dwelltime: add standard errors based on hessian approximation

changelog.md

@@ -17,6 +17,7 @@
 * Added parameter `titles` to customize title of each subplot in [`Kymo.plot_with_channels()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.kymo.Kymo.html#lumicks.pylake.kymo.Kymo.plot_with_channels).
 * Added [`KymoTrack.sample_from_channel()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.kymotracker.kymotrack.KymoTrack.html#lumicks.pylake.kymotracker.kymotrack.KymoTrack.sample_from_channel) to downsample channel data to the time points of a kymotrack.
 * Added support for file names with spaces in [`lk.download_from_doi()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.download_from_doi.html#lumicks.pylake.download_from_doi).
+* Added `err_amplitudes` and `err_lifetimes` to [`DwelltimeModel`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.DwelltimeModel.html). These return asymptotic standard errors and should only be used for well identified models.
 
 ## v1.5.3 | 2024-10-29
 

lumicks/pylake/fitting/parameters.py

@@ -43,6 +43,7 @@ def __init__(
         fixed=False,
         shared=False,
         unit=None,
+        stderr=None,
     ):
         """Model parameter
 
@@ -90,7 +91,7 @@ def __init__(
         from the data. See also: :meth:`~lumicks.pylake.FdFit.profile_likelihood()`.
         """
 
-        self.stderr = None
+        self.stderr = stderr
         """Standard error of this parameter.
 
         Standard errors are calculated after fitting the model. These asymptotic errors are based

lumicks/pylake/fitting/profile_likelihood.py

@@ -624,17 +624,27 @@ def chi2(self):
     def p(self):
         return self.parameters[:, self.profile_info.profiled_parameter_index]
 
-    def plot(self, *, significance_level=None, **kwargs):
+    def plot(self, *, significance_level=None, std_err=None, **kwargs):
         """Plot profile likelihood
 
         Parameters
         ----------
         significance_level : float, optional
             Desired significance level  (resulting in a 100 * (1 - alpha)% confidence interval) to
             plot. Default is the significance level specified when the profile was generated.
+        std_err : float | None
+            If provided, also make a quadratic plot based on a standard error.
         """
         import matplotlib.pyplot as plt
 
+        if std_err:
+            x = np.arange(-3 * std_err, 3 * std_err, 0.1 * std_err)
+            plt.plot(
+                self.p[np.argmin(self.chi2)] + x,
+                self.profile_info.minimum_chi2 + x**2 / (2 * std_err**2),
+                "k--",
+            )
+
         dash_length = 5
         plt.plot(self.p, self.chi2, **kwargs)
 

lumicks/pylake/kymotracker/tests/test_kymotrack.py

@@ -173,7 +173,7 @@ def test_kymotrackgroup_remove(blank_kymo, remove, remaining):
     tracks = KymoTrackGroup(src_tracks)
     for track in remove:
         tracks.remove(src_tracks[track])
-    for track, should_be_present in zip(src_tracks, remaining):
+    for track in src_tracks:
         if remaining:
             assert track in tracks
         else:
@@ -300,9 +300,10 @@ def test_kymotrack_merge():
     time_idx = ([1, 2, 3, 4, 5], [6, 7, 8], [6, 7, 8], [1, 2, 3])
     pos_idx = ([1, 1, 1, 3, 3], [4, 4, 4], [9, 9, 9], [10, 10, 10])
 
-    make_tracks = lambda: KymoTrackGroup(
-        [KymoTrack(t, p, kymo, "green", 0) for t, p in zip(time_idx, pos_idx)]
-    )
+    def make_tracks():
+        return KymoTrackGroup(
+            [KymoTrack(t, p, kymo, "green", 0) for t, p in zip(time_idx, pos_idx)]
+        )
 
     # connect first two
     tracks = make_tracks()
@@ -873,6 +874,7 @@ def test_fit_binding_times_nonzero(blank_kymo, blank_kymo_track_args):
         np.testing.assert_equal(dwelltime_model.dwelltimes, [4, 4, 4, 4])
         np.testing.assert_equal(dwelltime_model._observation_limits[0], 4)
         np.testing.assert_allclose(dwelltime_model.lifetimes[0], [0.4])
+        np.testing.assert_allclose(dwelltime_model.err_lifetimes[0], 0.199994, rtol=1e-5)
 
 
 def test_fit_binding_times_empty():
@@ -1174,10 +1176,11 @@ def make_coordinates(length, divisor):
 
     good_tracks = KymoTrackGroup([track for j, track in enumerate(tracks) if j in (0, 3, 4)])
 
