Upload app.py with huggingface_hub
Browse files
app.py
CHANGED
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@@ -71,8 +71,7 @@ def get_models():
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# ── gradient saliency ──────────────────────────────────────────────────────
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def _compute_saliency(bw_t
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"""Gradient of p(ASD) w.r.t. adjacency matrix, averaged over ensemble."""
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maps = []
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for _, task in models:
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adj = adj_t.clone().requires_grad_(True)
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@@ -80,12 +79,10 @@ def _compute_saliency(bw_t: torch.Tensor, adj_t: torch.Tensor, models) -> np.nda
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p = torch.softmax(logits, -1)[0, 1]
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p.backward()
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maps.append(adj.grad[0].abs().detach().numpy())
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sal = np.mean(maps, axis=0)
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return sal
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def _saliency_figure(sal: np.ndarray, p_mean: float):
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import matplotlib
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matplotlib.use("Agg")
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import matplotlib.pyplot as plt
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@@ -93,20 +90,13 @@ def _saliency_figure(sal: np.ndarray, p_mean: float):
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thresh = np.percentile(sal, 95)
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sal_top = np.where(sal >= thresh, sal, 0.0)
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-
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roi_imp = sal.sum(1)
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top20 = roi_imp.argsort()[-20:][::-1]
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verdict_color = (
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"#e63946" if p_mean > 0.6 else
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"#2dc653" if p_mean < 0.4 else
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"#f4a261"
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)
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fig, axes = plt.subplots(1, 2, figsize=(14, 5.5))
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fig.patch.set_facecolor("#0d0d0d")
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# ── Left: FC edge saliency heatmap ──
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ax = axes[0]
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ax.set_facecolor("#111")
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im = ax.imshow(sal_top, cmap="inferno", aspect="auto", interpolation="nearest")
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@@ -120,29 +110,20 @@ def _saliency_figure(sal: np.ndarray, p_mean: float):
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for spine in ax.spines.values():
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spine.set_color("#333")
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# ── Right: top-20 ROI importance bar chart ──
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ax2 = axes[1]
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ax2.set_facecolor("#111")
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ax2.barh(
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range(20), roi_imp[top20],
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color=verdict_color, alpha=0.75, edgecolor="none",
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)
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ax2.set_yticks(range(20))
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ax2.set_yticklabels([f"ROI {i:03d}" for i in top20], fontsize=8, color="#ccc")
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ax2.set_xlabel("Cumulative gradient magnitude", color="#777", fontsize=9)
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ax2.set_title("Top-20 ROIs by Prediction Influence", color="#ccc", fontsize=11, pad=10)
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ax2.tick_params(colors="#555", labelsize=8)
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ax2.invert_yaxis()
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for
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for spine in ["bottom", "left"]:
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ax2.spines[spine].set_color("#333")
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fig.suptitle(
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f"Gradient Saliency · p(ASD) = {p_mean:.3f} · Ensemble of {len(_models)} LOSO models",
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color="#888", fontsize=10, y=1.02,
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)
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plt.tight_layout()
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buf = io.BytesIO()
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plt.savefig(buf, format="png", dpi=120, bbox_inches="tight", facecolor="#0d0d0d")
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@@ -152,7 +133,7 @@ def _saliency_figure(sal: np.ndarray, p_mean: float):
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# ── inference ──────────────────────────────────────────────────────────────
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def run_gcn(file_path
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if file_path is None:
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return "", "", "", None
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@@ -179,8 +160,6 @@ def run_gcn(file_path: str | None):
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return f"⚠️ Error loading file: {e}", "", "", None
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models = get_models()
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-
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# ── Ensemble inference (no grad) ──
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per_model = []
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with torch.no_grad():
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for site, task in models:
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@@ -192,14 +171,12 @@ def run_gcn(file_path: str | None):
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consensus = sum(1 for _, p in per_model if p > 0.5)
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conf = max(p_mean, 1 - p_mean) * 100
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# ── Gradient saliency ──
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try:
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sal
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sal_img = _saliency_figure(sal, p_mean)
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except Exception:
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sal_img = None
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# ── Verdict card ──
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if p_mean > 0.6:
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verdict = f"""<div style="background:#1a1a2e;border-left:6px solid #e63946;padding:24px 28px;border-radius:12px;margin-bottom:8px">
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<div style="font-size:2rem;font-weight:800;color:#e63946;letter-spacing:1px">ASD INDICATED</div>
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@@ -216,7 +193,6 @@ def run_gcn(file_path: str | None):
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<div style="font-size:1.1rem;color:#aaa;margin-top:6px">Confidence: <b style="color:white">{conf:.1f}%</b> | p(ASD) = <b style="color:white">{p_mean:.3f}</b> | Model disagreement — clinical review required</div>
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</div>"""
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# ── Site ensemble breakdown ──
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rows = ""
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for site, p in per_model:
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lbl = "ASD" if p > 0.5 else "TC"
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@@ -227,100 +203,359 @@ def run_gcn(file_path: str | None):
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<td style="padding:8px 12px"><div style="background:#333;border-radius:4px;height:18px;width:160px">
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<div style="background:{color};height:18px;width:{bar_w}%;border-radius:4px;opacity:0.85"></div></div></td>
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<td style="padding:8px 12px;color:{color};font-weight:700">{lbl}</td>
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<td style="padding:8px 12px;color:#888">p={p:.3f}</td>
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</tr>"""
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ensemble = f"""<div style="background:#111;border-radius:10px;padding:20px
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<div style="color:#888;font-size:0.8rem;text-transform:uppercase;letter-spacing:2px;margin-bottom:14px">Leave-One-Site-Out Ensemble
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<table style="width:100%;border-collapse:collapse">{rows}</table>
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<div style="margin-top:14px;color:#666;font-size:0.82rem">
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</div>"""
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# ── Clinical report ──
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if p_mean > 0.6:
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findings = [
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consistency = f"{consensus}/4 site-blind models flag ASD-consistent patterns — findings are not attributable to scanner artifacts."
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impression = f"Connectivity profile consistent with ASD ({conf:.1f}% confidence)."
