Spaces:
Running on Zero
Running on Zero
Upload 8 files
Browse files- .gitattributes +3 -0
- README.md +41 -15
- app.py +499 -0
- llm.py +118 -0
- requirements.txt +11 -0
- test_audio/.DS_Store +0 -0
- test_audio/clips/D0420-S1-T01_clip.wav +3 -0
- test_audio/clips/D0420-S2-T01_clip.wav +3 -0
- test_audio/clips/D0420-S3-T01_clip.wav +3 -0
.gitattributes
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@@ -33,3 +33,6 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
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*.zip filter=lfs diff=lfs merge=lfs -text
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*.zst filter=lfs diff=lfs merge=lfs -text
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*tfevents* filter=lfs diff=lfs merge=lfs -text
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*.zip filter=lfs diff=lfs merge=lfs -text
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*.zst filter=lfs diff=lfs merge=lfs -text
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*tfevents* filter=lfs diff=lfs merge=lfs -text
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test_audio/clips/D0420-S1-T01_clip.wav filter=lfs diff=lfs merge=lfs -text
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test_audio/clips/D0420-S2-T01_clip.wav filter=lfs diff=lfs merge=lfs -text
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test_audio/clips/D0420-S3-T01_clip.wav filter=lfs diff=lfs merge=lfs -text
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README.md
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@@ -1,15 +1,41 @@
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# AI Medical Scribe
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Pipeline: audio file -> MedASR (transcription) -> MedGemma 4B, `google/medgemma-4b-it`
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(SOAP note) -> Gradio UI.
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Both models are gated on the Hugging Face Hub, so whichever environment runs
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this needs an HF token with access to `google/medasr` and `google/medgemma-4b-it`.
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## Setup (local)
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```bash
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python3.12 -m venv venv
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source venv/bin/activate
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pip install -r requirements.txt
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hf auth login # token needs access to the gated google/medasr and google/medgemma-4b-it repos
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```
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Model weights are pulled straight from the Hub on first run (no local
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`models/` download step needed anymore). To point at a local copy instead,
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set `MEDASR_MODEL_ID` / `MEDGEMMA_MODEL_ID` to a local directory.
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## Run (local)
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```bash
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python app.py
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```
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Opens a local Gradio app: pick a wav/mp3 file, click Run, see the MedASR
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transcript, the generated SOAP note, and per-step timing.
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## Deploying to Hugging Face Spaces (ZeroGPU)
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1. Create a Space with SDK "Gradio" and hardware "ZeroGPU".
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2. Push this repo's contents to the Space: `app.py`, `llm.py`,
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`requirements.txt`, `README.md`, `test_audio/clips/*.wav`.
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3. In the Space's Settings -> Variables and secrets, add a secret `HF_TOKEN`
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set to a token with access to the gated `google/medasr` and
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`google/medgemma-4b-it` repos. `huggingface_hub` reads this automatically.
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4. `llm.py`'s `run_pipeline` is decorated with `@spaces.GPU`, so ZeroGPU
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attaches a GPU only for the duration of that call; both the ASR and
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SOAP-note models load lazily on first invocation.
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app.py
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| 1 |
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"""AI medical scribe: audio -> MedASR transcript -> MedGemma SOAP note."""
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import os
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import gradio as gr
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from llm import run_pipeline
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_CLIPS_DIR = os.path.join(
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os.path.dirname(os.path.abspath(__file__)), "test_audio", "clips"
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)
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SAMPLES = {
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"Sample 1 — Psychiatric referral": os.path.join(
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_CLIPS_DIR, "D0420-S1-T01_clip.wav"
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),
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"Sample 2 — Mood check-in": os.path.join(_CLIPS_DIR, "D0420-S2-T01_clip.wav"),
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"Sample 3 — Sleep & nightmares": os.path.join(_CLIPS_DIR, "D0420-S3-T01_clip.wav"),
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}
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# Hardcoded light palette only — no Gradio theme / dark mode.
