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1		-== **Overview** ==
	1	+==== **Overview** ====
2	2
3		-Neurodiagnoses develops a **tridimensional diagnostic framework** for **CNS diseases**, incorporating **AI-powered annotation tools** to improve **interpretability, standardization, and clinical utility.**
	3	+This project 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**.
4	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).
	5	+=== **Workflow** ===
10	10
11		-By applying **machine learning models**, Neurodiagnoses generates **structured, explainable diagnostic outputs** to assist **clinical decision-making** and **biomarker-driven patient stratification.**
	7	+1. (((
	8	+**We Use GitHub to [[Store and develop AI models, scripts, and annotation pipelines.>>https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/discussions]]**
12	12
	10	+* Create a **GitHub repository** for AI scripts and models.
	11	+* Use **GitHub Projects** to manage research milestones.
	12	+)))
	13	+1. (((
	14	+**We Use EBRAINS for Data & Collaboration**
	15	+
	16	+* Store **biomarker and neuroimaging data** in **EBRAINS Buckets**.
	17	+* Run **Jupyter Notebooks** in **EBRAINS Lab** to test AI models.
	18	+* Use **EBRAINS Wiki** for structured documentation and research discussion.
	19	+)))
	20	+
13	13	----
14	14
15		-== **Data Integration & External Databases** ==
	23	+=== **1. Data Integration** ===
16	16
17		-=== **How to Use External Databases in Neurodiagnoses** ===
	25	+== Overview ==
18	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	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]]
	28	+Neurodiagnoses integrates clinical data via the **EBRAINS Medical Informatics Platform (MIP)**. MIP federates decentralized clinical data, allowing Neurodiagnoses to securely access and process sensitive information for AI-based diagnostics.
23	23
24		-=== **Register for Access** ===
	30	+== How It Works ==
25	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	29
30		-=== **Download & Prepare Data** ===
	33	+1. (((
	34	+**Authentication & API Access:**
31	31
32		-Once access is granted, download datasets **following compliance guidelines** and **format requirements** for integration.
	36	+* Users must have an **EBRAINS account**.
	37	+* Neurodiagnoses uses **secure API endpoints** to fetch clinical data (e.g., from the **Federation for Dementia**).
	38	+)))
	39	+1. (((
	40	+**Data Mapping & Harmonization:**
33	33
34		-**Supported File Formats**
	42	+* Retrieved data is **normalized** and converted to standard formats (.csv, .json).
	43	+* Data from **multiple sources** is harmonized to ensure consistency for AI processing.
	44	+)))
	45	+1. (((
	46	+**Security & Compliance:**
35	35
36		-* **Tabular Data**: .csv, .tsv
37		-* **Neuroimaging Data**: .nii, .dcm
38		-* **Genomic Data**: .fasta, .vcf
39		-* **Clinical Metadata**: .json, .xml
	48	+* All data access is **logged and monitored**.
	49	+* Data remains on **MIP servers** using **federated learning techniques** when possible.
	50	+* Access is granted only after signing a **Data Usage Agreement (DUA)**.
	51	+)))
40	40
41		-**Mandatory Fields for Integration**
	53	+== Implementation Steps ==
42	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	49
50		-=== **Upload Data to Neurodiagnoses** ===
	56	+1. Clone the repository.
	57	+1. Configure your **EBRAINS API credentials** in mip_integration.py.
	58	+1. Run the script to **download and harmonize clinical data**.
	59	+1. Process the data for **AI model training**.
51	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]]
	61	+For more detailed instructions, please refer to the **[[MIP Documentation>>url:https://mip.ebrains.eu/]]**.
54	54
55		-**For large datasets, please contact project administrators before uploading.**
	63	+----
56	56
57		-=== **Integrate Data into AI Models** ===
	65	+= Data Processing & Integration with Clinica.Run =
58	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	62
63		-**Reference:** [[Data Processing Guide>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/data_processing.md]]
	68	+== Overview ==
64	64
65		-----
66	66
67		-== **AI-Powered Annotation & Machine Learning Models** ==
	71	+Neurodiagnoses now supports **Clinica.Run**, an open-source neuroimaging platform designed for **multimodal data processing and reproducible neuroscience workflows**.
68	68
69		-Neurodiagnoses applies **advanced machine learning models** to classify CNS diseases, extract features from **biomarkers and neuroimaging**, and provide **AI-powered annotation.**
	73	+== How It Works ==
70	70
71		-=== **AI Model Categories** ===
72	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
	76	+1. (((
	77	+**Neuroimaging Preprocessing:**
79	79
80		-**Reference:** [[AI Model Documentation>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/models.md]]
	79	+* MRI, PET, EEG data is preprocessed using **Clinica.Run pipelines**.
	80	+* Supports **longitudinal and cross-sectional analyses**.
