Add SISTER-Lite interactive lookup app

.gitignore

@@ -1,5 +1,6 @@
 __pycache__/
 *.py[cod]
+.venv/
 .ipynb_checkpoints/
 results/raw/*.npz
 

data/sister_lite/sister_lite_grid.csv

@@ -0,0 +1,20 @@
+model,g_k1,g_to,bcl_ms,verapamil,valid,captured_beats,stimuli_count,analysis_beats,apd90_rsd_last5,apd90_ms,ca_amplitude_um,apd_alt_ms,ca_alt_relative,strong_alternans_probability,valid_denominator_n,strong_positive_n,discard_reason,source_label
+Paci,0.1,1.0,475,true,true,50,50,25,0.021,245,0.19,199.1,1.267,1.000,20,20,,low_ik1_confirmation
+Paci,0.1,1.0,500,true,true,50,50,25,0.024,252,0.18,157.8,1.046,0.900,20,18,,low_ik1_confirmation
+Paci,0.1,1.0,525,true,true,50,50,25,0.028,264,0.16,111.5,0.874,0.750,20,15,,low_ik1_confirmation
+Paci,0.25,1.0,500,true,true,50,50,25,0.031,271,0.17,58.2,0.361,0.579,57,33,,internal_validation_57_9_percent
+Paci,0.25,1.0,500,false,true,50,50,25,0.026,284,0.22,31.6,0.181,0.329,73,24,,internal_validation_32_9_percent
+Paci,0.25,1.0,475,true,true,50,50,25,0.034,267,0.15,34.8,0.143,0.420,50,21,,curated_low_gk1_window
+Paci,0.25,1.0,525,true,true,50,50,25,0.029,276,0.18,27.4,0.126,0.310,55,17,,curated_low_gk1_window
+Paci,0.4,1.0,500,true,true,50,50,25,0.018,302,0.21,19.4,0.109,0.180,50,9,,curated_weak_edge
+Paci,0.5,1.0,500,true,true,50,50,25,0.015,315,0.23,11.7,0.071,0.084,83,7,,internal_validation_8_4_percent
+Paci,1.0,1.0,500,true,true,50,50,25,0.012,318,0.19,5.4,0.034,0.020,50,1,,rescued_repolarization_reserve
+Paci,1.5,1.0,500,true,true,50,50,25,0.008,326,0.20,1.4,0.018,0.000,60,0,,high_gk1_negative_control
+Paci,1.5,1.0,500,false,true,50,50,25,0.006,342,0.26,0.9,0.009,0.000,60,0,,high_gk1_negative_control
+ORd,0.25,1.0,500,true,true,50,50,25,0.003,283,0.10,0.9,0.015,0.000,15,0,,ord_key_conditions_0_of_15
+ORd,0.25,1.0,500,false,true,50,50,25,0.002,286,0.11,0.7,0.012,0.000,15,0,,ord_adult_negative_control
+ORd,1.5,1.0,500,true,true,50,50,25,0.004,313,0.13,0.6,0.010,0.000,15,0,,ord_high_gk1_negative_control
+Grandi,0.25,1.0,500,true,true,50,50,25,0.006,295,0.12,3.1,0.026,0.000,12,0,,adult_calibrated_placeholder_negative
+Grandi,1.5,1.0,500,true,true,50,50,25,0.004,321,0.14,1.0,0.011,0.000,12,0,,adult_calibrated_placeholder_negative
+Paci,0.03,1.0,500,true,false,0,0,0,,0,0,0,0,0,0,0,g_k1_out_of_tested_range,parameter_guard
+Paci,2.1,1.0,500,true,false,0,0,0,,0,0,0,0,0,0,0,g_k1_out_of_tested_range,parameter_guard

environment.yml

@@ -10,3 +10,7 @@ dependencies:
   - pip
   - pip:
       - pypdf>=5.0
+      - fastapi>=0.136
+      - uvicorn>=0.46
+      - pytest>=9.0
+      - httpx>=0.28

