.. _notebooks/index: Notebook Gallery ================ Here, you can find static renders of EncoderMap's example notebooks. You can run them interactively on Google Colab or MyBinder. You can also run them on your local machine by cloning EncoderMap's repository. .. code-block:: :bash: $ git clone https://github.com/AG-Peter/encodermap && encodermap $ pip install -r requirements.txt && pip install md_requirements.txt $ cd tutorials $ jupyter-notebook Starter Notebooks ----------------- The starter notebooks help you with your first steps with EncoderMap. .. grid:: 3 .. grid-item-card:: Basic Cube Example :margin: 2 0 0 0 :img-bottom: ../_static/starter_nb_01_basic_thumbnail.png :img-alt: A cube with colored vertices. :link: starter_nb/starter_nb_01_basic :link-type: doc Get started with EncoderMap .. grid-item-card:: Advanced Asp7 :margin: 2 0 0 0 :img-bottom: ../_static/starter_nb_02_advanced_thumbnail.png :img-alt: the Mybinder logo :link: starter_nb/starter_nb_02_advanced :link-type: doc Advanced EncoderMap usage with MD data .. grid-item-card:: Your Data :margin: 2 0 0 0 :img-bottom: ../_static/starter_nb_03_your_data_thumbnail.png :img-alt: the Mybinder logo :link: starter_nb/starter_nb_03_your_data :link-type: doc Upload your own data and use this notebook Notebooks intermediate ---------------------- The advanced notebooks introduce more advanced techniques and explore more novel features of EncoderMap. .. grid:: 1 .. grid-item-card:: Training diverse topologies :margin: 2 0 0 0 :img-alt: Img description. :img-bottom: ../_static/glu7_generated.gif :link: intermediate_nb/sparse :link-type: doc Training diverse topologies Notebooks MD ------------ The MD notebooks contain more detailed descriptions of how EncoderMap deals with MD data. It helps you in saving and loading large MD datasets and using them to train EncoderMap. It also helps you in understanding the terms `feature space` and `collective variable`. .. grid:: 1 .. grid-item-card:: Trajectory Ensembles :margin: 2 0 0 0 :img-bottom: ../_static/md_nb_01_traj_ensemble_thumbnail.png :img-alt: Img description. :link: md_nb/md_nb_01_traj_ensemble :link-type: doc Trajectory Ensembles Notebooks Customization ----------------------- These notebooks help you in customizing EncoderMap. These tools can assist you in understanding how EncoderMap trains on your data. Furthermore, you will learn how to implement new cost functions and vary the training rate of the Neural Network. .. grid:: 4 .. grid-item-card:: Custom Scalars :margin: 2 0 0 0 :img-bottom: ../_static/customization_nb_01_scalars_thumbnail.png :img-alt: Img description. :link: customization_nb/customization_nb_01_scalars :link-type: doc Monitor in TensorBoard .. grid-item-card:: Custom Loss :margin: 2 0 0 0 :img-bottom: ../_static/customization_nb_02_loss_thumbnail.png :img-alt: Img description. :link: customization_nb/customization_nb_02_loss :link-type: doc Add new loss functions .. grid-item-card:: Custom Images :margin: 2 0 0 0 :img-bottom: ../_static/customization_nb_03_images_thumbnail.png :img-alt: Img description. :link: customization_nb/customization_nb_03_images :link-type: doc Write images to TensorBoard .. grid-item-card:: Learning Rate Scheduler :margin: 2 0 0 0 :img-bottom: ../_static/customization_nb_04_lr_thumbnail.png :img-alt: Img description. :link: customization_nb/customization_nb_04_lr :link-type: doc Adjust the learning rate Notebooks Publication --------------------- These notebooks contain the analysis code of an upcoming publication ""EncoderMap III: A dimensionality reduction package for feature exploration in molecular simulations" featuring the new version of the EncoderMap package. Trained network weights are available upon reasonable request by raising an issue on GitHub: https://github.com/AG-Peter/encodermap/issues, or by contacting the authors of the publication. .. grid:: 4 .. grid-item-card:: Figure1 :margin: 2 0 0 0 :img-bottom: ../_static/figure1_thumbnail.png :img-alt: Img description. :link: publication/figure1 :link-type: doc Notebook to create figure1 of the publication .. grid-item-card:: Figure2 :margin: 2 0 0 0 :img-bottom: ../_static/figure2_thumbnail.png :img-alt: Img description. :link: publication/figure2 :link-type: doc Notebook to create figure2 of the publication .. grid-item-card:: Figure3 :margin: 2 0 0 0 :img-bottom: ../_static/figure3_thumbnail.png :img-alt: Img description. :link: publication/figure3 :link-type: doc Notebook to create figure3 of the publication .. grid-item-card:: Figure5 :margin: 2 0 0 0 :img-bottom: ../_static/figure5_thumbnail.png :img-alt: Img description. :link: publication/figure5 :link-type: doc Notebook to create figure5 of the publication .. toctree:: :maxdepth: 3 :caption: Starter Notebooks starter_nb/starter_nb_01_basic starter_nb/starter_nb_02_advanced starter_nb/starter_nb_03_your_data .. toctree:: :maxdepth: 3 :caption: MD Notebooks md_nb/md_nb_01_traj_ensemble .. toctree:: :maxdepth: 3 :caption: Customization Notebooks customization_nb/customization_nb_01_scalars customization_nb/customization_nb_02_loss customization_nb/customization_nb_03_images customization_nb/customization_nb_04_lr .. toctree:: :maxdepth: 3 :caption: Publication Notebooks publication/figure1 publication/figure2 publication/figure3 publication/figure5 .. toctree:: :maxdepth: 3 :caption: Static Code Examples static_code