gradient of the log-marginal likelihood with respect to the kernel
hyperparameters at position theta.
Only returned when eval_gradient is True.
"""
| /usr/src/app/target_test_cases/failed_tests_GaussianProcessRegressor.log_marginal_likelihood.txt | def log_marginal_likelihood(
self, theta=None, eval_gradient=False, clone_kernel=True
):
"""Return log-marginal likelihood of theta for training data.
Parameters
----------
theta : array-like of shape (n_kernel_params,) default=None
Kernel hyperparameters for which the log-marginal likelihood is
evaluated. If None, the precomputed log_marginal_likelihood
of ``self.kernel_.theta`` is returned.
eval_gradient : bool, default=False
If True, the gradient of the log-marginal likelihood with respect
to the kernel hyperparameters at position theta is returned
additionally. If True, theta must not be None.
clone_kernel : bool, default=True
If True, the kernel attribute is copied. If False, the kernel
attribute is modified, but may result in a performance improvement.
Returns
-------
log_likelihood : float
Log-marginal likelihood of theta for training data.
log_likelihood_gradient : ndarray of shape (n_kernel_params,), optional
Gradient of the log-marginal likelihood with respect to the kernel
hyperparameters at position theta.
Only returned when eval_gradient is True.
"""
if theta is None:
if eval_gradient:
raise ValueError("Gradient can only be evaluated for theta!=None")
return self.log_marginal_likelihood_value_
if clone_kernel:
kernel = self.kernel_.clone_with_theta(theta)
else:
kernel = self.kernel_
kernel.theta = theta
if eval_gradient:
K, K_gradient = kernel(self.X_train_, eval_gradient=True)
else:
K = kernel(self.X_train_)
# Alg. 2.1, page 19, line 2 -> L = cholesky(K + sigma^2 I)
K[np.diag_indices_from(K)] += self.alpha
try:
L = cholesky(K, lower=GPR_CHOLESKY_LOWER, check_finite=False)
except np.linalg.LinAlgError:
return (-np.inf, np.zeros_like(theta)) if eval_gradient else -np.inf
# Support multi-dimensional output of self.y_train_
y_train = self.y_train_
if y_train.ndim == 1:
y_train = y_train[:, np.newaxis]
# Alg 2.1, page 19, line 3 -> alpha = L^T \ (L \ y)
alpha = cho_solve((L, GPR_CHOLESKY_LOWER), y_train, check_finite=False)
# Alg 2.1, page 19, line 7
# -0.5 . y^T . alpha - sum(log(diag(L))) - n_samples / 2 log(2*pi)
# y is originally thought to be a (1, n_samples) row vector. However,
# in multioutputs, y is of shape (n_samples, 2) and we need to compute
# y^T . alpha for each output, independently using einsum. Thus, it
# is equivalent to:
# for output_idx in range(n_outputs):
# log_likelihood_dims[output_idx] = (
# y_train[:, [output_idx]] @ alpha[:, [output_idx]]
# )
log_likelihood_dims = -0.5 * np.einsum("ik,ik->k", y_train, alpha)
log_likelihood_dims -= np.log(np.diag(L)).sum()
log_likelihood_dims -= K.shape[0] / 2 * np.log(2 * np.pi)
# the log likehood is sum-up across the outputs
log_likelihood = log_likelihood_dims.sum(axis=-1)
if eval_gradient:
# Eq. 5.9, p. 114, and footnote 5 in p. 114
# 0.5 * trace((alpha . alpha^T - K^-1) . K_gradient)
# alpha is supposed to be a vector of (n_samples,) elements. With
# multioutputs, alpha is a matrix of size (n_samples, n_outputs).
# Therefore, we want to construct a matrix of
# (n_samples, n_samples, n_outputs) equivalent to
# for output_idx in range(n_outputs):
# output_alpha = alpha[:, [output_idx]]
# inner_term[..., output_idx] = output_alpha @ output_alpha.T
inner_term = np.einsum("ik,jk->ijk", alpha, alpha)
# compute K^-1 of shape (n_samples, n_samples)
K_inv = cho_solve(
(L, GPR_CHOLESKY_LOWER), np.eye(K.shape[0]), check_finite=False
)
# create a new axis to use broadcasting between inner_term and
# K_inv
inner_term -= K_inv[..., np.newaxis]
# Since we are interested about the trace of
# inner_term @ K_gradient, we don't explicitly compute the
# matrix-by-matrix operation and instead use an einsum. Therefore
# it is equivalent to:
# for param_idx in range(n_kernel_params):
# for output_idx in range(n_output):
# log_likehood_gradient_dims[param_idx, output_idx] = (
# inner_term[..., output_idx] @
# K_gradient[..., param_idx]
# )
log_likelihood_gradient_dims = 0.5 * np.einsum(
"ijl,jik->kl", inner_term, K_gradient
)
# the log likehood gradient is the sum-up across the outputs
log_likelihood_gradient = log_likelihood_gradient_dims.sum(axis=-1)
if eval_gradient:
return log_likelihood, log_likelihood_gradient
else:
return log_likelihood
| GaussianProcessRegressor.log_marginal_likelihood | Self-Contained |
scikit-learn | 59 | sklearn/gaussian_process/_gpr.py | def predict(self, X, return_std=False, return_cov=False):
"""Predict using the Gaussian process regression model.
We can also predict based on an unfitted model by using the GP prior.
In addition to the mean of the predictive distribution, optionally also
returns its standard deviation (`return_std=True`) or covariance
(`return_cov=True`). Note that at most one of the two can be requested.
Parameters
----------
X : array-like of shape (n_samples, n_features) or list of object
Query points where the GP is evaluated.
return_std : bool, default=False
If True, the standard-deviation of the predictive distribution at
the query points is returned along with the mean.
return_cov : bool, default=False
If True, the covariance of the joint predictive distribution at
the query points is returned along with the mean.
Returns
-------
y_mean : ndarray of shape (n_samples,) or (n_samples, n_targets)
Mean of predictive distribution at query points.
y_std : ndarray of shape (n_samples,) or (n_samples, n_targets), optional
Standard deviation of predictive distribution at query points.
Only returned when `return_std` is True.
y_cov : ndarray of shape (n_samples, n_samples) or \
(n_samples, n_samples, n_targets), optional
Covariance of joint predictive distribution at query points.
Only returned when `return_cov` is True.
"""
| /usr/src/app/target_test_cases/failed_tests_GaussianProcessRegressor.predict.txt | def predict(self, X, return_std=False, return_cov=False):
"""Predict using the Gaussian process regression model.
We can also predict based on an unfitted model by using the GP prior.
In addition to the mean of the predictive distribution, optionally also
returns its standard deviation (`return_std=True`) or covariance
(`return_cov=True`). Note that at most one of the two can be requested.
Parameters
----------
X : array-like of shape (n_samples, n_features) or list of object
Query points where the GP is evaluated.
return_std : bool, default=False
If True, the standard-deviation of the predictive distribution at
the query points is returned along with the mean.
return_cov : bool, default=False
If True, the covariance of the joint predictive distribution at
the query points is returned along with the mean.
Returns
-------
y_mean : ndarray of shape (n_samples,) or (n_samples, n_targets)
Mean of predictive distribution at query points.
y_std : ndarray of shape (n_samples,) or (n_samples, n_targets), optional
Standard deviation of predictive distribution at query points.
Only returned when `return_std` is True.
y_cov : ndarray of shape (n_samples, n_samples) or \
(n_samples, n_samples, n_targets), optional
Covariance of joint predictive distribution at query points.
Only returned when `return_cov` is True.
"""
if return_std and return_cov:
raise RuntimeError(
"At most one of return_std or return_cov can be requested."
)
if self.kernel is None or self.kernel.requires_vector_input:
dtype, ensure_2d = "numeric", True
else:
dtype, ensure_2d = None, False
X = validate_data(self, X, ensure_2d=ensure_2d, dtype=dtype, reset=False)
if not hasattr(self, "X_train_"): # Unfitted;predict based on GP prior
if self.kernel is None:
kernel = C(1.0, constant_value_bounds="fixed") * RBF(
1.0, length_scale_bounds="fixed"
)
else:
kernel = self.kernel
n_targets = self.n_targets if self.n_targets is not None else 1
y_mean = np.zeros(shape=(X.shape[0], n_targets)).squeeze()
if return_cov:
y_cov = kernel(X)
if n_targets > 1:
y_cov = np.repeat(
np.expand_dims(y_cov, -1), repeats=n_targets, axis=-1
)
return y_mean, y_cov
elif return_std:
y_var = kernel.diag(X)
if n_targets > 1:
y_var = np.repeat(
np.expand_dims(y_var, -1), repeats=n_targets, axis=-1
)
return y_mean, np.sqrt(y_var)
else:
return y_mean
else: # Predict based on GP posterior
# Alg 2.1, page 19, line 4 -> f*_bar = K(X_test, X_train) . alpha
K_trans = self.kernel_(X, self.X_train_)
y_mean = K_trans @ self.alpha_
# undo normalisation
y_mean = self._y_train_std * y_mean + self._y_train_mean
# if y_mean has shape (n_samples, 1), reshape to (n_samples,)
if y_mean.ndim > 1 and y_mean.shape[1] == 1:
y_mean = np.squeeze(y_mean, axis=1)
# Alg 2.1, page 19, line 5 -> v = L \ K(X_test, X_train)^T
V = solve_triangular(
self.L_, K_trans.T, lower=GPR_CHOLESKY_LOWER, check_finite=False
)
if return_cov:
# Alg 2.1, page 19, line 6 -> K(X_test, X_test) - v^T. v
y_cov = self.kernel_(X) - V.T @ V
# undo normalisation
y_cov = np.outer(y_cov, self._y_train_std**2).reshape(*y_cov.shape, -1)
# if y_cov has shape (n_samples, n_samples, 1), reshape to
# (n_samples, n_samples)
if y_cov.shape[2] == 1:
y_cov = np.squeeze(y_cov, axis=2)
return y_mean, y_cov
elif return_std:
# Compute variance of predictive distribution
# Use einsum to avoid explicitly forming the large matrix
# V^T @ V just to extract its diagonal afterward.
y_var = self.kernel_.diag(X).copy()
y_var -= np.einsum("ij,ji->i", V.T, V)
# Check if any of the variances is negative because of
# numerical issues. If yes: set the variance to 0.
y_var_negative = y_var < 0
if np.any(y_var_negative):
warnings.warn(
"Predicted variances smaller than 0. "
"Setting those variances to 0."
