vbi 0.1.3__tar.gz → 0.2__tar.gz

vbi-0.2/Dockerfile

@@ -0,0 +1,51 @@
+FROM nvidia/cuda:11.8.0-cudnn8-runtime-ubuntu20.04
+
+# Set environment to avoid interactive prompts
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Install system dependencies
+RUN apt-get update && apt-get install -y \
+    python3.10 \
+    python3-pip \
+    build-essential \
+    gcc \
+    g++ \
+    libatlas-base-dev \
+    libopenblas-dev \
+    libhdf5-dev \
+    swig \
+    tzdata \
+    && ln -s /usr/bin/python3 /usr/bin/python \
+    && rm -rf /var/lib/apt/lists/*
+
+# Set timezone (e.g., UTC) to avoid configuration prompts
+RUN echo "Etc/UTC" > /etc/timezone && \
+    ln -fs /usr/share/zoneinfo/Etc/UTC /etc/localtime && \
+    dpkg-reconfigure -f noninteractive tzdata
+
+WORKDIR /app
+
+RUN pip install --upgrade pip
+
+RUN pip install --no-cache-dir \
+    hatchling \
+    setuptools>=45 \
+    wheel \
+    swig>=4.0
+
+COPY . .
+
+RUN pip install . --no-cache-dir
+RUN pip install cupy-cuda11x
+
+# Install Jupyter Notebook and related packages
+RUN pip install --no-cache-dir \
+    notebook \
+    ipykernel \
+    ipython
+
+EXPOSE 8888
+
+# Set the default command (modify as needed)
+# CMD ["python", "-c", "from vbi.utils import test_imports; test_imports()"]
+CMD ["jupyter", "notebook", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"]

{vbi-0.1.3/vbi.egg-info → vbi-0.2}/PKG-INFO

@@ -1,14 +1,13 @@
 Metadata-Version: 2.4
 Name: vbi
-Version: 0.1.3
+Version: 0.2
 Summary: Virtual brain inference.
 Author-email: Abolfazl Ziaeemehr <a.ziaeemehr@gmail.com>, Meysam Hashemi <meysam.hashemi@gmail.com>, Marmaduke Woodman <marmaduke.woodman@gmail.com>
-License: MIT
+License-Expression: Apache-2.0
 Project-URL: homepage, https://ziaeemehr.github.io/vbi_paper/
 Project-URL: repository, https://github.com/Ziaeemehr/vbi_paper
 Classifier: Programming Language :: Python :: 3
 Classifier: Topic :: Scientific/Engineering :: Information Analysis
-Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Operating System :: OS Independent
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
@@ -75,11 +74,17 @@ Dynamic: license-file
 ```bash
     conda env create --name vbi python=3.10
     conda activate vbi
+    # from pip: Recommended
+    pip install vbi
+    # from source: More recent update
     git clone https://github.com/ins-amu/vbi.git
     cd vbi
     pip install .
 
     # pip install -e .[all,dev,docs]
+    
+    # To skip C++ compilation, use the following environment variable and install from source:
+    SKIP_CPP=1 pip install -e . 
 ```
 