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CUSTOM_CSS = """
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:root, :root.dark, :root .dark, .dark, html, body {
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color-scheme: light !important;
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--radius: 0.9rem;
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--bg: #f6f7fb;
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--bg-glow: radial-gradient(ellipse 70% 40% at 15% -10%, rgba(59,130,246,0.07), transparent),
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radial-gradient(ellipse 60% 40% at 100% 0%, rgba(139,92,246,0.06), transparent);
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--card: #ffffff;
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--card-alt: #f2f4f9;
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--border: #e3e7f0;
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--fg: #10131c;
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--muted: #667085;
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--primary: #3b82f6;
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--primary-hover: #2563eb;
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--shadow: 0 1px 2px rgba(16,24,40,0.06), 0 1px 0 rgba(16,24,40,0.02);
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/* Override Gradio tokens so dark class / system preference cannot darken the UI */
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--body-background-fill: #f6f7fb !important;
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--background-fill-primary: #f6f7fb !important;
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--background-fill-secondary: #ffffff !important;
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--block-background-fill: #ffffff !important;
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--block-border-color: #e3e7f0 !important;
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--border-color-primary: #e3e7f0 !important;
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--body-text-color: #10131c !important;
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--body-text-color-subdued: #667085 !important;
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--neutral-50: #f8fafc !important;
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--neutral-100: #f1f5f9 !important;
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--neutral-200: #e2e8f0 !important;
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--neutral-300: #cbd5e1 !important;
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--neutral-400: #94a3b8 !important;
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--neutral-500: #64748b !important;
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--neutral-600: #475569 !important;
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--neutral-700: #334155 !important;
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--neutral-800: #1e293b !important;
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--neutral-900: #0f172a !important;
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--neutral-950: #020617 !important;
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--input-background-fill: #f2f4f9 !important;
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--input-border-color: #e3e7f0 !important;
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}
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* { box-sizing: border-box; }
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html, body, gradio-app, .gradio-container, .main, .wrap, .contain,
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| 66 |
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#root, .app, .fillable, .dark, .dark body, body.dark {
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background: #f6f7fb !important;
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| 68 |
+
background-color: #f6f7fb !important;
|
| 69 |
+
background-image: var(--bg-glow) !important;
|
| 70 |
+
background-attachment: fixed !important;
|
| 71 |
+
color: #10131c !important;
|
| 72 |
+
font-family: 'Inter', system-ui, sans-serif !important;
