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1 -== **Overview** ==
1 +**Neurodiagnoses AI** is an open-source, AI-driven framework designed to enhance the diagnosis and prognosis of central nervous system (CNS) disorders. It 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) **and** **Disease Knowledge Transfer (DKT), which standardizes disease and biomarker classification across all CNS diseases, facilitating cross-disease AI training.
2 2  
3 -Neurodiagnoses develops a tridimensional diagnostic framework for CNS diseases, incorporating AI-powered annotation tools to improve interpretability, standardization, and clinical utility. The methodology integrates multi-modal data, including genetic, neuroimaging, neurophysiological, and biomarker datasets, and applies machine learning models to generate structured, explainable diagnostic outputs.
3 +**Neuromarker: Generalized Biomarker Ontology**
4 4  
5 -----
5 +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.
6 6  
7 -== **How to Use External Databases in Neurodiagnoses** ==
7 +**Recommended Software**
8 8  
9 -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.
9 +There is a suite of software that can help implement the workflow needed in Neurodiagnoses. Find a list of recommendations [[here>>https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/recommended_software]].
10 10  
11 -=== **Potential Data Sources** ===
11 +**Core Biomarker Categories**
12 12  
13 -Neurodiagnoses maintains an updated list of potential biomedical databases relevant to neurodegenerative diseases.
13 +Within the Neurodiagnoses AI framework, biomarkers are categorized as follows:
14 14  
15 -* Reference: [[List of Potential Databases>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/data/sources/list_of_potential_databases]]
15 +|=**Category**|=**Description**
16 +|**Molecular Biomarkers**|Omics-based markers (genomic, transcriptomic, proteomic, metabolomic, lipidomic)
17 +|**Neuroimaging Biomarkers**|Structural (MRI, CT), Functional (fMRI, PET), Molecular Imaging (tau, amyloid, α-synuclein)
18 +|**Fluid Biomarkers**|CSF, plasma, blood-based markers for tau, amyloid, α-synuclein, TDP-43, GFAP, NfL, autoantiboides
19 +|**Neurophysiological Biomarkers**|EEG, MEG, evoked potentials (ERP), sleep-related markers
20 +|**Digital Biomarkers**|Gait analysis, cognitive/speech biomarkers, wearables data, EHR-based markers
21 +|**Clinical Phenotypic Markers**|Standardized clinical scores (MMSE, MoCA, CDR, UPDRS, ALSFRS, UHDRS)
22 +|**Genetic Biomarkers**|Risk alleles (APOE, LRRK2, MAPT, C9orf72, PRNP) and polygenic risk scores
23 +|**Environmental & Lifestyle Factors**|Toxins, infections, diet, microbiome, comorbidities
16 16  
17 -=== **1. Register for Access** ===
25 +**Integrating External Databases into Neurodiagnoses**
18 18  
19 -Each external database requires individual registration and access approval. Follow the official guidelines of each database provider.
27 +To enhance diagnostic precision, Neurodiagnoses AI incorporates data from multiple biomedical and neurological research databases. Researchers can integrate external datasets by following these steps:
20 20  
21 -* Ensure that you have completed all ethical approvals and data access agreements before integrating datasets into Neurodiagnoses.
22 -* Some repositories require a Data Usage Agreement (DUA) before downloading sensitive medical data.
29 +1. (((
30 +**Register for Access**
23 23  
24 -=== **2. Download & Prepare Data** ===
32 +* Each external database requires individual registration and access approval.
33 +* Ensure compliance with ethical approvals and data usage agreements before integrating datasets into Neurodiagnoses.
34 +* Some repositories may require a Data Usage Agreement (DUA) for sensitive medical data.
35 +)))
36 +1. (((
37 +**Download & Prepare Data**
25 25  
26 -Once access is granted, download datasets while complying with data usage policies. Ensure that the files meet Neurodiagnoses’ format requirements for smooth integration.
39 +* Download datasets while adhering to database usage policies.
