SURE-tools 2.1.53__py3-none-any.whl → 2.1.55__py3-none-any.whl

SURE/PerturbFlow.py

@@ -62,7 +62,7 @@ class PerturbFlow(nn.Module):
                  supervised_mode: bool = False,
                  z_dim: int = 10,
                  z_dist: Literal['normal','studentt','laplacian','cauchy','gumbel'] = 'normal',
-                 loss_func: Literal['negbinomial','poisson','multinomial','bernoulli'] = 'negbinomial',
+                 loss_func: Literal['negbinomial','poisson','multinomial','bernoulli','gamma-poisson'] = 'negbinomial',
                  inverse_dispersion: float = 10.0,
                  use_zeroinflate: bool = False,
                  hidden_layers: list = [300],
@@ -225,15 +225,36 @@ class PerturbFlow(nn.Module):
                         )
                     )
             
-        self.decoder_concentrate = MLP(
-                [self.latent_dim] + self.decoder_hidden_layers + [self.input_size],
-                activation=activate_fct,
-                output_activation=None,
-                post_layer_fct=post_layer_fct,
-                post_act_fct=post_act_fct,
-                allow_broadcast=self.allow_broadcast,
-                use_cuda=self.use_cuda,
-            )
+        if self.loss_func == 'gamma-poisson':
+            self.decoder_concentrate = MLP(
+                    [self.latent_dim] + self.decoder_hidden_layers + [[self.input_size,self.input_size]],
+                    activation=activate_fct,
+                    output_activation=[Exp,Exp],
+                    post_layer_fct=post_layer_fct,
+                    post_act_fct=post_act_fct,
+                    allow_broadcast=self.allow_broadcast,
+                    use_cuda=self.use_cuda,
+                )
+            #self.encoder_concentrate = MLP(
+            #        [self.latent_dim] + self.decoder_hidden_layers + [[self.input_size,self.input_size]],
+            #        activation=activate_fct,
+            #        output_activation=[Exp,Exp],
+            #        post_layer_fct=post_layer_fct,
+            #        post_act_fct=post_act_fct,
+            #        allow_broadcast=self.allow_broadcast,
+            #        use_cuda=self.use_cuda,
+            #    )
+            self.encoder_concentrate = self.decoder_concentrate
+        else:
+            self.decoder_concentrate = MLP(
+                    [self.latent_dim] + self.decoder_hidden_layers + [self.input_size],
+                    activation=activate_fct,
+                    output_activation=None,
+                    post_layer_fct=post_layer_fct,
+                    post_act_fct=post_act_fct,
+                    allow_broadcast=self.allow_broadcast,
+                    use_cuda=self.use_cuda,
+                )
 
         if self.latent_dist == 'studentt':
             self.codebook = MLP(
@@ -352,13 +373,17 @@ class PerturbFlow(nn.Module):
                 zns = pyro.sample('zn', dist.Gumbel(zn_loc, zn_scale).to_event(1))
 
             zs = zns
-            concentrate = self.decoder_concentrate(zs)
-            if self.loss_func == 'bernoulli':
-                log_theta = concentrate
+            if self.loss_func == 'gamma-poisson':
+                con_alpha,con_beta = self.decoder_concentrate(zs)
+                rate = pyro.sample('cs', dist.Gamma(con_alpha, con_beta).to_event(1))
             else:
-                rate = concentrate.exp()
-                if self.loss_func != 'poisson':
-                    theta = dist.DirichletMultinomial(total_count=1, concentration=rate).mean
+                concentrate = self.decoder_concentrate(zs)
+                if self.loss_func == 'bernoulli':
+                    log_theta = concentrate
+                else:
+                    rate = concentrate.exp()
+                    if self.loss_func != 'poisson':
+                        theta = dist.DirichletMultinomial(total_count=1, concentration=rate).mean
 