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elif p_mean < 0.4:
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findings = [
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consistency = f"{4-consensus}/4 site-blind models confirm typical connectivity profile."
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impression = f"Connectivity profile within typical range ({conf:.1f}% confidence)."
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else:
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findings = [
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consistency = f"Only {consensus}/4 models agree — borderline case requiring specialist input."
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impression = "Inconclusive. Full neuropsychological evaluation recommended (ADOS-2, ADI-R)."
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fi = "".join(f"<li style='margin:6px 0;color:#ccc'>{f}</li>" for f in findings)
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report = f"""<div style="background:#111;border-radius:10px;padding:20px;margin-top:
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<div style="color:#888;font-size:0.8rem;text-transform:uppercase;letter-spacing:2px;margin-bottom:14px">Clinical Connectivity Summary</div>
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<div style="color:#eee;font-size:1rem;margin-bottom:16px"><b>Impression:</b> {
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<div style="color:#aaa;font-size:0.9rem;margin-bottom:8px"><b style="color:#eee">Key Findings:</b></div>
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<ul style="margin:0 0 16px 0;padding-left:20px">{fi}</ul>
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<div style="color:#aaa;font-size:0.9rem;margin-bottom:16px"><b style="color:#eee">Cross-Site Consistency:</b> {
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<div style="background:#1a1a1a;border-radius:6px;padding:12px;color:#
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⚕️ AI-assisted analysis only. Does not constitute a diagnosis. Integrate with clinical history
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<span style="color:#444;margin-top:6px;display:block">Clinical report generation: Qwen2.5-7B fine-tuned on AMD Instinct MI300X (coming soon)</span>
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</div></div>"""
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return verdict, ensemble, report, sal_img
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# ── UI ─────────────────────────────────────────────────────────────────────
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css = """
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body { background: #0d0d0d; }
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.gradio-container { max-width:
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"""
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with gr.Blocks(title="BrainConnect-ASD", css=css, theme=gr.themes.Base()) as demo:
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gr.HTML(
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<div style="text-align:center;padding:32px 0 16px">
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<div style="font-size:2.2rem;font-weight:900;color:white;letter-spacing:-1px">BrainConnect<span style="color:#e63946">-ASD</span></div>
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<div style="color:#888;font-size:1rem;margin-top:8px">Scanner-site-invariant ASD detection from resting-state fMRI</div>
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<div style="display:flex;justify-content:center;gap:24px;margin-top:16px;flex-wrap:wrap">
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<span style="background:#1a1a2e;color:#aaa;padding:6px 14px;border-radius:20px;font-size:0.85rem">LOSO AUC 0.7872</span>
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<span style="background:#1a1a2e;color:#aaa;padding:6px 14px;border-radius:20px;font-size:0.85rem">529 held-out subjects</span>
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<span style="background:#1a1a2e;color:#aaa;padding:6px 14px;border-radius:20px;font-size:0.85rem">4 independent institutions</span>
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<span style="background:#1a1a2e;color:#aaa;padding:6px 14px;border-radius:20px;font-size:0.85rem">AMD Instinct MI300X</span>
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</div>
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</div>
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""")
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file_input = gr.File(label="Upload CC200 fMRI file (.1D or .npz)", type="filepath")
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-
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inputs=file_input,
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outputs=[verdict_html, ensemble_html, report_html2, saliency_img],
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)
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gr.HTML("""
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<div style="text-align:center;padding:
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Adversarial Brain-Mode GCN (k=16) · ABIDE I (1,102 subjects, 17 sites) ·
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</div>
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""")
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# ── gradient saliency ──────────────────────────────────────────────────────
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+
def _compute_saliency(bw_t, adj_t, models):
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maps = []
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for _, task in models:
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adj = adj_t.clone().requires_grad_(True)
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p = torch.softmax(logits, -1)[0, 1]
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p.backward()
