diff --git a/constraints.txt b/constraints.txt
index b020ae118d6..ed7da64301d 100644
--- a/constraints.txt
+++ b/constraints.txt
@@ -2,7 +2,7 @@
 # See: https://docs.astral.sh/uv/pip/compile/#adding-constraints
 
 # Constrain PyTorch versions to the same versions in install-dev.sh
-torch==2.5.1
+torch==2.8.0
 torchvision==0.20.1
 
 # Security upgrades
diff --git a/docs/requirements.txt b/docs/requirements.txt
index 7e56e774d79..300cafcf973 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -2,6 +2,6 @@ mkdocs==1.4.2
 mkdocstrings==0.20.0
 mkdocstrings-python==1.3.0
 mkdocs-macros-plugin==0.7.0
-mkdocs-include-markdown-plugin==4.0.0
+mkdocs-include-markdown-plugin==7.1.8
 # Transitive dependency, pinned to avoid error in #3393
 mkdocs_autorefs==1.3.1
diff --git a/pyproject.toml b/pyproject.toml
index 58ff2f99192..fd5afadcc13 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -339,7 +339,7 @@ medhelm = [
     "lxml~=5.3",
     "openpyxl~=3.1",
     "python-docx~=1.1",
-    "transformers~=4.45,<4.50",
+    "transformers>=4.45,<5.0",
 ]
 
 audiolm = [
diff --git a/requirements.txt b/requirements.txt
index a9e80c88790..dda33914dc7 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -260,7 +260,7 @@ preshed==3.0.10
 progressbar2==4.5.0
 propcache==0.3.2
 proto-plus==1.26.1
-protobuf==3.19.6 ; python_full_version >= '3.13'
+protobuf==4.25.8 ; python_full_version >= '3.13'
 protobuf==5.29.5 ; python_full_version < '3.13'
 psutil==7.0.0
 pyarrow==21.0.0
@@ -352,7 +352,7 @@ tensorboard-data-server==0.7.2 ; python_full_version < '3.13'
 tensorboard-plugin-wit==1.8.1 ; python_full_version >= '3.13'
 tensorflow==2.11.1 ; python_full_version >= '3.13'
 tensorflow==2.18.1 ; python_full_version < '3.10' or (python_full_version >= '3.11' and python_full_version < '3.13')
-tensorflow==2.20.0 ; python_full_version == '3.10.*'
+tensorflow==2.12.1 ; python_full_version == '3.10.*'
 tensorflow-estimator==2.11.0 ; python_full_version >= '3.13'
 tensorflow-hub==0.16.1 ; python_full_version >= '3.13' and sys_platform != 'darwin'
 tensorflow-io-gcs-filesystem==0.37.1 ; python_full_version < '3.10' or python_full_version == '3.11.*' or (python_full_version >= '3.13' and platform_machine != 'arm64') or (python_full_version >= '3.13' and sys_platform != 'darwin')
@@ -374,12 +374,12 @@ tokenizers==0.21.2
 toml==0.10.2
 tomli==2.2.1 ; python_full_version < '3.11'
 toolz==1.0.0
-torch==2.5.1
+torch==2.8.0
 torch-fidelity==0.3.0
 torchmetrics==0.11.4
 torchvision==0.20.1
 tqdm==4.67.1
-transformers==4.52.4
+transformers==4.53.0
 transformers-stream-generator==0.0.5
 treescope==0.1.9 ; python_full_version >= '3.10'
 trio==0.30.0