dspin 1.0.2__tar.gz → 1.0.3__tar.gz

{dspin-1.0.2/dspin.egg-info → dspin-1.0.3}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.1
 Name: dspin
-Version: 1.0.2
-Summary: Python implementation of 'D-SPIN constructs gene regulatory network models from multiplexed scRNA-seq data revealing organizing principles of cellular perturbation response'
+Version: 1.0.3
+Summary: Regulatory network models from single-cell perturbation profiling
 Home-page: https://github.com/JialongJiang/DSPIN
 Author: Jialong Jiang
 Author-email: jiangjl@caltech.edu

{dspin-1.0.2 → dspin-1.0.3}/dspin/dspin_abstract.py

@@ -195,19 +195,19 @@ class AbstractDSPIN(ABC):
                   'cur_j': np.zeros((num_spin, num_spin)),
                   'cur_h': np.zeros((num_spin, num_sample)),
                   'save_path': self.save_path}
-        params.update({'lambda_l1_j': 0.01,
+        params.update({'lambda_l1_j': 0.001,
                        'lambda_l1_h': 0,
                        'lambda_l2_j': 0,
-                       'lambda_l2_h': 0.05,
+                       'lambda_l2_h': 0.005,
                        'lambda_prior_h': 0})
         params.update({'backtrack_gap': 20,
                        'backtrack_tol': 4})
 
         if method == 'maximum_likelihood':
-            params['stepsz'] = 0.1
+            params['stepsz'] = 0.2
         elif method == 'mcmc_maximum_likelihood':
             params['stepsz'] = 0.01
-            params['mcmc_samplingsz'] = 2e5
+            params['mcmc_samplingsz'] = 5e5
             params['mcmc_samplingmix'] = 1e3
             params['mcmc_samplegap'] = 1
         else:
@@ -249,7 +249,7 @@ class AbstractDSPIN(ABC):
 
         if method == 'auto':
             if example_list is not None:
-                if len(example_list) > 10:
+                if len(example_list) > 30:
                     method = 'pseudo_likelihood'
             else:
                 samp_list = np.unique(self.adata.obs[sample_col_name])
@@ -300,7 +300,7 @@ class AbstractDSPIN(ABC):
                 unique_sample_batch = unique_sample_batch.loc[self.samp_list]
                 sample_batch_dict = unique_sample_batch['batch'].to_dict()
         
-        self._relative_responses = compute_relative_responses(self._responses, self.samp_list, sample_to_control_dict, sample_batch_dict)
+            self._relative_responses = compute_relative_responses(self._responses, self.samp_list, sample_to_control_dict, sample_batch_dict)
 
 
 class GeneDSPIN(AbstractDSPIN):

{dspin-1.0.2 → dspin-1.0.3/dspin.egg-info}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.1
 Name: dspin
-Version: 1.0.2
-Summary: Python implementation of 'D-SPIN constructs gene regulatory network models from multiplexed scRNA-seq data revealing organizing principles of cellular perturbation response'
+Version: 1.0.3
+Summary: Regulatory network models from single-cell perturbation profiling
 Home-page: https://github.com/JialongJiang/DSPIN
 Author: Jialong Jiang
 Author-email: jiangjl@caltech.edu

{dspin-1.0.2 → dspin-1.0.3}/setup.py

@@ -21,7 +21,7 @@ install_requires = [
 # ]
 
 # Managing your version (adjust accordingly)
-version = "1.0.2"  # You can manage versioning in a more sophisticated way if needed
+version = "1.0.3"  # You can manage versioning in a more sophisticated way if needed
 
 # Long description (usually a README file)
 readme = open("README_PyPI.md").read()  # Adjust the file name if necessary
@@ -29,7 +29,7 @@ readme = open("README_PyPI.md").read()  # Adjust the file name if necessary
 setup(
     name="dspin",
     version=version,
-    description="Python implementation of 'D-SPIN constructs gene regulatory network models from multiplexed scRNA-seq data revealing organizing principles of cellular perturbation response'",
+    description="Regulatory network models from single-cell perturbation profiling",
     author="Jialong Jiang",
     author_email="jiangjl@caltech.edu",
     packages=find_packages(),