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5		-= //A new tridimensional diagnostic framework for CNS diseases// =
	5	+= My Collab's Extended Title =
6	6
7		-This project is focused on developing a novel nosological and diagnostic framework for CNS diseases by using advanced AI techniques and integrating data from neuroimaging, biomarkers, and biomedical ontologies.
8		-We aim to create a structured, interpretable, and scalable diagnostic tool.
	7	+My collab's subtitle
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16		-= What is this about and what can I find here? =
	15	+= What can I find here? =
17	17
18		-= **Overview** =
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	21	+= Who has access? =
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22		-The classification and diagnosis of **central nervous system (CNS) diseases** have long been constrained by **traditional phenotype-based approaches**, which often fail to capture the **complex pathophysiological mechanisms, molecular biomarkers, and neuroanatomical changes** that drive disease progression. **Neurodegenerative and psychiatric disorders**, for example, exhibit significant **clinical overlap, co-pathology, and heterogeneity**, making current diagnostic models insufficient.
23		-
24		-This project proposes a **new diagnostic framework**—one that **shifts from symptom-based classifications** to an **etiology-driven, tridimensional system**. By integrating **genetics, proteomics, neuroimaging, computational modeling, and AI-powered annotations**, this approach aims to provide a **more precise, scalable, and biologically grounded method for diagnosing and managing CNS diseases**.
25		-
26		-The **AI-powered annotation system** plays a critical role by **structuring, interpreting, and tracking multi-modal data**, ensuring **real-time disease progression analysis, clinician decision support, and personalized treatment pathways**.
27		-
28		-=== **Project Aim** ===
29		-
30		-The project aims to develop a **tridimensional diagnostic framework** with an **AI-powered annotation system**, integrating **etiology, molecular biomarkers, and neuroanatomoclinical correlations** for **precise, standardized, and scalable CNS disease diagnostics**.
31		-
32		-The //Tridimensional Diagnostic Framework// redefines CNS diseases can be classified and diagnosed by focusing on:
33		-
34		-* **Axis 1**: Etiology (genetic or other causes of diseases).
35		-* **Axis 2**: Molecular Markers (biomarkers).
36		-* **Axis 3**: Neuroanatomoclinical correlations (linking clinical symptoms to structural changes in the nervous system).
37		-
38		-This methodology enables:
39		-
40		-* Greater precision in diagnosis.
41		-* Integration of incomplete datasets using AI-driven probabilistic modeling.
42		-* Stratification of patients for personalized treatment.
43		-
44		-== **The Role of AI-Powered Annotation** ==
45		-
46		-To enhance **standardization, interpretability, and clinical application**, the framework integrates **an AI-powered annotation system**, which:
47		-
48		-* **Assigns structured metadata tags** to diagnostic features.
49		-* **Provides real-time contextual explanations** for AI-based classifications.
50		-* **Tracks longitudinal disease progression** using timestamped AI annotations.
51		-* **Improves AI model transparency** through interpretability tools (e.g., SHAP analysis).
52		-* **Facilitates decision-making for clinicians** by linking annotations to standardized biomedical ontologies (SNOMED, HPO).
53		-
54		-== **The case of neurodegenerative diseases** ==
55		-
56		-There have been described these 3 diagnostic axes:
57		-
58		-[[Neurodegenerative diseases can be studied and classified in a tridimensional scheme with three axes: anatomic–clinical, molecular, and etiologic. CSF, cerebrospinal fluid; FDG, fluorodeoxyglucose; MRI, magnetic resonance imaging; PET, positron emission tomography.>>image:tridimensional.png||alt="tridimensional view of neurodegenerative diseases"]]
59		-
60		-* (((
61		-**Axis 1: Etiology**
62		-
63		-* //Description//: Focuses on genetic and sporadic causes, identifying risk factors and potential triggers.
64		-* //Examples//: APOE ε4 as a genetic risk factor, or cardiovascular health affecting NDD progression.
65		-* //Tests//: Genetic testing, lifestyle, and cardiovascular screening.
	23	+Describe the audience of this collab.
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67		-* (((
68		-**Axis 2: Molecular Markers**
69	69
70		-* //Description//: Analyzes primary (amyloid-beta, tau) and secondary biomarkers (NFL, GFAP) for tracking disease progression.
71		-* //Examples//: CSF amyloid-beta concentrations to confirm Alzheimer’s pathology.
72		-* //Tests//: Blood/CSF biomarkers, PET imaging (Tau-PET, Amyloid-PET).
73		-)))
74		-* (((
75		-**Axis 3: Neuroanatomoclinical**
76	76
77		-* //Description//: Links clinical symptoms to neuroanatomical changes, such as atrophy or functional impairments.
78		-* //Examples//: Hippocampal atrophy correlating with memory deficits.
79		-* //Tests//: MRI volumetrics, FDG-PET, neuropsychological evaluations.
80		-)))
81		-
82		-== **Applications** ==
83		-
84		-This system enhances:
85		-
86		-* **Research**: By stratifying patients, reduces cohort heterogeneity in clinical trials.
87		-* **Clinical Practice**: Provides dynamic diagnostic annotations with timestamps for longitudinal tracking.
88		-
89		-== How to Contribute ==
90		-
91		-* Access the `/docs` folder for guidelines.
92		-* Use `/code` for the latest AI pipelines.
93		-* Share feedback and ideas in the wiki discussion pages.
94		-
95		-== Key Objectives ==
96		-
97		-* Develop interpretable AI models for diagnosis and progression tracking.
98		-* Integrate data from Human Phenotype Ontology (HPO), Gene Ontology (GO), and other biomedical resources.
99		-* Foster collaboration among neuroscientists, AI researchers, and clinicians.
100		-
101		-== Who has access? ==
102		-
103		-We welcome contributions from the global community. Let’s build the future of neurological diagnostics together!
104		-)))
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107		-
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109		-
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113	113	{{box title="**Contents**"}}
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114	114	{{toc/}}
115	115	{{/box}}
116	116
117		-== Main contents ==
118		-
119		-* `/docs`: Documentation and contribution guidelines.
120		-* `/code`: Machine learning pipelines and scripts.
121		-* `/data`: Sample datasets for testing.
122		-* `/outputs`: Generated models, visualizations, and reports.
123		-* [[Methodology>>url:https://wiki.ebrains.eu/bin/view/Collabs/neurodiagnoses/Methodology/]]
124		-* [[Results>>url:https://wiki.ebrains.eu/bin/view/Collabs/neurodiagnoses/Results/]]
125		-* [[to-do-list>>to-do-list]]
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