)
y_var[y_var_negative] = 0.0
# undo normalisation
y_var = np.outer(y_var, self._y_train_std**2).reshape(*y_var.shape, -1)
# if y_var has shape (n_samples, 1), reshape to (n_samples,)
if y_var.shape[1] == 1:
y_var = np.squeeze(y_var, axis=1)
return y_mean, np.sqrt(y_var)
else:
return y_mean
| GaussianProcessRegressor.predict | Repo-Level |
scikit-learn | 66 | sklearn/decomposition/_incremental_pca.py | def partial_fit(self, X, y=None, check_input=True):
"""Incremental fit with X. All of X is processed as a single batch.
Parameters
----------
X : array-like of shape (n_samples, n_features)
Training data, where `n_samples` is the number of samples and
`n_features` is the number of features.
y : Ignored
Not used, present for API consistency by convention.
check_input : bool, default=True
Run check_array on X.
Returns
-------
self : object
Returns the instance itself.
"""
| /usr/src/app/target_test_cases/failed_tests_IncrementalPCA.partial_fit.txt | def partial_fit(self, X, y=None, check_input=True):
"""Incremental fit with X. All of X is processed as a single batch.
Parameters
----------
X : array-like of shape (n_samples, n_features)
Training data, where `n_samples` is the number of samples and
`n_features` is the number of features.
y : Ignored
Not used, present for API consistency by convention.
check_input : bool, default=True
Run check_array on X.
Returns
-------
self : object
Returns the instance itself.
"""
first_pass = not hasattr(self, "components_")
if check_input:
if sparse.issparse(X):
raise TypeError(
"IncrementalPCA.partial_fit does not support "
"sparse input. Either convert data to dense "
"or use IncrementalPCA.fit to do so in batches."
)
X = validate_data(
self,
X,
copy=self.copy,
dtype=[np.float64, np.float32],
force_writeable=True,
reset=first_pass,
)
n_samples, n_features = X.shape
if first_pass:
self.components_ = None
if self.n_components is None:
if self.components_ is None:
self.n_components_ = min(n_samples, n_features)
else:
self.n_components_ = self.components_.shape[0]
elif not self.n_components <= n_features:
raise ValueError(
"n_components=%r invalid for n_features=%d, need "
"more rows than columns for IncrementalPCA "
"processing" % (self.n_components, n_features)
)
elif not self.n_components <= n_samples:
raise ValueError(
"n_components=%r must be less or equal to "
"the batch number of samples "
"%d." % (self.n_components, n_samples)
)
else:
self.n_components_ = self.n_components
if (self.components_ is not None) and (
self.components_.shape[0] != self.n_components_
):
raise ValueError(
"Number of input features has changed from %i "
"to %i between calls to partial_fit! Try "
"setting n_components to a fixed value."
% (self.components_.shape[0], self.n_components_)
)
# This is the first partial_fit
if not hasattr(self, "n_samples_seen_"):
self.n_samples_seen_ = 0
self.mean_ = 0.0
self.var_ = 0.0
# Update stats - they are 0 if this is the first step
col_mean, col_var, n_total_samples = _incremental_mean_and_var(
X,
last_mean=self.mean_,
last_variance=self.var_,
last_sample_count=np.repeat(self.n_samples_seen_, X.shape[1]),
)
n_total_samples = n_total_samples[0]
# Whitening
if self.n_samples_seen_ == 0:
# If it is the first step, simply whiten X
X -= col_mean
else:
col_batch_mean = np.mean(X, axis=0)
X -= col_batch_mean
# Build matrix of combined previous basis and new data
mean_correction = np.sqrt(
(self.n_samples_seen_ / n_total_samples) * n_samples
) * (self.mean_ - col_batch_mean)
X = np.vstack(
(
self.singular_values_.reshape((-1, 1)) * self.components_,
X,
mean_correction,
)
)
U, S, Vt = linalg.svd(X, full_matrices=False, check_finite=False)
U, Vt = svd_flip(U, Vt, u_based_decision=False)
explained_variance = S**2 / (n_total_samples - 1)
explained_variance_ratio = S**2 / np.sum(col_var * n_total_samples)
self.n_samples_seen_ = n_total_samples
self.components_ = Vt[: self.n_components_]
self.singular_values_ = S[: self.n_components_]
self.mean_ = col_mean
self.var_ = col_var
self.explained_variance_ = explained_variance[: self.n_components_]
self.explained_variance_ratio_ = explained_variance_ratio[: self.n_components_]
# we already checked `self.n_components <= n_samples` above
if self.n_components_ not in (n_samples, n_features):
self.noise_variance_ = explained_variance[self.n_components_ :].mean()
else:
self.noise_variance_ = 0.0
return self
| IncrementalPCA.partial_fit | Repo-Level |
scikit-learn | 70 | sklearn/impute/_iterative.py | def fit_transform(self, X, y=None, **params):
"""Fit the imputer on `X` and return the transformed `X`.
Parameters
----------
X : array-like, shape (n_samples, n_features)
Input data, where `n_samples` is the number of samples and
`n_features` is the number of features.
y : Ignored
Not used, present for API consistency by convention.
**params : dict
Parameters routed to the `fit` method of the sub-estimator via the
metadata routing API.
.. versionadded:: 1.5
Only available if
`sklearn.set_config(enable_metadata_routing=True)` is set. See
:ref:`Metadata Routing User Guide <metadata_routing>` for more
details.
Returns
-------
Xt : array-like, shape (n_samples, n_features)
The imputed input data.
"""
| /usr/src/app/target_test_cases/failed_tests_IterativeImputer.fit_transform.txt | def fit_transform(self, X, y=None, **params):
"""Fit the imputer on `X` and return the transformed `X`.
Parameters
----------
X : array-like, shape (n_samples, n_features)
Input data, where `n_samples` is the number of samples and
`n_features` is the number of features.
y : Ignored
Not used, present for API consistency by convention.
**params : dict
Parameters routed to the `fit` method of the sub-estimator via the
metadata routing API.
.. versionadded:: 1.5
Only available if
`sklearn.set_config(enable_metadata_routing=True)` is set. See
:ref:`Metadata Routing User Guide <metadata_routing>` for more
details.
Returns
-------
Xt : array-like, shape (n_samples, n_features)
The imputed input data.
"""
_raise_for_params(params, self, "fit")
routed_params = process_routing(
self,
"fit",
**params,
)
self.random_state_ = getattr(
self, "random_state_", check_random_state(self.random_state)
)
if self.estimator is None:
from ..linear_model import BayesianRidge
self._estimator = BayesianRidge()
else:
self._estimator = clone(self.estimator)
self.imputation_sequence_ = []
self.initial_imputer_ = None
X, Xt, mask_missing_values, complete_mask = self._initial_imputation(
X, in_fit=True
)
super()._fit_indicator(complete_mask)
X_indicator = super()._transform_indicator(complete_mask)
if self.max_iter == 0 or np.all(mask_missing_values):
self.n_iter_ = 0
return super()._concatenate_indicator(Xt, X_indicator)
# Edge case: a single feature, we return the initial imputation.
if Xt.shape[1] == 1:
self.n_iter_ = 0
return super()._concatenate_indicator(Xt, X_indicator)
self._min_value = self._validate_limit(self.min_value, "min", X.shape[1])
self._max_value = self._validate_limit(self.max_value, "max", X.shape[1])
if not np.all(np.greater(self._max_value, self._min_value)):
raise ValueError("One (or more) features have min_value >= max_value.")
# order in which to impute
# note this is probably too slow for large feature data (d > 100000)
# and a better way would be good.
# see: https://goo.gl/KyCNwj and subsequent comments
ordered_idx = self._get_ordered_idx(mask_missing_values)
self.n_features_with_missing_ = len(ordered_idx)
abs_corr_mat = self._get_abs_corr_mat(Xt)
n_samples, n_features = Xt.shape
if self.verbose > 0:
print("[IterativeImputer] Completing matrix with shape %s" % (X.shape,))
start_t = time()
if not self.sample_posterior:
Xt_previous = Xt.copy()
normalized_tol = self.tol * np.max(np.abs(X[~mask_missing_values]))
for self.n_iter_ in range(1, self.max_iter + 1):
if self.imputation_order == "random":
ordered_idx = self._get_ordered_idx(mask_missing_values)
for feat_idx in ordered_idx:
neighbor_feat_idx = self._get_neighbor_feat_idx(
n_features, feat_idx, abs_corr_mat
)
Xt, estimator = self._impute_one_feature(
Xt,
mask_missing_values,
feat_idx,
neighbor_feat_idx,
estimator=None,
fit_mode=True,
params=routed_params.estimator.fit,
)
estimator_triplet = _ImputerTriplet(
feat_idx, neighbor_feat_idx, estimator
)
self.imputation_sequence_.append(estimator_triplet)
if self.verbose > 1:
print(
"[IterativeImputer] Ending imputation round "
"%d/%d, elapsed time %0.2f"
% (self.n_iter_, self.max_iter, time() - start_t)
)
if not self.sample_posterior:
inf_norm = np.linalg.norm(Xt - Xt_previous, ord=np.inf, axis=None)
if self.verbose > 0:
print(
"[IterativeImputer] Change: {}, scaled tolerance: {} ".format(
inf_norm, normalized_tol
)
)
if inf_norm < normalized_tol:
if self.verbose > 0:
print("[IterativeImputer] Early stopping criterion reached.")
break
Xt_previous = Xt.copy()
else:
if not self.sample_posterior:
warnings.warn(
"[IterativeImputer] Early stopping criterion not reached.",
ConvergenceWarning,
)
_assign_where(Xt, X, cond=~mask_missing_values)
return super()._concatenate_indicator(Xt, X_indicator)
| IterativeImputer.fit_transform | Repo-Level |
scikit-learn | 72 | sklearn/preprocessing/_discretization.py | def fit(self, X, y=None, sample_weight=None):
"""
Fit the estimator.