 ## Using Docker
@@ -143,14 +148,28 @@ We welcome contributions to the VBI project! If you have suggestions, bug report
 ## Citation
 
 ```bibtex
-@article{VBI,
-  author = {Ziaeemehr, Abolfazl and Woodman, Marmaduke and Domide, Lia and Petkoski, Spase and Jirsa, Viktor and Hashemi, Meysam},
-  title = {Virtual Brain Inference (VBI): A flexible and integrative toolkit for efficient probabilistic inference on virtual brain models},
-  journal = {bioRxiv},
-  year = {2025},
-  doi = {10.1101/2025.01.21.633922},
-  url = {https://doi.org/10.1101/2025.01.21.633922},
-  abstract = {Network neuroscience has proven essential for understanding the principles and mechanisms underlying complex brain (dys)function and cognition. In this context, whole-brain network modeling--also known as virtual brain modeling--combines computational models of brain dynamics (placed at each network node) with individual brain imaging data (to coordinate and connect the nodes), advancing our understanding of the complex dynamics of the brain and its neurobiological underpinnings. However, there remains a critical need for automated model inversion tools to estimate control (bifurcation) parameters at large scales and across neuroimaging modalities, given their varying spatio-temporal resolutions. This study aims to address this gap by introducing a flexible and integrative toolkit for efficient Bayesian inference on virtual brain models, called Virtual Brain Inference (VBI). This open-source toolkit provides fast simulations, taxonomy of feature extraction, efficient data storage and loading, and probabilistic machine learning algorithms, enabling biophysically interpretable inference from non-invasive and invasive recordings. Through in-silico testing, we demonstrate the accuracy and reliability of inference for commonly used whole-brain network models and their associated neuroimaging data. VBI shows potential to improve hypothesis evaluation in network neuroscience through uncertainty quantification, and contribute to advances in precision medicine by enhancing the predictive power of virtual brain models.}
+@article{VBI, 
+title={Virtual Brain Inference (VBI): A flexible and integrative toolkit for efficient probabilistic inference on virtual brain models},
+author={Ziaeemehr, Abolfazl and Woodman, Marmaduke and Domide, Lia and Petkoski, Spase and Jirsa, Viktor and Hashemi, Meysam},
+DOI={10.7554/elife.106194.1}, 
+url={http://dx.doi.org/10.7554/eLife.106194.1}, 
+publisher={eLife Sciences Publications, Ltd}, 
+year={2025}, 
+abstract = {Network neuroscience has proven essential for understanding the principles and mechanisms
+underlying complex brain (dys)function and cognition. In this context, whole-brain network modeling–
+also known as virtual brain modeling–combines computational models of brain dynamics (placed at each network node)
+with individual brain imaging data (to coordinate and connect the nodes), advancing our understanding of
+the complex dynamics of the brain and its neurobiological underpinnings. However, there remains a critical
+need for automated model inversion tools to estimate control (bifurcation) parameters at large scales
+associated with neuroimaging modalities, given their varying spatio-temporal resolutions.
+This study aims to address this gap by introducing a flexible and integrative toolkit for efficient Bayesian inference
+on virtual brain models, called Virtual Brain Inference (VBI). This open-source toolkit provides fast simulations,
+taxonomy of feature extraction, efficient data storage and loading, and probabilistic machine learning algorithms,
+enabling biophysically interpretable inference from non-invasive and invasive recordings.
+Through in-silico testing, we demonstrate the accuracy and reliability of inference for commonly used
+whole-brain network models and their associated neuroimaging data. VBI shows potential to improve hypothesis
+evaluation in network neuroscience through uncertainty quantification, and contribute to advances in precision
+medicine by enhancing the predictive power of virtual brain models.}
 }
 ```
 

{vbi-0.1.3 → vbi-0.2}/README.md

@@ -20,11 +20,17 @@
 ```bash
     conda env create --name vbi python=3.10
     conda activate vbi
+    # from pip: Recommended
+    pip install vbi
+    # from source: More recent update
     git clone https://github.com/ins-amu/vbi.git
     cd vbi
     pip install .
 
     # pip install -e .[all,dev,docs]
+    
+    # To skip C++ compilation, use the following environment variable and install from source:
+    SKIP_CPP=1 pip install -e . 
 ```
 
