From ab09e96a1fe75fb49f4e9833114d35c89ffc0b60 Mon Sep 17 00:00:00 2001
From: sebapersson <sebastian.persson1@gmail.com>
Date: Mon, 25 May 2026 12:11:26 +0100
Subject: [PATCH 1/6] Add software support page

---
 doc/format.rst           |  2 +-
 doc/index.rst            |  2 +-
 doc/introduction.rst     | 10 +++++-----
 doc/layers.rst           | 30 +++++++++++++++---------------
 doc/software_support.rst | 19 +++++++++++++++++++
 5 files changed, 41 insertions(+), 22 deletions(-)
 create mode 100644 doc/software_support.rst

diff --git a/doc/format.rst b/doc/format.rst
index 8fb6bd57..aecbaca2 100644
--- a/doc/format.rst
+++ b/doc/format.rst
@@ -125,7 +125,7 @@ keyword ``array`` in the relevant PEtab table entry.
 Semantically, assigning ``array`` is interpreted as a global assignment to an
 array variable whose potentially condition-specific values are provided in an
 array data file. Therefore, specifying ``array`` is only valid in the
-:ref:`hybridization table <_hybrid_table>` and the
+:ref:`hybridization table <hybrid_table>` and the
 :ref:`parameter Table <parameter_table>`, where assignments apply across all
 PEtab experiments.
 
diff --git a/doc/index.rst b/doc/index.rst
index 0f08e33f..84ef29d6 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -10,7 +10,7 @@ PEtab SciML - Scientific Machine Learning Format and Tooling
 
    Introduction <introduction>
    Getting Started <examples/getting_started/getting_started.ipynb>
-   trouble
+   software_support
    Contributing <_tmp/CONTRIBUTING>
 
 .. toctree::
diff --git a/doc/introduction.rst b/doc/introduction.rst
index 020b751c..550ea83f 100644
--- a/doc/introduction.rst
+++ b/doc/introduction.rst
@@ -63,10 +63,11 @@ How to read the documentation
 -----------------------------
 
 If you are new to PEtab SciML, start with the
-:doc:`Getting Started tutorial <tutorial>`. It is a prerequisite for the
-How-to guides, which cover different model scenarios (e.g., Neural ODEs, ML
-model upstream of the ODE). For a complete description of all options when
-defining a SciML problem, see the :doc:`Format specification <format>`.
+:doc:`Getting Started tutorial <examples/getting_started/getting_started>`
+It is a prerequisite for the How-to guides, which cover different model
+scenarios (e.g., Neural ODEs, ML model upstream of the ODE). For a complete
+description of all options when defining a SciML problem, see the
+:doc:`Format specification <format>`.
 
 Why a SciML data format?
 ------------------------
@@ -97,7 +98,6 @@ Getting Help with and Extending PEtab SciML
 
 If you run into problems:
 
-- Check the :doc:`Troubleshooting <trouble>` section of the documentation.
 - If you encounter unexpected behavior or a bug, please open an
   `issue <https://github.com/PEtab-dev/petab_sciml/issues/>`_ on GitHub
 
diff --git a/doc/layers.rst b/doc/layers.rst
index d7708fb4..532dfb2e 100644
--- a/doc/layers.rst
+++ b/doc/layers.rst
@@ -1,22 +1,22 @@
 .. _layers_activation:
 
-Supported Layers and Activation Functions
-=======================================================================
+Neural-network YAML format
+==========================
 
-The PEtab SciML NN model YAML format supports numerous
+The PEtab SciML neural network (NN) model YAML format supports numerous
 standard neural network layers and activation functions. Layer names and
-associated keyword arguments follow the PyTorch naming scheme. PyTorch
-is used because it is currently the most popular machine learning
-framework, and its comprehensive documentation makes it easy to look up
-details for any specific layer or activation function.
+associated keyword arguments follow the PyTorch naming scheme. PyTorch is used
+because it is currently the most popular machine learning framework, and its
+comprehensive documentation makes it easy to look up details for any specific
+layer or activation function.
 
-If support is lacking for a layer or activation function you would like
-to see, please file an issue on
+If support is lacking for a layer or activation function you would like to see,
+please file an issue on
 `GitHub <https://github.com/PEtab-dev/petab_sciml/issues>`__.
 