Parameters
----------
X : array-like of shape (n_samples, n_features)
Data to be discretized.
y : None
Ignored. This parameter exists only for compatibility with
:class:`~sklearn.pipeline.Pipeline`.
sample_weight : ndarray of shape (n_samples,)
Contains weight values to be associated with each sample.
Cannot be used when `strategy` is set to `"uniform"`.
.. versionadded:: 1.3
Returns
-------
self : object
Returns the instance itself.
"""
| /usr/src/app/target_test_cases/failed_tests_KBinsDiscretizer.fit.txt | def fit(self, X, y=None, sample_weight=None):
"""
Fit the estimator.
Parameters
----------
X : array-like of shape (n_samples, n_features)
Data to be discretized.
y : None
Ignored. This parameter exists only for compatibility with
:class:`~sklearn.pipeline.Pipeline`.
sample_weight : ndarray of shape (n_samples,)
Contains weight values to be associated with each sample.
Cannot be used when `strategy` is set to `"uniform"`.
.. versionadded:: 1.3
Returns
-------
self : object
Returns the instance itself.
"""
X = validate_data(self, X, dtype="numeric")
if self.dtype in (np.float64, np.float32):
output_dtype = self.dtype
else: # self.dtype is None
output_dtype = X.dtype
n_samples, n_features = X.shape
if sample_weight is not None and self.strategy == "uniform":
raise ValueError(
"`sample_weight` was provided but it cannot be "
"used with strategy='uniform'. Got strategy="
f"{self.strategy!r} instead."
)
if self.subsample is not None and n_samples > self.subsample:
# Take a subsample of `X`
X = resample(
X,
replace=False,
n_samples=self.subsample,
random_state=self.random_state,
)
n_features = X.shape[1]
n_bins = self._validate_n_bins(n_features)
if sample_weight is not None:
sample_weight = _check_sample_weight(sample_weight, X, dtype=X.dtype)
bin_edges = np.zeros(n_features, dtype=object)
for jj in range(n_features):
column = X[:, jj]
col_min, col_max = column.min(), column.max()
if col_min == col_max:
warnings.warn(
"Feature %d is constant and will be replaced with 0." % jj
)
n_bins[jj] = 1
bin_edges[jj] = np.array([-np.inf, np.inf])
continue
if self.strategy == "uniform":
bin_edges[jj] = np.linspace(col_min, col_max, n_bins[jj] + 1)
elif self.strategy == "quantile":
quantiles = np.linspace(0, 100, n_bins[jj] + 1)
if sample_weight is None:
bin_edges[jj] = np.asarray(np.percentile(column, quantiles))
else:
bin_edges[jj] = np.asarray(
[
_weighted_percentile(column, sample_weight, q)
for q in quantiles
],
dtype=np.float64,
)
elif self.strategy == "kmeans":
from ..cluster import KMeans # fixes import loops
# Deterministic initialization with uniform spacing
uniform_edges = np.linspace(col_min, col_max, n_bins[jj] + 1)
init = (uniform_edges[1:] + uniform_edges[:-1])[:, None] * 0.5
# 1D k-means procedure
km = KMeans(n_clusters=n_bins[jj], init=init, n_init=1)
centers = km.fit(
column[:, None], sample_weight=sample_weight
).cluster_centers_[:, 0]
# Must sort, centers may be unsorted even with sorted init
centers.sort()
bin_edges[jj] = (centers[1:] + centers[:-1]) * 0.5
bin_edges[jj] = np.r_[col_min, bin_edges[jj], col_max]
# Remove bins whose width are too small (i.e., <= 1e-8)
if self.strategy in ("quantile", "kmeans"):
mask = np.ediff1d(bin_edges[jj], to_begin=np.inf) > 1e-8
bin_edges[jj] = bin_edges[jj][mask]
if len(bin_edges[jj]) - 1 != n_bins[jj]:
warnings.warn(
"Bins whose width are too small (i.e., <= "
"1e-8) in feature %d are removed. Consider "
"decreasing the number of bins." % jj
)
n_bins[jj] = len(bin_edges[jj]) - 1
self.bin_edges_ = bin_edges
self.n_bins_ = n_bins
if "onehot" in self.encode:
self._encoder = OneHotEncoder(
categories=[np.arange(i) for i in self.n_bins_],
sparse_output=self.encode == "onehot",
dtype=output_dtype,
)
# Fit the OneHotEncoder with toy datasets
# so that it's ready for use after the KBinsDiscretizer is fitted
self._encoder.fit(np.zeros((1, len(self.n_bins_))))
return self
| KBinsDiscretizer.fit | Repo-Level |
scikit-learn | 75 | sklearn/cluster/_kmeans.py | def fit(self, X, y=None, sample_weight=None):
"""Compute k-means clustering.
Parameters
----------
X : {array-like, sparse matrix} of shape (n_samples, n_features)
Training instances to cluster. It must be noted that the data
will be converted to C ordering, which will cause a memory
copy if the given data is not C-contiguous.
If a sparse matrix is passed, a copy will be made if it's not in
CSR format.
y : Ignored
Not used, present here for API consistency by convention.
sample_weight : array-like of shape (n_samples,), default=None
The weights for each observation in X. If None, all observations
are assigned equal weight. `sample_weight` is not used during
initialization if `init` is a callable or a user provided array.
.. versionadded:: 0.20
Returns
-------
self : object
Fitted estimator.
"""
| /usr/src/app/target_test_cases/failed_tests_KMeans.fit.txt | def fit(self, X, y=None, sample_weight=None):
"""Compute k-means clustering.
Parameters
----------
X : {array-like, sparse matrix} of shape (n_samples, n_features)
Training instances to cluster. It must be noted that the data
will be converted to C ordering, which will cause a memory
copy if the given data is not C-contiguous.
If a sparse matrix is passed, a copy will be made if it's not in
CSR format.
y : Ignored
Not used, present here for API consistency by convention.
sample_weight : array-like of shape (n_samples,), default=None
The weights for each observation in X. If None, all observations
are assigned equal weight. `sample_weight` is not used during
initialization if `init` is a callable or a user provided array.
.. versionadded:: 0.20
Returns
-------
self : object
Fitted estimator.
"""
X = validate_data(
self,
X,
accept_sparse="csr",
dtype=[np.float64, np.float32],
order="C",
copy=self.copy_x,
accept_large_sparse=False,
)
self._check_params_vs_input(X)
random_state = check_random_state(self.random_state)
sample_weight = _check_sample_weight(sample_weight, X, dtype=X.dtype)
self._n_threads = _openmp_effective_n_threads()
# Validate init array
init = self.init
init_is_array_like = _is_arraylike_not_scalar(init)
if init_is_array_like:
init = check_array(init, dtype=X.dtype, copy=True, order="C")
self._validate_center_shape(X, init)
# subtract of mean of x for more accurate distance computations
if not sp.issparse(X):
X_mean = X.mean(axis=0)
# The copy was already done above
X -= X_mean
if init_is_array_like:
init -= X_mean
# precompute squared norms of data points
x_squared_norms = row_norms(X, squared=True)
if self._algorithm == "elkan":
kmeans_single = _kmeans_single_elkan
else:
kmeans_single = _kmeans_single_lloyd
self._check_mkl_vcomp(X, X.shape[0])
best_inertia, best_labels = None, None
for i in range(self._n_init):
# Initialize centers
centers_init = self._init_centroids(
X,
x_squared_norms=x_squared_norms,
init=init,
random_state=random_state,
sample_weight=sample_weight,
)
if self.verbose:
print("Initialization complete")
# run a k-means once
labels, inertia, centers, n_iter_ = kmeans_single(
X,
sample_weight,
centers_init,
max_iter=self.max_iter,
verbose=self.verbose,
tol=self._tol,
n_threads=self._n_threads,
)
# determine if these results are the best so far
# we chose a new run if it has a better inertia and the clustering is
# different from the best so far (it's possible that the inertia is
# slightly better even if the clustering is the same with potentially
# permuted labels, due to rounding errors)
if best_inertia is None or (
inertia < best_inertia
and not _is_same_clustering(labels, best_labels, self.n_clusters)
):
best_labels = labels
best_centers = centers
best_inertia = inertia
best_n_iter = n_iter_
if not sp.issparse(X):
if not self.copy_x:
X += X_mean
best_centers += X_mean
distinct_clusters = len(set(best_labels))
if distinct_clusters < self.n_clusters:
warnings.warn(
"Number of distinct clusters ({}) found smaller than "
"n_clusters ({}). Possibly due to duplicate points "
"in X.".format(distinct_clusters, self.n_clusters),
ConvergenceWarning,
stacklevel=2,
)
self.cluster_centers_ = best_centers
self._n_features_out = self.cluster_centers_.shape[0]
self.labels_ = best_labels
self.inertia_ = best_inertia
self.n_iter_ = best_n_iter
return self
| KMeans.fit | Repo-Level |
scikit-learn | 77 | sklearn/impute/_knn.py | def transform(self, X):
"""Impute all missing values in X.
Parameters
----------
X : array-like of shape (n_samples, n_features)
The input data to complete.
Returns
-------
X : array-like of shape (n_samples, n_output_features)
The imputed dataset. `n_output_features` is the number of features
that is not always missing during `fit`.
"""
| /usr/src/app/target_test_cases/failed_tests_KNNImputer.transform.txt | def transform(self, X):
"""Impute all missing values in X.
Parameters
----------
X : array-like of shape (n_samples, n_features)
The input data to complete.
Returns
-------
X : array-like of shape (n_samples, n_output_features)
The imputed dataset. `n_output_features` is the number of features
that is not always missing during `fit`.