|
| 73 |
+
}
|
| 74 |
+
|
| 75 |
+
footer { display: none !important; }
|
| 76 |
+
.gradio-container {
|
| 77 |
+
max-width: 100% !important;
|
| 78 |
+
width: 100% !important;
|
| 79 |
+
margin: 0 !important;
|
| 80 |
+
padding: 0 clamp(1.25rem, 5vw, 4rem) !important;
|
| 81 |
+
min-height: 100vh !important;
|
| 82 |
+
}
|
| 83 |
+
|
| 84 |
+
/* Strip Gradio block chrome; only .card should paint a background. */
|
| 85 |
+
.block, .form, .gr-group, div[data-testid="block"], .gradio-container .padded {
|
| 86 |
+
background: transparent !important;
|
| 87 |
+
border: none !important;
|
| 88 |
+
box-shadow: none !important;
|
| 89 |
+
}
|
| 90 |
+
|
| 91 |
+
#top-bar {
|
| 92 |
+
display: flex;
|
| 93 |
+
align-items: center;
|
| 94 |
+
justify-content: space-between;
|
| 95 |
+
padding: 1.5rem 0 0 0;
|
| 96 |
+
}
|
| 97 |
+
#brand {
|
| 98 |
+
display: flex;
|
| 99 |
+
align-items: center;
|
| 100 |
+
gap: 0.6rem;
|
| 101 |
+
font-family: 'Outfit', sans-serif;
|
| 102 |
+
font-weight: 700;
|
| 103 |
+
font-size: 1.05rem;
|
| 104 |
+
color: #10131c !important;
|
| 105 |
+
}
|
| 106 |
+
#brand .logo-dot {
|
| 107 |
+
width: 10px; height: 10px; border-radius: 3px;
|
| 108 |
+
background: linear-gradient(135deg, #3b82f6, #8b5cf6);
|
| 109 |
+
box-shadow: 0 0 10px rgba(59,130,246,0.6);
|
| 110 |
+
}
|
| 111 |
+
|
| 112 |
+
#app-header {
|
| 113 |
+
text-align: center;
|
| 114 |
+
padding: 2.75rem 1rem 2.25rem 1rem;
|
| 115 |
+
}
|
| 116 |
+
#app-header .eyebrow {
|
| 117 |
+
display: inline-block;
|
| 118 |
+
font-size: 0.72rem;
|
| 119 |
+
font-weight: 600;
|
| 120 |
+
letter-spacing: 0.12em;
|
| 121 |
+
text-transform: uppercase;
|
| 122 |
+
color: #2563eb !important;
|
| 123 |
+
background: rgba(59,130,246,0.12);
|
| 124 |
+
border: 1px solid rgba(59,130,246,0.3);
|
| 125 |
+
padding: 0.3rem 0.9rem;
|
| 126 |
+
border-radius: 999px;
|
| 127 |
+
margin-bottom: 1.1rem;
|
| 128 |
+
}
|
| 129 |
+
#app-header h1 {
|
| 130 |
+
font-family: 'Outfit', sans-serif;
|
| 131 |
+
font-weight: 800;
|
| 132 |
+
font-size: clamp(2rem, 4vw, 2.9rem);
|
| 133 |
+
letter-spacing: -0.02em;
|
| 134 |
+
margin: 0 0 0.6rem 0;
|
| 135 |
+
color: #10131c !important;
|
| 136 |
+
}
|
| 137 |
+
#app-header p {
|
| 138 |
+
color: #667085 !important;
|
| 139 |
+
font-size: 1.02rem;
|
| 140 |
+
max-width: 640px;
|
| 141 |
+
margin: 0 auto;
|
| 142 |
+
line-height: 1.6;
|
| 143 |
+
}
|
| 144 |
+
|
| 145 |
+
.card {
|
| 146 |
+
background: #ffffff !important;
|
| 147 |
+
border: 1px solid #e3e7f0 !important;
|
| 148 |
+
border-radius: var(--radius) !important;
|
| 149 |
+
box-shadow: var(--shadow);
|
| 150 |
+
}
|
| 151 |
+
|
| 152 |
+
#control-row { align-items: stretch; gap: 1rem; }
|
| 153 |
+
|
| 154 |
+
#sample-panel { padding: 1.25rem !important; margin-bottom: 1rem; }
|
| 155 |
+
#sample-radio .wrap {
|
| 156 |
+
display: flex !important;
|
| 157 |
+
flex-wrap: wrap;
|
| 158 |
+
justify-content: center;
|
| 159 |
+
gap: 0.75rem;
|
| 160 |
+
background: transparent !important;
|
| 161 |
+
border: none !important;
|
| 162 |
+
}
|
| 163 |
+
#sample-radio label {
|
| 164 |
+
position: relative;
|
| 165 |
+
background: #f9fafc !important;
|
| 166 |
+
border: 1.5px solid #e3e7f0 !important;
|
| 167 |
+
border-radius: 0.65rem !important;
|
| 168 |
+
padding: 0.7rem 1.1rem 0.7rem 2.15rem !important;
|
| 169 |
+
font-size: 0.85rem !important;
|
| 170 |
+
font-weight: 600 !important;
|
| 171 |
+
text-transform: none !important;
|
| 172 |
+
letter-spacing: normal !important;
|
| 173 |
+
color: #10131c !important;
|
| 174 |
+
box-shadow: 0 1px 2px rgba(16,24,40,0.05);
|
| 175 |
+
cursor: pointer;
|
| 176 |
+
transition: background 0.15s ease, border-color 0.15s ease, box-shadow 0.15s ease, transform 0.1s ease;
|
| 177 |
+
}
|
| 178 |
+
/* custom radio dot, drawn in place of the hidden native input */
|
| 179 |
+
#sample-radio label::before {
|
| 180 |
+
content: "";
|
| 181 |
+
position: absolute;
|
| 182 |
+
left: 0.85rem;
|
| 183 |
+
top: 50%;
|
| 184 |
+
transform: translateY(-50%);
|
| 185 |
+
width: 15px;
|
| 186 |
+
height: 15px;
|
| 187 |
+
border-radius: 50%;
|
| 188 |
+
border: 1.5px solid #cbd5e1;
|
| 189 |
+
background: #ffffff;
|
| 190 |
+
