Update README.md

README.md

@@ -61,39 +61,102 @@ This project builds a **multi-agent system** for clinical decision support. A ce
 ---
 
 ## Architecture
-```mermaid
-flowchart LR
-  U[Clinician / User] -->|case, symptoms, meds| ORCH(MCP Orchestrator)
-  ORCH -->|route| AG1[Diagnostics Agent]
-  ORCH -->|route| AG2[Pharmacology Agent]
-  ORCH -->|route| AG3[Triage Agent]
-
-  subgraph RAG[Agentic RAG]
-    Q[Query Router] --> RET[Retriever (Node & Graph)]
-    RET --> KB1[(EMR/EHR)]
-    RET --> KB2[(PubMed)]
-    RET --> SR[Safety Rails: filters, provenance, sectioning]
-  end
-
-  AG1 --> RAG
-  AG2 --> RAG
-  AG3 --> RAG
-  RAG --> AG1
-  RAG --> AG2
-  RAG --> AG3
-
-  AG1 --> FUSE[Evidence Fusion & Self-Consistent Reasoning]
-  AG2 --> FUSE
-  AG3 --> FUSE
-  FUSE --> OUT[Final Report: summary, citations, cautions]
-
-  subgraph EVAL[Evaluation & QA]
-    M1[MedMCQA]
-    M2[PubMedQA]
-    SIM[Semantic Similarity Audits (biomedical embeddings)]
-    LR[Early-Stopping + LR Scheduling]
-  end
-  OUT -. logged .-> EVAL
+
+### *L1. System Overall*
+
+```plaintext
++------------------------+                                       +----------------------------+
+| 1. Clinician UI / EMR  |--C1: symptoms, meds, files ---------> | 2. MCP Orchestrator        |
+| plug-in (PHI-safe)     |                                       | FastAPI router, planning   |
++------------------------+                                       | safety, tracing (traceID)  |
+                                                                 +-------------+--------------+
+                                                                               |
+                                                                               | plan / route
+                                                                               v
+                                                       +-----------------------+-----------------------+
+                                                       |        3. Specialist LLM Agents              |
+                                                       | +-----------------+  +---------------------+ |
+                                                       | | Diagnostics     |  | Pharmacology (Rx)   | |
+                                                       | | differential Dx |  | DDI, dosing, contra.| |
+                                                       | +-----------------+  +---------------------+ |
+                                                       | +-----------------+  +---------------------+ |
+                                                       | | Triage          |  | Summarizer (SOAP)   | |
+                                                       | | urgency, dispo. |  | clinical notes      | |
+                                                       | +-----------------+  +---------------------+ |
+                                                       +-----------------------+-----------------------+
+                                                                               ^           ^    ^
+                                                                               |           |    |
+                                                                               | evidence  |    | evidence
+                                                                               |           |    |
++---------------------------+       evidence queries        +-------------------+-----------+----+----------+
+| 5. VectorDB / Long-Term   | <--------------------------- | 4. Agentic RAG (Query Router --> Retriever --> |
+| Memory (EMR+Lit embeds,   | ---------------------------> | Safety Rails)                                 |
+| chat turns, provenance)   |   store traces/embeddings    +-------------------+-------------------------+-+
++---------------------------+                                                      |                       |
+                                                                                   | top-k, citations      |
+                                                                                   v                       v
+                                                                            +-------------+        +---------------+
+                                                                            | 4c. Med KB  |        | 4d. EMR       |
+                                                                            | PubMed,     |        | summarizer    |
+                                                                            | guidelines  |        | (PHI-safe)    |
+                                                                            +-------------+        +---------------+
+
+                                                                               |
+                                                                               | answers + rationale + citations
+                                                                               v
+                                                     +-------------------------+------------------------+
+                                                     | 7. Evidence Fusion & Self-Consistency (MCP)     |
+                                                     | voting, SLM adjudication, risk flags, refusal   |
+                                                     +-------------------------+------------------------+