"""
check_is_fitted(self)
if not is_scalar_nan(self.missing_values):
ensure_all_finite = True
else:
ensure_all_finite = "allow-nan"
X = validate_data(
self,
X,
accept_sparse=False,
dtype=FLOAT_DTYPES,
force_writeable=True,
ensure_all_finite=ensure_all_finite,
copy=self.copy,
reset=False,
)
mask = _get_mask(X, self.missing_values)
mask_fit_X = self._mask_fit_X
valid_mask = self._valid_mask
X_indicator = super()._transform_indicator(mask)
# Removes columns where the training data is all nan
if not np.any(mask[:, valid_mask]):
# No missing values in X
if self.keep_empty_features:
Xc = X
Xc[:, ~valid_mask] = 0
else:
Xc = X[:, valid_mask]
# Even if there are no missing values in X, we still concatenate Xc
# with the missing value indicator matrix, X_indicator.
# This is to ensure that the output maintains consistency in terms
# of columns, regardless of whether missing values exist in X or not.
return super()._concatenate_indicator(Xc, X_indicator)
row_missing_idx = np.flatnonzero(mask[:, valid_mask].any(axis=1))
non_missing_fix_X = np.logical_not(mask_fit_X)
# Maps from indices from X to indices in dist matrix
dist_idx_map = np.zeros(X.shape[0], dtype=int)
dist_idx_map[row_missing_idx] = np.arange(row_missing_idx.shape[0])
def process_chunk(dist_chunk, start):
row_missing_chunk = row_missing_idx[start : start + len(dist_chunk)]
# Find and impute missing by column
for col in range(X.shape[1]):
if not valid_mask[col]:
# column was all missing during training
continue
col_mask = mask[row_missing_chunk, col]
if not np.any(col_mask):
# column has no missing values
continue
(potential_donors_idx,) = np.nonzero(non_missing_fix_X[:, col])
# receivers_idx are indices in X
receivers_idx = row_missing_chunk[np.flatnonzero(col_mask)]
# distances for samples that needed imputation for column
dist_subset = dist_chunk[dist_idx_map[receivers_idx] - start][
:, potential_donors_idx
]
# receivers with all nan distances impute with mean
all_nan_dist_mask = np.isnan(dist_subset).all(axis=1)
all_nan_receivers_idx = receivers_idx[all_nan_dist_mask]
if all_nan_receivers_idx.size:
col_mean = np.ma.array(
self._fit_X[:, col], mask=mask_fit_X[:, col]
).mean()
X[all_nan_receivers_idx, col] = col_mean
if len(all_nan_receivers_idx) == len(receivers_idx):
# all receivers imputed with mean
continue
# receivers with at least one defined distance
receivers_idx = receivers_idx[~all_nan_dist_mask]
dist_subset = dist_chunk[dist_idx_map[receivers_idx] - start][
:, potential_donors_idx
]
n_neighbors = min(self.n_neighbors, len(potential_donors_idx))
value = self._calc_impute(
dist_subset,
n_neighbors,
self._fit_X[potential_donors_idx, col],
mask_fit_X[potential_donors_idx, col],
)
X[receivers_idx, col] = value
# process in fixed-memory chunks
gen = pairwise_distances_chunked(
X[row_missing_idx, :],
self._fit_X,
metric=self.metric,
missing_values=self.missing_values,
ensure_all_finite=ensure_all_finite,
reduce_func=process_chunk,
)
for chunk in gen:
# process_chunk modifies X in place. No return value.
pass
if self.keep_empty_features:
Xc = X
Xc[:, ~valid_mask] = 0
else:
Xc = X[:, valid_mask]
return super()._concatenate_indicator(Xc, X_indicator)
| KNNImputer.transform | Repo-Level |
scikit-learn | 99 | sklearn/linear_model/_linear_loss.py | def gradient_hessian(
self,
coef,
X,
y,
sample_weight=None,
l2_reg_strength=0.0,
n_threads=1,
gradient_out=None,
hessian_out=None,
raw_prediction=None,
):
"""Computes gradient and hessian w.r.t. coef.
Parameters
----------
coef : ndarray of shape (n_dof,), (n_classes, n_dof) or (n_classes * n_dof,)
Coefficients of a linear model.
If shape (n_classes * n_dof,), the classes of one feature are contiguous,
i.e. one reconstructs the 2d-array via
coef.reshape((n_classes, -1), order="F").
X : {array-like, sparse matrix} of shape (n_samples, n_features)
Training data.
y : contiguous array of shape (n_samples,)
Observed, true target values.
sample_weight : None or contiguous array of shape (n_samples,), default=None
Sample weights.
l2_reg_strength : float, default=0.0
L2 regularization strength
n_threads : int, default=1
Number of OpenMP threads to use.
gradient_out : None or ndarray of shape coef.shape
A location into which the gradient is stored. If None, a new array
might be created.
hessian_out : None or ndarray
A location into which the hessian is stored. If None, a new array
might be created.
raw_prediction : C-contiguous array of shape (n_samples,) or array of \
shape (n_samples, n_classes)
Raw prediction values (in link space). If provided, these are used. If
None, then raw_prediction = X @ coef + intercept is calculated.
Returns
-------
gradient : ndarray of shape coef.shape
The gradient of the loss.
hessian : ndarray
Hessian matrix.
hessian_warning : bool
True if pointwise hessian has more than half of its elements non-positive.
"""
| /usr/src/app/target_test_cases/failed_tests_LinearModelLoss.gradient_hessian.txt | def gradient_hessian(
self,
coef,
X,
y,
sample_weight=None,
l2_reg_strength=0.0,
n_threads=1,
gradient_out=None,
hessian_out=None,
raw_prediction=None,
):
"""Computes gradient and hessian w.r.t. coef.
Parameters
----------
coef : ndarray of shape (n_dof,), (n_classes, n_dof) or (n_classes * n_dof,)
Coefficients of a linear model.
If shape (n_classes * n_dof,), the classes of one feature are contiguous,
i.e. one reconstructs the 2d-array via
coef.reshape((n_classes, -1), order="F").
X : {array-like, sparse matrix} of shape (n_samples, n_features)
Training data.
y : contiguous array of shape (n_samples,)
Observed, true target values.
sample_weight : None or contiguous array of shape (n_samples,), default=None
Sample weights.
l2_reg_strength : float, default=0.0
L2 regularization strength
n_threads : int, default=1
Number of OpenMP threads to use.
gradient_out : None or ndarray of shape coef.shape
A location into which the gradient is stored. If None, a new array
might be created.
hessian_out : None or ndarray
A location into which the hessian is stored. If None, a new array
might be created.
raw_prediction : C-contiguous array of shape (n_samples,) or array of \
shape (n_samples, n_classes)
Raw prediction values (in link space). If provided, these are used. If
None, then raw_prediction = X @ coef + intercept is calculated.
Returns
-------
gradient : ndarray of shape coef.shape
The gradient of the loss.
hessian : ndarray
Hessian matrix.
hessian_warning : bool
True if pointwise hessian has more than half of its elements non-positive.
"""
n_samples, n_features = X.shape
n_dof = n_features + int(self.fit_intercept)
if raw_prediction is None:
weights, intercept, raw_prediction = self.weight_intercept_raw(coef, X)
else:
weights, intercept = self.weight_intercept(coef)
grad_pointwise, hess_pointwise = self.base_loss.gradient_hessian(
y_true=y,
raw_prediction=raw_prediction,
sample_weight=sample_weight,
n_threads=n_threads,
)
sw_sum = n_samples if sample_weight is None else np.sum(sample_weight)
grad_pointwise /= sw_sum
hess_pointwise /= sw_sum
# For non-canonical link functions and far away from the optimum, the pointwise
# hessian can be negative. We take care that 75% of the hessian entries are
# positive.
hessian_warning = np.mean(hess_pointwise <= 0) > 0.25
hess_pointwise = np.abs(hess_pointwise)
if not self.base_loss.is_multiclass:
# gradient
if gradient_out is None:
grad = np.empty_like(coef, dtype=weights.dtype)
else:
grad = gradient_out
grad[:n_features] = X.T @ grad_pointwise + l2_reg_strength * weights
if self.fit_intercept:
grad[-1] = grad_pointwise.sum()
# hessian
if hessian_out is None:
hess = np.empty(shape=(n_dof, n_dof), dtype=weights.dtype)
else:
hess = hessian_out
if hessian_warning:
# Exit early without computing the hessian.
return grad, hess, hessian_warning
# TODO: This "sandwich product", X' diag(W) X, is the main computational
# bottleneck for solvers. A dedicated Cython routine might improve it
# exploiting the symmetry (as opposed to, e.g., BLAS gemm).
if sparse.issparse(X):
hess[:n_features, :n_features] = (
X.T
@ sparse.dia_matrix(
(hess_pointwise, 0), shape=(n_samples, n_samples)
)
@ X
).toarray()
else:
# np.einsum may use less memory but the following, using BLAS matrix
# multiplication (gemm), is by far faster.
WX = hess_pointwise[:, None] * X
hess[:n_features, :n_features] = np.dot(X.T, WX)
if l2_reg_strength > 0:
# The L2 penalty enters the Hessian on the diagonal only. To add those
# terms, we use a flattened view on the array.
hess.reshape(-1)[
: (n_features * n_dof) : (n_dof + 1)
] += l2_reg_strength
if self.fit_intercept:
# With intercept included as added column to X, the hessian becomes
# hess = (X, 1)' @ diag(h) @ (X, 1)
# = (X' @ diag(h) @ X, X' @ h)
# ( h @ X, sum(h))
# The left upper part has already been filled, it remains to compute
# the last row and the last column.
Xh = X.T @ hess_pointwise
hess[:-1, -1] = Xh
hess[-1, :-1] = Xh
hess[-1, -1] = hess_pointwise.sum()
else:
# Here we may safely assume HalfMultinomialLoss aka categorical
# cross-entropy.
raise NotImplementedError
return grad, hess, hessian_warning
| LinearModelLoss.gradient_hessian | File-Level |
scikit-learn | 100 | sklearn/linear_model/_linear_loss.py | def gradient_hessian_product(
self, coef, X, y, sample_weight=None, l2_reg_strength=0.0, n_threads=1
):
"""Computes gradient and hessp (hessian product function) w.r.t. coef.