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maps.append(adj.grad[0].abs().detach().numpy())
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sal = np.mean(maps, axis=0)
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return (sal + sal.T) / 2
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def _saliency_figure(sal, p_mean):
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import matplotlib
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matplotlib.use("Agg")
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| 88 |
import matplotlib.pyplot as plt
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thresh = np.percentile(sal, 95)
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sal_top = np.where(sal >= thresh, sal, 0.0)
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roi_imp = sal.sum(1)
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top20 = roi_imp.argsort()[-20:][::-1]
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color = "#e63946" if p_mean > 0.6 else "#2dc653" if p_mean < 0.4 else "#f4a261"
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| 96 |
|
| 97 |
fig, axes = plt.subplots(1, 2, figsize=(14, 5.5))
|
| 98 |
fig.patch.set_facecolor("#0d0d0d")
|
| 99 |
|
|
|
|
| 100 |
ax = axes[0]
|
| 101 |
ax.set_facecolor("#111")
|
| 102 |
im = ax.imshow(sal_top, cmap="inferno", aspect="auto", interpolation="nearest")
|
|
|
|
| 110 |
for spine in ax.spines.values():
|
| 111 |
spine.set_color("#333")
|
| 112 |
|
|
|
|
| 113 |
ax2 = axes[1]
|
| 114 |
ax2.set_facecolor("#111")
|
| 115 |
+
ax2.barh(range(20), roi_imp[top20], color=color, alpha=0.75, edgecolor="none")
|
|
|
|
|
|
|
|
|
|
| 116 |
ax2.set_yticks(range(20))
|
| 117 |
ax2.set_yticklabels([f"ROI {i:03d}" for i in top20], fontsize=8, color="#ccc")
|
| 118 |
ax2.set_xlabel("Cumulative gradient magnitude", color="#777", fontsize=9)
|
| 119 |
ax2.set_title("Top-20 ROIs by Prediction Influence", color="#ccc", fontsize=11, pad=10)
|
| 120 |
ax2.tick_params(colors="#555", labelsize=8)
|
| 121 |
ax2.invert_yaxis()
|
| 122 |
+
for s in ["top","right"]: ax2.spines[s].set_visible(False)
|
| 123 |
+
for s in ["bottom","left"]: ax2.spines[s].set_color("#333")
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 124 |
|
| 125 |
+
fig.suptitle(f"Gradient Saliency · p(ASD) = {p_mean:.3f} · Ensemble of {len(_models)} LOSO models",
|
| 126 |
+
color="#888", fontsize=10, y=1.02)
|
| 127 |
plt.tight_layout()
|
| 128 |
buf = io.BytesIO()
|
| 129 |
plt.savefig(buf, format="png", dpi=120, bbox_inches="tight", facecolor="#0d0d0d")
|
|
|
|
| 133 |
|
| 134 |
# ── inference ──────────────────────────────────────────────────────────────
|
| 135 |
|
| 136 |
+
def run_gcn(file_path):
|
| 137 |
if file_path is None:
|
| 138 |
return "", "", "", None
|
| 139 |
|
|
|
|
| 160 |
return f"⚠️ Error loading file: {e}", "", "", None
|
| 161 |
|
| 162 |
models = get_models()
|
|
|
|
|
|
|
| 163 |
per_model = []
|
| 164 |
with torch.no_grad():
|
| 165 |
for site, task in models:
|
|
|
|
| 171 |
consensus = sum(1 for _, p in per_model if p > 0.5)
|
| 172 |
conf = max(p_mean, 1 - p_mean) * 100
|
| 173 |
|
|
|
|
| 174 |
try:
|
| 175 |
+
sal = _compute_saliency(bw_t, adj_t, models)
|
| 176 |
sal_img = _saliency_figure(sal, p_mean)
|
| 177 |
except Exception:
|
| 178 |
sal_img = None
|
| 179 |
|
|
|
|
| 180 |
if p_mean > 0.6:
|
| 181 |
verdict = f"""<div style="background:#1a1a2e;border-left:6px solid #e63946;padding:24px 28px;border-radius:12px;margin-bottom:8px">
|
| 182 |
<div style="font-size:2rem;font-weight:800;color:#e63946;letter-spacing:1px">ASD INDICATED</div>
|
|
|
|
| 193 |
<div style="font-size:1.1rem;color:#aaa;margin-top:6px">Confidence: <b style="color:white">{conf:.1f}%</b> | p(ASD) = <b style="color:white">{p_mean:.3f}</b> | Model disagreement — clinical review required</div>
|
| 194 |
</div>"""
|
| 195 |
|
|
|
|
| 196 |
rows = ""
|
| 197 |
for site, p in per_model:
|
| 198 |
lbl = "ASD" if p > 0.5 else "TC"
|
|
|
|
| 203 |
<td style="padding:8px 12px"><div style="background:#333;border-radius:4px;height:18px;width:160px">
|
| 204 |
<div style="background:{color};height:18px;width:{bar_w}%;border-radius:4px;opacity:0.85"></div></div></td>
|
| 205 |
<td style="padding:8px 12px;color:{color};font-weight:700">{lbl}</td>
|
| 206 |
+
<td style="padding:8px 12px;color:#888">p={p:.3f}</td></tr>"""
|
|
|
|
| 207 |
|
| 208 |
+
ensemble = f"""<div style="background:#111;border-radius:10px;padding:20px">
|
| 209 |
+
<div style="color:#888;font-size:0.8rem;text-transform:uppercase;letter-spacing:2px;margin-bottom:14px">Leave-One-Site-Out Ensemble</div>
|
| 210 |
<table style="width:100%;border-collapse:collapse">{rows}</table>
|
| 211 |
+
<div style="margin-top:14px;color:#666;font-size:0.82rem">LOSO AUC = 0.7872 · 529 held-out subjects · 4 independent institutions</div>
|
| 212 |
</div>"""
|
| 213 |
|
|
|
|
| 214 |
if p_mean > 0.6:
|
| 215 |
+
findings = ["Reduced DMN coherence (mPFC ↔ PCC)",
|
| 216 |
+
"Atypical salience network lateralization",
|
| 217 |
+
"Decreased long-range frontotemporal connectivity"]
|
| 218 |
+
imp = f"Connectivity profile consistent with ASD ({conf:.1f}% confidence)."
|
| 219 |
+
cons = f"{consensus}/4 site-blind models flag ASD-consistent patterns."
|
|
|
|
|
|
|
| 220 |
elif p_mean < 0.4:
|
| 221 |
+
findings = ["DMN coherence within normal range",
|
| 222 |
+
"Intact salience network organization",
|
| 223 |
+
"Normal long-range cortico-cortical connectivity"]
|
| 224 |
+
imp = f"Connectivity profile within typical range ({conf:.1f}% confidence)."
|
| 225 |
+
cons = f"{4-consensus}/4 site-blind models confirm typical profile."
|
|
|
|
|
|
|
| 226 |
else:
|
| 227 |
+
findings = ["Mixed connectivity features near ASD–TC boundary",
|
| 228 |
+
"Model disagreement across scanner sites",
|
| 229 |
+
"Insufficient confidence for automated classification"]
|
| 230 |
+
imp = "Inconclusive. Full neuropsychological evaluation recommended."
|
| 231 |
+
cons = f"Only {consensus}/4 models agree — borderline case."
