def __init__(self,
expect,
got,
name=None,
data=None,
P_LARGER=0.9,
regression=True,
ax=None,
alphabet=None,
expect_label=None,
got_label=None,
verbose=1):
"""Compare vectors.
Arguments:
- Specifying data for comparison two methods:
1) `expect`, `got`: two numeric one-dimensional arrays which we'd like
to compare (the argument names come for software testing). This
method requires argument `data=None`.
2) `data`: instance of `DataFrame`, expects arguments `expect` and `got`
to be column labels.
- `name`: name of this comparison.
Note:
- when plotting `expect` is the y-axis, `got` is the x-axis. This is by
convention that `expect` is the dependent variable (regression target).
TODO:
- Add an option to drop NaNs and continue comparison.
- Indicate which dimensions have the largest errors.
- Add option to allow alignment/matchings?
"""
self.name = name
if isinstance(alphabet, Alphabet):
alphabet = alphabet.tolist()
if isinstance(expect, dict) and isinstance(got, dict):
alphabet = list(expect.keys()) if alphabet is None else alphabet
assert set(got.keys()) == set(alphabet), \
'Keys differ.\n got keys = %s\n want keys = %s' % (set(got.keys()), set(alphabet))
expect = [expect[k] for k in alphabet]
got = [got[k] for k in alphabet]
if isinstance(expect, np.ndarray) and isinstance(got, np.ndarray):
assert expect.shape == got.shape, [expect.shape, got.shape]
expect = expect.flatten()
got = got.flatten()
if data is not None:
assert isinstance(expect, (int, str)), \
'expected a column name got %s' % type(expect)
assert isinstance(got, (int, str)), \
'expected a column name got %s' % type(got)
if expect_label is None:
expect_label = expect
if got_label is None:
got_label = got
expect = data[expect]
got = data[got]
else:
if expect_label is None:
expect_label = 'expect'
if got_label is None:
got_label = 'got'
expect = np.asarray(expect)
got = np.asarray(got)
data = pd.DataFrame({expect_label: expect, got_label: got})
assert expect.shape == got.shape, [expect.shape, got.shape]
[n] = expect.shape
self.expect = expect
self.got = got
self.alphabet = alphabet
self.ax = ax
self.got_label = got_label
self.expect_label = expect_label
self.n = n
self.coeff = None
self.tests = tests = []
# Check that vectors are finite.
if not np.isfinite(expect).all():
tests.append([
'expect finite',
progress(np.isfinite(expect).sum(), n), False
])
if not np.isfinite(got).all():
tests.append(
['got finite',
progress(np.isfinite(got).sum(), n), False])
ne = norm(expect)
ng = norm(got)
ok = abs(ne - ng) / ne < 0.01 if ne != 0 else True
if n > 1:
tests.append(['norms', '[%g, %g]' % (ne, ng), ok])
F = zero_retrieval(expect, got)
tests.append(['zero F1', F, F > 0.99])
if n > 1:
#self.cosine = cosine(expect, got)
#tests.append(['cosine', self.cosine, (self.cosine > 0.99999)]) # cosine similarities must be really high.
self.pearson = 1.0 if ne == ng == 0 else pearsonr(expect, got)[0]
tests.append(['pearson', self.pearson, (self.pearson > 0.99999)])
self.spearman = spearmanr(expect, got)[0]
tests.append(
['spearman', self.spearman, (self.spearman > 0.99999)])
# TODO: this check should probably take into account the scale of the data.
d = linf(expect, got)
self.max_err = d
tests.append(['Linf', d, d < 1e-8])
# same sign check (weak agreement, but useful sanity check -- especially
# for gradients)
x = expect
y = got
s = np.asarray(~((x >= 0) ^ (y >= 0)), dtype=int)
p = s.sum() * 100.0 / len(s)
tests.append(
['same-sign',
'%s%% (%s/%s)' % (p, s.sum(), len(s)), p == 100.0])
# relative error
r = relative_difference(expect, got)
r = np.max(r[np.isfinite(r)])
tests.append(['max rel err', r, r <= 0.01])
self.max_relative_error = r
self.max_rel_err = r
# TODO: suggest that if relative error is high and rescaled error is low (or
# something to do wtih regression residuals) that maybe there is a
# (hopefully) simple fix via scale/offset.
# TODO: can provide descriptive statistics for each vector
#tests.append(['range (expect)', [expect.min(), expect.max()], 2])
#tests.append(['range (got) ', [got.min(), got.max()], 2])
# regression and rescaled error only valid for n >= 2
if n >= 2:
es = abs(expect).max()
gs = abs(got).max()
if es == 0:
es = 1
if gs == 0:
gs = 1
if 0:
# rescaled error
E = expect / es
G = got / gs
R = abs(E - G)
r = np.mean(R)
tests.append(['mean rescaled error', r, r <= 1e-5])
if regression:
self.regression()
if n >= 2:
# These tests check if one of the datasets is consistently larger than the
# other. The threshold for error is based on `P_LARGER` ("percent larger").
L = ((expect - got) > 0).sum()
if L >= P_LARGER * n:
tests.append(['expect is larger', progress(L, n), 0])
L = ((got - expect) > 0).sum()
if L >= P_LARGER * n:
tests.append(['got is larger', progress(L, n), 0])
self.tests = tests
if verbose:
self.message()
def __init__(self, want, have, name=None, data=None, P_LARGER=0.9,
regression=True, ax=None, alphabet=None,
want_label=None, have_label=None, verbose=1):
"""Compare vectors.