Parameters
----------
coef : ndarray of shape (n_dof,), (n_classes, n_dof) or (n_classes * n_dof,)
Coefficients of a linear model.
If shape (n_classes * n_dof,), the classes of one feature are contiguous,
i.e. one reconstructs the 2d-array via
coef.reshape((n_classes, -1), order="F").
X : {array-like, sparse matrix} of shape (n_samples, n_features)
Training data.
y : contiguous array of shape (n_samples,)
Observed, true target values.
sample_weight : None or contiguous array of shape (n_samples,), default=None
Sample weights.
l2_reg_strength : float, default=0.0
L2 regularization strength
n_threads : int, default=1
Number of OpenMP threads to use.
Returns
-------
gradient : ndarray of shape coef.shape
The gradient of the loss.
hessp : callable
Function that takes in a vector input of shape of gradient and
and returns matrix-vector product with hessian.
"""
| /usr/src/app/target_test_cases/failed_tests_LinearModelLoss.gradient_hessian_product.txt | def gradient_hessian_product(
self, coef, X, y, sample_weight=None, l2_reg_strength=0.0, n_threads=1
):
"""Computes gradient and hessp (hessian product function) w.r.t. coef.
Parameters
----------
coef : ndarray of shape (n_dof,), (n_classes, n_dof) or (n_classes * n_dof,)
Coefficients of a linear model.
If shape (n_classes * n_dof,), the classes of one feature are contiguous,
i.e. one reconstructs the 2d-array via
coef.reshape((n_classes, -1), order="F").
X : {array-like, sparse matrix} of shape (n_samples, n_features)
Training data.
y : contiguous array of shape (n_samples,)
Observed, true target values.
sample_weight : None or contiguous array of shape (n_samples,), default=None
Sample weights.
l2_reg_strength : float, default=0.0
L2 regularization strength
n_threads : int, default=1
Number of OpenMP threads to use.
Returns
-------
gradient : ndarray of shape coef.shape
The gradient of the loss.
hessp : callable
Function that takes in a vector input of shape of gradient and
and returns matrix-vector product with hessian.
"""
(n_samples, n_features), n_classes = X.shape, self.base_loss.n_classes
n_dof = n_features + int(self.fit_intercept)
weights, intercept, raw_prediction = self.weight_intercept_raw(coef, X)
sw_sum = n_samples if sample_weight is None else np.sum(sample_weight)
if not self.base_loss.is_multiclass:
grad_pointwise, hess_pointwise = self.base_loss.gradient_hessian(
y_true=y,
raw_prediction=raw_prediction,
sample_weight=sample_weight,
n_threads=n_threads,
)
grad_pointwise /= sw_sum
hess_pointwise /= sw_sum
grad = np.empty_like(coef, dtype=weights.dtype)
grad[:n_features] = X.T @ grad_pointwise + l2_reg_strength * weights
if self.fit_intercept:
grad[-1] = grad_pointwise.sum()
# Precompute as much as possible: hX, hX_sum and hessian_sum
hessian_sum = hess_pointwise.sum()
if sparse.issparse(X):
hX = (
sparse.dia_matrix((hess_pointwise, 0), shape=(n_samples, n_samples))
@ X
)
else:
hX = hess_pointwise[:, np.newaxis] * X
if self.fit_intercept:
# Calculate the double derivative with respect to intercept.
# Note: In case hX is sparse, hX.sum is a matrix object.
hX_sum = np.squeeze(np.asarray(hX.sum(axis=0)))
# prevent squeezing to zero-dim array if n_features == 1
hX_sum = np.atleast_1d(hX_sum)
# With intercept included and l2_reg_strength = 0, hessp returns
# res = (X, 1)' @ diag(h) @ (X, 1) @ s
# = (X, 1)' @ (hX @ s[:n_features], sum(h) * s[-1])
# res[:n_features] = X' @ hX @ s[:n_features] + sum(h) * s[-1]
# res[-1] = 1' @ hX @ s[:n_features] + sum(h) * s[-1]
def hessp(s):
ret = np.empty_like(s)
if sparse.issparse(X):
ret[:n_features] = X.T @ (hX @ s[:n_features])
else:
ret[:n_features] = np.linalg.multi_dot([X.T, hX, s[:n_features]])
ret[:n_features] += l2_reg_strength * s[:n_features]
if self.fit_intercept:
ret[:n_features] += s[-1] * hX_sum
ret[-1] = hX_sum @ s[:n_features] + hessian_sum * s[-1]
return ret
else:
# Here we may safely assume HalfMultinomialLoss aka categorical
# cross-entropy.
# HalfMultinomialLoss computes only the diagonal part of the hessian, i.e.
# diagonal in the classes. Here, we want the matrix-vector product of the
# full hessian. Therefore, we call gradient_proba.
grad_pointwise, proba = self.base_loss.gradient_proba(
y_true=y,
raw_prediction=raw_prediction,
sample_weight=sample_weight,
n_threads=n_threads,
)
grad_pointwise /= sw_sum
grad = np.empty((n_classes, n_dof), dtype=weights.dtype, order="F")
grad[:, :n_features] = grad_pointwise.T @ X + l2_reg_strength * weights
if self.fit_intercept:
grad[:, -1] = grad_pointwise.sum(axis=0)
# Full hessian-vector product, i.e. not only the diagonal part of the
# hessian. Derivation with some index battle for input vector s:
# - sample index i
# - feature indices j, m
# - class indices k, l
# - 1_{k=l} is one if k=l else 0
# - p_i_k is the (predicted) probability that sample i belongs to class k
# for all i: sum_k p_i_k = 1
# - s_l_m is input vector for class l and feature m
# - X' = X transposed
#
# Note: Hessian with dropping most indices is just:
# X' @ p_k (1(k=l) - p_l) @ X
#
# result_{k j} = sum_{i, l, m} Hessian_{i, k j, m l} * s_l_m
# = sum_{i, l, m} (X')_{ji} * p_i_k * (1_{k=l} - p_i_l)
# * X_{im} s_l_m
# = sum_{i, m} (X')_{ji} * p_i_k
# * (X_{im} * s_k_m - sum_l p_i_l * X_{im} * s_l_m)
#
# See also https://github.com/scikit-learn/scikit-learn/pull/3646#discussion_r17461411 # noqa
def hessp(s):
s = s.reshape((n_classes, -1), order="F") # shape = (n_classes, n_dof)
if self.fit_intercept:
s_intercept = s[:, -1]
s = s[:, :-1] # shape = (n_classes, n_features)
else:
s_intercept = 0
tmp = X @ s.T + s_intercept # X_{im} * s_k_m
tmp += (-proba * tmp).sum(axis=1)[:, np.newaxis] # - sum_l ..
tmp *= proba # * p_i_k
if sample_weight is not None:
tmp *= sample_weight[:, np.newaxis]
# hess_prod = empty_like(grad), but we ravel grad below and this
# function is run after that.
hess_prod = np.empty((n_classes, n_dof), dtype=weights.dtype, order="F")
hess_prod[:, :n_features] = (tmp.T @ X) / sw_sum + l2_reg_strength * s
if self.fit_intercept:
hess_prod[:, -1] = tmp.sum(axis=0) / sw_sum
if coef.ndim == 1:
return hess_prod.ravel(order="F")
else:
return hess_prod
if coef.ndim == 1:
return grad.ravel(order="F"), hessp
return grad, hessp
| LinearModelLoss.gradient_hessian_product | File-Level |
scikit-learn | 103 | sklearn/linear_model/_base.py | def fit(self, X, y, sample_weight=None):
"""
Fit linear model.
Parameters
----------
X : {array-like, sparse matrix} of shape (n_samples, n_features)
Training data.
y : array-like of shape (n_samples,) or (n_samples, n_targets)
Target values. Will be cast to X's dtype if necessary.
sample_weight : array-like of shape (n_samples,), default=None
Individual weights for each sample.
.. versionadded:: 0.17
parameter *sample_weight* support to LinearRegression.
Returns
-------
self : object
Fitted Estimator.
"""
| /usr/src/app/target_test_cases/failed_tests_LinearRegression.fit.txt | def fit(self, X, y, sample_weight=None):
"""
Fit linear model.
Parameters
----------
X : {array-like, sparse matrix} of shape (n_samples, n_features)
Training data.
y : array-like of shape (n_samples,) or (n_samples, n_targets)
Target values. Will be cast to X's dtype if necessary.
sample_weight : array-like of shape (n_samples,), default=None
Individual weights for each sample.
.. versionadded:: 0.17
parameter *sample_weight* support to LinearRegression.
Returns
-------
self : object
Fitted Estimator.