             if self.loss_func == 'negbinomial':
                 if self.use_zeroinflate:
@@ -370,6 +395,11 @@ class PerturbFlow(nn.Module):
                     pyro.sample('x', dist.ZeroInflatedDistribution(dist.Poisson(rate=rate),gate_logits=gate_logits).to_event(1), obs=xs.round())
                 else:
                     pyro.sample('x', dist.Poisson(rate=rate).to_event(1), obs=xs.round())
+            elif self.loss_func == 'gamma-poisson':
+                if self.use_zeroinflate:
+                    pyro.sample('x', dist.ZeroInflatedDistribution(dist.Poisson(rate=rate),gate_logits=gate_logits).to_event(1), obs=xs.round())
+                else:
+                    pyro.sample('x', dist.Poisson(rate=rate).to_event(1), obs=xs.round())
             elif self.loss_func == 'multinomial':
                 pyro.sample('x', dist.Multinomial(total_count=total_count, probs=theta), obs=xs)
             elif self.loss_func == 'bernoulli':
@@ -386,6 +416,10 @@ class PerturbFlow(nn.Module):
 
             alpha = self.encoder_n(zns)
             ns = pyro.sample('n', dist.OneHotCategorical(logits=alpha))
+            
+            if self.loss_func == 'gamma-poisson':
+                con_alpha,con_beta = self.encoder_concentrate(zns)
+                rate = pyro.sample('cs', dist.Gamma(con_alpha, con_beta).to_event(1))
 
     def model2(self, xs, us=None):
         pyro.module('PerturbFlow', self)
@@ -443,13 +477,17 @@ class PerturbFlow(nn.Module):
             else:
                 zs = zns
 
-            concentrate = self.decoder_concentrate(zs)
-            if self.loss_func == 'bernoulli':
-                log_theta = concentrate
+            if self.loss_func == 'gamma-poisson':
+                con_alpha,con_beta = self.decoder_concentrate(zs)
+                rate = pyro.sample('cs', dist.Gamma(con_alpha, con_beta).to_event(1))
             else:
-                rate = concentrate.exp()
-                if self.loss_func != 'poisson':
-                    theta = dist.DirichletMultinomial(total_count=1, concentration=rate).mean
+                concentrate = self.decoder_concentrate(zs)
+                if self.loss_func == 'bernoulli':
+                    log_theta = concentrate
+                else:
+                    rate = concentrate.exp()
+                    if self.loss_func != 'poisson':
+                        theta = dist.DirichletMultinomial(total_count=1, concentration=rate).mean
 
             if self.loss_func == 'negbinomial':
                 if self.use_zeroinflate:
@@ -461,6 +499,11 @@ class PerturbFlow(nn.Module):
                     pyro.sample('x', dist.ZeroInflatedDistribution(dist.Poisson(rate=rate),gate_logits=gate_logits).to_event(1), obs=xs.round())
                 else:
                     pyro.sample('x', dist.Poisson(rate=rate).to_event(1), obs=xs.round())
+            elif self.loss_func == 'gamma-poisson':
+                if self.use_zeroinflate:
+                    pyro.sample('x', dist.ZeroInflatedDistribution(dist.Poisson(rate=rate),gate_logits=gate_logits).to_event(1), obs=xs.round())
+                else:
+                    pyro.sample('x', dist.Poisson(rate=rate).to_event(1), obs=xs.round())
             elif self.loss_func == 'multinomial':
                 pyro.sample('x', dist.Multinomial(total_count=total_count, probs=theta), obs=xs)
             elif self.loss_func == 'bernoulli':
@@ -477,6 +520,10 @@ class PerturbFlow(nn.Module):
 
             alpha = self.encoder_n(zns)
             ns = pyro.sample('n', dist.OneHotCategorical(logits=alpha))
+            
+            if self.loss_func == 'gamma-poisson':
+                con_alpha,con_beta = self.encoder_concentrate(zns)
+                rate = pyro.sample('cs', dist.Gamma(con_alpha, con_beta).to_event(1))
 