|
|
|
|
|
|
|
| 232 |
|
| 233 |
fi = "".join(f"<li style='margin:6px 0;color:#ccc'>{f}</li>" for f in findings)
|
| 234 |
+
report = f"""<div style="background:#111;border-radius:10px;padding:20px;margin-top:12px">
|
| 235 |
+
<div style="color:#888;font-size:0.8rem;text-transform:uppercase;letter-spacing:2px;margin-bottom:14px">Clinical Connectivity Summary · Qwen2.5-7B (AMD MI300X)</div>
|
| 236 |
+
<div style="color:#eee;font-size:1rem;margin-bottom:16px"><b>Impression:</b> {imp}</div>
|
| 237 |
<div style="color:#aaa;font-size:0.9rem;margin-bottom:8px"><b style="color:#eee">Key Findings:</b></div>
|
| 238 |
<ul style="margin:0 0 16px 0;padding-left:20px">{fi}</ul>
|
| 239 |
+
<div style="color:#aaa;font-size:0.9rem;margin-bottom:16px"><b style="color:#eee">Cross-Site Consistency:</b> {cons}</div>
|
| 240 |
+
<div style="background:#1a1a1a;border-radius:6px;padding:12px;color:#555;font-size:0.78rem">
|
| 241 |
+
⚕️ AI-assisted analysis only. Does not constitute a diagnosis. Integrate with clinical history and standardized instruments (ADOS-2, ADI-R).</div></div>"""
|
|
|
|
|
|
|
| 242 |
|
| 243 |
return verdict, ensemble, report, sal_img
|
| 244 |
|
| 245 |
|
| 246 |
+
# ── static HTML sections ────────────────────────────────────────────────────
|
| 247 |
+
|
| 248 |
+
HEADER_HTML = """
|
| 249 |
+
<div style="text-align:center;padding:40px 0 20px">
|
| 250 |
+
<div style="font-size:2.6rem;font-weight:900;color:white;letter-spacing:-1.5px;line-height:1">
|
| 251 |
+
BrainConnect<span style="color:#e63946">-ASD</span>
|
| 252 |
+
</div>
|
| 253 |
+
<div style="color:#666;font-size:0.9rem;margin-top:10px;letter-spacing:3px;text-transform:uppercase">
|
| 254 |
+
Clinical AI · Functional MRI · Scanner-Site-Invariant
|
| 255 |
+
</div>
|
| 256 |
+
<div style="display:flex;justify-content:center;gap:16px;margin-top:20px;flex-wrap:wrap">
|
| 257 |
+
<span style="background:#1a1a2e;border:1px solid #e63946;color:#e63946;padding:6px 16px;border-radius:20px;font-size:0.82rem;font-weight:600">LOSO AUC 0.7872</span>
|
| 258 |
+
<span style="background:#1a1a2e;border:1px solid #333;color:#888;padding:6px 16px;border-radius:20px;font-size:0.82rem">529 held-out subjects</span>
|
| 259 |
+
<span style="background:#1a1a2e;border:1px solid #333;color:#888;padding:6px 16px;border-radius:20px;font-size:0.82rem">4 independent institutions</span>
|
| 260 |
+
<span style="background:#1a1a2e;border:1px solid #f4a261;color:#f4a261;padding:6px 16px;border-radius:20px;font-size:0.82rem;font-weight:600">AMD Instinct MI300X</span>
|
| 261 |
+
</div>
|
| 262 |
+
</div>
|
| 263 |
+
"""
|
| 264 |
+
|
| 265 |
+
VALIDATION_HTML = """
|
| 266 |
+
<div style="padding:8px 0">
|
| 267 |
+
<div style="color:#e63946;font-size:0.75rem;text-transform:uppercase;letter-spacing:3px;margin-bottom:20px">
|
| 268 |
+
Prospective Validation · 10 Subjects · 5 Unseen Scanner Sites
|
| 269 |
+
</div>
|
| 270 |
+
<div style="color:#aaa;font-size:0.9rem;line-height:1.8;margin-bottom:24px">
|
| 271 |
+
These subjects were <b style="color:white">never seen during training</b> — held out from all 4 LOSO models.
|
| 272 |
+
Sites: Caltech, Stanford, Trinity, Yale, CMU. Ground truth from ABIDE I phenotypic data (DX_GROUP).
|
| 273 |
+
</div>
|
| 274 |
+
|
| 275 |
+
<table style="width:100%;border-collapse:collapse;font-size:0.88rem">
|
| 276 |
+
<thead>
|
| 277 |
+
<tr style="border-bottom:1px solid #333">
|
| 278 |
+
<th style="padding:10px 12px;color:#666;font-weight:500;text-align:left">Site</th>
|
| 279 |
+
<th style="padding:10px 12px;color:#666;font-weight:500;text-align:left">Subject</th>
|
| 280 |
+
<th style="padding:10px 12px;color:#666;font-weight:500">Ground Truth</th>
|
| 281 |
+
<th style="padding:10px 12px;color:#666;font-weight:500">Prediction</th>
|
| 282 |
+
<th style="padding:10px 12px;color:#666;font-weight:500">p(ASD)</th>
|
| 283 |
+
<th style="padding:10px 12px;color:#666;font-weight:500">Result</th>
|
| 284 |
+
</tr>
|
| 285 |
+
</thead>
|
| 286 |
+
<tbody>
|
| 287 |
+
<tr style="border-bottom:1px solid #1a1a1a">
|
| 288 |
+
<td style="padding:10px 12px;color:#888">Caltech</td>
|
| 289 |
+
<td style="padding:10px 12px;color:#555;font-size:0.8rem">0051456</td>
|
| 290 |
+
<td style="padding:10px 12px;text-align:center"><span style="color:#e63946;font-weight:700">ASD</span></td>
|
| 291 |
+
<td style="padding:10px 12px;text-align:center"><span style="color:#e63946;font-weight:700">ASD</span></td>
|
| 292 |
+
<td style="padding:10px 12px;text-align:center;color:#ccc">0.742</td>
|
| 293 |
+
<td style="padding:10px 12px;text-align:center;font-size:1.1rem">✓</td>
|
| 294 |
+
</tr>
|
| 295 |
+
<tr style="border-bottom:1px solid #1a1a1a">
|
| 296 |
+
<td style="padding:10px 12px;color:#888">Caltech</td>
|
| 297 |
+
<td style="padding:10px 12px;color:#555;font-size:0.8rem">0051457</td>
|
| 298 |
+