"""
n_jobs_ = self.n_jobs
accept_sparse = False if self.positive else ["csr", "csc", "coo"]
X, y = validate_data(
self,
X,
y,
accept_sparse=accept_sparse,
y_numeric=True,
multi_output=True,
force_writeable=True,
)
has_sw = sample_weight is not None
if has_sw:
sample_weight = _check_sample_weight(
sample_weight, X, dtype=X.dtype, ensure_non_negative=True
)
# Note that neither _rescale_data nor the rest of the fit method of
# LinearRegression can benefit from in-place operations when X is a
# sparse matrix. Therefore, let's not copy X when it is sparse.
copy_X_in_preprocess_data = self.copy_X and not sp.issparse(X)
X, y, X_offset, y_offset, X_scale = _preprocess_data(
X,
y,
fit_intercept=self.fit_intercept,
copy=copy_X_in_preprocess_data,
sample_weight=sample_weight,
)
if has_sw:
# Sample weight can be implemented via a simple rescaling. Note
# that we safely do inplace rescaling when _preprocess_data has
# already made a copy if requested.
X, y, sample_weight_sqrt = _rescale_data(
X, y, sample_weight, inplace=copy_X_in_preprocess_data
)
if self.positive:
if y.ndim < 2:
self.coef_ = optimize.nnls(X, y)[0]
else:
# scipy.optimize.nnls cannot handle y with shape (M, K)
outs = Parallel(n_jobs=n_jobs_)(
delayed(optimize.nnls)(X, y[:, j]) for j in range(y.shape[1])
)
self.coef_ = np.vstack([out[0] for out in outs])
elif sp.issparse(X):
X_offset_scale = X_offset / X_scale
if has_sw:
def matvec(b):
return X.dot(b) - sample_weight_sqrt * b.dot(X_offset_scale)
def rmatvec(b):
return X.T.dot(b) - X_offset_scale * b.dot(sample_weight_sqrt)
else:
def matvec(b):
return X.dot(b) - b.dot(X_offset_scale)
def rmatvec(b):
return X.T.dot(b) - X_offset_scale * b.sum()
X_centered = sparse.linalg.LinearOperator(
shape=X.shape, matvec=matvec, rmatvec=rmatvec
)
if y.ndim < 2:
self.coef_ = lsqr(X_centered, y)[0]
else:
# sparse_lstsq cannot handle y with shape (M, K)
outs = Parallel(n_jobs=n_jobs_)(
delayed(lsqr)(X_centered, y[:, j].ravel())
for j in range(y.shape[1])
)
self.coef_ = np.vstack([out[0] for out in outs])
else:
self.coef_, _, self.rank_, self.singular_ = linalg.lstsq(X, y)
self.coef_ = self.coef_.T
if y.ndim == 1:
self.coef_ = np.ravel(self.coef_)
self._set_intercept(X_offset, y_offset, X_scale)
return self
| LinearRegression.fit | Repo-Level |
scikit-learn | 114 | sklearn/cluster/_kmeans.py | def fit(self, X, y=None, sample_weight=None):
"""Compute the centroids on X by chunking it into mini-batches.
Parameters
----------
X : {array-like, sparse matrix} of shape (n_samples, n_features)
Training instances to cluster. It must be noted that the data
will be converted to C ordering, which will cause a memory copy
if the given data is not C-contiguous.
If a sparse matrix is passed, a copy will be made if it's not in
CSR format.
y : Ignored
Not used, present here for API consistency by convention.
sample_weight : array-like of shape (n_samples,), default=None
The weights for each observation in X. If None, all observations
are assigned equal weight. `sample_weight` is not used during
initialization if `init` is a callable or a user provided array.
.. versionadded:: 0.20
Returns
-------
self : object
Fitted estimator.
"""
| /usr/src/app/target_test_cases/failed_tests_MiniBatchKMeans.fit.txt | def fit(self, X, y=None, sample_weight=None):
"""Compute the centroids on X by chunking it into mini-batches.
Parameters
----------
X : {array-like, sparse matrix} of shape (n_samples, n_features)
Training instances to cluster. It must be noted that the data
will be converted to C ordering, which will cause a memory copy
if the given data is not C-contiguous.
If a sparse matrix is passed, a copy will be made if it's not in
CSR format.
y : Ignored
Not used, present here for API consistency by convention.
sample_weight : array-like of shape (n_samples,), default=None
The weights for each observation in X. If None, all observations
are assigned equal weight. `sample_weight` is not used during
initialization if `init` is a callable or a user provided array.
.. versionadded:: 0.20
Returns
-------
self : object
Fitted estimator.
"""
X = validate_data(
self,
X,
accept_sparse="csr",
dtype=[np.float64, np.float32],
order="C",
accept_large_sparse=False,
)
self._check_params_vs_input(X)
random_state = check_random_state(self.random_state)
sample_weight = _check_sample_weight(sample_weight, X, dtype=X.dtype)
self._n_threads = _openmp_effective_n_threads()
n_samples, n_features = X.shape
# Validate init array
init = self.init
if _is_arraylike_not_scalar(init):
init = check_array(init, dtype=X.dtype, copy=True, order="C")
self._validate_center_shape(X, init)
self._check_mkl_vcomp(X, self._batch_size)
# precompute squared norms of data points
x_squared_norms = row_norms(X, squared=True)
# Validation set for the init
validation_indices = random_state.randint(0, n_samples, self._init_size)
X_valid = X[validation_indices]
sample_weight_valid = sample_weight[validation_indices]
# perform several inits with random subsets
best_inertia = None
for init_idx in range(self._n_init):
if self.verbose:
print(f"Init {init_idx + 1}/{self._n_init} with method {init}")
# Initialize the centers using only a fraction of the data as we
# expect n_samples to be very large when using MiniBatchKMeans.
cluster_centers = self._init_centroids(
X,
x_squared_norms=x_squared_norms,
init=init,
random_state=random_state,
init_size=self._init_size,
sample_weight=sample_weight,
)
# Compute inertia on a validation set.
_, inertia = _labels_inertia_threadpool_limit(
X_valid,
sample_weight_valid,
cluster_centers,
n_threads=self._n_threads,
)
if self.verbose:
print(f"Inertia for init {init_idx + 1}/{self._n_init}: {inertia}")
if best_inertia is None or inertia < best_inertia:
init_centers = cluster_centers
best_inertia = inertia
centers = init_centers
centers_new = np.empty_like(centers)
# Initialize counts
self._counts = np.zeros(self.n_clusters, dtype=X.dtype)
# Attributes to monitor the convergence
self._ewa_inertia = None
self._ewa_inertia_min = None
self._no_improvement = 0
# Initialize number of samples seen since last reassignment
self._n_since_last_reassign = 0
n_steps = (self.max_iter * n_samples) // self._batch_size
with _get_threadpool_controller().limit(limits=1, user_api="blas"):
# Perform the iterative optimization until convergence
for i in range(n_steps):
# Sample a minibatch from the full dataset
minibatch_indices = random_state.randint(0, n_samples, self._batch_size)
# Perform the actual update step on the minibatch data
batch_inertia = _mini_batch_step(
X=X[minibatch_indices],
sample_weight=sample_weight[minibatch_indices],
centers=centers,
centers_new=centers_new,
weight_sums=self._counts,
random_state=random_state,
random_reassign=self._random_reassign(),
reassignment_ratio=self.reassignment_ratio,
verbose=self.verbose,
n_threads=self._n_threads,
)
if self._tol > 0.0:
centers_squared_diff = np.sum((centers_new - centers) ** 2)
else:
centers_squared_diff = 0
centers, centers_new = centers_new, centers
# Monitor convergence and do early stopping if necessary
if self._mini_batch_convergence(
i, n_steps, n_samples, centers_squared_diff, batch_inertia
):
break
self.cluster_centers_ = centers
self._n_features_out = self.cluster_centers_.shape[0]
self.n_steps_ = i + 1
self.n_iter_ = int(np.ceil(((i + 1) * self._batch_size) / n_samples))
if self.compute_labels:
self.labels_, self.inertia_ = _labels_inertia_threadpool_limit(
X,
sample_weight,
self.cluster_centers_,
n_threads=self._n_threads,
)
else:
self.inertia_ = self._ewa_inertia * n_samples
return self
| MiniBatchKMeans.fit | Repo-Level |
scikit-learn | 115 | sklearn/cluster/_kmeans.py | def partial_fit(self, X, y=None, sample_weight=None):
"""Update k means estimate on a single mini-batch X.
Parameters
----------
X : {array-like, sparse matrix} of shape (n_samples, n_features)
Training instances to cluster. It must be noted that the data
will be converted to C ordering, which will cause a memory copy
if the given data is not C-contiguous.
If a sparse matrix is passed, a copy will be made if it's not in
CSR format.
y : Ignored
Not used, present here for API consistency by convention.
sample_weight : array-like of shape (n_samples,), default=None
The weights for each observation in X. If None, all observations
are assigned equal weight. `sample_weight` is not used during
initialization if `init` is a callable or a user provided array.
Returns
-------
self : object
Return updated estimator.
"""
| /usr/src/app/target_test_cases/failed_tests_MiniBatchKMeans.partial_fit.txt | def partial_fit(self, X, y=None, sample_weight=None):
"""Update k means estimate on a single mini-batch X.
Parameters
----------
X : {array-like, sparse matrix} of shape (n_samples, n_features)
Training instances to cluster. It must be noted that the data
will be converted to C ordering, which will cause a memory copy
if the given data is not C-contiguous.
If a sparse matrix is passed, a copy will be made if it's not in
CSR format.
y : Ignored
Not used, present here for API consistency by convention.
sample_weight : array-like of shape (n_samples,), default=None
The weights for each observation in X. If None, all observations
are assigned equal weight. `sample_weight` is not used during
initialization if `init` is a callable or a user provided array.
Returns
-------
self : object
Return updated estimator.
"""
has_centers = hasattr(self, "cluster_centers_")
X = validate_data(
self,
X,
accept_sparse="csr",
dtype=[np.float64, np.float32],
order="C",
accept_large_sparse=False,
reset=not has_centers,
)
self._random_state = getattr(
self, "_random_state", check_random_state(self.random_state)
)
sample_weight = _check_sample_weight(sample_weight, X, dtype=X.dtype)
self.n_steps_ = getattr(self, "n_steps_", 0)
# precompute squared norms of data points
x_squared_norms = row_norms(X, squared=True)
if not has_centers:
# this instance has not been fitted yet (fit or partial_fit)
self._check_params_vs_input(X)
self._n_threads = _openmp_effective_n_threads()
# Validate init array
init = self.init
if _is_arraylike_not_scalar(init):
init = check_array(init, dtype=X.dtype, copy=True, order="C")
self._validate_center_shape(X, init)
self._check_mkl_vcomp(X, X.shape[0])
# initialize the cluster centers
self.cluster_centers_ = self._init_centroids(
X,
x_squared_norms=x_squared_norms,
init=init,
random_state=self._random_state,
init_size=self._init_size,
sample_weight=sample_weight,
)
# Initialize counts
self._counts = np.zeros(self.n_clusters, dtype=X.dtype)
# Initialize number of samples seen since last reassignment
self._n_since_last_reassign = 0
with _get_threadpool_controller().limit(limits=1, user_api="blas"):
_mini_batch_step(
X,
sample_weight=sample_weight,
centers=self.cluster_centers_,
centers_new=self.cluster_centers_,
weight_sums=self._counts,
random_state=self._random_state,
random_reassign=self._random_reassign(),
reassignment_ratio=self.reassignment_ratio,
verbose=self.verbose,
n_threads=self._n_threads,
)
if self.compute_labels:
self.labels_, self.inertia_ = _labels_inertia_threadpool_limit(
X,
sample_weight,
self.cluster_centers_,
n_threads=self._n_threads,
)
self.n_steps_ += 1
self._n_features_out = self.cluster_centers_.shape[0]
return self
| MiniBatchKMeans.partial_fit | Repo-Level |
scikit-learn | 120 | sklearn/linear_model/_coordinate_descent.py | def fit(self, X, y):
"""Fit MultiTaskElasticNet model with coordinate descent.