40 +* (((
41 +Ensure files meet Neurodiagnoses format requirements:
27 27  
28 -==== **Supported File Formats** ====
43 +|=**Data Type**|=**Accepted Formats**
44 +|**Tabular Data**|.csv, .tsv
45 +|**Neuroimaging**|.nii, .dcm
46 +|**Genomic Data**|.fasta, .vcf
47 +|**Clinical Metadata**|.json, .xml
48 +)))
49 +* (((
50 +**Mandatory Fields for Integration**:
29 29  
30 -* Tabular Data: .csv, .tsv
31 -* Neuroimaging Data: .nii, .dcm
32 -* Genomic Data: .fasta, .vcf
33 -* Clinical Metadata: .json, .xml
52 +* Subject ID: Unique patient identifier
53 +* Diagnosis: Standardized disease classification
54 +* Biomarkers: CSF, plasma, or imaging biomarkers
55 +* Genetic Data: Whole-genome or exome sequencing
56 +* Neuroimaging Metadata: MRI/PET acquisition parameters
57 +)))
58 +)))
59 +1. (((
60 +**Upload Data to Neurodiagnoses**
34 34  
35 -==== **Mandatory Fields for Integration** ====
36 -
37 -|=Field Name|=Description
38 -|Subject ID|Unique patient identifier
39 -|Diagnosis|Standardized disease classification
40 -|Biomarkers|CSF, plasma, or imaging biomarkers
41 -|Genetic Data|Whole-genome or exome sequencing
42 -|Neuroimaging Metadata|MRI/PET acquisition parameters
43 -
44 -=== **3. Upload Data to Neurodiagnoses** ===
45 -
46 -Once preprocessed, data can be uploaded to EBRAINS or GitHub.
47 -
48 48  * (((
49 49  **Option 1: Upload to EBRAINS Bucket**
50 50  
51 -* Location: [[EBRAINS Neurodiagnoses Bucket>>url:https://wiki.ebrains.eu/bin/view/Collabs/neurodiagnoses/Bucket]]
65 +* Location: EBRAINS Neurodiagnoses Bucket
52 52  * Ensure correct metadata tagging before submission.
53 53  )))
54 54  * (((
55 55  **Option 2: Contribute via GitHub Repository**
56 56  
57 -* Location: [[GitHub Data Repository>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/tree/main/data]]
58 -* Create a new folder under /data/ and include dataset description.
71 +* Location: GitHub Data Repository
72 +* Create a new folder under /data/ and include a dataset description.
73 +* For large datasets, contact project administrators before uploading.
59 59  )))
75 +)))
76 +1. (((
77 +**Integrate Data into AI Models**
60 60  
61 -//Note: For large datasets, please contact the project administrators before uploading.//
62 -
63 -=== **4. Integrate Data into AI Models** ===
64 -
65 -Once uploaded, datasets must be harmonized and formatted before AI model training.
66 -
67 -==== **Steps for Data Integration** ====
68 -
69 69  * Open Jupyter Notebooks on EBRAINS to run preprocessing scripts.
70 70  * Standardize neuroimaging and biomarker formats using harmonization tools.
71 -* Use machine learning models to handle missing data and feature extraction.
81 +* Utilize machine learning models to handle missing data and feature extraction.
72 72  * Train AI models with newly integrated patient cohorts.
73 -* 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]].
74 74  
75 -----
84 +**Reference**: See docs/data_processing.md for detailed instructions.