Arguments:
- Specifying data for comparison two methods:
1) `want`, `have`: two numeric one-dimensional arrays which we'd like
to compare (the argument names come for software testing). This
method requires argument `data=None`.
2) `data`: instance of `DataFrame`, expects arguments `want` and `have`
to be column labels.
- `name`: name of this comparison.
Note:
- when plotting `want` is the y-axis, `have` is the x-axis. This is by
convention that `want` is the dependent variable (regression target).
TODO:
- Add an option to drop NaNs and continue comparison.
- Indicate which dimensions have the largest errors.
- Add option to allow alignment/matchings?
"""
self.name = name
if isinstance(alphabet, Alphabet):
alphabet = list(alphabet)
if isinstance(want, dict) and isinstance(have, dict):
alphabet = list(want.keys() | have.keys()) if alphabet is None else alphabet
#assert set(have.keys()) == set(alphabet), \
# 'Keys differ.\n have keys = %s\n want keys = %s' % (set(have.keys()), set(alphabet))
want = [want.get(k, 0) for k in alphabet]
have = [have.get(k, 0) for k in alphabet]
if isinstance(want, np.ndarray) and isinstance(have, np.ndarray):
assert alphabet is None
alphabet = Alphabet(dict(np.ndenumerate(want)).keys())
assert want.shape == have.shape, [want.shape, have.shape]
want = want.flatten()
have = have.flatten()
if data is not None:
# assert isinstance(want, (int, str)), \
# 'expected a column name have %s' % type(want)
# assert isinstance(have, (int, str)), \
# 'expected a column name have %s' % type(have)
if want_label is None: want_label = want
if have_label is None: have_label = have
want = data[want]
have = data[have]
else:
if want_label is None: want_label = 'want'
if have_label is None: have_label = 'have'
want = np.asarray(want)
have = np.asarray(have)
data = pd.DataFrame({want_label: want, have_label: have})
assert want.shape == have.shape, [want.shape, have.shape]
[n] = want.shape
self.want = want
self.have = have
self.alphabet = alphabet
self.ax = ax
self.have_label = have_label
self.want_label = want_label
self.n = n
self.coeff = None
self.tests = tests = []
# Check that vectors are finite.
if not np.isfinite(want).all():
tests.append(['want finite', progress(np.isfinite(want).sum(), n), False])
if not np.isfinite(have).all():
tests.append(['have finite', progress(np.isfinite(have).sum(), n), False])
ne = norm(want)
ng = norm(have)
ok = abs(ne-ng)/ne < 0.01 if ne != 0 else True
if n > 1:
tests.append(['norms', '[%g, %g]' % (ne, ng), ok])
#F = zero_retrieval(want, have)
#tests.append(['zero F1', F, F > 0.99])
# Correlation statistics
if n > 1:
#self.cosine = cosine(want, have)
#tests.append(['cosine', self.cosine, (self.cosine > 0.99999)]) # cosine similarities must be really high.
self.pearson = 1.0 if ne == ng == 0 else pearsonr(want, have)[0]
tests.append(['pearson', self.pearson, (self.pearson > 0.99999)])
self.spearman = spearmanr(want, have)[0]
tests.append(['spearman', self.spearman, (self.spearman > 0.99999)])
# TODO: this check should probably take into account the scale of the data.
d = linf(want, have)
self.max_err = d
tests.append(['ℓ∞', d, None])
tests.append(['ℓ₂', np.linalg.norm(want - have), None])
# same sign check (weak agreement, but useful sanity check -- especially
# for gradients)
x = want
y = have
s = np.asarray(~((x >= 0) ^ (y >= 0)), dtype=int)
p = s.sum() * 100.0 / len(s)
tests.append(['same-sign', f'{p:.2f}% ({s.sum()}/{len(s)})', p == 100.0])
# relative error
r = relative_difference(want, have)
r = np.max(r[np.isfinite(r)])
#tests.append(['max rel err', r, r <= 0.01])
self.max_relative_error = r
self.max_rel_err = r
# TODO: suggest that if relative error is high and rescaled error is low (or
# something to do wtih regression residuals) that maybe there is a
# (hopefully) simple fix via scale/offset.
# TODO: can provide descriptive statistics for each vector
#tests.append(['range (want)', [want.min(), want.max()], 2])
#tests.append(['range (have) ', [have.min(), have.max()], 2])
# regression and rescaled error only valid for n >= 2
# if n >= 2:
# es = abs(want).max()
# gs = abs(have).max()
# if es == 0:
# es = 1
# if gs == 0:
# gs = 1
# if 0:
# # rescaled error
# E = want / es
# G = have / gs
# R = abs(E - G)
# r = np.mean(R)
# tests.append(['mean rescaled error', r, r <= 1e-5])
if regression:
self.regression()
if n >= 2:
# These tests check if one of the datasets is consistently larger than the
# other. The threshold for error is based on `P_LARGER` ("percent larger").
L = ((want-have) > 0).sum()
if L >= P_LARGER * n:
tests.append(['want is larger', progress(L, n), 0])
L = ((have-want) > 0).sum()
if L >= P_LARGER * n:
tests.append(['have is larger', progress(L, n), 0])
self.tests = tests
if verbose:
self.message()