	81	+)))
	82	+1. (((
	83	+**Automated Biomarker Extraction:**
81	81
	85	+* Standardized extraction of **volumetric, metabolic, and functional biomarkers**.
	86	+* Integration with machine learning models in Neurodiagnoses.
	87	+)))
	88	+1. (((
	89	+**Data Security & Compliance:**
	90	+
	91	+* Clinica.Run operates in **compliance with GDPR and HIPAA**.
	92	+* Neuroimaging data remains **within the original storage environment**.
	93	+)))
	94	+
	95	+== Implementation Steps ==
	96	+
	97	+
	98	+1. Install **Clinica.Run** dependencies.
	99	+1. Configure your **Clinica.Run pipeline** in clinica_run_config.json.
	100	+1. Run the pipeline for **preprocessing and biomarker extraction**.
	101	+1. Use processed neuroimaging data for **AI-driven diagnostics** in Neurodiagnoses.
	102	+
	103	+For further information, refer to **[[Clinica.Run Documentation>>url:https://clinica.run/]]**.
	104	+
	105	+==== ====
	106	+
	107	+==== **Data Sources** ====
	108	+
	109	+[[List of potential sources of databases>>https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/data/sources/list_of_potential_databases]]
	110	+
	111	+**Biomedical Ontologies & Databases:**
	112	+
	113	+* **Human Phenotype Ontology (HPO)** for symptom annotation.
	114	+* **Gene Ontology (GO)** for molecular and cellular processes.
	115	+
	116	+**Dimensionality Reduction and Interpretability:**
	117	+
	118	+* **Evaluate interpretability** using metrics like the **Area Under the Interpretability Curve (AUIC)**.
	119	+* **Leverage [[DEIBO>>https://github.com/Mellandd/DEIBO]] (Data-driven Embedding Interpretation Based on Ontologies)** to connect model dimensions to ontology concepts.
	120	+
	121	+**Neuroimaging & EEG/MEG Data:**
	122	+
	123	+* **MRI volumetric measures** for brain atrophy tracking.
	124	+* **EEG functional connectivity patterns** (AI-Mind).
	125	+
	126	+**Clinical & Biomarker Data:**
	127	+
	128	+* **CSF biomarkers** (Amyloid-beta, Tau, Neurofilament Light).
	129	+* **Sleep monitoring and actigraphy data** (ADIS).
	130	+
	131	+**Federated Learning Integration:**
	132	+
	133	+* **Secure multi-center data harmonization** (PROMINENT).
	134	+
82	82	----
83	83
84		-== **Clinical Decision Support & Tridimensional Diagnostic Framework** ==
	137	+==== **Annotation System for Multi-Modal Data** ====
85	85
86		-Neurodiagnoses generates **structured AI reports** for clinicians, combining:
	139	+To ensure **structured integration of diverse datasets**, **Neurodiagnoses** will implement an **AI-driven annotation system**, which will:
87	87
88		-**Probabilistic Diagnosis:** AI-generated ranking of potential diagnoses.
89		-**Tridimensional Classification:** Standardized diagnostic reports based on:
	141	+* **Assign standardized metadata tags** to diagnostic features.
	142	+* **Provide contextual explanations** for AI-based classifications.
	143	+* **Track temporal disease progression annotations** to identify long-term trends.
90	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.
	145	+----
94	94
95		-**Reference:** [[Tridimensional Classification Guide>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/classification.md]]
	147	+=== **2. AI-Based Analysis** ===
96	96
	149	+==== **Machine Learning & Deep Learning Models** ====
	150	+
	151	+**Risk Prediction Models:**
	152	+
	153	+* **LETHE’s cognitive risk prediction model** integrated into the annotation framework.
	154	+
	155	+**Biomarker Classification & Probabilistic Imputation:**
	156	+
	157	+* **KNN Imputer** and **Bayesian models** used for handling **missing biomarker data**.
	158	+
	159	+**Neuroimaging Feature Extraction:**
	160	+
	161	+* **MRI & EEG data** annotated with **neuroanatomical feature labels**.
	162	+
	163	+==== **AI-Powered Annotation System** ====
	164	+
	165	+* Uses **SHAP-based interpretability tools** to explain model decisions.
	166	+* Generates **automated clinical annotations** in structured reports.
	167	+* Links findings to **standardized medical ontologies** (e.g., **SNOMED, HPO**).
	168	+
97	97	----
98	98
99		-== **Data Security, Compliance & Federated Learning** ==
	171	+=== **3. Diagnostic Framework & Clinical Decision Support** ===
100	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.
	173	+==== **Tridimensional Diagnostic Axes** ====
104	104
105		-**Reference:** [[Data Protection & Federated Learning>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/security.md]]
	175	+**Axis 1: Etiology (Pathogenic Mechanisms)**
106	106
	177	+* Classification based on **genetic markers, cellular pathways, and environmental risk factors**.
	178	+* **AI-assisted annotation** provides **causal interpretations** for clinical use.