85 +)))
76 76  
77 -== **Database Sources Table** ==
87 +**AI-Driven Biomarker Categorization**
78 78  
79 -=== **Where to Insert This** ===
89 +Neurodiagnoses employs advanced AI models for biomarker classification:
80 80  
81 -* GitHub: [[docs/data_sources.md>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/data_sources.md]]
82 -* EBRAINS Wiki: Collabs/neurodiagnoses/Data Sources
91 +|=**Model Type**|=**Application**
92 +|**Graph Neural Networks (GNNs)**|Identify shared biomarker pathways across diseases
93 +|**Contrastive Learning**|Distinguish overlapping vs. unique biomarkers
94 +|**Multimodal Transformer Models**|Integrate imaging, omics, and clinical data
83 83  
84 -=== **Key Databases for Neurodiagnoses** ===
96 +**Collaboration & Partnerships**
85 85  
86 -|=Database|=Focus Area|=Data Type|=Access Link
87 -|ADNI|Alzheimer's Disease|MRI, PET, CSF, cognitive tests|ADNI
88 -|PPMI|Parkinson’s Disease|Imaging, biospecimens|[[PPMI>>url:https://www.ppmi-info.org/]]
89 -|GP2|Genetic Data for PD|Whole-genome sequencing|[[GP2>>url:https://gp2.org/]]
90 -|Enroll-HD|Huntington’s Disease|Clinical, genetic, imaging|[[Enroll-HD>>url:https://enroll-hd.org/]]
91 -|GAAIN|Alzheimer's & Cognitive Decline|Multi-source data aggregation|[[GAAIN>>url:https://www.gaain.org/]]
92 -|UK Biobank|Population-wide studies|Genetic, imaging, health records|[[UK Biobank>>url:https://www.ukbiobank.ac.uk/]]
93 -|DPUK|Dementia & Aging|Imaging, genetics, lifestyle factors|[[DPUK>>url:https://www.dementiasplatform.uk/]]
94 -|PRION Registry|Prion Diseases|Clinical and genetic data|[[PRION Registry>>url:https://www.prionalliance.org/]]
95 -|DECIPHER|Rare Genetic Disorders|Genomic variants|DECIPHER
98 +Neurodiagnoses actively seeks partnerships with data providers to:
96 96  
97 -If you know a relevant dataset, submit a proposal in [[GitHub Issues>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/issues]].
98 -
99 -----
100 -
101 -== **Collaboration & Partnerships** ==
102 -
103 -=== **Where to Insert This** ===
104 -
105 -* GitHub: [[docs/collaboration.md>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/collaboration.md]]
106 -* EBRAINS Wiki: Collabs/neurodiagnoses/Collaborations
107 -
108 -=== **Partnering with Data Providers** ===
109 -
110 -Beyond using existing datasets, Neurodiagnoses seeks partnerships with data repositories to:
111 -
112 -* Enable direct API-based data integration for real-time processing.
100 +* Enable API-based data integration for real-time processing.
113 113  * Co-develop harmonized AI-ready datasets with standardized annotations.
114 114  * Secure funding opportunities through joint grant applications.
115 115  
116 -=== **Interested in Partnering?** ===
104 +**Interested in Partnering?**
117 117  
118 118  If you represent a research consortium or database provider, reach out to explore data-sharing agreements.
119 119  
120 -* Contact: [[info@neurodiagnoses.com>>mailto:info@neurodiagnoses.com]]
108 +**Contact**: [[info@neurodiagnoses.com>>mailto:info@neurodiagnoses.com]]
121 121  
122 -----
110 +**Final Notes**
123 123  
124 -== **Final Notes** ==
112 +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.
125 125  
126 -Neurodiagnoses continuously expands its data ecosystem to support AI-driven clinical decision-making. Researchers and institutions are encouraged to contribute new datasets and methodologies.
114 +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.
127 127  
128 -For additional technical documentation:
116 +**For additional technical documentation and collaboration opportunities:**
129 129  
130 -* [[GitHub Repository>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses]]
131 -* [[EBRAINS Collaboration Page>>url:https://wiki.ebrains.eu/bin/view/Collabs/neurodiagnoses/]]
118 +* **GitHub Repository:** [[Neurodiagnoses GitHub>>url:https://github.com/neurodiagnoses]]
119 +* **EBRAINS Collaboration Page:** [[EBRAINS Neurodiagnoses>>url:https://ebrains.eu/collabs/neurodiagnoses]]
132 132  
133 -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.
121 +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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