diff --git a/MODULE.bazel b/MODULE.bazel
index 8c469c7fa..8f441fc47 100644
--- a/MODULE.bazel
+++ b/MODULE.bazel
@@ -4,7 +4,7 @@ pyrovelocity MODULE
 
 module(
     name = "pyrovelocity",
-    version = "0.4.0b2",
+    version = "0.4.0b3",
     compatibility_level = 1,
 )
 
diff --git a/Makefile b/Makefile
index 9ba541cff..01f821a4f 100644
--- a/Makefile
+++ b/Makefile
@@ -913,8 +913,8 @@ approve-prs: ## Approve github pull requests from bots: PR_ENTRIES="2-5 10 12-18
 		fi; \
 	done
 
-PREVIOUS_VERSION := 0.4.0b1
-NEXT_VERSION := 0.4.0b2
+PREVIOUS_VERSION := 0.4.0b2
+NEXT_VERSION := 0.4.0b3
 VERSION_FILES := \
 	pyproject.toml \
 	conda/colab/construct.yaml \
diff --git a/conda/colab/construct.yaml b/conda/colab/construct.yaml
index 349becd58..be9faa22a 100644
--- a/conda/colab/construct.yaml
+++ b/conda/colab/construct.yaml
@@ -1,5 +1,5 @@
 name: pyrovelocity-colab
-version: 0.4.0b2
+version: 0.4.0b3
 
 channels:
   - pytorch
diff --git a/containers/gpu.Dockerfile b/containers/gpu.Dockerfile
index 1a7f1eda7..5a91a373b 100644
--- a/containers/gpu.Dockerfile
+++ b/containers/gpu.Dockerfile
@@ -77,7 +77,7 @@ COPY . /root
 # development
 RUN pip install --no-deps -e .
 # distribution
-# RUN pip install pyrovelocity==0.4.0b2
+# RUN pip install pyrovelocity==0.4.0b3
 
 ARG tag
 ENV FLYTE_INTERNAL_IMAGE $tag
diff --git a/containers/pkg.Dockerfile b/containers/pkg.Dockerfile
index 1b8266ff5..3d047a222 100644
--- a/containers/pkg.Dockerfile
+++ b/containers/pkg.Dockerfile
@@ -34,7 +34,7 @@ COPY . /root
 # development
 RUN pip install --no-deps -e .
 # distribution
-# RUN pip install pyrovelocity==0.4.0b2
+# RUN pip install pyrovelocity==0.4.0b3
 
 ARG tag
 ENV FLYTE_INTERNAL_IMAGE $tag
diff --git a/docs/source/notebooks/pyrovelocity_colab_template.ipynb b/docs/source/notebooks/pyrovelocity_colab_template.ipynb
index bef8f6879..02e6cf309 100644
--- a/docs/source/notebooks/pyrovelocity_colab_template.ipynb
+++ b/docs/source/notebooks/pyrovelocity_colab_template.ipynb
@@ -70,7 +70,7 @@
         }
       ],
       "source": [
-        "pyrovelocity_version = \"0.4.0b2\"\n",
+        "pyrovelocity_version = \"0.4.0b3\"\n",
         "pyrovelocity_colab_script_url = (\n",
         "    \"https://storage.googleapis.com/pyrovelocity/data/scripts/\"\n",
         "    + f\"pyrovelocity-colab-{pyrovelocity_version}-Linux-x86_64.sh\"\n",
diff --git a/pyproject.toml b/pyproject.toml
index f2986adcc..853ea12b4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pyrovelocity"
-version = "0.4.0b2"
+version = "0.4.0b3"
 packages = [{ include = "pyrovelocity", from = "src" }]
 description = "A multivariate RNA Velocity model to estimate future cell states with uncertainty using probabilistic modeling with pyro."
 authors = ["pyrovelocity team"]
diff --git a/scripts/conda b/scripts/conda
index 0d03f9b9e..6ff82dce9 100755
--- a/scripts/conda
+++ b/scripts/conda
@@ -3,7 +3,7 @@
 set -euo pipefail
 
 PACKAGE_NAME="pyrovelocity"
-PACKAGE_VERSION="0.4.0b2"
+PACKAGE_VERSION="0.4.0b3"
 CONDA_BUILD_STRING="pyhff70e4c"
 CONDA_BUILD_NUMBER="0"
 # CONDA_CHANNEL_LABEL="pyrovelocity_dev"
@@ -32,7 +32,7 @@ Example:
 
     ./conda \\
     --name pyrovelocity \\
-    --version 0.4.0b2.dev1 \\
+    --version 0.4.0b3.dev1 \\
     --build-string pyhff70e4c \\
     --build-number 0 \\
     --label pyrovelocity_dev
@@ -67,9 +67,9 @@ PACKAGE_SPEC="conda-forge/label/\
 $CONDA_CHANNEL_LABEL::\
 $PACKAGE_NAME=$PACKAGE_VERSION=$CONDA_BUILD_STRING"_"$CONDA_BUILD_NUMBER"
 
-BLUE="\0.4.0b2;34;1m"
+BLUE="\0.4.0b3;34;1m"
 BOLD="\033[1m"
-NO_COLOR="\0.4.0b2m"
+NO_COLOR="\0.4.0b3m"
 if [ "$USE_COLOR" = false ]; then
     BLUE=""
     BOLD=""