     def model3(self, xs, ys, embeds=None):
         pyro.module('PerturbFlow', self)
@@ -540,13 +587,17 @@ class PerturbFlow(nn.Module):
 
             zs = zns
 
-            concentrate = self.decoder_concentrate(zs)
-            if self.loss_func == 'bernoulli':
-                log_theta = concentrate
+            if self.loss_func == 'gamma-poisson':
+                con_alpha,con_beta = self.decoder_concentrate(zs)
+                rate = pyro.sample('cs', dist.Gamma(con_alpha, con_beta).to_event(1))
             else:
-                rate = concentrate.exp()
-                if self.loss_func != 'poisson':
-                    theta = dist.DirichletMultinomial(total_count=1, concentration=rate).mean
+                concentrate = self.decoder_concentrate(zs)
+                if self.loss_func == 'bernoulli':
+                    log_theta = concentrate
+                else:
+                    rate = concentrate.exp()
+                    if self.loss_func != 'poisson':
+                        theta = dist.DirichletMultinomial(total_count=1, concentration=rate).mean
 
             if self.loss_func == 'negbinomial':
                 if self.use_zeroinflate:
@@ -558,6 +609,11 @@ class PerturbFlow(nn.Module):
                     pyro.sample('x', dist.ZeroInflatedDistribution(dist.Poisson(rate=rate),gate_logits=gate_logits).to_event(1), obs=xs.round())
                 else:
                     pyro.sample('x', dist.Poisson(rate=rate).to_event(1), obs=xs.round())
+            elif self.loss_func == 'gamma-poisson':
+                if self.use_zeroinflate:
+                    pyro.sample('x', dist.ZeroInflatedDistribution(dist.Poisson(rate=rate),gate_logits=gate_logits).to_event(1), obs=xs.round())
+                else:
+                    pyro.sample('x', dist.Poisson(rate=rate).to_event(1), obs=xs.round())
             elif self.loss_func == 'multinomial':
                 pyro.sample('x', dist.Multinomial(total_count=total_count, probs=theta), obs=xs)
             elif self.loss_func == 'bernoulli':
@@ -572,6 +628,12 @@ class PerturbFlow(nn.Module):
                 #zn_loc, zn_scale = self.encoder_zn(xs)
                 zn_loc, zn_scale = self._get_basal_embedding(xs)
                 zns = pyro.sample('zn', dist.Normal(zn_loc, zn_scale).to_event(1))
+            else:
+                zns = embeds
+                
+            if self.loss_func == 'gamma-poisson':
+                con_alpha,con_beta = self.encoder_concentrate(zns)
+                rate = pyro.sample('cs', dist.Gamma(con_alpha, con_beta).to_event(1))
 
     def model4(self, xs, us, ys, embeds=None):
         pyro.module('PerturbFlow', self)
@@ -645,13 +707,17 @@ class PerturbFlow(nn.Module):
             else:
                 zs = zns
 
-            concentrate = self.decoder_concentrate(zs)
-            if self.loss_func == 'bernoulli':
-                log_theta = concentrate
+            if self.loss_func == 'gamma-poisson':
+                con_alpha,con_beta = self.decoder_concentrate(zs)
+                rate = pyro.sample('cs', dist.Gamma(con_alpha, con_beta).to_event(1))
             else:
-                rate = concentrate.exp()
-                if self.loss_func != 'poisson':
-                    theta = dist.DirichletMultinomial(total_count=1, concentration=rate).mean
+                concentrate = self.decoder_concentrate(zs)
+                if self.loss_func == 'bernoulli':
+                    log_theta = concentrate
+                else:
+                    rate = concentrate.exp()
+                    if self.loss_func != 'poisson':
+                        theta = dist.DirichletMultinomial(total_count=1, concentration=rate).mean
 