-The table below lists the supported and tested neural network layers
-along with links to their respective PyTorch documentation.
-Additionally, the table indicates which tools support each layer.
+The table below lists the supported and tested neural network layers along with
+links to their respective PyTorch documentation. Additionally, the table
+indicates which tools support each layer.
 
 +--------------------------------------------------------------+----+---+
 | layer                                                        | PE | A |
@@ -122,9 +122,9 @@ Additionally, the table indicates which tools support each layer.
 Supported Activation Function
 -----------------------------
 
-The table below lists the supported and tested activation functions
-along with links to their respective PyTorch documentation.
-Additionally, the table indicates which tools support each layer.
+The table below lists the supported and tested activation functions along with
+links to their respective PyTorch documentation. Additionally, the table
+indicates which tools support each layer.
 
 +--------------------------------------------------------------+----+---+
 | Function                                                     | PE | A |
diff --git a/doc/software_support.rst b/doc/software_support.rst
new file mode 100644
index 00000000..1e4ed1d2
--- /dev/null
+++ b/doc/software_support.rst
@@ -0,0 +1,19 @@
+.. _software_support:
+
+Software support
+================
+
+Tools that support importing PEtab-SciML problems for downstream tasks (e.g.
+simulation and model training), listed alphabetically are:
+
+- `AMICI <https://github.com/ICB-DCM/AMICI/>`__
+  (`Example <https://github.com/ICB-DCM/AMICI/blob/master/python/examples/example_petab/petab.ipynb>`__)
+- `PEtab.jl <https://github.com/sebapersson/PEtab.jl>`__
+  (`Example <https://sebapersson.github.io/PEtab.jl/stable/tutorials/sciml/standard_format/>`__)
+
+If your tool supports PEtab-SciML and you would like it listed here, please
+`open an issue <https://github.com/PEtab-dev/petab_sciml/issues>`__.
+
+Both AMICI and PEtab.jl support the PEtab-SciML neural-network YAML format.
+For supported layers and activation functions, see the
+:ref:`Neural-network YAML format <layers_activation>` page.

From 5b364c2d0be75f86c7befff5dd64eb92b65112e9 Mon Sep 17 00:00:00 2001
From: Sebastian Persson <46872750+sebapersson@users.noreply.github.com>
Date: Tue, 26 May 2026 07:51:55 +0100
Subject: [PATCH 2/6] Apply suggestions from code review

Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com>
---
 doc/introduction.rst     | 2 +-
 doc/layers.rst           | 2 +-
 doc/software_support.rst | 6 +++---
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/doc/introduction.rst b/doc/introduction.rst
index 550ea83f..c479d461 100644
--- a/doc/introduction.rst
+++ b/doc/introduction.rst
@@ -65,7 +65,7 @@ How to read the documentation
 If you are new to PEtab SciML, start with the
 :doc:`Getting Started tutorial <examples/getting_started/getting_started>`
 It is a prerequisite for the How-to guides, which cover different model
-scenarios (e.g., Neural ODEs, ML model upstream of the ODE). For a complete
+scenarios (e.g., Neural ODEs, or ML model upstream of the ODE). For a complete
 description of all options when defining a SciML problem, see the
 :doc:`Format specification <format>`.
 
diff --git a/doc/layers.rst b/doc/layers.rst
index 532dfb2e..82a14aa5 100644
--- a/doc/layers.rst
+++ b/doc/layers.rst
@@ -1,6 +1,6 @@
 .. _layers_activation:
 
-Neural-network YAML format
+Neural network YAML format
 ==========================
 
 The PEtab SciML neural network (NN) model YAML format supports numerous
diff --git a/doc/software_support.rst b/doc/software_support.rst
index 1e4ed1d2..e09a5d4a 100644
--- a/doc/software_support.rst
+++ b/doc/software_support.rst
@@ -6,7 +6,7 @@ Software support
 Tools that support importing PEtab-SciML problems for downstream tasks (e.g.
 simulation and model training), listed alphabetically are:
 
-- `AMICI <https://github.com/ICB-DCM/AMICI/>`__
+- `AMICI <https://github.com/AMICI-dev/AMICI>`__
   (`Example <https://github.com/ICB-DCM/AMICI/blob/master/python/examples/example_petab/petab.ipynb>`__)
 - `PEtab.jl <https://github.com/sebapersson/PEtab.jl>`__
   (`Example <https://sebapersson.github.io/PEtab.jl/stable/tutorials/sciml/standard_format/>`__)
@@ -14,6 +14,6 @@ simulation and model training), listed alphabetically are:
 If your tool supports PEtab-SciML and you would like it listed here, please
 `open an issue <https://github.com/PEtab-dev/petab_sciml/issues>`__.
 