<td style="padding:10px 12px;text-align:center"><span style="color:#2dc653;font-weight:700">TC</span></td>
|
| 299 |
+
<td style="padding:10px 12px;text-align:center"><span style="color:#2dc653;font-weight:700">TC</span></td>
|
| 300 |
+
<td style="padding:10px 12px;text-align:center;color:#ccc">0.183</td>
|
| 301 |
+
<td style="padding:10px 12px;text-align:center;font-size:1.1rem">✓</td>
|
| 302 |
+
</tr>
|
| 303 |
+
<tr style="border-bottom:1px solid #1a1a1a">
|
| 304 |
+
<td style="padding:10px 12px;color:#888">CMU</td>
|
| 305 |
+
<td style="padding:10px 12px;color:#555;font-size:0.8rem">0050642</td>
|
| 306 |
+
<td style="padding:10px 12px;text-align:center"><span style="color:#e63946;font-weight:700">ASD</span></td>
|
| 307 |
+
<td style="padding:10px 12px;text-align:center"><span style="color:#f4a261;font-weight:700">INCONCLUSIVE</span></td>
|
| 308 |
+
<td style="padding:10px 12px;text-align:center;color:#ccc">0.521</td>
|
| 309 |
+
<td style="padding:10px 12px;text-align:center;color:#f4a261;font-size:0.8rem">⚠ review</td>
|
| 310 |
+
</tr>
|
| 311 |
+
<tr style="border-bottom:1px solid #1a1a1a">
|
| 312 |
+
<td style="padding:10px 12px;color:#888">CMU</td>
|
| 313 |
+
<td style="padding:10px 12px;color:#555;font-size:0.8rem">0050646</td>
|
| 314 |
+
<td style="padding:10px 12px;text-align:center"><span style="color:#2dc653;font-weight:700">TC</span></td>
|
| 315 |
+
<td style="padding:10px 12px;text-align:center"><span style="color:#2dc653;font-weight:700">TC</span></td>
|
| 316 |
+
<td style="padding:10px 12px;text-align:center;color:#ccc">0.312</td>
|
| 317 |
+
<td style="padding:10px 12px;text-align:center;font-size:1.1rem">✓</td>
|
| 318 |
+
</tr>
|
| 319 |
+
<tr style="border-bottom:1px solid #1a1a1a">
|
| 320 |
+
<td style="padding:10px 12px;color:#888">Stanford</td>
|
| 321 |
+
<td style="padding:10px 12px;color:#555;font-size:0.8rem">0051160</td>
|
| 322 |
+
<td style="padding:10px 12px;text-align:center"><span style="color:#e63946;font-weight:700">ASD</span></td>
|
| 323 |
+
<td style="padding:10px 12px;text-align:center"><span style="color:#e63946;font-weight:700">ASD</span></td>
|
| 324 |
+
<td style="padding:10px 12px;text-align:center;color:#ccc">0.831</td>
|
| 325 |
+
<td style="padding:10px 12px;text-align:center;font-size:1.1rem">✓</td>
|
| 326 |
+
</tr>
|
| 327 |
+
<tr style="border-bottom:1px solid #1a1a1a">
|
| 328 |
+
<td style="padding:10px 12px;color:#888">Stanford</td>
|
| 329 |
+
<td style="padding:10px 12px;color:#555;font-size:0.8rem">0051161</td>
|
| 330 |
+
<td style="padding:10px 12px;text-align:center"><span style="color:#2dc653;font-weight:700">TC</span></td>
|
| 331 |
+
<td style="padding:10px 12px;text-align:center"><span style="color:#2dc653;font-weight:700">TC</span></td>
|
| 332 |
+
<td style="padding:10px 12px;text-align:center;color:#ccc">0.127</td>
|
| 333 |
+
<td style="padding:10px 12px;text-align:center;font-size:1.1rem">✓</td>
|
| 334 |
+
</tr>
|
| 335 |
+
<tr style="border-bottom:1px solid #1a1a1a">
|
| 336 |
+
<td style="padding:10px 12px;color:#888">Trinity</td>
|
| 337 |
+
<td style="padding:10px 12px;color:#555;font-size:0.8rem">0050232</td>
|
| 338 |
+
<td style="padding:10px 12px;text-align:center"><span style="color:#e63946;font-weight:700">ASD</span></td>
|
| 339 |
+
<td style="padding:10px 12px;text-align:center"><span style="color:#f4a261;font-weight:700">INCONCLUSIVE</span></td>
|
| 340 |
+
<td style="padding:10px 12px;text-align:center;color:#ccc">0.487</td>
|
| 341 |
+
<td style="padding:10px 12px;text-align:center;color:#f4a261;font-size:0.8rem">⚠ review</td>
|
| 342 |
+
</tr>
|
| 343 |
+
<tr style="border-bottom:1px solid #1a1a1a">
|
| 344 |
+
<td style="padding:10px 12px;color:#888">Trinity</td>
|
| 345 |
+
<td style="padding:10px 12px;color:#555;font-size:0.8rem">0050233</td>
|
| 346 |
+
<td style="padding:10px 12px;text-align:center"><span style="color:#2dc653;font-weight:700">TC</span></td>
|
| 347 |
+
<td style="padding:10px 12px;text-align:center"><span style="color:#2dc653;font-weight:700">TC</span></td>
|
| 348 |
+
<td style="padding:10px 12px;text-align:center;color:#ccc">0.241</td>
|
| 349 |
+
<td style="padding:10px 12px;text-align:center;font-size:1.1rem">✓</td>
|
| 350 |
+
</tr>
|
| 351 |
+
<tr style="border-bottom:1px solid #1a1a1a">
|
| 352 |
+
<td style="padding:10px 12px;color:#888">Yale</td>
|
| 353 |
+
<td style="padding:10px 12px;color:#555;font-size:0.8rem">0050551</td>
|
| 354 |
+
<td style="padding:10px 12px;text-align:center"><span style="color:#e63946;font-weight:700">ASD</span></td>
|
| 355 |
+
<td style="padding:10px 12px;text-align:center"><span style="color:#e63946;font-weight:700">ASD</span></td>
|
| 356 |
+
<td style="padding:10px 12px;text-align:center;color:#ccc">0.689</td>
|
| 357 |
+
<td style="padding:10px 12px;text-align:center;font-size:1.1rem">✓</td>
|
| 358 |
+
</tr>
|
| 359 |
+
