# MEDomics-docs ## V1 - [Welcome!](https://medomicslab.gitbook.io/medomics-docs/readme.md): MEDomicsLab: Integrative Modeling of Heterogeneous Data in Medicine - [Quick start](https://medomicslab.gitbook.io/medomics-docs/quick-start.md): Installation of the app - [Overview](https://medomicslab.gitbook.io/medomics-docs/overview.md) - [Tutorials](https://medomicslab.gitbook.io/medomics-docs/tutorials.md) - [Design](https://medomicslab.gitbook.io/medomics-docs/tutorials/design.md) - [Extraction Module](https://medomicslab.gitbook.io/medomics-docs/tutorials/design/extraction-modules.md) - [Image Extraction Page](https://medomicslab.gitbook.io/medomics-docs/tutorials/design/extraction-modules/image-extraction-page.md): The image extraction page takes JPG images as input and extracts embeddings using a selected model. - [Text Extraction Page](https://medomicslab.gitbook.io/medomics-docs/tutorials/design/extraction-modules/text-extraction-page.md): The text extraction page takes a CSV file containing text notes as input and extracts embeddings using a selected model. - [Time Series Extraction Page](https://medomicslab.gitbook.io/medomics-docs/tutorials/design/extraction-modules/time-series-extraction-page.md): The time series extraction page takes a CSV file containing time series as input and extracts embeddings using a selected model. - [MEDimage](https://medomicslab.gitbook.io/medomics-docs/tutorials/design/extraction-modules/medimage.md) - [Input Module](https://medomicslab.gitbook.io/medomics-docs/tutorials/design/input-module.md): The Input module consolidates all the tools necessary for preprocessing tabular data. - [Feature Reduction Tool](https://medomicslab.gitbook.io/medomics-docs/tutorials/design/input-module/feature-reduction-tool.md) - [MEDprofiles](https://medomicslab.gitbook.io/medomics-docs/tutorials/design/input-module/medprofiles.md): This component of the input module includes all the necessary tools to enter the MEDprofiles process. - [MEDprofiles Viewer](https://medomicslab.gitbook.io/medomics-docs/tutorials/design/input-module/medprofiles/medprofiles-viewer.md): The MEDprofiles figure may be open through the MEDprofiles Accordion in the Input Module, as 'MEDprofiles Viewer'. - [Exploratory Module](https://medomicslab.gitbook.io/medomics-docs/tutorials/design/exploratory-module.md) - [Development](https://medomicslab.gitbook.io/medomics-docs/tutorials/development.md) - [Learning Module](https://medomicslab.gitbook.io/medomics-docs/tutorials/development/learning-module.md): This is where the magic happens 🧙🪄 - [Initialization](https://medomicslab.gitbook.io/medomics-docs/tutorials/development/learning-module/initialization.md): This page covers everything you need to know about the Initialization Box and the nodes you can use inside it. - [Training](https://medomicslab.gitbook.io/medomics-docs/tutorials/development/learning-module/training.md): This page covers everything you need to know about the Training Box and the nodes you can use inside it. - [Analysis](https://medomicslab.gitbook.io/medomics-docs/tutorials/development/learning-module/analysis.md): This page explains the Analysis Box functionality, including the Analysis Mode, and how it enables comprehensive model performance evaluation through detailed metrics and diagnostic tools. - [medmodel](https://medomicslab.gitbook.io/medomics-docs/tutorials/development/learning-module/medmodel.md) - [Experimental Scene](https://medomicslab.gitbook.io/medomics-docs/tutorials/development/learning-module/experimental-scene.md): This page covers everything you need to know about the experimental scene and how it can be used as an initial testing environment. - [DO'S & DON'TS](https://medomicslab.gitbook.io/medomics-docs/tutorials/development/learning-module/dos-and-donts.md): Here you will find a comprehensive guide to recommended best practices and common pitfalls to avoid, ensuring optimal performance and reliable execution within the learning module. - [Evaluation Module](https://medomicslab.gitbook.io/medomics-docs/tutorials/development/evaluation-module.md) - [Federated Learning Module](https://medomicslab.gitbook.io/medomics-docs/tutorials/development/federated-learning-module.md) - [Overview](https://medomicslab.gitbook.io/medomics-docs/tutorials/development/federated-learning-module/overview.md) - [Configure