From 5d3386c16d0665dadd81e496306073399b16857b Mon Sep 17 00:00:00 2001
From: user <59329744+dilpath@users.noreply.github.com>
Date: Wed, 22 Jul 2026 14:44:42 +0200
Subject: [PATCH 1/2] add silu support, fix neural_nets typo

---
 doc/examples/getting_started/problem.yaml   | 2 +-
 doc/examples/how_to_dmms/problem.yaml       | 2 +-
 doc/examples/how_to_neural_ode/problem.yaml | 2 +-
 doc/examples/how_to_observable/problem.yaml | 2 +-
 doc/layers.rst                              | 3 +++
 petab_sciml/problem_utils/neural_ode.py     | 2 +-
 tests/problem_utils/test_neural_ode.py      | 6 ++++--
 7 files changed, 12 insertions(+), 7 deletions(-)

diff --git a/doc/examples/getting_started/problem.yaml b/doc/examples/getting_started/problem.yaml
index c24db02b..31ca7a55 100644
--- a/doc/examples/getting_started/problem.yaml
+++ b/doc/examples/getting_started/problem.yaml
@@ -18,7 +18,7 @@ extensions:
       - "net1_ps.hdf5"
     hybridization_files:
       - "hybridization.tsv"
-    neural_nets:
+    neural_networks:
       net1:
         location: "net1.yaml"
         static: false
diff --git a/doc/examples/how_to_dmms/problem.yaml b/doc/examples/how_to_dmms/problem.yaml
index 1ddb6987..1c56d889 100644
--- a/doc/examples/how_to_dmms/problem.yaml
+++ b/doc/examples/how_to_dmms/problem.yaml
@@ -19,7 +19,7 @@ extensions:
       - "net3_input2.hdf5"
     hybridization_files:
       - "hybridization.tsv"
-    neural_nets:
+    neural_networks:
       net3:
         location: "net3.yaml"
         static: true
diff --git a/doc/examples/how_to_neural_ode/problem.yaml b/doc/examples/how_to_neural_ode/problem.yaml
index 1804dfa6..8911f5f6 100644
--- a/doc/examples/how_to_neural_ode/problem.yaml
+++ b/doc/examples/how_to_neural_ode/problem.yaml
@@ -18,7 +18,7 @@ extensions:
       - net1_ps.hdf5
     hybridization_files:
       - hybridization.tsv
-    neural_nets:
+    neural_networks:
       net1:
         location: net1.yaml
         static: false
diff --git a/doc/examples/how_to_observable/problem.yaml b/doc/examples/how_to_observable/problem.yaml
index c24db02b..31ca7a55 100644
--- a/doc/examples/how_to_observable/problem.yaml
+++ b/doc/examples/how_to_observable/problem.yaml
@@ -18,7 +18,7 @@ extensions:
       - "net1_ps.hdf5"
     hybridization_files:
       - "hybridization.tsv"
-    neural_nets:
+    neural_networks:
       net1:
         location: "net1.yaml"
         static: false
diff --git a/doc/layers.rst b/doc/layers.rst
index d7708fb4..f52c2bef 100644
--- a/doc/layers.rst
+++ b/doc/layers.rst
@@ -176,6 +176,9 @@ Additionally, the table indicates which tools support each layer.
 | moid <https://pytorch.org/docs/stable/generated/torch.nn.fun |    |   |
 | ctional.hardsigmoid.html#torch.nn.functional.hardsigmoid>`__ |    |   |
 +--------------------------------------------------------------+----+---+
+| `silu <https://pytorch.org/docs/stable/generated/torch.nn    | ✔️ |   |
+| .functional.silu.html#torch.nn.functional.silu>`__           |    |   |
++--------------------------------------------------------------+----+---+
 | `mish <https://pytorch.org/docs/stable/generate              | ✔️ |   |
 | d/torch.nn.functional.mish.html#torch.nn.functional.mish>`__ |    |   |
 +--------------------------------------------------------------+----+---+
diff --git a/petab_sciml/problem_utils/neural_ode.py b/petab_sciml/problem_utils/neural_ode.py
index 927ae133..ded40478 100644
--- a/petab_sciml/problem_utils/neural_ode.py
+++ b/petab_sciml/problem_utils/neural_ode.py
@@ -208,7 +208,7 @@ def create_neural_ode_problem(
             "sciml": {
                 "version": "0.1.0",
                 "required": True,
-                "neural_nets": {
+                "neural_networks": {
                     network_name: {
                         "location": network_filename,
                         "pre_initialization": False,
diff --git a/tests/problem_utils/test_neural_ode.py b/tests/problem_utils/test_neural_ode.py
index c3f41832..07c07854 100644
--- a/tests/problem_utils/test_neural_ode.py
+++ b/tests/problem_utils/test_neural_ode.py
@@ -152,9 +152,11 @@ def test_create_neural_ode_problem(dir_tmp):
         assert problem["model_files"]["model"]["location"] == "model.xml"
         assert problem["measurement_files"][0] == "measurements.tsv"
 
-        assert "net1" in problem["extensions"]["sciml"]["neural_nets"]
+        assert "net1" in problem["extensions"]["sciml"]["neural_networks"]
         assert (
-            problem["extensions"]["sciml"]["neural_nets"]["net1"]["location"]
+            problem["extensions"]["sciml"]["neural_networks"]["net1"][
+                "location"
+            ]
             == "net1.yaml"
         )
         assert "array_files" in problem["extensions"]["sciml"]

From 70551c6706239542ac81eeb69166538a7dda5b45 Mon Sep 17 00:00:00 2001
From: user <59329744+dilpath@users.noreply.github.com>
Date: Thu, 23 Jul 2026 19:07:57 +0200
Subject: [PATCH 2/2] review: swish

---
 doc/layers.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/layers.rst b/doc/layers.rst
index f52c2bef..7d7c3529 100644
--- a/doc/layers.rst
+++ b/doc/layers.rst
@@ -176,8 +176,8 @@ Additionally, the table indicates which tools support each layer.
 | moid <https://pytorch.org/docs/stable/generated/torch.nn.fun |    |   |
 | ctional.hardsigmoid.html#torch.nn.functional.hardsigmoid>`__ |    |   |
 +--------------------------------------------------------------+----+---+
-| `silu <https://pytorch.org/docs/stable/generated/torch.nn    | ✔️ |   |
-| .functional.silu.html#torch.nn.functional.silu>`__           |    |   |
+| `silu (swish) <https://pytorch.org/docs/stable/generated/    | ✔️ |   |
+| torch.nn.functional.silu.html#torch.nn.functional.silu>`__   |    |   |
 +--------------------------------------------------------------+----+---+
 | `mish <https://pytorch.org/docs/stable/generate              | ✔️ |   |
 | d/torch.nn.functional.mish.html#torch.nn.functional.mish>`__ |    |   |