Fix calculation of fit weights

Author: nkanazawa1989

qiskit_experiments/curve_analysis/curve_analysis.py

@@ -316,20 +316,30 @@ def _run_curve_fit(
 
         valid_uncertainty = np.all(np.isfinite(curve_data.y_err))
 
+        model_weights = {}
+        if valid_uncertainty:
+            for model in models:
+                sub_yerr = curve_data.get_subset_of(model._name).y_err
+                if len(sub_yerr) == 0:
+                    continue
+                nonzero_yerr = np.where(np.isclose(sub_yerr, 0.0), np.finfo(float).eps, sub_yerr)
+                raw_weights = 1 / nonzero_yerr
+                # Remove outlier. When all sample values are the same with sample average,
+                # or sampling error is zero with shot-weighted average,
+                # some yerr values might be very close to zero, yielding significant weights.
+                # With such outlier, the fit doesn't sense residual of other data points.
+                maximum_weight = np.percentile(raw_weights, 90)
+                model_weights[model._name] = np.clip(raw_weights, 0.0, maximum_weight)
+
         # Objective function for minimize. This computes composite residuals of sub models.
         def _objective(_params):
             ys = []
             for model in models:
                 sub_data = curve_data.get_subset_of(model._name)
-                with np.errstate(divide="ignore"):
-                    # Ignore numpy runtime warning.
-                    # Zero y_err point introduces infinite weight,
-                    # but this should be managed by LMFIT.
-                    weights = 1.0 / sub_data.y_err if valid_uncertainty else None
                 yi = model._residual(
                     params=_params,
                     data=sub_data.y,
-                    weights=weights,
+                    weights=model_weights.get(model._name, None),
                     x=sub_data.x,
                 )
                 ys.append(yi)

releasenotes/notes/fix-curve-fit-weights-fb43d3aa5ed1c91c.yaml

@@ -0,0 +1,9 @@
+---
+fixes:
+  - |
+    Fix calculation of weight for curve fitting. Previously the weights of data points to obtain
+    the residual of fit curve were computed by the inverse of the error bars of y data. 
+    This may yield significant weights on certain data points when their error bar is small or zero,
+    and this can cause the local overfit to these data points. 
+    To avoid this edge case of small error bars, computed weights are now clipped at 90 percentile. 
+    This update might slightly change the outcome of fit.

test/curve_analysis/test_baseclass.py

@@ -440,6 +440,49 @@ def test_end_to_end_parallel_analysis(self):
         self.assertAlmostEqual(taus[0].value.nominal_value, tau1, delta=0.1)
         self.assertAlmostEqual(taus[1].value.nominal_value, tau2, delta=0.1)
 
+    def test_end_to_end_zero_yerr(self):
+        """Integration test for an edge case of having zero y error.
+
+        When the error bar is zero, the fit weights to compute residual tend to become larger.
+        When the weight is too much significant, the result locally overfits to
+        certain data points with smaller or zero y error.
+        """
+        analysis = CurveAnalysis(models=[ExpressionModel(expr="amp * x**2", name="test")])
+        analysis.set_options(
+            data_processor=DataProcessor(input_key="counts", data_actions=[Probability("1")]),
+            result_parameters=["amp"],
+            average_method="sample",  # Use sample average to make some yerr = 0
+            plot=False,
+            p0={"amp": 0.2},
+        )
+
+        amp = 0.3
+        x = np.linspace(0, 1, 100)
+        y = amp * x**2
+
+        # Replace small y values with zero.
+        # Since mock function samples count dictionary from binomial distribution,
+        # y=0 (or 1) yield always the same count dictionary
+        # and hence y error becomes zero with sample averaging.
+        # In this case, amp = 0 may yield the best result.
+        y[0] = 0
+        y[1] = 0
+        y[2] = 0
+
+        test_data1 = self.single_sampler(x, y, seed=123)
+        test_data2 = self.single_sampler(x, y, seed=124)
+        test_data3 = self.single_sampler(x, y, seed=125)
+
+        expdata = ExperimentData(experiment=FakeExperiment())
+        expdata.add_data(test_data1.data())
+        expdata.add_data(test_data2.data())
+        expdata.add_data(test_data3.data())
+
+        result = analysis.run(expdata)
+        self.assertExperimentDone(result)
+
+        self.assertAlmostEqual(result.analysis_results("amp").value.nominal_value, amp, delta=0.1)
+
     def test_get_init_params(self):
         """Integration test for getting initial parameter from overview entry."""
 

test/library/calibration/test_ramsey_xy.py

@@ -56,7 +56,7 @@ def test_end_to_end(self, freq_shift: float):
 
         This test also checks that we can pickup frequency shifts with different signs.
         """
-        test_tol = 0.01
+        test_tol = 0.03
         abs_tol = max(1e3, abs(freq_shift) * test_tol)
 
         exp_helper = RamseyXYHelper()