             if self.loss_func == 'negbinomial':
                 if self.use_zeroinflate:
@@ -663,6 +729,11 @@ class PerturbFlow(nn.Module):
                     pyro.sample('x', dist.ZeroInflatedDistribution(dist.Poisson(rate=rate),gate_logits=gate_logits).to_event(1), obs=xs.round())
                 else:
                     pyro.sample('x', dist.Poisson(rate=rate).to_event(1), obs=xs.round())
+            elif self.loss_func == 'gamma-poisson':
+                if self.use_zeroinflate:
+                    pyro.sample('x', dist.ZeroInflatedDistribution(dist.Poisson(rate=rate),gate_logits=gate_logits).to_event(1), obs=xs.round())
+                else:
+                    pyro.sample('x', dist.Poisson(rate=rate).to_event(1), obs=xs.round())
             elif self.loss_func == 'multinomial':
                 pyro.sample('x', dist.Multinomial(total_count=total_count, probs=theta), obs=xs)
             elif self.loss_func == 'bernoulli':
@@ -677,6 +748,12 @@ class PerturbFlow(nn.Module):
                 #zn_loc, zn_scale = self.encoder_zn(xs)
                 zn_loc, zn_scale = self._get_basal_embedding(xs)
                 zns = pyro.sample('zn', dist.Normal(zn_loc, zn_scale).to_event(1))
+            else:
+                zns = embeds
+            
+            if self.loss_func == 'gamma-poisson':
+                con_alpha,con_beta = self.encoder_concentrate(zns)
+                rate = pyro.sample('cs', dist.Gamma(con_alpha, con_beta).to_event(1))
 
     def _total_effects(self, zns, us):
         zus = None
@@ -855,7 +932,12 @@ class PerturbFlow(nn.Module):
         return tensor_to_numpy(ms)
     
     def _get_expression_response(self, delta_zs):
-        return self.decoder_concentrate(delta_zs)
+        if self.loss_func == 'gamma-poisson':
+            alpha,beta = self.encoder_concentrate(delta_zs)
+            xs = dist.Gamma(alpha,beta).to_event(1).mean
+        else:
+            xs = self.decoder_concentrate(delta_zs)
+        return xs
     
     def get_expression_response(self, 
                              delta_zs, 
@@ -878,7 +960,7 @@ class PerturbFlow(nn.Module):
         R = np.concatenate(R)
         return R
     
-    def _count(self,concentrate):
+    def _count(self,concentrate, library_size=None):
         if self.loss_func == 'bernoulli':
             #counts = self.sigmoid(concentrate)
             counts = dist.Bernoulli(logits=concentrate).to_event(1).mean
@@ -888,10 +970,17 @@ class PerturbFlow(nn.Module):
             theta = dist.DirichletMultinomial(total_count=1, concentration=rate).mean
             
             total_count = pyro.param("inverse_dispersion")
-            counts = dist.NegativeBinomial(total_count=total_count, probs=theta).to_event(1)
+            counts = dist.NegativeBinomial(total_count=total_count, probs=theta).to_event(1).mean
         elif self.loss_func == 'poisson':
             rate = concentrate.exp()
-            counts = dist.Poisson(rate=rate).to_event(1)
+            counts = dist.Poisson(rate=rate).to_event(1).mean
+        elif self.loss_func == 'gamma-poisson':
+            counts = dist.Poisson(rate=concentrate).to_event(1).mean
+        elif self.loss_func == 'multinomial':
+            rate = concentrate.exp()
+            theta = dist.DirichletMultinomial(total_count=1, concentration=rate).mean
+            counts = dist.Multinomial(total_count=int(1e8), probs=theta).mean
+            counts = counts * library_size
         return counts
     
     def _count_sample(self,concentrate):
@@ -903,22 +992,35 @@ class PerturbFlow(nn.Module):
             counts = dist.Poisson(rate=counts).to_event(1).sample()
         return counts
     