-Both AMICI and PEtab.jl support the PEtab-SciML neural-network YAML format.
+Both AMICI and PEtab.jl support the PEtab SciML neural network YAML format.
 For supported layers and activation functions, see the
-:ref:`Neural-network YAML format <layers_activation>` page.
+:ref:`Neural network YAML format <layers>` page.

From b691e781bf350479c9eec6154ba03262d78fd3e1 Mon Sep 17 00:00:00 2001
From: sebapersson <sebastian.persson1@gmail.com>
Date: Tue, 26 May 2026 07:56:11 +0100
Subject: [PATCH 3/6] Remove trouble.rst

---
 doc/trouble.rst | 2 --
 1 file changed, 2 deletions(-)
 delete mode 100644 doc/trouble.rst

diff --git a/doc/trouble.rst b/doc/trouble.rst
deleted file mode 100644
index 4edddddf..00000000
--- a/doc/trouble.rst
+++ /dev/null
@@ -1,2 +0,0 @@
-Troubleshooting
-===============

From a6319d26499be8bacd63abdf3f3009d5967b6659 Mon Sep 17 00:00:00 2001
From: sebapersson <sebastian.persson1@gmail.com>
Date: Tue, 26 May 2026 08:03:00 +0100
Subject: [PATCH 4/6] Fix broken links

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

diff --git a/doc/software_support.rst b/doc/software_support.rst
index e09a5d4a..312416e6 100644
--- a/doc/software_support.rst
+++ b/doc/software_support.rst
@@ -9,11 +9,11 @@ simulation and model training), listed alphabetically are:
 - `AMICI <https://github.com/AMICI-dev/AMICI>`__
   (`Example <https://github.com/ICB-DCM/AMICI/blob/master/python/examples/example_petab/petab.ipynb>`__)
 - `PEtab.jl <https://github.com/sebapersson/PEtab.jl>`__
-  (`Example <https://sebapersson.github.io/PEtab.jl/stable/tutorials/sciml/standard_format/>`__)
+  (`Example <https://sebapersson.github.io/PEtab.jl/stable/tutorials/sciml/standard_format>`__)
 
 If your tool supports PEtab-SciML and you would like it listed here, please
 `open an issue <https://github.com/PEtab-dev/petab_sciml/issues>`__.
 
 Both AMICI and PEtab.jl support the PEtab SciML neural network YAML format.
 For supported layers and activation functions, see the
-:ref:`Neural network YAML format <layers>` page.
+:ref:`Neural network YAML format <layers_activation>` page.

From dc755544c818c7cf411341df5d73e075016522a5 Mon Sep 17 00:00:00 2001
From: Branwen Snelling <branwen.snelling@crick.ac.uk>
Date: Tue, 26 May 2026 10:27:48 +0100
Subject: [PATCH 5/6] update supported layers and link

---
 doc/layers.rst           | 332 +++++++++++++++++++--------------------
 doc/software_support.rst |   2 +-
 2 files changed, 167 insertions(+), 167 deletions(-)

diff --git a/doc/layers.rst b/doc/layers.rst
index 82a14aa5..ec93105e 100644
--- a/doc/layers.rst
+++ b/doc/layers.rst
@@ -18,106 +18,106 @@ The table below lists the supported and tested neural network layers along with
 links to their respective PyTorch documentation. Additionally, the table
 indicates which tools support each layer.
 