+                                                                               |
+                                                                               v
++------------------------+       final report (summary, plan, citations, cautions)       +--------------------+
+| 1. Clinician UI / EMR  | <----------------------------------------------------------------- | 8. Evaluation & |
+|  (display result)      |                                                                     |    QA Harness   |
++------------------------+ --------------------- telemetry / traces -------------------------> | MedMCQA,        |
+                                                                                               | PubMedQA, sim   |
+                                                                                               | audits, LR ctrl |
+                                                                                               +-----------------+
+```
+
+### *L2. Agentic RAG Internals*
+
+```plaintext
++----------------------------- 4. Agentic RAG ----------------------------------------------+
+| Inputs: symptoms, vitals, meds, files, chat LTM snippets                                   |
+|                                                                                            |
+|  +-----------------+     +-----------------+     +--------------------+                    |
+|  | 4b Query Router | --> | 4b Rewriter     | --> | 4b/RET Retriever   | -- top-k -->      |
+|  | (Node / Graph)  |     | (expand/disamb) |     | (vector + keyword) |                  |
+|  +--------+--------+     +-----------------+     +----------+---------+                  |
+|           |                                         filter τ  |                           |
+|  +--------v--------+                                   +------v------+     +-----------+ |
+|  | 4 SR Safety     |  allowlist, section filters,      | 4c Med KB   |     | 4d EMR    | |
+|  | Rails           |  dedupe, provenance enforcement   | (PubMed/GL) |     | Summarizer| |
+|  +--------+--------+                                   +------+------ +     +-----+-----+ |
+|           |                                                   |                  |       |
+|  +--------v--------+                                   +------v------+     +-----v-----+ |
+|  | 5 VectorDB/LTM  | <---- write embeddings/traces ----| evidence    |     | patient   | |
+|  | (embeds+proven.)|                                   | bundle      |     | snippets  | |
+|  +-----------------+                                   +-------------+     +-----------+ |
++------------------------------------------------------------------------------------------+
+Outputs: Evidence bundle [{snippet, section, citation, similarity}], EMR summary, provenance map
+```
+
+### *L3. Single-turn Dataflow*
+
+```plaintext
+Clinician --> UI/EMR --> MCP Orchestrator --> RAG (Router --> Retriever --> SafetyRails)
+            ^                                        |                                   \
+            |                                        v                                    \
+            |                                   EMR Summarizer ----------------------------\
+            |                                                                                 \
+            \------------------------------ Final Report <----- Evidence Fusion <---- Agents (Dx/Rx/Triage)
+                                                     |                      ^                 /
+                                                     |                      |                /
+                                                     +--> VectorDB/LTM -----+----- write ----
+                                                                                     \
+                                                                                      --> Evaluation/QA
 ```
 
 ---
@@ -142,36 +205,6 @@ flowchart LR
 
 ---
 
-## Repository Structure
-
-```
-├─ apps/
-│  ├─ orchestrator/           # MCP planner/router, self-consistency, fusion
-│  ├─ agent_diagnostics/      # differential logic, red flags, uncertainty
-│  ├─ agent_pharmacology/     # DDIs, dosing, contraindications
-│  └─ agent_triage/           # urgency/disposition policy
-├─ rag/
-│  ├─ pipelines/              # Node & Graph RAG, safety rails
-│  ├─ build_index.py          # EMR/EHR + PubMed indexing
-│  └─ server.py               # retrieval API with citation payloads
-├─ training/
-│  ├─ datasets/               # loaders for curated/synthetic cases
-│  ├─ augmentation/           # QAC, counterfactuals, back-translation
-│  ├─ finetune/               # KD, LoRA/QLoRA, GRPO loops
-│  ��─ configs/                # seeds, LR schedules, early-stopping
-├─ eval/
-│  ├─ medmcqa/                # benchmark harness
-│  ├─ pubmedqa/               # benchmark harness
-│  └─ semantics/              # embedding audits, hallucination metrics
-├─ docs/                      # design notes, risk register, policies
-├─ scripts/                   # utilities, data prep, CI hooks
-├─ requirements.txt
-├─ .env.example
-└─ LICENSE
-```
-
----
-
 ## Roadmap
 
 * [ ] Expand specialty coverage (cardiology, oncology, paediatrics).
@@ -219,7 +252,4 @@ https://huggingface.co/MedAI-COS30018
 ---
 
 ## License
-Apache-2.0.
-
-
-
+MIT License.