requirements.txt

@@ -3,3 +3,7 @@ matplotlib>=3.8
 pandas>=2.0
 scipy>=1.10
 pypdf>=5.0
+fastapi>=0.136
+uvicorn>=0.46
+pytest>=9.0
+httpx>=0.28

src/run_sister_lite.py

@@ -0,0 +1,3 @@
+from src.sister_lite.api import app
+
+__all__ = ["app"]

src/sister_lite/__init__.py

@@ -0,0 +1,5 @@
+"""SISTER-Lite web lookup package."""
+
+from .service import SisterLookupService
+
+__all__ = ["SisterLookupService"]

src/sister_lite/api.py

@@ -0,0 +1,114 @@
+from __future__ import annotations
+
+from pathlib import Path
+from uuid import uuid4
+
+from fastapi import FastAPI, HTTPException, Query
+from fastapi.responses import FileResponse
+from fastapi.staticfiles import StaticFiles
+from pydantic import BaseModel, Field
+
+from .models import LookupParameters
+from .service import SisterLookupService
+
+STATIC_DIR = Path(__file__).resolve().parent / "static"
+
+app = FastAPI(
+    title="SISTER-Lite",
+    description="Structure-Informed Stress Testing of Electrophysiological Risk for open-science hypothesis generation.",
+    version="0.1.0",
+)
+app.mount("/static", StaticFiles(directory=STATIC_DIR), name="static")
+
+service = SisterLookupService()
+JOBS: dict[str, dict[str, object]] = {}
+
+
+class SimulationRequest(BaseModel):
+    model: str = Field(default="Paci")
+    g_k1: float = Field(default=0.25, ge=0.0, le=2.5)
+    g_to: float = Field(default=1.0, ge=0.1, le=2.0)
+    bcl_ms: float = Field(default=500.0, ge=300.0, le=800.0)
+    verapamil: bool = Field(default=True)
+
+
+class OptimizeRequest(BaseModel):
+    target_apd_alt_ms: float = Field(default=25.0, ge=0.0, le=250.0)
+    model: str = Field(default="Paci")
+    verapamil: bool = Field(default=True)
+
+
+@app.get("/")
+def index() -> FileResponse:
+    return FileResponse(STATIC_DIR / "index.html")
+
+
+@app.get("/api/health")
+def health() -> dict[str, object]:
+    return {"status": "ok", "grid_rows": len(service.rows)}
+
+
+@app.get("/api/lookup")
+def lookup_get(
+    model: str = Query(default="Paci"),
+    g_k1: float = Query(default=0.25, ge=0.0, le=2.5),
+    g_to: float = Query(default=1.0, ge=0.1, le=2.0),
+    bcl_ms: float = Query(default=500.0, ge=300.0, le=800.0),
+    verapamil: bool = Query(default=True),
+) -> dict[str, object]:
+    return _lookup(SimulationRequest(model=model, g_k1=g_k1, g_to=g_to, bcl_ms=bcl_ms, verapamil=verapamil))
+
+
+@app.post("/api/lookup")
+def lookup_post(request: SimulationRequest) -> dict[str, object]:
+    return _lookup(request)
+
+
+@app.post("/api/simulate")
+def simulate(request: SimulationRequest) -> dict[str, object]:
+    result = _lookup(request)
+    job_id = f"sister-lite-{uuid4().hex[:12]}"
+    JOBS[job_id] = {"status": "completed", "result": result}
+    return {"job_id": job_id, "status": "completed", "result": result}
+
+
+@app.get("/api/status/{job_id}")
+def status(job_id: str) -> dict[str, object]:
+    job = JOBS.get(job_id)
+    if job is None:
+        raise HTTPException(status_code=404, detail="Unknown job_id")
+    return {"job_id": job_id, **job}
+
+
+@app.get("/api/compare")
+def compare(
+    g_k1: float = Query(default=0.25, ge=0.0, le=2.5),
+    g_to: float = Query(default=1.0, ge=0.1, le=2.0),
+    bcl_ms: float = Query(default=500.0, ge=300.0, le=800.0),
+    verapamil: bool = Query(default=True),
+) -> dict[str, object]:
+    try:
+        return service.compare_models(LookupParameters("Paci", g_k1, bcl_ms, verapamil, g_to))
+    except ValueError as exc:
+        raise HTTPException(status_code=422, detail=str(exc)) from exc
+
+
+@app.post("/api/optimize")
+def optimize(request: OptimizeRequest) -> dict[str, object]:
+    try:
+        rows = service.optimize(request.target_apd_alt_ms, request.model, request.verapamil)
+    except ValueError as exc:
+        raise HTTPException(status_code=422, detail=str(exc)) from exc
+    return {
+        "target_apd_alt_ms": request.target_apd_alt_ms,
+        "candidates": rows,
+        "method": "nearest precomputed SISTER-Lite grid search; BoTorch-ready API contract",
+    }
+
+
+def _lookup(request: SimulationRequest) -> dict[str, object]:
+    try:
+        result = service.lookup(LookupParameters(request.model, request.g_k1, request.bcl_ms, request.verapamil, request.g_to))
+    except ValueError as exc:
+        raise HTTPException(status_code=422, detail=str(exc)) from exc
+    return service.to_dict(result)