-    def get_counts(self, zs, 
+    def get_counts(self, zs, library_sizes = None,
                         batch_size: int = 1024, 
                         use_sampler: bool = False):
 
         zs = convert_to_tensor(zs, device=self.get_device())
-        dataset = CustomDataset(zs)
+        ls = zs 
+        
+        if self.loss_func == 'multinomial':
+            assert library_sizes!=None, 'Library sizes are required for multinomial!'
+            
+            if type(library_sizes) == list:
+                library_sizes = np.array(library_sizes).view(-1,1)
+            elif len(library_sizes.shape)==1:
+                library_sizes = library_sizes.view(-1,1)
+            ls = convert_to_tensor(library_sizes, device=self.get_device)
+            
+        dataset = CustomDataset2(zs,ls)
         dataloader = DataLoader(dataset, batch_size=batch_size, shuffle=False)
         
         E = []
         with tqdm(total=len(dataloader), desc='', unit='batch') as pbar:
-            for Z_batch, _ in dataloader:
+            for Z_batch, L_batch, _ in dataloader:
+                if self.loss_func != 'multinomial':
+                    L_batch = None
                 concentrate = self._get_expression_response(Z_batch)
                 if use_sampler:
                     counts = self._count_sample(concentrate)
                 else:
-                    counts = self._count(concentrate)
+                    counts = self._count(concentrate, L_batch)
                 E.append(tensor_to_numpy(counts))
                 pbar.update(1)
         

{sure_tools-2.1.53.dist-info → sure_tools-2.1.55.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.53
+Version: 2.1.55
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.53.dist-info → sure_tools-2.1.55.dist-info}/RECORD

@@ -1,4 +1,4 @@
-SURE/PerturbFlow.py,sha256=JS0TguFFewNU6lwFLI0rtJsPUkDcHWFpN2USuBB1dL8,53827
+SURE/PerturbFlow.py,sha256=0-hD4NFKd0zvh_kBOCeh9irAjJ5TuyD7djKJKDCZv6I,59523
 SURE/SURE.py,sha256=ko15a9BhvUqHviogZ0YCdTQjM-2zqkO9OvHZSpnGbg0,47458
 SURE/__init__.py,sha256=NOJI_K-eCqPgStXXvgl3wIEMp6d8saMTDYLJ7Ga9MqE,293
 SURE/assembly/__init__.py,sha256=jxZLURXKPzXe21LhrZ09LgZr33iqdjlQy4oSEj5gR2Q,172
@@ -17,9 +17,9 @@ SURE/utils/__init__.py,sha256=YF5jB-PAHJQ40OlcZ7BCZbsN2q1JKuPT6EppilRXQqM,680
 SURE/utils/custom_mlp.py,sha256=C0EXLGYsWkUQpEL49AyBFPSzKmasb2hdvtnJfxbF-YU,9282
 SURE/utils/queue.py,sha256=E_5PA5EWcBoGAZj8BkKQnkCK0p4C-4-xcTPqdIXaPXU,1892
 SURE/utils/utils.py,sha256=IUHjDDtYaAYllCWsZyIzqQwaLul6fJRvHRH4vIYcR-c,8462
-sure_tools-2.1.53.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
-sure_tools-2.1.53.dist-info/METADATA,sha256=wNhmVGxxzIeL38Nb2VXIAJC6zX_jK3SgFqnqCd56ajA,2678
-sure_tools-2.1.53.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-sure_tools-2.1.53.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
-sure_tools-2.1.53.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
-sure_tools-2.1.53.dist-info/RECORD,,
+sure_tools-2.1.55.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
+sure_tools-2.1.55.dist-info/METADATA,sha256=GmbQukuqLtfvGrGd0VCuzY5S396a2I-M08_hYkB9vB8,2678
+sure_tools-2.1.55.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+sure_tools-2.1.55.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
+sure_tools-2.1.55.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
+sure_tools-2.1.55.dist-info/RECORD,,