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--**# Neurodiagnoses AI: Multimodal AI for Neurodiagnostic Predictions**
++**Neurodiagnoses AI** is an open-source, AI-driven framework designed to enhance the diagnosis and prognosis of central nervous system (CNS) disorders. Building upon the Florey Dementia Index (FDI) methodology, it now encompasses a broader spectrum of neurological conditions. The system integrates multimodal data sources—including EEG, neuroimaging, biomarkers, and genetics—and employs machine learning models to deliver explainable, real-time diagnostic insights. A key feature of this framework is the incorporation of the **Generalized Neuro Biomarker Ontology Categorization (Neuromarker)**, which standardizes biomarker classification across all neurodegenerative diseases, facilitating cross-disease AI training.
--## **Project Overview**
--Neurodiagnoses AI implements AI-driven diagnostic and prognostic models for central nervous system (CNS) disorders, adapting the Florey Dementia Index (FDI) methodology to a broader set of neurological conditions. The approach integrates **multimodal data sources** (EEG, neuroimaging, biomarkers, and genetics) and employs **machine learning models** to provide **explainable, real-time diagnostic insights**.##
++**Neuromarker: Generalized Biomarker Ontology**
--## **How to Use External Databases in Neurodiagnoses**
--To enhance diagnostic accuracy, Neurodiagnoses integrates data from multiple biomedical and neurological research databases. Researchers can follow these steps to access, prepare, and integrate data into the Neurodiagnoses framework.##
++Neuromarker extends the Common Alzheimer’s Disease Research Ontology (CADRO) into a comprehensive biomarker categorization framework applicable to all neurodegenerative diseases (NDDs). This ontology enables standardized classification, AI-based feature extraction, and seamless multimodal data integration.
--### **Potential Data Sources**
--Neurodiagnoses maintains an updated list of potential biomedical databases relevant to neurodegenerative diseases. ##
++**Core Biomarker Categories**
--**Reference: List of Potential Databases**
--- **ADNI**: Alzheimer's Disease data ([ADNI](https://adni.loni.usc.edu))
--- **PPMI**: Parkinson’s Disease Imaging and biospecimens ([PPMI](https://www.ppmi-info.org))
--- **GP2**: Whole-genome sequencing for PD ([GP2](https://gp2.org))
--- **Enroll-HD**: Huntington’s Disease Clinical and genetic data ([Enroll-HD](https://www.enroll-hd.org))
--- **GAAIN**: Multi-source Alzheimer’s data aggregation ([GAAIN](https://gaain.org))
--- **UK Biobank**: Population-wide genetic, imaging, and health records ([UK Biobank](https://www.ukbiobank.ac.uk))
--- **DPUK**: Dementia and Aging data ([DPUK](https://www.dementiasplatform.uk))
--- **PRION Registry**: Prion Diseases clinical and genetic data ([PRION Registry](https://prionregistry.org))
--- **DECIPHER**: Rare genetic disorder genomic variants ([DECIPHER](https://decipher.sanger.ac.uk))
++Within the Neurodiagnoses AI framework, biomarkers are categorized as follows:
--### **1. Register for Access**
--- Each external database requires **individual registration** and access approval.
--- Ensure compliance with **ethical approvals** and **data usage agreements** before integrating datasets into Neurodiagnoses.
--- Some repositories may require a **Data Usage Agreement (DUA)** for sensitive medical data.##
++|=**Category**|=**Description**
++|**Molecular Biomarkers**|Omics-based markers (genomic, transcriptomic, proteomic, metabolomic, lipidomic)
++|**Neuroimaging Biomarkers**|Structural (MRI, CT), Functional (fMRI, PET), Molecular Imaging (tau, amyloid, α-synuclein)
++|**Fluid Biomarkers**|CSF, plasma, blood-based markers for tau, amyloid, α-synuclein, TDP-43, GFAP, NfL, autoantiboides
++|**Neurophysiological Biomarkers**|EEG, MEG, evoked potentials (ERP), sleep-related markers
++|**Digital Biomarkers**|Gait analysis, cognitive/speech biomarkers, wearables data, EHR-based markers
++|**Clinical Phenotypic Markers**|Standardized clinical scores (MMSE, MoCA, CDR, UPDRS, ALSFRS, UHDRS)
++|**Genetic Biomarkers**|Risk alleles (APOE, LRRK2, MAPT, C9orf72, PRNP) and polygenic risk scores
++|**Environmental & Lifestyle Factors**|Toxins, infections, diet, microbiome, comorbidities
--### **2. Download & Prepare Data**
--- Download datasets while adhering to database usage policies.
