Wiki source code of to-do-list

Last modified by manuelmenendez on 2025/02/08 17:21
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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.
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5 == 1. Data Management & Integration ==
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8 **Data Acquisition & Storage:**
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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.
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14 **Data Conversion & Format:**
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16 * Convert all datasets to standardized formats (.csv, .json, .h5) to facilitate AI processing.
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19 **Data Harmonization:**
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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).
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25 **Federated Learning:**
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27 * Enable federated learning techniques to train AI models on multi-center data without sharing raw patient data (ensuring GDPR compliance).
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32 == 2. AI-Based Risk Prediction & Diagnosis ==
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35 **Predictive Modeling:**
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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.
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41 **Training with Multi-Modal Data:**
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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.
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47 **Diagnostic Annotation System:**
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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.
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59 == 3. EEG, Neuroimaging & Sleep Analysis ==
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62 **EEG/MEG Analysis:**
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64 * Process EEG/MEG data using tools like MNE-Python.
65 * Apply spectral analysis and connectivity metrics to derive EEG biomarkers for dementia detection.
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68 **Sleep Monitoring:**
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70 * Integrate sleep data from wearables (smartwatches, headbands) as early biomarkers.
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73 **Neuroimaging Analysis:**
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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.
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81 == 4. Clinical Validation & Pilot Testing ==
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84 **Pilot Study Design:**
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86 * Design a multicenter pilot study to validate AI-generated diagnostic scores.
87 * Recruit a clinical validation cohort from European research hospitals.
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90 **Performance Evaluation:**
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92 * Compare AI-based diagnoses with traditional clinician diagnoses.
93 * Develop and track validation metrics (e.g., AUROC, precision-recall, false positive rates).
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96 **Feedback and Refinement:**
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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.
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104 == 5. Ethical, Regulatory & GDPR Compliance ==
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107 **Regulatory Compliance:**
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109 * Ensure all AI models comply with relevant regulations (e.g., EU AI Act, GDPR).
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112 **Privacy Preservation:**
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114 * Implement privacy-preserving techniques (Federated Learning, Differential Privacy) to protect patient data.
115 * Develop data anonymization pipelines prior to AI processing.
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118 **Consent & Data Governance:**
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120 * Establish consent management systems for patient data contributions.
121 * Ensure interoperability with hospital Electronic Health Record (EHR) systems.
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126 == 6. EBRAINS Deployment & Cloud Infrastructure ==
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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.
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138 == 7. Interactive Web Application for Clinicians & Researchers ==
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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.
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152 == 8. Cross-Project Collaborations ==
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155 **External Partnerships:**
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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.
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163 **Open-Source Community:**
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165 * Encourage contributions via GitHub (code improvements, new features) and EBRAINS discussion pages (research and validation).
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170 == 9. Long-Term Expansion & Future Goals ==
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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.
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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/]]