Parameters
----------
X : ndarray of shape (n_samples, n_features)
Data.
y : ndarray of shape (n_samples, n_targets)
Target. Will be cast to X's dtype if necessary.
Returns
-------
self : object
Fitted estimator.
Notes
-----
Coordinate descent is an algorithm that considers each column of
data at a time hence it will automatically convert the X input
as a Fortran-contiguous numpy array if necessary.
To avoid memory re-allocation it is advised to allocate the
initial data in memory directly using that format.
"""
| /usr/src/app/target_test_cases/failed_tests_MultiTaskElasticNet.fit.txt | def fit(self, X, y):
"""Fit MultiTaskElasticNet model with coordinate descent.
Parameters
----------
X : ndarray of shape (n_samples, n_features)
Data.
y : ndarray of shape (n_samples, n_targets)
Target. Will be cast to X's dtype if necessary.
Returns
-------
self : object
Fitted estimator.
Notes
-----
Coordinate descent is an algorithm that considers each column of
data at a time hence it will automatically convert the X input
as a Fortran-contiguous numpy array if necessary.
To avoid memory re-allocation it is advised to allocate the
initial data in memory directly using that format.
"""
# Need to validate separately here.
# We can't pass multi_output=True because that would allow y to be csr.
check_X_params = dict(
dtype=[np.float64, np.float32],
order="F",
force_writeable=True,
copy=self.copy_X and self.fit_intercept,
)
check_y_params = dict(ensure_2d=False, order="F")
X, y = validate_data(
self, X, y, validate_separately=(check_X_params, check_y_params)
)
check_consistent_length(X, y)
y = y.astype(X.dtype)
if hasattr(self, "l1_ratio"):
model_str = "ElasticNet"
else:
model_str = "Lasso"
if y.ndim == 1:
raise ValueError("For mono-task outputs, use %s" % model_str)
n_samples, n_features = X.shape
n_targets = y.shape[1]
X, y, X_offset, y_offset, X_scale = _preprocess_data(
X, y, fit_intercept=self.fit_intercept, copy=False
)
if not self.warm_start or not hasattr(self, "coef_"):
self.coef_ = np.zeros(
(n_targets, n_features), dtype=X.dtype.type, order="F"
)
l1_reg = self.alpha * self.l1_ratio * n_samples
l2_reg = self.alpha * (1.0 - self.l1_ratio) * n_samples
self.coef_ = np.asfortranarray(self.coef_) # coef contiguous in memory
random = self.selection == "random"
(
self.coef_,
self.dual_gap_,
self.eps_,
self.n_iter_,
) = cd_fast.enet_coordinate_descent_multi_task(
self.coef_,
l1_reg,
l2_reg,
X,
y,
self.max_iter,
self.tol,
check_random_state(self.random_state),
random,
)
# account for different objective scaling here and in cd_fast
self.dual_gap_ /= n_samples
self._set_intercept(X_offset, y_offset, X_scale)
# return self for chaining fit and predict calls
return self
| MultiTaskElasticNet.fit | Repo-Level |
scikit-learn | 123 | sklearn/neighbors/_nca.py | def fit(self, X, y):
"""Fit the model according to the given training data.
Parameters
----------
X : array-like of shape (n_samples, n_features)
The training samples.
y : array-like of shape (n_samples,)
The corresponding training labels.
Returns
-------
self : object
Fitted estimator.
"""
| /usr/src/app/target_test_cases/failed_tests_NeighborhoodComponentsAnalysis.fit.txt | def fit(self, X, y):
"""Fit the model according to the given training data.
Parameters
----------
X : array-like of shape (n_samples, n_features)
The training samples.
y : array-like of shape (n_samples,)
The corresponding training labels.
Returns
-------
self : object
Fitted estimator.
"""
# Validate the inputs X and y, and converts y to numerical classes.
X, y = validate_data(self, X, y, ensure_min_samples=2)
check_classification_targets(y)
y = LabelEncoder().fit_transform(y)
# Check the preferred dimensionality of the projected space
if self.n_components is not None and self.n_components > X.shape[1]:
raise ValueError(
"The preferred dimensionality of the "
f"projected space `n_components` ({self.n_components}) cannot "
"be greater than the given data "
f"dimensionality ({X.shape[1]})!"
)
# If warm_start is enabled, check that the inputs are consistent
if (
self.warm_start
and hasattr(self, "components_")
and self.components_.shape[1] != X.shape[1]
):
raise ValueError(
f"The new inputs dimensionality ({X.shape[1]}) does not "
"match the input dimensionality of the "
f"previously learned transformation ({self.components_.shape[1]})."
)
# Check how the linear transformation should be initialized
init = self.init
if isinstance(init, np.ndarray):
init = check_array(init)
# Assert that init.shape[1] = X.shape[1]
if init.shape[1] != X.shape[1]:
raise ValueError(
f"The input dimensionality ({init.shape[1]}) of the given "
"linear transformation `init` must match the "
f"dimensionality of the given inputs `X` ({X.shape[1]})."
)
# Assert that init.shape[0] <= init.shape[1]
if init.shape[0] > init.shape[1]:
raise ValueError(
f"The output dimensionality ({init.shape[0]}) of the given "
"linear transformation `init` cannot be "
f"greater than its input dimensionality ({init.shape[1]})."
)
# Assert that self.n_components = init.shape[0]
if self.n_components is not None and self.n_components != init.shape[0]:
raise ValueError(
"The preferred dimensionality of the "
f"projected space `n_components` ({self.n_components}) does"
" not match the output dimensionality of "
"the given linear transformation "
f"`init` ({init.shape[0]})!"
)
# Initialize the random generator
self.random_state_ = check_random_state(self.random_state)
# Measure the total training time
t_train = time.time()
# Compute a mask that stays fixed during optimization:
same_class_mask = y[:, np.newaxis] == y[np.newaxis, :]
# (n_samples, n_samples)
# Initialize the transformation
transformation = np.ravel(self._initialize(X, y, init))
# Create a dictionary of parameters to be passed to the optimizer
disp = self.verbose - 2 if self.verbose > 1 else -1
optimizer_params = {
"method": "L-BFGS-B",
"fun": self._loss_grad_lbfgs,
"args": (X, same_class_mask, -1.0),
"jac": True,
"x0": transformation,
"tol": self.tol,
"options": dict(maxiter=self.max_iter, disp=disp),
"callback": self._callback,
}
# Call the optimizer
self.n_iter_ = 0
opt_result = minimize(**optimizer_params)
# Reshape the solution found by the optimizer
self.components_ = opt_result.x.reshape(-1, X.shape[1])
# Stop timer
t_train = time.time() - t_train
if self.verbose:
cls_name = self.__class__.__name__
# Warn the user if the algorithm did not converge
if not opt_result.success:
warn(
"[{}] NCA did not converge: {}".format(
cls_name, opt_result.message
),
ConvergenceWarning,
)
print("[{}] Training took {:8.2f}s.".format(cls_name, t_train))
return self
| NeighborhoodComponentsAnalysis.fit | Repo-Level |
scikit-learn | 131 | sklearn/multiclass.py | def partial_fit(self, X, y, classes=None, **partial_fit_params):
"""Partially fit underlying estimators.
Should be used when memory is inefficient to train all data. Chunks
of data can be passed in several iteration, where the first call
should have an array of all target variables.
Parameters
----------
X : {array-like, sparse matrix) of shape (n_samples, n_features)
Data.
y : array-like of shape (n_samples,)
Multi-class targets.
classes : array, shape (n_classes, )
Classes across all calls to partial_fit.
Can be obtained via `np.unique(y_all)`, where y_all is the
target vector of the entire dataset.
This argument is only required in the first call of partial_fit
and can be omitted in the subsequent calls.
**partial_fit_params : dict
Parameters passed to the ``estimator.partial_fit`` method of each
sub-estimator.
.. versionadded:: 1.4
Only available if `enable_metadata_routing=True`. See
:ref:`Metadata Routing User Guide <metadata_routing>` for more
details.
Returns
-------
self : object
The partially fitted underlying estimator.
"""
| /usr/src/app/target_test_cases/failed_tests_OneVsOneClassifier.partial_fit.txt | def partial_fit(self, X, y, classes=None, **partial_fit_params):
"""Partially fit underlying estimators.
Should be used when memory is inefficient to train all data. Chunks
of data can be passed in several iteration, where the first call
should have an array of all target variables.
Parameters
----------
X : {array-like, sparse matrix) of shape (n_samples, n_features)
Data.
y : array-like of shape (n_samples,)
Multi-class targets.
classes : array, shape (n_classes, )
Classes across all calls to partial_fit.
Can be obtained via `np.unique(y_all)`, where y_all is the
target vector of the entire dataset.
This argument is only required in the first call of partial_fit
and can be omitted in the subsequent calls.
**partial_fit_params : dict
Parameters passed to the ``estimator.partial_fit`` method of each
sub-estimator.
.. versionadded:: 1.4
Only available if `enable_metadata_routing=True`. See
:ref:`Metadata Routing User Guide <metadata_routing>` for more
details.
Returns
-------
self : object
The partially fitted underlying estimator.
