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15	15	(((
16	16	= What is this about and what can I find here? =
17	17
18		-== **Overview** ==
	18	+= **Overview** =
19	19
	20	+
	21	+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.
	22	+
	23	+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**.
	24	+
	25	+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**.
	26	+
	27	+=== **Project Aim** ===
	28	+
	29	+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**.
	30	+
20	20	The //Tridimensional Diagnostic Framework// redefines CNS diseases can be classified and diagnosed by focusing on:
21	21
22	22	* **Axis 1**: Etiology (genetic or other causes of diseases).
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23	23	* **Axis 2**: Molecular Markers (biomarkers).
24	24	* **Axis 3**: Neuroanatomoclinical correlations (linking clinical symptoms to structural changes in the nervous system).
25	25
26		-
27		-[[For instance, 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"]]
28		-
29		-
30	30	This methodology enables:
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32	32	* Greater precision in diagnosis.
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33	33	* Integration of incomplete datasets using AI-driven probabilistic modeling.
34	34	* Stratification of patients for personalized treatment.
35	35
	43	+== **The Role of AI-Powered Annotation** ==
	44	+
	45	+To enhance **standardization, interpretability, and clinical application**, the framework integrates **an AI-powered annotation system**, which:
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	47	+* **Assigns structured metadata tags** to diagnostic features.
	48	+* **Provides real-time contextual explanations** for AI-based classifications.
	49	+* **Tracks longitudinal disease progression** using timestamped AI annotations.
	50	+* **Improves AI model transparency** through interpretability tools (e.g., SHAP analysis).
	51	+* **Facilitates decision-making for clinicians** by linking annotations to standardized biomedical ontologies (SNOMED, HPO).
	52	+
36	36	== **The case of neurodegenerative diseases** ==
37	37
38	38	There have been described these 3 diagnostic axes:
39	39
	57	+[[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"]]
	58	+
40	40	* (((
41	41	**Axis 1: Etiology**
42	42
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66	66	* **Research**: By stratifying patients, reduces cohort heterogeneity in clinical trials.
67	67	* **Clinical Practice**: Provides dynamic diagnostic annotations with timestamps for longitudinal tracking.
68	68
69		-== Who has access? ==
70		-
71		-We welcome contributions from the global community. Let’s build the future of neurological diagnostics together!
72		-
73	73	== How to Contribute ==
74	74
75	75	* Access the `/docs` folder for guidelines.
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81	81	* Develop interpretable AI models for diagnosis and progression tracking.
82	82	* Integrate data from Human Phenotype Ontology (HPO), Gene Ontology (GO), and other biomedical resources.
83	83	* Foster collaboration among neuroscientists, AI researchers, and clinicians.
	99	+
	100	+== Who has access? ==
	101	+
	102	+We welcome contributions from the global community. Let’s build the future of neurological diagnostics together!
84	84	)))
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	109	+
87	87	(% class="col-xs-12 col-sm-4" %)
88	88	(((
89	89	{{box title="**Contents**"}}
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97	97	* `/data`: Sample datasets for testing.
98	98	* `/outputs`: Generated models, visualizations, and reports.
99	99	* [[Methodology>>url:https://wiki.ebrains.eu/bin/view/Collabs/neurodiagnoses/Methodology/]]
	123	+* [[Notebooks>>Notebooks]]
100	100	* [[Results>>url:https://wiki.ebrains.eu/bin/view/Collabs/neurodiagnoses/Results/]]
101	101	* [[to-do-list>>to-do-list]]
102	102	)))