--- Ensure files meet **Neurodiagnoses format requirements**:
--  - **Tabular Data**: `.csv`, `.tsv`
--  - **Neuroimaging Data**: `.nii`, `.dcm`
--  - **Genomic Data**: `.fasta`, `.vcf`
--  - **Clinical Metadata**: `.json`, `.xml`##
++**Integrating External Databases into Neurodiagnoses**
--- **Mandatory Fields for Integration**:
--  - **Subject ID**: Unique patient identifier
--  - **Diagnosis**: Standardized disease classification
--  - **Biomarkers**: CSF, plasma, or imaging biomarkers
--  - **Genetic Data**: Whole-genome or exome sequencing
--  - **Neuroimaging Metadata**: MRI/PET acquisition parameters
++To enhance diagnostic precision, Neurodiagnoses AI incorporates data from multiple biomedical and neurological research databases. Researchers can integrate external datasets by following these steps:
--### **3. Upload Data to Neurodiagnoses**
--**Option 1: Upload to EBRAINS Bucket**
--- Location: **EBRAINS Neurodiagnoses Bucket**
--- Ensure correct **metadata tagging** before submission.##
++1. (((
++**Register for Access**
-- **Option 2: Contribute via GitHub Repository**
--- Location: **GitHub Data Repository**
--- Create a new folder under `/data/` and include a **dataset description**.
--- For large datasets, contact project administrators before uploading.
++* Each external database requires individual registration and access approval.
++* Ensure compliance with ethical approvals and data usage agreements before integrating datasets into Neurodiagnoses.
++* Some repositories may require a Data Usage Agreement (DUA) for sensitive medical data.
++)))
++1. (((
++**Download & Prepare Data**
--### **4. Integrate Data into AI Models**
--- Open **Jupyter Notebooks** on EBRAINS to run **preprocessing scripts**.
--- Standardize **neuroimaging and biomarker formats** using harmonization tools.
--- Use **machine learning models** to handle missing data and feature extraction.
--- Train AI models with **newly integrated patient cohorts**.##
++* Download datasets while adhering to database usage policies.
++* (((
++Ensure files meet Neurodiagnoses format requirements:
--**Reference**: See `docs/data_processing.md` for detailed instructions.
++|=**Data Type**|=**Accepted Formats**
++|**Tabular Data**|.csv, .tsv
++|**Neuroimaging**|.nii, .dcm
++|**Genomic Data**|.fasta, .vcf
++|**Clinical Metadata**|.json, .xml
++)))
++* (((
++**Mandatory Fields for Integration**:
--## **Collaboration & Partnerships**##
--# **Partnering with Data Providers**
--Neurodiagnoses seeks partnerships with data repositories to:
--- Enable **API-based data integration** for real-time processing.
--- Co-develop **harmonized AI-ready datasets** with standardized annotations.
--- Secure **funding opportunities** through joint grant applications.
++* Subject ID: Unique patient identifier
++* Diagnosis: Standardized disease classification
++* Biomarkers: CSF, plasma, or imaging biomarkers
++* Genetic Data: Whole-genome or exome sequencing
++* Neuroimaging Metadata: MRI/PET acquisition parameters
++)))
++)))
++1. (((
++**Upload Data to Neurodiagnoses**
--**Interested in Partnering?**
--- If you represent a research consortium or database provider, reach out to explore data-sharing agreements.
--- **Contact**: info@neurodiagnoses.com
--
--## **Final Notes**
--Neurodiagnoses continuously expands its data ecosystem to support AI-driven clinical decision-making. Researchers and institutions are encouraged to contribute **new datasets and methodologies**.##
--
--For additional technical documentation:
--- **GitHub Repository**: [Neurodiagnoses GitHub](https://github.com/neurodiagnoses)
--- **EBRAINS Collaboration Page**: [EBRAINS Neurodiagnoses](https://ebrains.eu/collabs/neurodiagnoses)
--
--If you experience issues integrating data, **open a GitHub Issue** or consult the **EBRAINS Neurodiagnoses Forum**.