-+--------------------------------------------------------------+----+---+
-| layer                                                        | PE | A |
-|                                                              | ta | M |
-|                                                              | b. | I |
-|                                                              | jl | C |
-|                                                              |    | I |
-+==============================================================+====+===+
-| `Linear <https://pytorch.org/do                              | ✔️ |   |
-| cs/stable/generated/torch.nn.Linear.html#torch.nn.Linear>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `Bilinear <https://pytorch.org/docs/s                        | ✔️ |   |
-| table/generated/torch.nn.Bilinear.html#torch.nn.Bilinear>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `Flatten <https://pytorch.org/docs                           | ✔️ |   |
-| /stable/generated/torch.nn.Flatten.html#torch.nn.Flatten>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `Dropout <https://pytorch.org/docs                           | ✔️ |   |
-| /stable/generated/torch.nn.Dropout.html#torch.nn.Dropout>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `Dropout1d <https://pytorch.org/docs/sta                     | ✔️ |   |
-| ble/generated/torch.nn.Dropout1d.html#torch.nn.Dropout1d>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `Dropout2d <https://pytorch.org/docs/sta                     | ✔️ |   |
-| ble/generated/torch.nn.Dropout2d.html#torch.nn.Dropout2d>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `Dropout3d <https://pytorch.org/docs/sta                     | ✔️ |   |
-| ble/generated/torch.nn.Dropout3d.html#torch.nn.Dropout3d>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `AlphaDropout <https://pytorch.org/docs/stable/ge            | ✔️ |   |
-| nerated/torch.nn.AlphaDropout.html#torch.nn.AlphaDropout>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `Conv1d <https://pytorch.org/do                              | ✔️ |   |
-| cs/stable/generated/torch.nn.Conv1d.html#torch.nn.Conv1d>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `Conv2d <https://pytorch.org/do                              | ✔️ |   |
-| cs/stable/generated/torch.nn.Conv2d.html#torch.nn.Conv2d>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `Conv3d <https://pytorch.org/do                              | ✔️ |   |
-| cs/stable/generated/torch.nn.Conv3d.html#torch.nn.Conv3d>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `ConvTranspose1d <https://pytorch.org/docs/stable/generate   | ✔️ |   |
-| d/torch.nn.ConvTranspose1d.html#torch.nn.ConvTranspose1d>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `ConvTranspose2d <https://pytorch.org/docs/stable/generate   | ✔️ |   |
-| d/torch.nn.ConvTranspose2d.html#torch.nn.ConvTranspose2d>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `ConvTranspose3d <https://pytorch.org/docs/stable/generate   | ✔️ |   |
-| d/torch.nn.ConvTranspose3d.html#torch.nn.ConvTranspose3d>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `MaxPool1d <https://pytorch.org/docs/sta                     | ✔️ |   |
-| ble/generated/torch.nn.MaxPool1d.html#torch.nn.MaxPool1d>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `MaxPool2d <https://pytorch.org/docs/sta                     | ✔️ |   |
-| ble/generated/torch.nn.MaxPool2d.html#torch.nn.MaxPool2d>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `MaxPool3d <https://pytorch.org/docs/sta                     | ✔️ |   |
-| ble/generated/torch.nn.MaxPool3d.html#torch.nn.MaxPool3d>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `AvgPool1d <https://pytorch.org/docs/sta                     | ✔️ |   |
-| ble/generated/torch.nn.AvgPool1d.html#torch.nn.AvgPool1d>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `AvgPool2d <https://pytorch.org/docs/sta                     | ✔️ |   |
-| ble/generated/torch.nn.AvgPool2d.html#torch.nn.AvgPool2d>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `AvgPool3d <https://pytorch.org/docs/sta                     | ✔️ |   |
-| ble/generated/torch.nn.AvgPool3d.html#torch.nn.AvgPool3d>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `LPPool1 <https://pytorch.org/docs/s                         | ✔️ |   |
-| table/generated/torch.nn.LPPool1d.html#torch.nn.LPPool1d>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `LPPool2 <https://pytorch.org/docs/s                         | ✔️ |   |
-| table/generated/torch.nn.LPPool2d.html#torch.nn.LPPool2d>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `LPPool3 <https://pytorch.org/docs/s                         | ✔️ |   |
-| table/generated/torch.nn.LPPool3d.html#torch.nn.LPPool3d>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `Ada                                                         | ✔️ |   |
-| ptiveMaxPool1d <https://pytorch.org/docs/stable/generated/to |    |   |
-| rch.nn.AdaptiveMaxPool1d.html#torch.nn.AdaptiveMaxPool1d>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `Ada                                                         | ✔️ |   |
-| ptiveMaxPool2d <https://pytorch.org/docs/stable/generated/to |    |   |
-| rch.nn.AdaptiveMaxPool2d.html#torch.nn.AdaptiveMaxPool2d>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `Ada                                                         | ✔️ |   |
-| ptiveMaxPool3d <https://pytorch.org/docs/stable/generated/to |    |   |
-| rch.nn.AdaptiveMaxPool3d.html#torch.nn.AdaptiveMaxPool3d>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `Ada                                                         | ✔️ |   |
-| ptiveAvgPool1d <https://pytorch.org/docs/stable/generated/to |    |   |
-| rch.nn.AdaptiveAvgPool1d.html#torch.nn.AdaptiveAvgPool1d>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `Ada                                                         | ✔️ |   |
-| ptiveAvgPool2d <https://pytorch.org/docs/stable/generated/to |    |   |
-| rch.nn.AdaptiveAvgPool2d.html#torch.nn.AdaptiveAvgPool2d>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `Ada                                                         | ✔️ |   |
-| ptiveAvgPool3d <https://pytorch.org/docs/stable/generated/to |    |   |
-| rch.nn.AdaptiveAvgPool3d.html#torch.nn.AdaptiveAvgPool3d>`__ |    |   |
-+--------------------------------------------------------------+----+---+