 ## Using Docker
@@ -88,14 +94,28 @@ We welcome contributions to the VBI project! If you have suggestions, bug report
 ## Citation
 
 ```bibtex
-@article{VBI,
-  author = {Ziaeemehr, Abolfazl and Woodman, Marmaduke and Domide, Lia and Petkoski, Spase and Jirsa, Viktor and Hashemi, Meysam},
-  title = {Virtual Brain Inference (VBI): A flexible and integrative toolkit for efficient probabilistic inference on virtual brain models},
-  journal = {bioRxiv},
-  year = {2025},
-  doi = {10.1101/2025.01.21.633922},
-  url = {https://doi.org/10.1101/2025.01.21.633922},
-  abstract = {Network neuroscience has proven essential for understanding the principles and mechanisms underlying complex brain (dys)function and cognition. In this context, whole-brain network modeling--also known as virtual brain modeling--combines computational models of brain dynamics (placed at each network node) with individual brain imaging data (to coordinate and connect the nodes), advancing our understanding of the complex dynamics of the brain and its neurobiological underpinnings. However, there remains a critical need for automated model inversion tools to estimate control (bifurcation) parameters at large scales and across neuroimaging modalities, given their varying spatio-temporal resolutions. This study aims to address this gap by introducing a flexible and integrative toolkit for efficient Bayesian inference on virtual brain models, called Virtual Brain Inference (VBI). This open-source toolkit provides fast simulations, taxonomy of feature extraction, efficient data storage and loading, and probabilistic machine learning algorithms, enabling biophysically interpretable inference from non-invasive and invasive recordings. Through in-silico testing, we demonstrate the accuracy and reliability of inference for commonly used whole-brain network models and their associated neuroimaging data. VBI shows potential to improve hypothesis evaluation in network neuroscience through uncertainty quantification, and contribute to advances in precision medicine by enhancing the predictive power of virtual brain models.}
+@article{VBI, 
+title={Virtual Brain Inference (VBI): A flexible and integrative toolkit for efficient probabilistic inference on virtual brain models},
+author={Ziaeemehr, Abolfazl and Woodman, Marmaduke and Domide, Lia and Petkoski, Spase and Jirsa, Viktor and Hashemi, Meysam},
+DOI={10.7554/elife.106194.1}, 
+url={http://dx.doi.org/10.7554/eLife.106194.1}, 
+publisher={eLife Sciences Publications, Ltd}, 
+year={2025}, 
+abstract = {Network neuroscience has proven essential for understanding the principles and mechanisms
+underlying complex brain (dys)function and cognition. In this context, whole-brain network modeling–
+also known as virtual brain modeling–combines computational models of brain dynamics (placed at each network node)
+with individual brain imaging data (to coordinate and connect the nodes), advancing our understanding of
+the complex dynamics of the brain and its neurobiological underpinnings. However, there remains a critical
+need for automated model inversion tools to estimate control (bifurcation) parameters at large scales
+associated with neuroimaging modalities, given their varying spatio-temporal resolutions.
+This study aims to address this gap by introducing a flexible and integrative toolkit for efficient Bayesian inference
+on virtual brain models, called Virtual Brain Inference (VBI). This open-source toolkit provides fast simulations,
+taxonomy of feature extraction, efficient data storage and loading, and probabilistic machine learning algorithms,
+enabling biophysically interpretable inference from non-invasive and invasive recordings.
+Through in-silico testing, we demonstrate the accuracy and reliability of inference for commonly used
+whole-brain network models and their associated neuroimaging data. VBI shows potential to improve hypothesis
+evaluation in network neuroscience through uncertainty quantification, and contribute to advances in precision
+medicine by enhancing the predictive power of virtual brain models.}
 }
 ```
 

{vbi-0.1.3 → vbi-0.2}/docs/examples/mpr_sde_cpp.ipynb

@@ -4,7 +4,12 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# MPR model in C++ "
+    "# MPR model in C++ \n",
+    "\n",
+    "# [Montbrio SDE model, C++](https://github.com/Ziaeemehr/vbi_paper/blob/main/docs/examples/mpr_sde_cpp.ipynb)\n",
+    "\n",
+    "\n",
+    "<a href=\"https://colab.research.google.com/github/Ziaeemehr/vbi_paper/blob/main/docs/examples/mpr_sde_cpp.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
    ]
   },
   {