-    warning_string = lambda n_discarded: (
-        f"{n_discarded} tracks were shorter than the specified min_length "
-        "and discarded from the analysis."
-    )
+    def warning_string(n_discarded):
+        return (
+            f"{n_discarded} tracks were shorter than the specified min_length and discarded "
+            f"from the analysis."
+        )
 
     # test algorithms with default min_length
     with pytest.warns(RuntimeWarning, match=warning_string(3)):

lumicks/pylake/population/dwelltime.py

@@ -8,6 +8,7 @@
 
 from lumicks.pylake.fitting.parameters import Params, Parameter
 from lumicks.pylake.fitting.profile_likelihood import ProfileLikelihood1D
+from lumicks.pylake.fitting.detail.derivative_manipulation import numerical_jacobian
 
 
 @dataclass(frozen=True)
@@ -98,8 +99,10 @@ def fit_func(params, lb, ub, fitted):
         )
         parameters = Params(
             **{
-                key: Parameter(param, lower_bound=lb, upper_bound=ub)
-                for key, param, (lb, ub) in zip(keys, dwelltime_model._parameters, bounds)
+                key: Parameter(param, lower_bound=lb, upper_bound=ub, stderr=std_err)
+                for key, param, (lb, ub), std_err in zip(
+                    keys, dwelltime_model._parameters, bounds, dwelltime_model._std_errs
+                )
             }
         )
 
@@ -194,7 +197,7 @@ def n_components(self):
         """Number of components in the model."""
         return self.model.n_components
 
-    def plot(self, alpha=None):
+    def plot(self, alpha=None, *, with_stderr=False, **kwargs):
         """Plot the profile likelihoods for the parameters of a model.
 
         Confidence interval is indicated by the region where the profile crosses the chi squared
@@ -206,16 +209,26 @@ def plot(self, alpha=None):
             Significance level. Confidence intervals are calculated as 100 * (1 - alpha)%. The
             default value of `None` results in using the significance level applied when
             profiling (default: 0.05).
+        with_stderr : bool
+            Also show bounds based on standard errors.
         """
         import matplotlib.pyplot as plt
 
+        std_errs = self.model._std_errs[~np.isnan(self.model._std_errs)]
         if self.n_components == 1:
-            next(iter(self.profiles.values())).plot(significance_level=alpha)
+            next(iter(self.profiles.values())).plot(
+                significance_level=alpha,
+                std_err=std_errs[0] if with_stderr else None,
+            )
         else:
             plot_idx = np.reshape(np.arange(1, len(self.profiles) + 1), (-1, 2)).T.flatten()
-            for idx, profile in zip(plot_idx, self.profiles.values()):
+            for par_idx, (idx, profile) in enumerate(zip(plot_idx, self.profiles.values())):
                 plt.subplot(self.n_components, 2, idx)
-                profile.plot(significance_level=alpha)
+                profile.plot(
+                    significance_level=alpha,
+                    std_err=std_errs[par_idx] if with_stderr else None,
+                    **kwargs,
+                )
 
 
 @dataclass(frozen=True)
@@ -332,7 +345,7 @@ def _sample(optimized, iterations) -> np.ndarray:
             )
             sample, min_obs, max_obs = to_resample[choices, :].T
 
-            result, _ = _exponential_mle_optimize(
+            result, _, _ = _exponential_mle_optimize(
                 optimized.n_components,
                 sample,
                 min_obs,
@@ -575,7 +588,7 @@ def __init__(
             if value is not None
         }
 
-        self._parameters, self._log_likelihood = _exponential_mle_optimize(
+        self._parameters, self._log_likelihood, self._std_errs = _exponential_mle_optimize(
             n_components,
             dwelltimes,
             min_observation_time,
@@ -619,6 +632,34 @@ def lifetimes(self):
         """Lifetime parameter (in time units) of each model component."""
         return self._parameters[self.n_components :]
 