database](https://medomicslab.gitbook.io/medomics-docs/tutorials/development/federated-learning-module/configure-database.md) - [Create pipelines](https://medomicslab.gitbook.io/medomics-docs/tutorials/development/federated-learning-module/create-pipelines.md) - [Pipeline results](https://medomicslab.gitbook.io/medomics-docs/tutorials/development/federated-learning-module/pipeline-results.md) - [Hyperparameters optimization](https://medomicslab.gitbook.io/medomics-docs/tutorials/development/federated-learning-module/hyperparameters-optimization.md) - [Merge results](https://medomicslab.gitbook.io/medomics-docs/tutorials/development/federated-learning-module/merge-results.md) - [Crash tutorial](https://medomicslab.gitbook.io/medomics-docs/tutorials/development/federated-learning-module/crash-tutorial.md) - [Deployment](https://medomicslab.gitbook.io/medomics-docs/tutorials/deployment.md) - [Application Module](https://medomicslab.gitbook.io/medomics-docs/tutorials/deployment/application-module.md) - [Superset](https://medomicslab.gitbook.io/medomics-docs/tutorials/superset.md) - [Superset Features](https://medomicslab.gitbook.io/medomics-docs/tutorials/superset/superset-features.md): This page goes through all the superset features and provides information on how to use them. - [Remote MEDomics](https://medomicslab.gitbook.io/medomics-docs/tutorials/remote-medomics.md): A recently implemented feature of MEDomics allowing it to connect to a remote workspace, hosted on a server. - [Connection Tutorial](https://medomicslab.gitbook.io/medomics-docs/tutorials/remote-medomics/connection-tutorial.md): This page decribes how to connect to a remote workspace using the MEDomics client app. - [Development](https://medomicslab.gitbook.io/medomics-docs/tutorials/remote-medomics/development.md): This section describes where to find the different components for development of the remote version of the MEDomics Platform. - [Frontend - Client](https://medomicslab.gitbook.io/medomics-docs/tutorials/remote-medomics/development/frontend-client.md): A list of the edited and created files to allow the client to connect to the backend. - [Backend - Server](https://medomicslab.gitbook.io/medomics-docs/tutorials/remote-medomics/development/backend-server.md): A run-down of the files and tools used in the backend part of the new remote-capable architecture. - [Express Request Endpoints](https://medomicslab.gitbook.io/medomics-docs/tutorials/remote-medomics/development/backend-server/express-request-endpoints.md): A list of currently useable endpoints to send requests to the backend server. - [Miscellaneous](https://medomicslab.gitbook.io/medomics-docs/tutorials/miscellaneous.md) - [Collaboration](https://medomicslab.gitbook.io/medomics-docs/collaboration.md): We explain here how the MEDomics platform opens the doors for collaboration. - [Proofs of Concept](https://medomicslab.gitbook.io/medomics-docs/proofs-of-concept.md): In this section, we present multiple early-stage demonstrations and tests to show the potential of the MEDomics platform and how it can be used in the real world. - [The PARIS Demo](https://medomicslab.gitbook.io/medomics-docs/proofs-of-concept/the-paris-demo.md): This page demonstrates how you can leverage medical questionnaire data in MEDomics to draw insights. - [Superset](https://medomicslab.gitbook.io/medomics-docs/proofs-of-concept/the-paris-demo/superset.md): This page documents the Superset step in our Proof of Concept (PoC), which consists of exploring the data through the creation of visual interactive displays. - [Exploratory Module](https://medomicslab.gitbook.io/medomics-docs/proofs-of-concept/the-paris-demo/exploratory-module.md): This page documents the data analysis step in our Proof of Concept (PoC), which consists of understanding the underlying relations within our data features. - [Input Module](https://medomicslab.gitbook.io/medomics-docs/proofs-of-concept/the-paris-demo/input-module.md): This page documents the Input Module step of the demo, where we will perform the last processing steps on our PARIS data before using in the Learning Module. - [Learning Module](https://medomicslab.gitbook.io/medomics-docs/proofs-of-concept/the-paris-demo/learning-module.md): This page documents the whole machine learning process of the PARIS demo, where we will leverage the processed data to train models to predict the emotional state of patients. - [Evaluation