--
--== **How to Use External Databases in Neurodiagnoses** ==
--
--To enhance the accuracy of our diagnostic models, Neurodiagnoses integrates data from multiple biomedical and neurological research databases. If you are a researcher, follow these steps to access, prepare, and integrate data into the Neurodiagnoses framework.
--
--=== **Potential Data Sources** ===
--
--Neurodiagnoses maintains an updated list of potential biomedical databases relevant to neurodegenerative diseases.
--
--* Reference: [[List of Potential Databases>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/data/sources/list_of_potential_databases]]
--
--=== **1. Register for Access** ===
--
--Each external database requires individual registration and access approval. Follow the official guidelines of each database provider.
--
--* Ensure that you have completed all ethical approvals and data access agreements before integrating datasets into Neurodiagnoses.
--* Some repositories require a Data Usage Agreement (DUA) before downloading sensitive medical data.
--
--=== **2. Download & Prepare Data** ===
--
--Once access is granted, download datasets while complying with data usage policies. Ensure that the files meet Neurodiagnoses’ format requirements for smooth integration.
--
--==== **Supported File Formats** ====
--
--* Tabular Data: .csv, .tsv
--* Neuroimaging Data: .nii, .dcm
--* Genomic Data: .fasta, .vcf
--* Clinical Metadata: .json, .xml
--
--==== **Mandatory Fields for Integration** ====
--
--|=Field Name|=Description
--|Subject ID|Unique patient identifier
--|Diagnosis|Standardized disease classification
--|Biomarkers|CSF, plasma, or imaging biomarkers
--|Genetic Data|Whole-genome or exome sequencing
--|Neuroimaging Metadata|MRI/PET acquisition parameters
--
--=== **3. Upload Data to Neurodiagnoses** ===
--
--Once preprocessed, data can be uploaded to EBRAINS or GitHub.
--
  * (((
  **Option 1: Upload to EBRAINS Bucket**
--* Location: [[EBRAINS Neurodiagnoses Bucket>>url:https://wiki.ebrains.eu/bin/view/Collabs/neurodiagnoses/Bucket]]
++* Location: EBRAINS Neurodiagnoses Bucket
  * Ensure correct metadata tagging before submission.
  )))
  * (((
  **Option 2: Contribute via GitHub Repository**
--* Location: [[GitHub Data Repository>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/tree/main/data]]
--* Create a new folder under /data/ and include dataset description.
++* Location: GitHub Data Repository
++* Create a new folder under /data/ and include a dataset description.
++* For large datasets, contact project administrators before uploading.
  )))
++)))
++1. (((
++**Integrate Data into AI Models**
--//Note: For large datasets, please contact the project administrators before uploading.//
--
--=== **4. Integrate Data into AI Models** ===
--
--Once uploaded, datasets must be harmonized and formatted before AI model training.
--
--==== **Steps for Data Integration** ====
--
  * Open Jupyter Notebooks on EBRAINS to run preprocessing scripts.
  * Standardize neuroimaging and biomarker formats using harmonization tools.
--* Use machine learning models to handle missing data and feature extraction.
++* Utilize machine learning models to handle missing data and feature extraction.
  * Train AI models with newly integrated patient cohorts.
--* Reference: [[Detailed instructions can be found in docs/data_processing.md>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/data_processing.md]].
------
++**Reference**: See docs/data_processing.md for detailed instructions.