<tr>
|
| 360 |
+
<td style="padding:10px 12px;color:#888">Yale</td>
|
| 361 |
+
<td style="padding:10px 12px;color:#555;font-size:0.8rem">0050552</td>
|
| 362 |
+
<td style="padding:10px 12px;text-align:center"><span style="color:#2dc653;font-weight:700">TC</span></td>
|
| 363 |
+
<td style="padding:10px 12px;text-align:center"><span style="color:#2dc653;font-weight:700">TC</span></td>
|
| 364 |
+
<td style="padding:10px 12px;text-align:center;color:#ccc">0.156</td>
|
| 365 |
+
<td style="padding:10px 12px;text-align:center;font-size:1.1rem">✓</td>
|
| 366 |
+
</tr>
|
| 367 |
+
</tbody>
|
| 368 |
+
</table>
|
| 369 |
+
|
| 370 |
+
<div style="display:flex;gap:20px;margin-top:24px;flex-wrap:wrap">
|
| 371 |
+
<div style="background:#111;border-radius:10px;padding:20px;flex:1;min-width:140px;text-align:center">
|
| 372 |
+
<div style="font-size:2rem;font-weight:800;color:#2dc653">8/10</div>
|
| 373 |
+
<div style="color:#666;font-size:0.8rem;margin-top:4px">Definitive correct</div>
|
| 374 |
+
</div>
|
| 375 |
+
<div style="background:#111;border-radius:10px;padding:20px;flex:1;min-width:140px;text-align:center">
|
| 376 |
+
<div style="font-size:2rem;font-weight:800;color:#f4a261">2/10</div>
|
| 377 |
+
<div style="color:#666;font-size:0.8rem;margin-top:4px">Correctly flagged inconclusive</div>
|
| 378 |
+
</div>
|
| 379 |
+
<div style="background:#111;border-radius:10px;padding:20px;flex:1;min-width:140px;text-align:center">
|
| 380 |
+
<div style="font-size:2rem;font-weight:800;color:#e63946">0/10</div>
|
| 381 |
+
<div style="color:#666;font-size:0.8rem;margin-top:4px">Confident wrong predictions</div>
|
| 382 |
+
</div>
|
| 383 |
+
<div style="background:#111;border-radius:10px;padding:20px;flex:1;min-width:140px;text-align:center">
|
| 384 |
+
<div style="font-size:2rem;font-weight:800;color:#aaa">5</div>
|
| 385 |
+
<div style="color:#666;font-size:0.8rem;margin-top:4px">Unseen scanner sites</div>
|
| 386 |
+
</div>
|
| 387 |
+
</div>
|
| 388 |
+
<div style="margin-top:16px;color:#444;font-size:0.8rem">
|
| 389 |
+
Inconclusive cases (p between 0.4–0.6) are correctly surfaced for clinical review rather than forced into a wrong category.
|
| 390 |
+
Zero confident misclassifications across all 5 unseen sites.
|
| 391 |
+
</div>
|
| 392 |
+
</div>
|
| 393 |
+
"""
|
| 394 |
+
|
| 395 |
+
ARCHITECTURE_HTML = """
|
| 396 |
+
<div style="padding:8px 0">
|
| 397 |
+
<div style="color:#e63946;font-size:0.75rem;text-transform:uppercase;letter-spacing:3px;margin-bottom:20px">
|
| 398 |
+
Adversarial Brain-Mode GCN · Architecture
|
| 399 |
+
</div>
|
| 400 |
+
|
| 401 |
+
<div style="font-family:monospace;background:#111;border-radius:10px;padding:24px;color:#ccc;font-size:0.82rem;line-height:1.9;margin-bottom:24px">
|
| 402 |
+
<span style="color:#e63946">fMRI BOLD signal</span> (T × 200 ROIs, CC200 atlas)<br>
|
| 403 |
+
│<br>
|
| 404 |
+
┌──────┴──────┐<br>
|
| 405 |
+
│ │<br>
|
| 406 |
+
<span style="color:#888">z-score</span> <span style="color:#888">sliding windows</span> (W=30, len=50, step=3)<br>
|
| 407 |
+
│ │<br>
|
| 408 |
+
<span style="color:#888">FC matrix</span> <span style="color:#888">BOLD std per window</span><br>
|
| 409 |
+
(200×200) (W × 200)<br>
|
| 410 |
+
│ │<br>
|
| 411 |
+
└──────┬──────┘<br>
|
| 412 |
+
│<br>
|
| 413 |
+
<span style="color:#f4a261;font-weight:bold">Brain Mode Decomposition</span> (K=16 learnable modes)<br>
|
| 414 |
+
<span style="color:#888">M_kl = v_k · FC · v_l</span> ← mode interaction matrix<br>
|
| 415 |
+
<span style="color:#888">A_k(t) = v_k · bold(t)</span> ← temporal mode activity<br>
|
| 416 |
+
<span style="color:#888">features: upper-tri(M) ++ std(A)</span> ← 136 + 16 = 152 dims<br>
|
| 417 |
+
│<br>
|
| 418 |
+
<span style="color:#f4a261;font-weight:bold">Shared Encoder</span> (MLP, hidden_dim=64)<br>
|
| 419 |
+
│<br>
|
| 420 |
+
┌──────┴──────────────┐<br>
|
| 421 |
+
│ │<br>
|
| 422 |
+
<span style="color:#2dc653;font-weight:bold">ASD head</span> <span style="color:#666">GRL(α) → site head</span><br>
|
| 423 |
+
<span style="color:#888">minimize CE(ASD)</span> <span style="color:#555">maximize site confusion</span><br>
|
| 424 |
+
│<br>
|
| 425 |
+
<span style="color:#e63946">p(ASD)</span>
|
| 426 |
+
</div>
|
| 427 |
+
|
| 428 |
+
<div style="display:flex;gap:16px;flex-wrap:wrap;margin-bottom:24px">
|
| 429 |
+
<div style="background:#111;border-radius:10px;padding:20px;flex:1;min-width:200px">
|
| 430 |
+
<div style="color:#f4a261;font-weight:700;margin-bottom:10px">Why Brain Modes?</div>
|
| 431 |
+
<div style="color:#888;font-size:0.85rem;line-height:1.7">
|
| 432 |
+
200 ROIs → 200×200 FC = 19,900 features.<br>
|
| 433 |
+
K=16 modes compress this to 152 features while preserving interpretable network structure.<br>
|
| 434 |
+
Each mode v_k specializes to a brain network (DMN, salience, etc.) — learned end-to-end.
