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slinderman · Jul 24, 2016 · 9e67b56 · 9e67b56
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Showing 54 changed files with 3 additions and 1 deletion.
diff --git a/.gitignore b/.gitignore
diff --git a/.gitmodules b/.gitmodules
diff --git a/README.md b/README.md
diff --git a/examples/collapsed_demo.py b/examples/collapsed_demo.py
diff --git a/examples/generate_synthetic_data.py b/examples/generate_synthetic_data.py
diff --git a/examples/gibbs_demo.py b/examples/gibbs_demo.py
diff --git a/examples/hmm_gibbs_demo.py b/examples/hmm_gibbs_demo.py
diff --git a/examples/negbinom/generate_synthetic_negbinom_data.py b/examples/negbinom/generate_synthetic_negbinom_data.py
diff --git a/examples/negbinom/gibbs_demo.py b/examples/negbinom/gibbs_demo.py
diff --git a/examples/negbinom/standard_demo.py b/examples/negbinom/standard_demo.py
diff --git a/examples/negbinom/svi_demo.py b/examples/negbinom/svi_demo.py
diff --git a/examples/negbinom/vb_demo.py b/examples/negbinom/vb_demo.py
diff --git a/examples/standard_demo.py b/examples/standard_demo.py
diff --git a/examples/svi_demo.py b/examples/svi_demo.py
diff --git a/examples/vb_demo.py b/examples/vb_demo.py
diff --git a/pyglm/__init__.py b/pyglm/__init__.py
diff --git a/pyglm/abstractions.py b/pyglm/abstractions.py
diff --git a/pyglm/distributions.py b/pyglm/distributions.py
diff --git a/pyglm/dynamic_models.py b/pyglm/dynamic_models.py
diff --git a/pyglm/internals/__init__.py b/pyglm/internals/__init__.py
diff --git a/pyglm/internals/activation.py b/pyglm/internals/activation.py
diff --git a/pyglm/internals/background.py b/pyglm/internals/background.py
diff --git a/pyglm/internals/bias.py b/pyglm/internals/bias.py
diff --git a/pyglm/internals/distributions.py b/pyglm/internals/distributions.py
diff --git a/pyglm/internals/negbin.pyx b/pyglm/internals/negbin.pyx
diff --git a/pyglm/internals/observations.py b/pyglm/internals/observations.py
diff --git a/pyglm/internals/parallel.py b/pyglm/internals/parallel.py
diff --git a/pyglm/internals/weights.py b/pyglm/internals/weights.py
@@ -573,6 +573,8 @@ def _collapsed_resample_A(self, n, P, J_prior, h_prior, J_post, h_post):
 
         for m in perm:
 
+            # TODO: Check if P[m,n] is deterministic
+
             # Compute the marginal prob with and without A[m,n]
             lps = np.zeros(2)
 

diff --git a/pyglm/models.py b/pyglm/models.py
diff --git a/pyglm/simple_models.py b/pyglm/simple_models.py
@@ -327,7 +327,7 @@ def fit(self, L1=True, cs=None):
             print " Max w: ", self.weights[n_post].max(), \
                   " Min w: ", self.weights[n_post].min()
 
-            assert abs(self.weights[n_post]).max() > 1e-6
+            # assert abs(self.weights[n_post]).max() > 1e-6
 
         print ""
 

diff --git a/pyglm/switching_models.py b/pyglm/switching_models.py
diff --git a/pyglm/utils/__init__.py b/pyglm/utils/__init__.py
diff --git a/pyglm/utils/basis.py b/pyglm/utils/basis.py
diff --git a/pyglm/utils/f2pyptr.h b/pyglm/utils/f2pyptr.h
diff --git a/pyglm/utils/fastinv.py b/pyglm/utils/fastinv.py
diff --git a/pyglm/utils/linalg.pxd b/pyglm/utils/linalg.pxd
diff --git a/pyglm/utils/linalg.pyx b/pyglm/utils/linalg.pyx
diff --git a/pyglm/utils/profiling.py b/pyglm/utils/profiling.py
diff --git a/pyglm/utils/utils.py b/pyglm/utils/utils.py
diff --git a/setup.py b/setup.py
diff --git a/test/debug_collapsed_resample_with_temp.py b/test/debug_collapsed_resample_with_temp.py
diff --git a/test/profile_gibbs.py b/test/profile_gibbs.py
diff --git a/test/profile_vb.py b/test/profile_vb.py
diff --git a/test/test_ais.py b/test/test_ais.py
diff --git a/test/test_collapsed_geweke.py b/test/test_collapsed_geweke.py
diff --git a/test/test_geweke.py b/test/test_geweke.py
diff --git a/test/test_lds.py b/test/test_lds.py
diff --git a/test/test_linalg.py b/test/test_linalg.py
diff --git a/test/test_matrix_inverse.py b/test/test_matrix_inverse.py
diff --git a/test/test_model_comparison.py b/test/test_model_comparison.py
diff --git a/test/test_single_neuron_gibbs.py b/test/test_single_neuron_gibbs.py
diff --git a/test/test_single_neuron_vb.py b/test/test_single_neuron_vb.py
diff --git a/test/test_synapses.py b/test/test_synapses.py
diff --git a/test/test_synth_recovery.py b/test/test_synth_recovery.py