"""
_raise_for_params(partial_fit_params, self, "partial_fit")
routed_params = process_routing(
self,
"partial_fit",
**partial_fit_params,
)
first_call = _check_partial_fit_first_call(self, classes)
if first_call:
self.estimators_ = [
clone(self.estimator)
for _ in range(self.n_classes_ * (self.n_classes_ - 1) // 2)
]
if len(np.setdiff1d(y, self.classes_)):
raise ValueError(
"Mini-batch contains {0} while it must be subset of {1}".format(
np.unique(y), self.classes_
)
)
X, y = validate_data(
self,
X,
y,
accept_sparse=["csr", "csc"],
ensure_all_finite=False,
reset=first_call,
)
check_classification_targets(y)
combinations = itertools.combinations(range(self.n_classes_), 2)
self.estimators_ = Parallel(n_jobs=self.n_jobs)(
delayed(_partial_fit_ovo_binary)(
estimator,
X,
y,
self.classes_[i],
self.classes_[j],
partial_fit_params=routed_params.estimator.partial_fit,
)
for estimator, (i, j) in zip(self.estimators_, (combinations))
)
self.pairwise_indices_ = None
if hasattr(self.estimators_[0], "n_features_in_"):
self.n_features_in_ = self.estimators_[0].n_features_in_
return self
| OneVsOneClassifier.partial_fit | Repo-Level |
scikit-learn | 133 | sklearn/multiclass.py | def partial_fit(self, X, y, classes=None, **partial_fit_params):
"""Partially fit underlying estimators.
Should be used when memory is inefficient to train all data.
Chunks of data can be passed in several iterations.
Parameters
----------
X : {array-like, sparse matrix} of shape (n_samples, n_features)
Data.
y : {array-like, sparse matrix} of shape (n_samples,) or (n_samples, n_classes)
Multi-class targets. An indicator matrix turns on multilabel
classification.
classes : array, shape (n_classes, )
Classes across all calls to partial_fit.
Can be obtained via `np.unique(y_all)`, where y_all is the
target vector of the entire dataset.
This argument is only required in the first call of partial_fit
and can be omitted in the subsequent calls.
**partial_fit_params : dict
Parameters passed to the ``estimator.partial_fit`` method of each
sub-estimator.
.. versionadded:: 1.4
Only available if `enable_metadata_routing=True`. See
:ref:`Metadata Routing User Guide <metadata_routing>` for more
details.
Returns
-------
self : object
Instance of partially fitted estimator.
"""
| /usr/src/app/target_test_cases/failed_tests_OneVsRestClassifier.partial_fit.txt | def partial_fit(self, X, y, classes=None, **partial_fit_params):
"""Partially fit underlying estimators.
Should be used when memory is inefficient to train all data.
Chunks of data can be passed in several iterations.
Parameters
----------
X : {array-like, sparse matrix} of shape (n_samples, n_features)
Data.
y : {array-like, sparse matrix} of shape (n_samples,) or (n_samples, n_classes)
Multi-class targets. An indicator matrix turns on multilabel
classification.
classes : array, shape (n_classes, )
Classes across all calls to partial_fit.
Can be obtained via `np.unique(y_all)`, where y_all is the
target vector of the entire dataset.
This argument is only required in the first call of partial_fit
and can be omitted in the subsequent calls.
**partial_fit_params : dict
Parameters passed to the ``estimator.partial_fit`` method of each
sub-estimator.
.. versionadded:: 1.4
Only available if `enable_metadata_routing=True`. See
:ref:`Metadata Routing User Guide <metadata_routing>` for more
details.
Returns
-------
self : object
Instance of partially fitted estimator.
"""
_raise_for_params(partial_fit_params, self, "partial_fit")
routed_params = process_routing(
self,
"partial_fit",
**partial_fit_params,
)
if _check_partial_fit_first_call(self, classes):
self.estimators_ = [clone(self.estimator) for _ in range(self.n_classes_)]
# A sparse LabelBinarizer, with sparse_output=True, has been
# shown to outperform or match a dense label binarizer in all
# cases and has also resulted in less or equal memory consumption
# in the fit_ovr function overall.
self.label_binarizer_ = LabelBinarizer(sparse_output=True)
self.label_binarizer_.fit(self.classes_)
if len(np.setdiff1d(y, self.classes_)):
raise ValueError(
(
"Mini-batch contains {0} while classes " + "must be subset of {1}"
).format(np.unique(y), self.classes_)
)
Y = self.label_binarizer_.transform(y)
Y = Y.tocsc()
columns = (col.toarray().ravel() for col in Y.T)
self.estimators_ = Parallel(n_jobs=self.n_jobs)(
delayed(_partial_fit_binary)(
estimator,
X,
column,
partial_fit_params=routed_params.estimator.partial_fit,
)
for estimator, column in zip(self.estimators_, columns)
)
if hasattr(self.estimators_[0], "n_features_in_"):
self.n_features_in_ = self.estimators_[0].n_features_in_
return self
| OneVsRestClassifier.partial_fit | Repo-Level |
Can Language Models Replace Programmers? REPOCOD Says 'Not Yet'
Large language models (LLMs) have achieved high accuracy, i.e., more than 90 pass@1, in solving Python coding problems in HumanEval and MBPP. Thus, a natural question is, whether LLMs achieve comparable code completion performance compared to human developers? Unfortunately, one cannot answer this question using existing manual crafted or simple (e.g., single-line) code generation benchmarks, since such tasks fail to represent real-world software development tasks. In addition, existing benchmarks often use poor code correctness metrics, providing misleading conclusions.
To address these challenges, we create REPOCOD, a code generation benchmark with 980 problems collected from 11 popular real-world projects, with more than 58% of them requiring file-level or repository-level context information. In addition, REPOCOD has the longest average canonical solution length (331.6 tokens) and the highest average cyclomatic complexity (9.00) compared to existing benchmarks. Each task in REPOCOD includes 313.5 developer-written test cases on average for better correctness evaluation. In our evaluations on ten LLMs, none of the models achieves more than 30 pass@1 on REPOCOD, disclosing the necessity of building stronger LLMs that can help developers in real-world software development.
For easier evaluation, we sample 200 of the hardest problems in REPOCOD to create REPOCOD-Lite, using the product of the prompt length and canonical solution length (in terms of line count) as an indicator of difficulty. From the three categories of questions—self-contained, file-level, and repo-level—we select 66, 67, and 67 samples respectively in descending order of the scores.
For more details on data collection and evaluation results, please refer to our arxiv preprint.
Examples code for downloading repositories, preparing repository snapshot, and running test cases for evaluation are propived at code
Check our Leaderboard for preliminary results using SOTA LLMs with RAG.
Usage
from datasets import load_dataset
data = load_dataset('lt-asset/REPOCOD_Lite')
print(data)
DatasetDict({
train: Dataset({
features: ['repository', 'repo_id', 'target_module_path', 'prompt', 'relavent_test_path', 'full_function', 'function_name'],
num_rows: 200
})
})
Data Fields
- repository: the source repository of the current sample
- repo_id: the unique index of the sample in the corresponding source repository
- target_module_path: the file path containing the current sample relative to the root of the source repository
- prompt: the developer provided function signature and docstring
- relavent_test_path: the path to the relevant test cases
- full_function: the canonical solution of the current sample
- function_name: the name of the target function (current sample)
Example
"repository": "seaborn", # collected from seaborn
"repo_id": "6", # first sample from seaborn
"target_module_path": "seaborn/_base.py", # the target function is in this path
"prompt": " def iter_data(
self, grouping_vars=None, *,
reverse=False, from_comp_data=False,
by_facet=True, allow_empty=False, dropna=True,
):
'''Generator for getting subsets of data defined by semantic variables.
Also injects "col" and "row" into grouping semantics.
Parameters
----------
grouping_vars : string or list of strings
Semantic variables that define the subsets of data.
reverse : bool
If True, reverse the order of iteration.
from_comp_data : bool
If True, use self.comp_data rather than self.plot_data
by_facet : bool
If True, add faceting variables to the set of grouping variables.
allow_empty : bool
If True, yield an empty dataframe when no observations exist for
combinations of grouping variables.
dropna : bool
If True, remove rows with missing data.
Yields
------
sub_vars : dict
Keys are semantic names, values are the level of that semantic.
sub_data : :class:`pandas.DataFrame`
Subset of ``plot_data`` for this combination of semantic values.
'''", # the function signature and docstring for the target function
"relevant_test_path": "/usr/src/app/target_test_cases/failed_tests_Continuous.label.txt", # Path to relevant tests for the function
"full_function": " def iter_data(
self, grouping_vars=None, *,
reverse=False, from_comp_data=False,
by_facet=True, allow_empty=False, dropna=True,
):
'''Generator for getting subsets of data defined by semantic variables.
Also injects "col" and "row" into grouping semantics.
Parameters
----------
grouping_vars : string or list of strings
Semantic variables that define the subsets of data.
reverse : bool
If True, reverse the order of iteration.
from_comp_data : bool
If True, use self.comp_data rather than self.plot_data
by_facet : bool
If True, add faceting variables to the set of grouping variables.
allow_empty : bool
If True, yield an empty dataframe when no observations exist for
combinations of grouping variables.
dropna : bool
If True, remove rows with missing data.
Yields
------
sub_vars : dict
Keys are semantic names, values are the level of that semantic.
sub_data : :class:`pandas.DataFrame`
Subset of ``plot_data`` for this combination of semantic values.
'''
if grouping_vars is None:
grouping_vars = []
...", # the full snippet of the target function, including the function signature and docstring for the target function
"function_name": "VectorPlotter.iter_data" # The name of the target function
Citation
@misc{liang2024repocod,
title={Can Language Models Replace Programmers? REPOCOD Says 'Not Yet'},
author={Shanchao Liang and Yiran Hu and Nan Jiang and Lin Tan},
year={2024},
eprint={2410.21647},
archivePrefix={arXiv},
primaryClass={cs.SE},
url={https://arxiv.org/abs/2410.21647},
}
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