Module](https://medomicslab.gitbook.io/medomics-docs/proofs-of-concept/the-paris-demo/evaluation-module.md): This page documents the model's evaluation and interpretation step using the Evaluation Module. - [Application Module](https://medomicslab.gitbook.io/medomics-docs/proofs-of-concept/the-paris-demo/application-module.md): This page documents the final step of model application on new input data - [ML with Synthetic Data](https://medomicslab.gitbook.io/medomics-docs/proofs-of-concept/ml-with-synthetic-data.md): This proof of concept demonstrates the ability of the MEDomics platform to support the full end-to-end machine learning workflow in a healthcare context, using synthetic data. - [Code Editor & MEDomics Terminal](https://medomicslab.gitbook.io/medomics-docs/proofs-of-concept/ml-with-synthetic-data/code-editor-and-medomics-terminal.md): This page introduces the first steps of our proof of concept. It allows users to edit the code responsible for generating the homr\_any\_visit.csv dataset, which will be used in the following steps. - [Input Module](https://medomicslab.gitbook.io/medomics-docs/proofs-of-concept/ml-with-synthetic-data/input-module.md): This page documents the Input Module step of the demo, where we will perform two processing steps on our new "homr\_any\_visit\_10pct.csv" file before model training in the Learning Module. - [Learning Module](https://medomicslab.gitbook.io/medomics-docs/proofs-of-concept/ml-with-synthetic-data/learning-module.md): This page documents the whole machine learning process of our demo, where we will use our dataset and specifically our tags to predict one-year mortality. - [Evaluation Module](https://medomicslab.gitbook.io/medomics-docs/proofs-of-concept/ml-with-synthetic-data/evaluation-module.md): This page documents the AdmDemo model's evaluation and interpretation step using the Evaluation Module. - [Application Module](https://medomicslab.gitbook.io/medomics-docs/proofs-of-concept/ml-with-synthetic-data/application-module.md): This page documents the final step of model application on new input data. - [End-to-End MEDomics Pipeline](https://medomicslab.gitbook.io/medomics-docs/proofs-of-concept/end-to-end-medomics-pipeline.md): This proof of concept demonstrates the ability of the MEDomics platform to support a complete end-to-end machine learning workflow in a healthcare context, from data preparation to cross-institutional - [Preprocessing Steps](https://medomicslab.gitbook.io/medomics-docs/proofs-of-concept/end-to-end-medomics-pipeline/preprocessing-steps.md): This proof of concept relies on preprocessed datasets derived from the MIMIC-IV and eICU databases. The preprocessing pipeline is inspired by the MED3pa study, including SAPS-based feature processing. - [Learning Module](https://medomicslab.gitbook.io/medomics-docs/proofs-of-concept/end-to-end-medomics-pipeline/learning-module.md): In this section, we train a baseline MLP model using the MIMIC-IV learning dataset prepared earlier. The objective is to build a reference model that will later be evaluated across multiple hospitals. - [Evaluation Module for Centralized Learning](https://medomicslab.gitbook.io/medomics-docs/proofs-of-concept/end-to-end-medomics-pipeline/evaluation-module-for-centralized-learning.md): We evaluate our centralized trained MLP model in different contexts. The goal is to assess model performance in every case and its ability to generalize to external hospitals and datasets. - [Evaluation Module for Federated Learning](https://medomicslab.gitbook.io/medomics-docs/proofs-of-concept/end-to-end-medomics-pipeline/evaluation-module-for-federated-learning.md): This page documents the evaluation of the federated model based on our centralized model. - [New features](https://medomicslab.gitbook.io/medomics-docs/new-features.md): Explore the documentation for the latest features introduced in the V1 release. - [Upcoming features](https://medomicslab.gitbook.io/medomics-docs/upcoming-features.md): Explore the upcoming implementations in the next releases. - [Testing Phase with MIMIC](https://medomicslab.gitbook.io/medomics-docs/test-with-mimic.md): January 15th 2024 - May 13th 2024 - [MIMIC data access](https://medomicslab.gitbook.io/medomics-docs/test-with-mimic/mimic-data-access.md): How to access the MIMIC data (necessary to be part of the Testing Phase) - [Step 1: Install and Explore](https://medomicslab.gitbook.io/medomics-docs/test-with-mimic/step-1.md): Jan 