+    @property
+    def err_amplitudes(self):
+        """Asymptotic standard error estimate on the model amplitudes.
+
+        Returns an asymptotic standard error on the amplitude parameters. These error estimates
+        are only reliable for estimates where a lot of data is available and the model does
+        not suffer from identifiability issues. To verify that these conditions are met, please
+        use either :meth:`DwelltimeModel.profile_likelihood()` method or
+        :meth:`DwelltimeModel.calculate_bootstrap()`.
+
+        Note that `np.nan` will be returned in case the parameter was either not estimated or no
+        error could be obtained."""
+        return self._std_errs[: self.n_components]
+
+    @property
+    def err_lifetimes(self):
+        """Asymptotic standard error estimate on the model lifetimes.
+
+        Returns an asymptotic standard error on the amplitude parameters. These error estimates
+        are only reliable for estimates where a lot of data is available and the model does
+        not suffer from identifiability issues. To verify that these conditions are met, please
+        use either :meth:`DwelltimeModel.profile_likelihood()` method or
+        :meth:`DwelltimeModel.calculate_bootstrap()`.
+
+        Note that `np.nan` will be returned in case the parameter was either not estimated or no
+        error could be obtained."""
+        return self._std_errs[self.n_components :]
+
     @property
     def rate_constants(self):
         """First order rate constant (units of per time) of each model component."""
@@ -1191,7 +1232,7 @@ def _handle_amplitude_constraint(
         else ()
     )
 
-    return fitted_param_mask, constraints, params
+    return fitted_param_mask, constraints, params, num_free_amps
 
 
 def _exponential_mle_bounds(n_components, min_observation_time, max_observation_time):
@@ -1207,6 +1248,24 @@ def _exponential_mle_bounds(n_components, min_observation_time, max_observation_
     )
 
 
+def _calculate_std_errs(jac_fun, constraints, num_free_amps, current_params, fitted_param_mask):
+    hessian_approx = numerical_jacobian(jac_fun, current_params[fitted_param_mask], dx=1e-6)
+
+    if constraints:
+        from scipy.linalg import null_space
+
+        # When we have a constraint, we should enforce it. We do this by projecting the Hessian
+        # onto the null space of the constraint and inverting it there. This null space only
+        # includes directions in which the constraint does not change (i.e. is fulfilled).
+        constraint = np.zeros((1, hessian_approx.shape[0]))
+        constraint[0, :num_free_amps] = -1
+        n = null_space(constraint)
+
+        return np.sqrt(np.diag(np.abs(n @ np.linalg.pinv(n.T @ hessian_approx @ n) @ n.T)))
+
+    return np.sqrt(np.diag(np.abs(np.linalg.pinv(hessian_approx))))
+
+
 def _exponential_mle_optimize(
     n_components,
     t,
@@ -1273,7 +1332,7 @@ def _exponential_mle_optimize(
 
     bounds = _exponential_mle_bounds(n_components, min_observation_time, max_observation_time)
 
-    fitted_param_mask, constraints, initial_guess = _handle_amplitude_constraint(
+    fitted_param_mask, constraints, initial_guess, num_free_amps = _handle_amplitude_constraint(
         n_components, initial_guess, fixed_param_mask
     )
 
@@ -1291,10 +1350,11 @@ def cost_fun(params):
         )
 
     def jac_fun(params):
-        current_params[fitted_param_mask] = params
+        jac_params = current_params.copy()
+        jac_params[fitted_param_mask] = params
 
         gradient = _exponential_mixture_log_likelihood_jacobian(
-            current_params,
+            jac_params,
             t=t,
             t_min=min_observation_time,
             t_max=max_observation_time,
@@ -1305,7 +1365,7 @@ def jac_fun(params):
 
     # Nothing to fit, return!
     if np.sum(fitted_param_mask) == 0:
-        return initial_guess, -cost_fun([])
+        return initial_guess, -cost_fun([]), np.full(initial_guess.shape, np.nan)
 
     # SLSQP is overly cautious when it comes to warning about bounds. The bound violations are
     # typically on the order of 1-2 ULP for a float32 and do not matter for our problem. Initially
@@ -1328,7 +1388,16 @@ def jac_fun(params):
 
     # output parameters as [amplitudes, lifetimes], -log_likelihood
     current_params[fitted_param_mask] = result.x
-    return current_params, -result.fun
+
+    if use_jacobian:
+        std_errs = np.full(current_params.shape, np.nan)
+        std_errs[fitted_param_mask] = _calculate_std_errs(
+            jac_fun, constraints, num_free_amps, current_params, fitted_param_mask
+        )
+    else:
+        std_errs = np.full(current_params.shape, np.nan)
+
+    return current_params, -result.fun, std_errs
 
 
 def _dwellcounts_from_statepath(statepath, exclude_ambiguous_dwells):