	179	+
	180	+**Axis 2: Molecular Markers & Biomarkers**
	181	+
	182	+* **Integration of CSF, blood, and neuroimaging biomarkers**.
	183	+* **Structured annotation** highlights **biological pathways linked to diagnosis**.
	184	+
	185	+**Axis 3: Neuroanatomoclinical Correlations**
	186	+
	187	+* **MRI and EEG data** provide anatomical and functional insights.
	188	+* **AI-generated progression maps** annotate **brain structure-function relationships**.
	189	+
107	107	----
108	108
109		-== **Data Processing & Integration with Clinica.Run** ==
	192	+=== **4. Computational Workflow & Annotation Pipelines** ===
110	110
111		-Neurodiagnoses now supports **Clinica.Run**, an **open-source neuroimaging platform** for **multimodal data processing.**
	194	+==== **Data Processing Steps** ====
112	112
113		-=== **How It Works** ===
	196	+**Data Ingestion:**
114	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.**
	198	+* **Harmonized datasets** stored in **EBRAINS Bucket**.
	199	+* **Preprocessing pipelines** clean and standardize data.
118	118
119		-=== **Implementation Steps** ===
	201	+**Feature Engineering:**
120	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.
	203	+* **AI models** extract **clinically relevant patterns** from **EEG, MRI, and biomarkers**.
124	124
125		-**Reference:** [[Clinica.Run Documentation>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/docs/clinica_run.md]]
	205	+**AI-Generated Annotations:**
126	126
	207	+* **Automated tagging** of diagnostic features in **structured reports**.
	208	+* **Explainability modules (SHAP, LIME)** ensure transparency in predictions.
	209	+
	210	+**Clinical Decision Support Integration:**
	211	+
	212	+* **AI-annotated findings** fed into **interactive dashboards**.
	213	+* **Clinicians can adjust, validate, and modify annotations**.
	214	+
127	127	----
128	128
129		-== **Collaborative Development & Research** ==
	217	+=== **5. Validation & Real-World Testing** ===
130	130
131		-**We Use GitHub to Develop AI Models & Store Research Data**
	219	+==== **Prospective Clinical Study** ====
132	132
133		-* **GitHub Repository:** AI model training scripts.
134		-* **GitHub Issues:** Tracks ongoing research questions.
135		-* **GitHub Wiki:** Project documentation & user guides.
	221	+* **Multi-center validation** of AI-based **annotations & risk stratifications**.
	222	+* **Benchmarking against clinician-based diagnoses**.
	223	+* **Real-world testing** of AI-powered **structured reporting**.
136	136
137		-**We Use EBRAINS for Data & Collaboration**
	225	+==== **Quality Assurance & Explainability** ====
138	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.
	227	+* **Annotations linked to structured knowledge graphs** for improved transparency.
	228	+* **Interactive annotation editor** allows clinicians to validate AI outputs.
142	142
143		-**Join the Project Forum:** [[GitHub Discussions>>url:https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/discussions]]
	230	+----
144	144
	232	+=== **6. Collaborative Development** ===
	233	+
	234	+The project is **open to contributions** from **researchers, clinicians, and developers**.
	235	+
	236	+**Key tools include:**
	237	+
	238	+* **Jupyter Notebooks**: For data analysis and pipeline development.
	239	+** Example: **probabilistic imputation**
	240	+* **Wiki Pages**: For documenting methods and results.
	241	+* **Drive and Bucket**: For sharing code, data, and outputs.
	242	+* **Collaboration with related projects**:
	243	+** Example: **Beyond the hype: AI in dementia – from early risk detection to disease treatment**
	244	+
145	145	----
146	146
147		-**For Additional Documentation:**
	247	+=== **7. Tools and Technologies** ===
148	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/]]
	249	+==== **Programming Languages:** ====
151	151
	251	+* **Python** for AI and data processing.
	252	+
	253	+==== **Frameworks:** ====
	254	+
	255	+* **TensorFlow** and **PyTorch** for machine learning.
	256	+* **Flask** or **FastAPI** for backend services.
	257	+
	258	+==== **Visualization:** ====
	259	+
	260	+* **Plotly** and **Matplotlib** for interactive and static visualizations.
	261	+
	262	+==== **EBRAINS Services:** ====
	263	+
	264	+* **Collaboratory Lab** for running Notebooks.
	265	+* **Buckets** for storing large datasets.
	266	+
152	152	----
153	153
154		-**Neurodiagnoses is Open for Contributions – Join Us Today!**
	269	+=== **Why This Matters** ===
	270	+
	271	+* The annotation system ensures that AI-generated insights are structured, interpretable, and clinically meaningful.
	272	+* It enables real-time tracking of disease progression across the three diagnostic axes.
	273	+* It facilitates integration with electronic health records and decision-support tools, improving AI adoption in clinical workflows.