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1		-This document outlines the full workflow for Neurodiagnoses—from data acquisition and AI model training to clinical validation, ethical compliance, cloud deployment, and future expansion into CNS Digital Twins.
	1	+== **1. Data Management & Integration** ==
2	2
3		-----
4		-
5		-== 1. Data Management & Integration ==
6		-
7		-* (((
8		-**Data Acquisition & Storage:**
9		-
10		-* Download raw data from external sources (e.g., ADNI, GP2, PPMI, Enroll-HD, UK Biobank, etc.).
11		-* Upload and organize datasets in EBRAINS Buckets and in the /datasets/ directory on GitHub.
12		-)))
13		-* (((
14		-**Data Conversion & Format:**
15		-
16		-* Convert all datasets to standardized formats (.csv, .json, .h5) to facilitate AI processing.
17		-)))
18		-* (((
19		-**Data Harmonization:**
20		-
	3	+* Upload and organize harmonized biomarker datasets (PROMINENT).
	4	+* Store EEG, sleep, and neuroimaging data in the EBRAINS Bucket.
	5	+* Convert all datasets to .csv, .json, or .h5 formats for easier AI processing.
21	21	* Implement automated data ingestion scripts to streamline updates from new sources.
22		-* Set up data harmonization methods to ensure consistency across different sources (e.g., genetics, neuroimaging, biomarkers, digital health).
23		-)))
24		-* (((
25		-**Federated Learning:**
	7	+* Set up data harmonization methods to ensure consistency across different sources.
	8	+* Enable Federated Learning to train AI models on multi-center data without sharing raw patient data (GDPR-compliant).
26	26
27		-* Enable federated learning techniques to train AI models on multi-center data without sharing raw patient data (ensuring GDPR compliance).
28		-)))
	10	+== **2. AI-Based Risk Prediction & Diagnosis** ==
29	29
30		-----
	12	+* Implement machine learning models for dementia risk stratification (LETHE).
	13	+* Develop AI-based probabilistic models for filling in missing data (KNN Imputer, Bayesian approaches).
	14	+* Train AI models using multi-modal data (biomarkers, EEG, MRI, and lifestyle factors).
	15	+* Store pretrained models in the /models/ directory for future use.
	16	+* Implement real-time AI-based diagnostic annotation for clinicians.
	17	+* Add confidence intervals to AI predictions for clinical decision support.
	18	+* Integrate Explainable AI (SHAP analysis) to ensure transparency and clinician trust.
	19	+* Implement deep learning for pattern recognition in neuroimaging data (MRI/PET-based feature extraction).
	20	+* Explore the use of Large Language Models (LLMs) for medical report summarization.
31	31
32		-== 2. AI-Based Risk Prediction & Diagnosis ==
	22	+== **3. EEG, Neuroimaging & Sleep Analysis** ==
33	33
34		-* (((
35		-**Predictive Modeling:**
	24	+* Process EEG/MEG data using MNE-Python (AI-Mind).
	25	+* Apply EEG biomarkers for dementia detection (spectral analysis, connectivity metrics).
	26	+* Integrate sleep monitoring data from ADIS (smartwatches, headbands) as an early biomarker.
	27	+* Use MRI volumetric analysis for assessing brain atrophy in high-risk patients.
	28	+* Implement functional MRI (fMRI) analysis to link neuroanatomical changes with cognitive function.
36	36
37		-* Implement machine learning models (e.g., Random Forest, Neural Networks) for dementia risk stratification.
38		-* Develop probabilistic models (e.g., KNN Imputer, Bayesian approaches) to handle missing data.
39		-)))
40		-* (((
41		-**Training with Multi-Modal Data:**
	30	+== **4. Clinical Validation & Pilot Testing** ==
42	42
43		-* Train AI models using data from biomarkers, EEG, MRI, and lifestyle factors.
44		-* Store pre-trained models in the /models/ directory for future use.
45		-)))
46		-* (((
47		-**Diagnostic Annotation System:**
48		-
49		-* Implement real-time AI-based diagnostic annotation that produces two types of reports for each case:
50		-** **Probabilistic Diagnosis:** Traditional diagnosis with associated probability percentages.
51		-** **Tridimensional Diagnosis:** A structured classification based on three axes—etiology, molecular markers, and neuroanatomoclinical correlations.
