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5		-= //A new tridimensional diagnostic framework for CNS diseases// =
	5	+= //A new tridimensional diagnostic framework for complex CNS diseases// =
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.
	7	+This project is focused on developing a novel nosological and diagnostic framework for complex CNS diseases by using advanced AI techniques and integrating data from neuroimaging, biomarkers, and biomedical ontologies.
8	8	We aim to create a structured, interpretable, and scalable diagnostic tool.
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18	18	= **Overview** =
19	19
20	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.
	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.
22	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**.
	23	+Neurodiagnoses is an open-source AI-powered diagnostic system designed for complex CNS disorders, including neurodegenerative diseases, autoimmune encephalopathies, prion disorders, and genetic syndromes. 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.
24	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		-
31	31	The //Tridimensional Diagnostic Framework// redefines CNS diseases can be classified and diagnosed by focusing on:
32	32
33	33	* **Axis 1**: Etiology (genetic or other causes of diseases).
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40	40	* Integration of incomplete datasets using AI-driven probabilistic modeling.
41	41	* Stratification of patients for personalized treatment.
42	42
43		-== **The Role of AI-Powered Annotation** ==
	37	+== **The role of AI-powered annotation** ==
44	44
45		-To enhance **standardization, interpretability, and clinical application**, the framework integrates **an AI-powered annotation system**, which:
	39	+To enhance standardization, interpretability, and clinical application, the framework integrates an AI-powered annotation system, which:
46	46
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).
	41	+* Assigns structured metadata tags to diagnostic features.
	42	+* Provides real-time contextual explanations for AI-based classifications.
	43	+* Tracks longitudinal disease progression using timestamped AI annotations.
	44	+* Improves AI model transparency through interpretability tools (e.g., SHAP analysis).
	45	+* Facilitates decision-making for clinicians by linking annotations to standardized biomedical ontologies (SNOMED, HPO).
52	52
	47	+Neurodiagnoses provides two complementary AI-driven diagnostic approaches:
	48	+
	49	+1. Traditional Probabilistic Diagnosis
	50	+
	51	+* AI provides multiple possible diagnoses, each assigned a probability percentage based on biomarker, imaging, and clinical data.
	52	+* Example Output:
	53	+** 75% Alzheimer's Disease
	54	+** 20% Lewy Body Dementia
	55	+** 5% Vascular Dementia
	56	+* Useful for differential diagnosis and treatment decision-making.
	57	+
	58	+2. Tridimensional Diagnosis
	59	+
	60	+* Diagnoses are structured based on:
	61	+(1) Etiology (genetic, autoimmune, metabolic, infectious)
	62	+(2) Molecular Biomarkers (amyloid-beta, tau, inflammatory markers, EEG patterns)
	63	+(3) Neuroanatomoclinical Correlations (brain atrophy, connectivity alterations)
	64	+* This approach enables precise disease subtyping and biologically meaningful classification, particularly useful to track progression over time.
	65	+
	66	+For every patient case, both systems will be offered, allowing clinicians to compare AI-generated probabilistic diagnosis with a structured tridimensional classification.
	67	+
	68	+
53	53	== **The case of neurodegenerative diseases** ==
54	54
55	55	There have been described these 3 diagnostic axes:
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62	62	* //Description//: Focuses on genetic and sporadic causes, identifying risk factors and potential triggers.
63	63	* //Examples//: APOE ε4 as a genetic risk factor, or cardiovascular health affecting NDD progression.
64	64	* //Tests//: Genetic testing, lifestyle, and cardiovascular screening.
	81	+
	82	+
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66	66	* (((
67	67	**Axis 2: Molecular Markers**
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69	69	* //Description//: Analyzes primary (amyloid-beta, tau) and secondary biomarkers (NFL, GFAP) for tracking disease progression.
70	70	* //Examples//: CSF amyloid-beta concentrations to confirm Alzheimer’s pathology.
71	71	* //Tests//: Blood/CSF biomarkers, PET imaging (Tau-PET, Amyloid-PET).
	90	+
	91	+
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73	73	* (((
74	74	**Axis 3: Neuroanatomoclinical**