Wiki source code of Methodology

Version 17.1 by manuelmenendez on 2025/02/09 13:01
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1 == **Overview** ==
2
3 Neurodiagnoses develops a **tridimensional diagnostic framework** for **CNS diseases**, incorporating **AI-powered annotation tools** to improve **interpretability, standardization, and clinical utility.**
4
5 This methodology integrates **multi-modal data**, including:
6 **Genetic data** (whole-genome sequencing, polygenic risk scores).
7 **Neuroimaging** (MRI, PET, EEG, MEG).
8 **Neurophysiological data** (EEG-based biomarkers, sleep actigraphy).
9 **CSF & Blood Biomarkers** (Amyloid-beta, Tau, Neurofilament Light).
10
11 By applying **machine learning models**, Neurodiagnoses generates **structured, explainable diagnostic outputs** to assist **clinical decision-making** and **biomarker-driven patient stratification.**
12
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14
15 == **Data Integration & External Databases** ==
16
17 === **How to Use External Databases in Neurodiagnoses** ===
18
19 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.
20
21 **Potential Data Sources**
22 **Reference:** [[List of Potential Databases>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/data/sources/list_of_potential_databases]]
23
24 === **Register for Access** ===
25
26 Each **external database** requires **individual registration** and approval.
27 ✔️ Follow the official **data access guidelines** of each provider.
28 ✔️ Ensure compliance with **ethical approvals** and **data-sharing agreements (DUAs).**
29
30 === **Download & Prepare Data** ===
31
32 Once access is granted, download datasets **following compliance guidelines** and **format requirements** for integration.
33
34 **Supported File Formats**
35
36 * **Tabular Data**: .csv, .tsv
37 * **Neuroimaging Data**: .nii, .dcm
38 * **Genomic Data**: .fasta, .vcf
39 * **Clinical Metadata**: .json, .xml
40
41 **Mandatory Fields for Integration**
42
43 |=**Field Name**|=**Description**
44 |**Subject ID**|Unique patient identifier
45 |**Diagnosis**|Standardized disease classification
46 |**Biomarkers**|CSF, plasma, or imaging biomarkers
47 |**Genetic Data**|Whole-genome or exome sequencing
48 |**Neuroimaging Metadata**|MRI/PET acquisition parameters
49
50 === **Upload Data to Neurodiagnoses** ===
51
52 **Option 1:** Upload to **EBRAINS Bucket** → [[Neurodiagnoses Data Storage>>url:https://wiki.ebrains.eu/bin/view/Collabs/neurodiagnoses/Bucket]]
53 **Option 2:** Contribute via **GitHub Repository** → [[GitHub Data Repository>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/tree/main/data]]
54
55 **For large datasets, please contact project administrators before uploading.**
56
57 === **Integrate Data into AI Models** ===
58
59 Use **Jupyter Notebooks** on EBRAINS for **data preprocessing.**
60 Standardize data using **harmonization tools.**
61 Train AI models with **newly integrated datasets.**
62
63 **Reference:** [[Data Processing Guide>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/data_processing.md]]
64
65 ----
66
67 == **AI-Powered Annotation & Machine Learning Models** ==
68
69 Neurodiagnoses applies **advanced machine learning models** to classify CNS diseases, extract features from **biomarkers and neuroimaging**, and provide **AI-powered annotation.**
70
71 === **AI Model Categories** ===
72
73 |=**Model Type**|=**Function**|=**Example Algorithms**
74 |**Probabilistic Diagnosis**|Assigns probability scores to multiple CNS disorders.|Random Forest, XGBoost, Bayesian Networks
75 |**Tridimensional Diagnosis**|Classifies disorders based on Etiology, Biomarkers, and Neuroanatomical Correlations.|CNNs, Transformers, Autoencoders
76 |**Biomarker Prediction**|Predicts missing biomarker values using regression.|KNN Imputation, Bayesian Estimation
77 |**Neuroimaging Feature Extraction**|Extracts patterns from MRI, PET, EEG.|CNNs, Graph Neural Networks
78 |**Clinical Decision Support**|Generates AI-driven diagnostic reports.|SHAP Explainability Tools
79
80 **Reference:** [[AI Model Documentation>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/models.md]]
81
82 ----
83
84 == **Clinical Decision Support & Tridimensional Diagnostic Framework** ==
85
86 Neurodiagnoses generates **structured AI reports** for clinicians, combining:
87
88 **Probabilistic Diagnosis:** AI-generated ranking of potential diagnoses.
89 **Tridimensional Classification:** Standardized diagnostic reports based on:
90
91 1. **Axis 1:** **Etiology** → Genetic, Autoimmune, Prion, Toxic, Vascular.
92 1. **Axis 2:** **Molecular Markers** → CSF, Neuroinflammation, EEG biomarkers.
93 1. **Axis 3:** **Neuroanatomoclinical Correlations** → MRI atrophy, PET.
94
95 **Reference:** [[Tridimensional Classification Guide>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/classification.md]]
96
97 ----
98
99 == **Data Security, Compliance & Federated Learning** ==
100
101 ✔ **Privacy-Preserving AI**: Implements **Federated Learning**, ensuring that patient data **never leaves** local institutions.
102 ✔ **Secure Data Access**: Data remains **stored in EBRAINS MIP servers** using **differential privacy techniques.**
103 ✔ **Ethical & GDPR Compliance**: Data-sharing agreements **must be signed** before use.
104
105 **Reference:** [[Data Protection & Federated Learning>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/security.md]]
106
107 ----
108
109 == **Data Processing & Integration with Clinica.Run** ==
110
111 Neurodiagnoses now supports **Clinica.Run**, an **open-source neuroimaging platform** for **multimodal data processing.**
112
113 === **How It Works** ===
114
115 ✔ **Neuroimaging Preprocessing**: MRI, PET, EEG data is preprocessed using **Clinica.Run pipelines.**
116 ✔ **Automated Biomarker Extraction**: Extracts volumetric, metabolic, and functional biomarkers.
117 ✔ **Data Security & Compliance**: Clinica.Run is **GDPR & HIPAA-compliant.**
118
119 === **Implementation Steps** ===
120
121 1. Install **Clinica.Run** dependencies.
122 1. Configure **Clinica.Run pipeline** in clinica_run_config.json.
123 1. Run **biomarker extraction pipelines** for AI-based diagnostics.
124
125 **Reference:** [[Clinica.Run Documentation>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/clinica_run.md]]
126
127 ----
128
129 == **Collaborative Development & Research** ==
130
131 **We Use GitHub to Develop AI Models & Store Research Data**
132
133 * **GitHub Repository:** AI model training scripts.
134 * **GitHub Issues:** Tracks ongoing research questions.
135 * **GitHub Wiki:** Project documentation & user guides.
136
137 **We Use EBRAINS for Data & Collaboration**
138
139 * **EBRAINS Buckets:** Large-scale neuroimaging and biomarker storage.
140 * **EBRAINS Jupyter Notebooks:** Cloud-based AI model execution.
141 * **EBRAINS Wiki:** Research documentation and updates.
142
143 **Join the Project Forum:** [[GitHub Discussions>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/discussions]]
144
145 ----
146
147 **For Additional Documentation:**
148
149 * **GitHub Repository:** [[Neurodiagnoses AI Models>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses]]
150 * **EBRAINS Wiki:** [[Neurodiagnoses Research Collaboration>>url:https://wiki.ebrains.eu/bin/view/Collabs/neurodiagnoses/]]
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153
154 **Neurodiagnoses is Open for Contributions – Join Us Today!**