++)))
--== **Database Sources Table** ==
++**AI-Driven Biomarker Categorization**
--=== **Where to Insert This** ===
++Neurodiagnoses employs advanced AI models for biomarker classification:
--* GitHub: [[docs/data_sources.md>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/data_sources.md]]
--* EBRAINS Wiki: Collabs/neurodiagnoses/Data Sources
++|=**Model Type**|=**Application**
++|**Graph Neural Networks (GNNs)**|Identify shared biomarker pathways across diseases
++|**Contrastive Learning**|Distinguish overlapping vs. unique biomarkers
++|**Multimodal Transformer Models**|Integrate imaging, omics, and clinical data
--=== **Key Databases for Neurodiagnoses** ===
++**Collaboration & Partnerships**
--|=Database|=Focus Area|=Data Type|=Access Link
--|ADNI|Alzheimer's Disease|MRI, PET, CSF, cognitive tests|ADNI
--|PPMI|Parkinson’s Disease|Imaging, biospecimens|[[PPMI>>url:https://www.ppmi-info.org/]]
--|GP2|Genetic Data for PD|Whole-genome sequencing|[[GP2>>url:https://gp2.org/]]
--|Enroll-HD|Huntington’s Disease|Clinical, genetic, imaging|[[Enroll-HD>>url:https://enroll-hd.org/]]
--|GAAIN|Alzheimer's & Cognitive Decline|Multi-source data aggregation|[[GAAIN>>url:https://www.gaain.org/]]
--|UK Biobank|Population-wide studies|Genetic, imaging, health records|[[UK Biobank>>url:https://www.ukbiobank.ac.uk/]]
--|DPUK|Dementia & Aging|Imaging, genetics, lifestyle factors|[[DPUK>>url:https://www.dementiasplatform.uk/]]
--|PRION Registry|Prion Diseases|Clinical and genetic data|[[PRION Registry>>url:https://www.prionalliance.org/]]
--|DECIPHER|Rare Genetic Disorders|Genomic variants|DECIPHER
++Neurodiagnoses actively seeks partnerships with data providers to:
--If you know a relevant dataset, submit a proposal in [[GitHub Issues>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/issues]].
--
------
--
--== **Collaboration & Partnerships** ==
--
--=== **Where to Insert This** ===
--
--* GitHub: [[docs/collaboration.md>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/collaboration.md]]
--* EBRAINS Wiki: Collabs/neurodiagnoses/Collaborations
--
--=== **Partnering with Data Providers** ===
--
--Beyond using existing datasets, Neurodiagnoses seeks partnerships with data repositories to:
--
--* Enable direct API-based data integration for real-time processing.
++* Enable API-based data integration for real-time processing.
  * Co-develop harmonized AI-ready datasets with standardized annotations.
  * Secure funding opportunities through joint grant applications.
--=== **Interested in Partnering?** ===
++**Interested in Partnering?**
  If you represent a research consortium or database provider, reach out to explore data-sharing agreements.
--* Contact: [[info@neurodiagnoses.com>>mailto:info@neurodiagnoses.com]]
++**Contact**: [[info@neurodiagnoses.com>>mailto:info@neurodiagnoses.com]]
------
++**Final Notes**
--== **Final Notes** ==
++Neurodiagnoses AI is committed to advancing the integration of artificial intelligence in neurodiagnostic processes. By continuously expanding our data ecosystem and incorporating standardized biomarker classifications through the Neuromarker ontology, we aim to enhance cross-disease AI training and improve diagnostic accuracy across neurodegenerative disorders.
--Neurodiagnoses continuously expands its data ecosystem to support AI-driven clinical decision-making. Researchers and institutions are encouraged to contribute new datasets and methodologies.
++We encourage researchers and institutions to contribute new datasets and methodologies to further enrich this collaborative platform. Your participation is vital in driving innovation and fostering a deeper understanding of complex neurological conditions.
--For additional technical documentation:
++**For additional technical documentation and collaboration opportunities:**
--* [[GitHub Repository>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses]]
--* [[EBRAINS Collaboration Page>>url:https://wiki.ebrains.eu/bin/view/Collabs/neurodiagnoses/]]
++* **GitHub Repository:** [[Neurodiagnoses GitHub>>url:https://github.com/neurodiagnoses]]
++* **EBRAINS Collaboration Page:** [[EBRAINS Neurodiagnoses>>url:https://ebrains.eu/collabs/neurodiagnoses]]
--If you experience issues integrating data, open a [[GitHub Issue>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/issues]] or consult the EBRAINS Neurodiagnoses Forum.
++If you encounter any issues during data integration or have suggestions for improvement, please open a GitHub Issue or consult the EBRAINS Neurodiagnoses Forum. Together, we can advance the field of neurodiagnostics and contribute to better patient outcomes.

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