++--------------------------------------------------------------+----+----+
+| layer                                                        | PE | A  |
+|                                                              | ta | M  |
+|                                                              | b. | I  |
+|                                                              | jl | C  |
+|                                                              |    | I  |
++==============================================================+====+====+
+| `Linear <https://pytorch.org/do                              | ✔️ | ✔️ |
+| cs/stable/generated/torch.nn.Linear.html#torch.nn.Linear>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `Bilinear <https://pytorch.org/docs/s                        | ✔️ |    |
+| table/generated/torch.nn.Bilinear.html#torch.nn.Bilinear>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `Flatten <https://pytorch.org/docs                           | ✔️ | ✔️ |
+| /stable/generated/torch.nn.Flatten.html#torch.nn.Flatten>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `Dropout <https://pytorch.org/docs                           | ✔️ |    |
+| /stable/generated/torch.nn.Dropout.html#torch.nn.Dropout>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `Dropout1d <https://pytorch.org/docs/sta                     | ✔️ |    |
+| ble/generated/torch.nn.Dropout1d.html#torch.nn.Dropout1d>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `Dropout2d <https://pytorch.org/docs/sta                     | ✔️ |    |
+| ble/generated/torch.nn.Dropout2d.html#torch.nn.Dropout2d>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `Dropout3d <https://pytorch.org/docs/sta                     | ✔️ |    |
+| ble/generated/torch.nn.Dropout3d.html#torch.nn.Dropout3d>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `AlphaDropout <https://pytorch.org/docs/stable/ge            | ✔️ |    |
+| nerated/torch.nn.AlphaDropout.html#torch.nn.AlphaDropout>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `Conv1d <https://pytorch.org/do                              | ✔️ | ✔️ |
+| cs/stable/generated/torch.nn.Conv1d.html#torch.nn.Conv1d>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `Conv2d <https://pytorch.org/do                              | ✔️ | ✔️ |
+| cs/stable/generated/torch.nn.Conv2d.html#torch.nn.Conv2d>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `Conv3d <https://pytorch.org/do                              | ✔️ | ✔️ |
+| cs/stable/generated/torch.nn.Conv3d.html#torch.nn.Conv3d>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `ConvTranspose1d <https://pytorch.org/docs/stable/generate   | ✔️ | ✔️ |
+| d/torch.nn.ConvTranspose1d.html#torch.nn.ConvTranspose1d>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `ConvTranspose2d <https://pytorch.org/docs/stable/generate   | ✔️ | ✔️ |
+| d/torch.nn.ConvTranspose2d.html#torch.nn.ConvTranspose2d>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `ConvTranspose3d <https://pytorch.org/docs/stable/generate   | ✔️ | ✔️ |
+| d/torch.nn.ConvTranspose3d.html#torch.nn.ConvTranspose3d>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `MaxPool1d <https://pytorch.org/docs/sta                     | ✔️ | ✔️ |
+| ble/generated/torch.nn.MaxPool1d.html#torch.nn.MaxPool1d>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `MaxPool2d <https://pytorch.org/docs/sta                     | ✔️ | ✔️ |
+| ble/generated/torch.nn.MaxPool2d.html#torch.nn.MaxPool2d>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `MaxPool3d <https://pytorch.org/docs/sta                     | ✔️ | ✔️ |
+| ble/generated/torch.nn.MaxPool3d.html#torch.nn.MaxPool3d>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `AvgPool1d <https://pytorch.org/docs/sta                     | ✔️ | ✔️ |
+| ble/generated/torch.nn.AvgPool1d.html#torch.nn.AvgPool1d>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `AvgPool2d <https://pytorch.org/docs/sta                     | ✔️ | ✔️ |
+| ble/generated/torch.nn.AvgPool2d.html#torch.nn.AvgPool2d>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `AvgPool3d <https://pytorch.org/docs/sta                     | ✔️ | ✔️ |
+| ble/generated/torch.nn.AvgPool3d.html#torch.nn.AvgPool3d>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `LPPool1 <https://pytorch.org/docs/s                         | ✔️ | ✔️ |
+| table/generated/torch.nn.LPPool1d.html#torch.nn.LPPool1d>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `LPPool2 <https://pytorch.org/docs/s                         | ✔️ | ✔️ |
+| table/generated/torch.nn.LPPool2d.html#torch.nn.LPPool2d>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `LPPool3 <https://pytorch.org/docs/s                         | ✔️ | ✔️ |
+| table/generated/torch.nn.LPPool3d.html#torch.nn.LPPool3d>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `Ada                                                         | ✔️ | ✔️ |
+| ptiveMaxPool1d <https://pytorch.org/docs/stable/generated/to |    |    |
+| rch.nn.AdaptiveMaxPool1d.html#torch.nn.AdaptiveMaxPool1d>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `Ada                                                         | ✔️ | ✔️ |
+| ptiveMaxPool2d <https://pytorch.org/docs/stable/generated/to |    |    |
+| rch.nn.AdaptiveMaxPool2d.html#torch.nn.AdaptiveMaxPool2d>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `Ada                                                         | ✔️ | ✔️ |
+| ptiveMaxPool3d <https://pytorch.org/docs/stable/generated/to |    |    |
+| rch.nn.AdaptiveMaxPool3d.html#torch.nn.AdaptiveMaxPool3d>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `Ada                                                         | ✔️ | ✔️ |
+| ptiveAvgPool1d <https://pytorch.org/docs/stable/generated/to |    |    |
+| rch.nn.AdaptiveAvgPool1d.html#torch.nn.AdaptiveAvgPool1d>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `Ada                                                         | ✔️ | ✔️ |
+| ptiveAvgPool2d <https://pytorch.org/docs/stable/generated/to |    |    |
+| rch.nn.AdaptiveAvgPool2d.html#torch.nn.AdaptiveAvgPool2d>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `Ada                                                         | ✔️ | ✔️ |
+| ptiveAvgPool3d <https://pytorch.org/docs/stable/generated/to |    |    |
+| rch.nn.AdaptiveAvgPool3d.html#torch.nn.AdaptiveAvgPool3d>`__ |    |    |
++--------------------------------------------------------------+----+----+
 