52		-* Integrate Explainable AI techniques (e.g., SHAP) to ensure transparency in predictions.
53		-* Explore advanced deep learning methods for pattern recognition in neuroimaging data.
54		-* Investigate the use of Large Language Models (LLMs) for summarizing and generating medical reports.
55		-)))
56		-
57		-----
58		-
59		-== 3. EEG, Neuroimaging & Sleep Analysis ==
60		-
61		-* (((
62		-**EEG/MEG Analysis:**
63		-
64		-* Process EEG/MEG data using tools like MNE-Python.
65		-* Apply spectral analysis and connectivity metrics to derive EEG biomarkers for dementia detection.
66		-)))
67		-* (((
68		-**Sleep Monitoring:**
69		-
70		-* Integrate sleep data from wearables (smartwatches, headbands) as early biomarkers.
71		-)))
72		-* (((
73		-**Neuroimaging Analysis:**
74		-
75		-* Utilize MRI volumetric analysis to assess brain atrophy in high-risk patients.
76		-* Implement functional MRI (fMRI) analysis to correlate neuroanatomical changes with cognitive function.
77		-)))
78		-
79		-----
80		-
81		-== 4. Clinical Validation & Pilot Testing ==
82		-
83		-* (((
84		-**Pilot Study Design:**
85		-
86		-* Design a multicenter pilot study to validate AI-generated diagnostic scores.
87		-* Recruit a clinical validation cohort from European research hospitals.
88		-)))
89		-* (((
90		-**Performance Evaluation:**
91		-
92		-* Compare AI-based diagnoses with traditional clinician diagnoses.
93		-* Develop and track validation metrics (e.g., AUROC, precision-recall, false positive rates).
94		-)))
95		-* (((
96		-**Feedback and Refinement:**
97		-
	32	+* Design a pilot study to validate AI-generated diagnostic scores.
	33	+* Recruit a multicenter clinical validation cohort across European research hospitals.
	34	+* Compare AI-based diagnoses with clinician-based diagnoses to measure performance.
	35	+* Develop validation metrics (e.g., AUROC, precision-recall, false positive rates).
	36	+* Conduct a prospective study to test predictive accuracy over time.
98	98	* Implement clinician feedback loops to refine the AI model based on real-world usage.
99		-* Publish validation results in peer-reviewed journals to enhance credibility.
100		-)))
	38	+* Publish validation results in peer-reviewed journals for credibility.
101	101
102		-----
	40	+== **5. Ethical, Regulatory & GDPR Compliance** ==
103	103
104		-== 5. Ethical, Regulatory & GDPR Compliance ==
	42	+* Ensure AI models comply with the EU AI Act for medical applications.
	43	+* Implement privacy-preserving AI techniques (Federated Learning, Differential Privacy).
	44	+* Develop patient data anonymization pipelines before AI processing.
	45	+* Secure ethics approval for data usage in clinical applications.
	46	+* Set up consent management systems for patient data contributions.
	47	+* Ensure interoperability with hospital Electronic Health Records (EHRs).
105	105
106		-* (((
107		-**Regulatory Compliance:**
	49	+== **6. EBRAINS Deployment & Cloud Infrastructure** ==
108	108
109		-* Ensure all AI models comply with relevant regulations (e.g., EU AI Act, GDPR).
110		-)))
111		-* (((
112		-**Privacy Preservation:**
	51	+* Deploy AI models on EBRAINS Cloud for real-time inference.
	52	+* Set up Jupyter Notebooks in EBRAINS Lab for collaborative development.
	53	+* Automate model training pipelines using GitHub Actions or EBRAINS’ HPC.
	54	+* Optimize computational efficiency to ensure AI inference runs on real-time clinical data.
113	113
114		-* Implement privacy-preserving techniques (Federated Learning, Differential Privacy) to protect patient data.
115		-* Develop data anonymization pipelines prior to AI processing.
116		-)))
117		-* (((
118		-**Consent & Data Governance:**
	56	+== **7. Interactive Web App for Clinicians & Researchers** ==
119	119
120		-* Establish consent management systems for patient data contributions.
121		-* Ensure interoperability with hospital Electronic Health Record (EHR) systems.
122		-)))
	58	+* Develop an interactive web-based AI diagnostic tool (Flask, FastAPI, or Streamlit).
	59	+* Allow clinicians to input biomarker data and get real-time AI predictions.