src/sister_lite/models.py

@@ -0,0 +1,64 @@
+from __future__ import annotations
+
+from dataclasses import dataclass
+from enum import StrEnum
+
+
+class Outcome(StrEnum):
+    INVALID = "invalid"
+    VALID_NEGATIVE = "valid_negative"
+    WEAK_ALTERNANS = "weak_alternans"
+    STRONG_POSITIVE = "strong_positive"
+
+
+@dataclass(frozen=True)
+class LookupParameters:
+    model: str
+    g_k1: float
+    bcl_ms: float
+    verapamil: bool
+    g_to: float = 1.0
+
+
+@dataclass(frozen=True)
+class SimulationRow:
+    model: str
+    g_k1: float
+    g_to: float
+    bcl_ms: float
+    verapamil: bool
+    valid: bool
+    captured_beats: int
+    stimuli_count: int
+    analysis_beats: int
+    apd90_rsd_last5: float | None
+    apd90_ms: float
+    ca_amplitude_um: float
+    apd_alt_ms: float
+    ca_alt_relative: float
+    strong_alternans_probability: float
+    valid_denominator_n: int
+    strong_positive_n: int
+    discard_reason: str
+    source_label: str
+
+
+@dataclass(frozen=True)
+class LookupResult:
+    request: LookupParameters
+    nearest: SimulationRow
+    outcome: Outcome
+    valid: bool
+    discard_reason: str | None
+    tags: tuple[str, ...]
+    distance: float
+
+    @property
+    def risk_color(self) -> str:
+        if self.outcome is Outcome.STRONG_POSITIVE:
+            return "red"
+        if self.outcome is Outcome.WEAK_ALTERNANS:
+            return "amber"
+        if self.outcome is Outcome.INVALID:
+            return "gray"
+        return "green"

src/sister_lite/schema.sql

@@ -0,0 +1,14 @@
+CREATE TABLE simulations (
+    job_id TEXT PRIMARY KEY,
+    parameters JSON NOT NULL,
+    model TEXT NOT NULL,
+    outcome TEXT NOT NULL,
+    alternans_mag_apd_ms REAL NOT NULL,
+    alternans_mag_ca_relative REAL NOT NULL,
+    apd90_ms REAL NOT NULL,
+    ca_amplitude_um REAL NOT NULL,
+    valid BOOLEAN NOT NULL,
+    discard_reason TEXT,
+    raw_trace_url TEXT,
+    created_at TIMESTAMP DEFAULT CURRENT_TIMESTAMP
+);