 Supported Activation Function
 -----------------------------
@@ -126,69 +126,69 @@ The table below lists the supported and tested activation functions along with
 links to their respective PyTorch documentation. Additionally, the table
 indicates which tools support each layer.
 
-+--------------------------------------------------------------+----+---+
-| Function                                                     | PE | A |
-|                                                              | ta | M |
-|                                                              | b. | I |
-|                                                              | jl | C |
-|                                                              |    | I |
-+==============================================================+====+===+
-| `relu <https://pytorch.org/docs/stable/generate              | ✔️ |   |
-| d/torch.nn.functional.relu.html#torch.nn.functional.relu>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `relu6 <https://pytorch.org/docs/stable/generated/           | ✔️ |   |
-| torch.nn.functional.relu6.html#torch.nn.functional.relu6>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `hardtanh <https://pytorch.org/docs/stable/generated/torch.  | ✔️ |   |
-| nn.functional.hardtanh.html#torch.nn.functional.hardtanh>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `h                                                           | ✔️ |   |
-| ardswish <https://pytorch.org/docs/stable/generated/torch.nn |    |   |
-| .functional.hardswish.html#torch.nn.functional.hardswish>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `selu <https://pytorch.org/docs/stable/generate              | ✔️ |   |
-| d/torch.nn.functional.selu.html#torch.nn.functional.selu>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `leak                                                        | ✔️ |   |
-| y_relu <https://pytorch.org/docs/stable/generated/torch.nn.f |    |   |
-| unctional.leaky_relu.html#torch.nn.functional.leaky_relu>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `gelu <https://pytorch.org/docs/stable/generate              | ✔️ |   |
-| d/torch.nn.functional.gelu.html#torch.nn.functional.gelu>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `tanh                                                        | ✔️ |   |
-| shrink <https://pytorch.org/docs/stable/generated/torch.nn.f |    |   |
-| unctional.tanhshrink.html#torch.nn.functional.tanhshrink>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `softsign <https://pytorch.org/docs/stable/generated/torch.  | ✔️ |   |
-| nn.functional.softsign.html#torch.nn.functional.softsign>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `softplus <https://pytorch.org/docs/stable/generated/torch.  | ✔️ |   |
-| nn.functional.softplus.html#torch.nn.functional.softplus>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `tanh <https://pytorch.org/docs/stable/generate              | ✔️ |   |
-| d/torch.nn.functional.tanh.html#torch.nn.functional.tanh>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `sigmoid <https://pytorch.org/docs/stable/generated/torc     | ✔️ |   |
-| h.nn.functional.sigmoid.html#torch.nn.functional.sigmoid>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `hardsig                                                     | ✔️ |   |
-| moid <https://pytorch.org/docs/stable/generated/torch.nn.fun |    |   |
-| ctional.hardsigmoid.html#torch.nn.functional.hardsigmoid>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `mish <https://pytorch.org/docs/stable/generate              | ✔️ |   |
-| d/torch.nn.functional.mish.html#torch.nn.functional.mish>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `elu <https://pytorch.org/docs/stable/genera                 | ✔️ |   |
-| ted/torch.nn.functional.elu.html#torch.nn.functional.elu>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `celu <https://pytorch.org/docs/stable/generate              | ✔️ |   |
-| d/torch.nn.functional.celu.html#torch.nn.functional.celu>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `softmax <https://pytorch.org/docs/stable/generated/torc     | ✔️ |   |
-| h.nn.functional.softmax.html#torch.nn.functional.softmax>`__ |    |   |
-+--------------------------------------------------------------+----+---+
-| `log_sof                                                     | ✔️ |   |
-| tmax <https://pytorch.org/docs/stable/generated/torch.nn.fun |    |   |
-| ctional.log_softmax.html#torch.nn.functional.log_softmax>`__ |    |   |
-+--------------------------------------------------------------+----+---+