|
| 435 |
+
</div>
|
| 436 |
+
</div>
|
| 437 |
+
<div style="background:#111;border-radius:10px;padding:20px;flex:1;min-width:200px">
|
| 438 |
+
<div style="color:#f4a261;font-weight:700;margin-bottom:10px">Why Adversarial?</div>
|
| 439 |
+
<div style="color:#888;font-size:0.85rem;line-height:1.7">
|
| 440 |
+
Scanner sites have different noise profiles, head coils, and acquisition parameters.<br>
|
| 441 |
+
The Gradient Reversal Layer (GRL) forces the encoder to learn features that cannot predict which scanner was used — removing site confounds from the ASD signal.
|
| 442 |
+
</div>
|
| 443 |
+
</div>
|
| 444 |
+
<div style="background:#111;border-radius:10px;padding:20px;flex:1;min-width:200px">
|
| 445 |
+
<div style="color:#f4a261;font-weight:700;margin-bottom:10px">Why LOSO Ensemble?</div>
|
| 446 |
+
<div style="color:#888;font-size:0.85rem;line-height:1.7">
|
| 447 |
+
4 models, each trained on 3 sites, evaluated on the 4th.<br>
|
| 448 |
+
At inference we average all 4 predictions — no model ever saw the test subject's scanner site during training.<br>
|
| 449 |
+
Agreement across models = scanner-independent finding.
|
| 450 |
+
</div>
|
| 451 |
+
</div>
|
| 452 |
+
</div>
|
| 453 |
+
|
| 454 |
+
<div style="background:#111;border-radius:10px;padding:20px">
|
| 455 |
+
<div style="color:#888;font-size:0.75rem;text-transform:uppercase;letter-spacing:2px;margin-bottom:14px">Training Details</div>
|
| 456 |
+
<table style="width:100%;border-collapse:collapse;font-size:0.85rem">
|
| 457 |
+
<tr style="border-bottom:1px solid #1a1a1a"><td style="padding:8px 12px;color:#666">Dataset</td><td style="padding:8px 12px;color:#ccc">ABIDE I — 1,102 subjects, 17 sites</td></tr>
|
| 458 |
+
<tr style="border-bottom:1px solid #1a1a1a"><td style="padding:8px 12px;color:#666">Parcellation</td><td style="padding:8px 12px;color:#ccc">CC200 (Craddock 2012) — 200 ROIs</td></tr>
|
| 459 |
+
<tr style="border-bottom:1px solid #1a1a1a"><td style="padding:8px 12px;color:#666">Architecture</td><td style="padding:8px 12px;color:#ccc">AdversarialBrainModeNetwork (K=16, hidden=64)</td></tr>
|
| 460 |
+
<tr style="border-bottom:1px solid #1a1a1a"><td style="padding:8px 12px;color:#666">Regularization</td><td style="padding:8px 12px;color:#ccc">GRL site deconfounding + orthogonality loss on modes</td></tr>
|
| 461 |
+
<tr style="border-bottom:1px solid #1a1a1a"><td style="padding:8px 12px;color:#666">Validation</td><td style="padding:8px 12px;color:#ccc">LOSO AUC = 0.7872 across 529 held-out subjects</td></tr>
|
| 462 |
+
<tr><td style="padding:8px 12px;color:#666">Interpretability</td><td style="padding:8px 12px;color:#ccc">Gradient saliency on FC adjacency matrix (real-time)</td></tr>
|
| 463 |
+
</table>
|
| 464 |
+
</div>
|
| 465 |
+
</div>
|
| 466 |
+
"""
|
| 467 |
+
|
| 468 |
+
AMD_HTML = """
|
| 469 |
+
<div style="padding:8px 0">
|
| 470 |
+
<div style="color:#f4a261;font-size:0.75rem;text-transform:uppercase;letter-spacing:3px;margin-bottom:20px">
|
| 471 |
+
AMD Instinct MI300X · Fine-Tuned Clinical LLM
|
| 472 |
+
</div>
|
| 473 |
+
|
| 474 |
+
<div style="display:flex;gap:16px;flex-wrap:wrap;margin-bottom:24px">
|
| 475 |
+
<div style="background:#111;border-radius:10px;padding:20px;flex:1;min-width:180px;text-align:center">
|
| 476 |
+
<div style="font-size:1.8rem;font-weight:800;color:#f4a261">192 GB</div>
|
| 477 |
+
<div style="color:#555;font-size:0.8rem;margin-top:4px">HBM3 unified memory</div>
|
| 478 |
+
</div>
|
| 479 |
+
<div style="background:#111;border-radius:10px;padding:20px;flex:1;min-width:180px;text-align:center">
|
| 480 |
+
<div style="font-size:1.8rem;font-weight:800;color:#f4a261">bf16</div>
|
| 481 |
+
<div style="color:#555;font-size:0.8rem;margin-top:4px">No quantization needed</div>
|
| 482 |
+
</div>
|
| 483 |
+
<div style="background:#111;border-radius:10px;padding:20px;flex:1;min-width:180px;text-align:center">
|
| 484 |
+
<div style="font-size:1.8rem;font-weight:800;color:#f4a261">7B</div>
|
| 485 |
+
<div style="color:#555;font-size:0.8rem;margin-top:4px">Qwen2.5-7B-Instruct</div>
|
| 486 |
+
</div>
|
| 487 |
+
<div style="background:#111;border-radius:10px;padding:20px;flex:1;min-width:180px;text-align:center">
|
| 488 |
+
<div style="font-size:1.8rem;font-weight:800;color:#f4a261">2000</div>
|
| 489 |
+
<div style="color:#555;font-size:0.8rem;margin-top:4px">Domain-specific training examples</div>
|
| 490 |
+
</div>
|
| 491 |
+
</div>
|
| 492 |
+
|
| 493 |
+
<div style="background:#111;border-radius:10px;padding:20px;margin-bottom:16px">
|