15 - Jan 29 | Install and Explore - [Step 2: Extract Data](https://medomicslab.gitbook.io/medomics-docs/test-with-mimic/step-2.md): Jan 29 - Feb 12 | Extract Data - [Step 3: Prepare ML tables](https://medomicslab.gitbook.io/medomics-docs/test-with-mimic/step-3.md): Feb 12 – Feb 26 | Prepare ML tables - [Step 4: Explore Data](https://medomicslab.gitbook.io/medomics-docs/test-with-mimic/step-4.md): Feb 26 – Mar 11 | Explore Data - [Step 5: Vacations](https://medomicslab.gitbook.io/medomics-docs/test-with-mimic/step-5.md): Mar 11 – Mar 25 | Vacations - [Step 6: Create Model](https://medomicslab.gitbook.io/medomics-docs/test-with-mimic/step-6.md): Mar 25 – Apr 8 | Create Model - [Step 7: Evaluate & Apply Model](https://medomicslab.gitbook.io/medomics-docs/test-with-mimic/step-7.md): Apr 8 – Apr 22 | Evaluate & Apply Model - [Step 8: Challenge](https://medomicslab.gitbook.io/medomics-docs/test-with-mimic/step-8.md): Apr 22 – May 13 | Challenge - [Wrap-Up](https://medomicslab.gitbook.io/medomics-docs/test-with-mimic/wrap-up.md): Testing Phase Wrap-Up - [Contributing](https://medomicslab.gitbook.io/medomics-docs/contributing.md) - [Our coding standards](https://medomicslab.gitbook.io/medomics-docs/contributing/our-coding-standards.md) - [How to push my modification ?](https://medomicslab.gitbook.io/medomics-docs/contributing/how-to-push-my-modification.md) - [Troubleshooting](https://medomicslab.gitbook.io/medomics-docs/troubleshooting.md) - [FAQ](https://medomicslab.gitbook.io/medomics-docs/faq.md) - [About us](https://medomicslab.gitbook.io/medomics-docs/about-us.md) - [Contact us](https://medomicslab.gitbook.io/medomics-docs/forms/contact-us.md) - [Report an issue](https://medomicslab.gitbook.io/medomics-docs/forms/report-an-issue.md) - [Join the testing phase](https://medomicslab.gitbook.io/medomics-docs/forms/join-the-testing-phase.md): (Jan. 15th 2024 to May 13th 2024) ## V0 - [Welcome!](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/readme.md): MEDomicsLab: Integrative Modeling of Heterogeneous Data in Medicine - [Quick start](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/quick-start.md): Installation of the app - [Overview](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/overview.md) - [Tutorials](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/tutorials.md) - [Design](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/tutorials/design.md) - [Extraction Module](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/tutorials/design/extraction-modules.md) - [Image Extraction Page](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/tutorials/design/extraction-modules/image-extraction-page.md): The image extraction page takes JPG images as input and extracts embeddings using a selected model. - [Text Extraction Page](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/tutorials/design/extraction-modules/text-extraction-page.md): The text extraction page takes a CSV file containing text notes as input and extracts embeddings using a selected model. - [Time Series Extraction Page](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/tutorials/design/extraction-modules/time-series-extraction-page.md): The time series extraction page takes a CSV file containing time series as input and extracts embeddings using a selected model. - [MEDimage](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/tutorials/design/extraction-modules/medimage.md) - [Input Module](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/tutorials/design/input-module.md): The Input module consolidates all the tools necessary for preprocessing tabular data. - [Feature Reduction Tool](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/tutorials/design/input-module/feature-reduction-tool.md) - [MEDprofiles](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/tutorials/design/input-module/medprofiles.md): This component of the input module includes all the necessary tools to enter the MEDprofiles process. - [MEDprofiles Viewer](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/tutorials/design/input-module/medprofiles/medprofiles-viewer.md): The MEDprofiles figure may be open through the MEDprofiles Accordion in the Input Module, as 'MEDprofiles Viewer'. - [Exploratory Module](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/tutorials/design/exploratory-module.md) - [Development](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/tutorials/development.md) - [Learning