++--------------------------------------------------------------+----+----+
+| Function                                                     | PE | A  |
+|                                                              | ta | M  |
+|                                                              | b. | I  |
+|                                                              | jl | C  |
+|                                                              |    | I  |
++==============================================================+====+====+
+| `relu <https://pytorch.org/docs/stable/generate              | ✔️ | ✔️ |
+| d/torch.nn.functional.relu.html#torch.nn.functional.relu>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `relu6 <https://pytorch.org/docs/stable/generated/           | ✔️ | ✔️ |
+| torch.nn.functional.relu6.html#torch.nn.functional.relu6>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `hardtanh <https://pytorch.org/docs/stable/generated/torch.  | ✔️ | ✔️ |
+| nn.functional.hardtanh.html#torch.nn.functional.hardtanh>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `h                                                           | ✔️ | ✔️ |
+| ardswish <https://pytorch.org/docs/stable/generated/torch.nn |    |    |
+| .functional.hardswish.html#torch.nn.functional.hardswish>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `selu <https://pytorch.org/docs/stable/generate              | ✔️ | ✔️ |
+| d/torch.nn.functional.selu.html#torch.nn.functional.selu>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `leak                                                        | ✔️ | ✔️ |
+| y_relu <https://pytorch.org/docs/stable/generated/torch.nn.f |    |    |
+| unctional.leaky_relu.html#torch.nn.functional.leaky_relu>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `gelu <https://pytorch.org/docs/stable/generate              | ✔️ | ✔️ |
+| d/torch.nn.functional.gelu.html#torch.nn.functional.gelu>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `tanh                                                        | ✔️ | ✔️ |
+| shrink <https://pytorch.org/docs/stable/generated/torch.nn.f |    |    |
+| unctional.tanhshrink.html#torch.nn.functional.tanhshrink>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `softsign <https://pytorch.org/docs/stable/generated/torch.  | ✔️ | ✔️ |
+| nn.functional.softsign.html#torch.nn.functional.softsign>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `softplus <https://pytorch.org/docs/stable/generated/torch.  | ✔️ | ✔️ |
+| nn.functional.softplus.html#torch.nn.functional.softplus>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `tanh <https://pytorch.org/docs/stable/generate              | ✔️ | ✔️ |
+| d/torch.nn.functional.tanh.html#torch.nn.functional.tanh>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `sigmoid <https://pytorch.org/docs/stable/generated/torc     | ✔️ | ✔️ |
+| h.nn.functional.sigmoid.html#torch.nn.functional.sigmoid>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `hardsig                                                     | ✔️ | ✔️ |
+| moid <https://pytorch.org/docs/stable/generated/torch.nn.fun |    |    |
+| ctional.hardsigmoid.html#torch.nn.functional.hardsigmoid>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `mish <https://pytorch.org/docs/stable/generate              | ✔️ | ✔️ |
+| d/torch.nn.functional.mish.html#torch.nn.functional.mish>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `elu <https://pytorch.org/docs/stable/genera                 | ✔️ | ✔️ |
+| ted/torch.nn.functional.elu.html#torch.nn.functional.elu>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `celu <https://pytorch.org/docs/stable/generate              | ✔️ | ✔️ |
+| d/torch.nn.functional.celu.html#torch.nn.functional.celu>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `softmax <https://pytorch.org/docs/stable/generated/torc     | ✔️ | ✔️ |
+| h.nn.functional.softmax.html#torch.nn.functional.softmax>`__ |    |    |
++--------------------------------------------------------------+----+----+
+| `log_sof                                                     | ✔️ | ✔️ |
+| tmax <https://pytorch.org/docs/stable/generated/torch.nn.fun |    |    |
+| ctional.log_softmax.html#torch.nn.functional.log_softmax>`__ |    |    |
++--------------------------------------------------------------+----+----+
diff --git a/doc/software_support.rst b/doc/software_support.rst
index 312416e6..0ebd1b6e 100644
--- a/doc/software_support.rst
+++ b/doc/software_support.rst
@@ -7,7 +7,7 @@ Tools that support importing PEtab-SciML problems for downstream tasks (e.g.
 simulation and model training), listed alphabetically are:
 