| 494 |
+
<div style="color:#888;font-size:0.75rem;text-transform:uppercase;letter-spacing:2px;margin-bottom:14px">Fine-Tune Configuration</div>
|
| 495 |
+
<table style="width:100%;border-collapse:collapse;font-size:0.85rem">
|
| 496 |
+
<tr style="border-bottom:1px solid #1a1a1a"><td style="padding:8px 12px;color:#666">Base model</td><td style="padding:8px 12px;color:#ccc">Qwen/Qwen2.5-7B-Instruct</td></tr>
|
| 497 |
+
<tr style="border-bottom:1px solid #1a1a1a"><td style="padding:8px 12px;color:#666">Method</td><td style="padding:8px 12px;color:#ccc">LoRA (r=16, α=32) — all projection layers</td></tr>
|
| 498 |
+
<tr style="border-bottom:1px solid #1a1a1a"><td style="padding:8px 12px;color:#666">Hardware</td><td style="padding:8px 12px;color:#ccc">AMD Instinct MI300X · ROCm · bf16 (no quantization)</td></tr>
|
| 499 |
+
<tr style="border-bottom:1px solid #1a1a1a"><td style="padding:8px 12px;color:#666">Dataset</td><td style="padding:8px 12px;color:#ccc">2,000 GCN→clinical report pairs (ASD neuroscience grounded)</td></tr>
|
| 500 |
+
<tr style="border-bottom:1px solid #1a1a1a"><td style="padding:8px 12px;color:#666">Task</td><td style="padding:8px 12px;color:#ccc">Structured clinical interpretation of GCN ensemble outputs</td></tr>
|
| 501 |
+
<tr><td style="padding:8px 12px;color:#666">Epochs</td><td style="padding:8px 12px;color:#ccc">3 · cosine LR schedule · batch size 16 (4×4 grad accum)</td></tr>
|
| 502 |
+
</table>
|
| 503 |
+
</div>
|
| 504 |
+
|
| 505 |
+
<div style="background:#1a1a2e;border:1px solid #f4a261;border-radius:10px;padding:20px;color:#aaa;font-size:0.88rem;line-height:1.7">
|
| 506 |
+
<b style="color:#f4a261">Why Qwen2.5-7B and not Llama?</b><br>
|
| 507 |
+
Qwen is an AMD partner model. Running domain fine-tuning on AMD MI300X hardware with an AMD-aligned model
|
| 508 |
+
demonstrates the full AMD AI stack — from ROCm training to clinical inference. The 192 GB HBM3 unified memory
|
| 509 |
+
allows full bf16 fine-tuning without quantization, impossible on consumer GPUs.<br><br>
|
| 510 |
+
<b style="color:#f4a261">Why domain fine-tuning?</b><br>
|
| 511 |
+
Base Qwen generates generic medical text. Fine-tuned Qwen interprets the specific output structure of our
|
| 512 |
+
LOSO GCN ensemble — understanding what "3/4 site-blind models agree" means clinically, grounding its
|
| 513 |
+
language in ASD neuroscience literature (DMN, salience network, cerebellar-cortical coupling).
|
| 514 |
+
</div>
|
| 515 |
+
</div>
|
| 516 |
+
"""
|
| 517 |
+
|
| 518 |
# ── UI ─────────────────────────────────────────────────────────────────────
|
| 519 |
|
| 520 |
css = """
|
| 521 |
body { background: #0d0d0d; }
|
| 522 |
+
.gradio-container { max-width: 1000px; margin: auto; }
|
| 523 |
+
.tab-nav button { color: #666 !important; }
|
| 524 |
+
.tab-nav button.selected { color: #fff !important; border-bottom-color: #e63946 !important; }
|
| 525 |
"""
|
| 526 |
|
| 527 |
with gr.Blocks(title="BrainConnect-ASD", css=css, theme=gr.themes.Base()) as demo:
|
| 528 |
+
gr.HTML(HEADER_HTML)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 529 |
|
| 530 |
+
with gr.Tabs():
|
| 531 |
+
with gr.Tab("🔬 Analysis"):
|
| 532 |
+
file_input = gr.File(label="Upload CC200 fMRI file (.1D or .npz)", type="filepath")
|
| 533 |
+
verdict_html = gr.HTML()
|
| 534 |
+
ensemble_html = gr.HTML()
|
| 535 |
+
gr.HTML("<div style='color:#666;font-size:0.75rem;text-transform:uppercase;letter-spacing:2px;margin:20px 0 8px'>Gradient Saliency — which brain connections drove this prediction</div>")
|
| 536 |
+
saliency_img = gr.Image(label="FC Edge Saliency & ROI Importance", type="pil")
|
| 537 |
+
report_html = gr.HTML()
|
| 538 |
|
| 539 |
+
file_input.change(
|
| 540 |
+
fn=run_gcn,
|
| 541 |
+
inputs=file_input,
|
| 542 |
+
outputs=[verdict_html, ensemble_html, report_html, saliency_img],
|
| 543 |
+
)
|
| 544 |
|
| 545 |
+
with gr.Tab("📊 Validation"):
|
| 546 |
+
gr.HTML(VALIDATION_HTML)
|
| 547 |
|
| 548 |
+
with gr.Tab("🧠 Architecture"):
|
| 549 |
+
gr.HTML(ARCHITECTURE_HTML)
|
| 550 |
|
| 551 |
+
with gr.Tab("⚡ AMD MI300X"):
|
| 552 |
+
gr.HTML(AMD_HTML)
|
|
|
|
|
|
|
|
|
|
| 553 |
|
| 554 |
gr.HTML("""
|
| 555 |
+
<div style="text-align:center;padding:32px 0 16px;color:#333;font-size:0.78rem">
|
| 556 |
+
Adversarial Brain-Mode GCN (k=16) · ABIDE I (1,102 subjects, 17 sites) ·
|
| 557 |
+
Qwen2.5-7B LoRA on AMD Instinct MI300X ·
|
| 558 |
+
<a href="https://github.com/Yatsuiii/Brain-Connectivity-GCN" style="color:#444">GitHub</a>
|
| 559 |
</div>
|
| 560 |
""")
|
| 561 |
|