	60	+* Enable PDF report generation for clinical decision-making.
	61	+* Integrate custom dashboards with risk stratification results.
	62	+* Deploy the tool on **neurodiagnoses.com** using Netlify, Vercel, or AWS.
123	123
124		-----
	64	+== **8. Cross-Project Collaborations** ==
125	125
126		-== 6. EBRAINS Deployment & Cloud Infrastructure ==
	66	+* Partner with AI-Mind for integrating EEG-based predictive models.
	67	+* Collaborate with LETHE on lifestyle-based cognitive decline risk scoring.
	68	+* Use PROMINENT’s multi-modal AI pipeline for refining dementia subtype classification.
	69	+* Leverage ADIS sleep monitoring research for non-invasive biomarker expansion.
	70	+* Expand partnerships with clinical institutions to increase dataset size.
127	127
128		-* **Cloud Deployment:**
129		-** Deploy AI models on the EBRAINS Cloud for real-time inference.
130		-* **Collaborative Development:**
131		-** Set up Jupyter Notebooks in EBRAINS Lab for collaborative development and testing.
132		-** Automate model training pipelines using GitHub Actions or EBRAINS HPC resources.
133		-* **Optimization:**
134		-** Optimize computational efficiency to enable real-time processing of clinical data.
	72	+== **9. Long-Term Expansion & Future Goals** ==
135	135
136		-----
137		-
138		-== 7. Interactive Web Application for Clinicians & Researchers ==
139		-
140		-* **Web App Development:**
141		-** Develop an interactive web-based diagnostic tool using frameworks such as Flask, FastAPI, or Streamlit.
142		-** Allow clinicians to input biomarker data and receive real-time AI predictions.
143		-* **Report Generation:**
144		-** Enable the generation of PDF reports for clinical decision support.
145		-* **Custom Dashboards:**
146		-** Integrate dashboards that display risk stratification results.
147		-* **Deployment:**
148		-** Deploy the web app on neurodiagnoses.com using hosting services like Netlify, Vercel, or AWS.
149		-
150		-----
151		-
152		-== 8. Cross-Project Collaborations ==
153		-
154		-* (((
155		-**External Partnerships:**
156		-
157		-* Collaborate with projects such as AI-Mind for EEG-based predictive modeling.
158		-* Work with LETHE for lifestyle-based cognitive decline risk scoring.
159		-* Leverage PROMINENT’s multi-modal AI pipeline to refine dementia subtype classification.
160		-* Expand partnerships with clinical institutions to enhance dataset diversity.
161		-)))
162		-* (((
163		-**Open-Source Community:**
164		-
165		-* Encourage contributions via GitHub (code improvements, new features) and EBRAINS discussion pages (research and validation).
166		-)))
167		-
168		-----
169		-
170		-== 9. Long-Term Expansion & Future Goals ==
171		-
172		-* **Disease Progression Modeling:**
173		-** Explore AI-powered models for tracking neurodegeneration over time.
174		-* **CNS Digital Twins:**
175		-** Develop CNS Digital Twins by integrating multi-omics data, neuroimaging, and digital health records to create personalized simulations of disease progression.
176		-* **Continuous Monitoring:**
177		-** Investigate the integration of wearable health tracking devices for ongoing cognitive assessment.
178		-* **Open-Access API:**
179		-** Create an API to allow global research collaborations with access to AI diagnostic tools.
180		-* **Sustainability & Updates:**
181		-** Regularly update the system with new data and algorithm improvements.
182		-** Establish long-term funding and partnership strategies to ensure sustainability.
183		-
184		-----
185		-
186		-=== Key Resources ===
187		-
188		-* **GitHub Repository:** [[Neurodiagnoses on GitHub>>https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/discussions]]
189		-* **EBRAINS Collaboratory:** [[Neurodiagnoses on EBRAINS>>url:https://wiki.ebrains.eu/bin/view/Collabs/neurodiagnoses/]]
	74	+* Explore AI-powered disease progression models for tracking neurodegeneration over time.
	75	+* Develop real-time multimodal patient monitoring (EEG, MRI, biomarkers, lifestyle).
	76	+* Investigate genomics and proteomics for precision diagnostics.
	77	+* Integrate wearable health tracking for continuous cognitive assessment.
	78	+* Create an open-access AI diagnostic API for global research collaborations.