 - `AMICI <https://github.com/AMICI-dev/AMICI>`__
-  (`Example <https://github.com/ICB-DCM/AMICI/blob/master/python/examples/example_petab/petab.ipynb>`__)
+  (`Example <https://amici.readthedocs.io/en/latest/examples/example_jax_petab/ExampleJaxPEtab.html>`__)
 - `PEtab.jl <https://github.com/sebapersson/PEtab.jl>`__
   (`Example <https://sebapersson.github.io/PEtab.jl/stable/tutorials/sciml/standard_format>`__)
 

From eebecb45163b146c0ce53be4dfa693e1251397a5 Mon Sep 17 00:00:00 2001
From: sebapersson <sebastian.persson1@gmail.com>
Date: Tue, 26 May 2026 10:45:13 +0100
Subject: [PATCH 6/6] Add Silu activation function

---
 doc/layers.rst | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/doc/layers.rst b/doc/layers.rst
index ec93105e..0c931a77 100644
--- a/doc/layers.rst
+++ b/doc/layers.rst
@@ -192,3 +192,6 @@ indicates which tools support each layer.
 | tmax <https://pytorch.org/docs/stable/generated/torch.nn.fun |    |    |
 | ctional.log_softmax.html#torch.nn.functional.log_softmax>`__ |    |    |
 +--------------------------------------------------------------+----+----+
+| `silu <https://docs.pytorch.org/docs/2.12/generated/torch.nn | ✔️ | ✔️ |
+| .functional.silu.html>`__                                    |    |    |
++--------------------------------------------------------------+----+----+