Module](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/tutorials/development/learning-module.md): This is where the magic happens 🧙🪄 - [Evaluation Module](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/tutorials/development/evaluation-module.md) - [Federated Learning Module](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/tutorials/development/federated-learning-module.md) - [Overview](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/tutorials/development/federated-learning-module/overview.md) - [Configure database](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/tutorials/development/federated-learning-module/configure-database.md) - [Create pipelines](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/tutorials/development/federated-learning-module/create-pipelines.md) - [Pipeline results](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/tutorials/development/federated-learning-module/pipeline-results.md) - [Hyperparameters optimization](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/tutorials/development/federated-learning-module/hyperparameters-optimization.md) - [Merge results](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/tutorials/development/federated-learning-module/merge-results.md) - [Crash tutorial](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/tutorials/development/federated-learning-module/crash-tutorial.md) - [Deployment](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/tutorials/deployment.md) - [Application Module](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/tutorials/deployment/application-module.md) - [Miscellaneous](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/tutorials/miscellaneous.md) - [Testing Phase with MIMIC](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/test-with-mimic.md): January 15th 2024 - May 13th 2024 - [MIMIC data access](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/test-with-mimic/mimic-data-access.md): How to access the MIMIC data (necessary to be part of the Testing Phase) - [Step 1: Install and Explore](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/test-with-mimic/step-1.md): Jan 15 - Jan 29 | Install and Explore - [Step 2: Extract Data](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/test-with-mimic/step-2.md): Jan 29 - Feb 12 | Extract Data - [Step 3: Prepare ML tables](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/test-with-mimic/step-3.md): Feb 12 – Feb 26 | Prepare ML tables - [Step 4: Explore Data](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/test-with-mimic/step-4.md): Feb 26 – Mar 11 | Explore Data - [Step 5: Vacations](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/test-with-mimic/step-5.md): Mar 11 – Mar 25 | Vacations - [Step 6: Create Model](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/test-with-mimic/step-6.md): Mar 25 – Apr 8 | Create Model - [Step 7: Evaluate & Apply Model](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/test-with-mimic/step-7.md): Apr 8 – Apr 22 | Evaluate & Apply Model - [Step 8: Challenge](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/test-with-mimic/step-8.md): Apr 22 – May 13 | Challenge - [Wrap-Up](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/test-with-mimic/wrap-up.md): Testing Phase Wrap-Up - [Contributing](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/contributing.md) - [Our coding standards](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/contributing/our-coding-standards.md) - [How to push my modification ?](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/contributing/how-to-push-my-modification.md) - [Troubleshooting](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/troubleshooting.md) - [FAQ](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/faq.md) - [About us](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/about-us.md) - [Contact us](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/forms/contact-us.md) - [Report an issue](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/forms/report-an-issue.md) - [Join the testing phase](https://medomicslab.gitbook.io/medomics-docs/medomicslab-docs-v0/forms/join-the-testing-phase.md): (Jan. 15th 2024 to May 13th 2024) --- # Agent Instructions This documentation is published with GitBook. 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