transition: border-color 0.15s ease, background 0.15s ease, box-shadow 0.15s ease;
|
| 191 |
+
}
|
| 192 |
+
#sample-radio label:hover {
|
| 193 |
+
border-color: #93c5fd !important;
|
| 194 |
+
box-shadow: 0 2px 8px rgba(59,130,246,0.12);
|
| 195 |
+
transform: translateY(-1px);
|
| 196 |
+
}
|
| 197 |
+
#sample-radio label:hover::before { border-color: #3b82f6; }
|
| 198 |
+
#sample-radio label:has(input:checked) {
|
| 199 |
+
background: #eaf1ff !important;
|
| 200 |
+
border-color: #3b82f6 !important;
|
| 201 |
+
color: #1d4ed8 !important;
|
| 202 |
+
box-shadow: 0 3px 12px rgba(59,130,246,0.25);
|
| 203 |
+
}
|
| 204 |
+
#sample-radio label:has(input:checked)::before {
|
| 205 |
+
border-color: #3b82f6;
|
| 206 |
+
background: #3b82f6;
|
| 207 |
+
box-shadow: inset 0 0 0 3px #ffffff;
|
| 208 |
+
}
|
| 209 |
+
#sample-radio input[type="radio"] { display: none; }
|
| 210 |
+
|
| 211 |
+
label span, .gr-form label {
|
| 212 |
+
color: #667085 !important;
|
| 213 |
+
font-weight: 500 !important;
|
| 214 |
+
font-size: 0.78rem !important;
|
| 215 |
+
letter-spacing: 0.03em;
|
| 216 |
+
text-transform: uppercase;
|
| 217 |
+
}
|
| 218 |
+
|
| 219 |
+
#audio-upload {
|
| 220 |
+
background: #ffffff !important;
|
| 221 |
+
border: 1px dashed #e3e7f0 !important;
|
| 222 |
+
border-radius: var(--radius) !important;
|
| 223 |
+
color: #10131c !important;
|
| 224 |
+
min-height: 220px;
|
| 225 |
+
}
|
| 226 |
+
#audio-upload:hover { border-color: #3b82f6 !important; }
|
| 227 |
+
#audio-upload .audio-container,
|
| 228 |
+
#audio-upload button.svelte-8prmba {
|
| 229 |
+
width: 100% !important;
|
| 230 |
+
background: transparent !important;
|
| 231 |
+
}
|
| 232 |
+
#audio-upload .wrap.svelte-1vmd51o {
|
| 233 |
+
width: 100% !important;
|
| 234 |
+
height: 100% !important;
|
| 235 |
+
background: transparent !important;
|
| 236 |
+
color: #10131c !important;
|
| 237 |
+
gap: 0.35rem;
|
| 238 |
+
}
|
| 239 |
+
#audio-upload .wrap.svelte-1vmd51o .icon-wrap {
|
| 240 |
+
color: #3b82f6 !important;
|
| 241 |
+
width: 34px !important;
|
| 242 |
+
height: 34px !important;
|
| 243 |
+
margin-bottom: 0.25rem;
|
| 244 |
+
}
|
| 245 |
+
#audio-upload .wrap.svelte-1vmd51o .or {
|
| 246 |
+
color: #94a3b8 !important;
|
| 247 |
+
font-size: 0.85rem !important;
|
| 248 |
+
}
|
| 249 |
+
|
| 250 |
+
button.primary, #run-btn button {
|
| 251 |
+
background: linear-gradient(180deg, #2563eb, #3b82f6) !important;
|
| 252 |
+
border: none !important;
|
| 253 |
+
border-radius: 0.75rem !important;
|
| 254 |
+
color: white !important;
|
| 255 |
+
font-weight: 700 !important;
|
| 256 |
+
font-size: 1rem !important;
|
| 257 |
+
letter-spacing: 0.01em;
|
| 258 |
+
box-shadow: 0 6px 20px rgba(59,130,246,0.35);
|
| 259 |
+
transition: transform 0.15s ease, box-shadow 0.15s ease;
|
| 260 |
+
}
|
| 261 |
+
button.primary:hover, #run-btn button:hover {
|
| 262 |
+
transform: translateY(-1px);
|
| 263 |
+
box-shadow: 0 8px 26px rgba(59,130,246,0.5);
|
| 264 |
+
}
|
| 265 |
+
#run-btn button { width: 100%; height: 3.1rem !important; }
|
| 266 |
+
#run-row { margin-top: 1rem; }
|
| 267 |
+
|
| 268 |
+
textarea, input[type="text"] {
|
| 269 |
+
background: #f2f4f9 !important;
|
| 270 |
+
border: 1px solid #e3e7f0 !important;
|
| 271 |
+
border-radius: 0.6rem !important;
|
| 272 |
+
color: #10131c !important;
|
| 273 |
+
font-family: 'Inter', monospace !important;
|
| 274 |
+
font-size: 0.92rem !important;
|
| 275 |
+
line-height: 1.55 !important;
|
| 276 |
+
}
|
| 277 |
+
|
| 278 |
+
#transcript-panel, #soap-panel, #timing-panel {
|
| 279 |
+
padding: 1.25rem !important;
|
| 280 |
+
}
|
| 281 |
+
|
| 282 |
+
.panel-title {
|
| 283 |
+
font-family: 'Outfit', sans-serif;
|
| 284 |
+
font-weight: 600;
|
| 285 |
+
font-size: 1.02rem;
|
| 286 |
+
color: #10131c !important;
|
| 287 |
+
margin-bottom: 0.9rem;
|
| 288 |
+
display: flex;
|
| 289 |
+
align-items: center;
|
| 290 |
+
gap: 0.5rem;
|
| 291 |
+
}
|
| 292 |
+
.panel-title .dot {
|
| 293 |
+
width: 8px; height: 8px; border-radius: 50%;
|
| 294 |
+
}
|
| 295 |
+
.dot-blue { background: #3b82f6; box-shadow: 0 0 8px #3b82f6; }
|
| 296 |
+
.dot-violet { background: #8b5cf6; box-shadow: 0 0 8px #8b5cf6; }
|
| 297 |
+
.dot-emerald { background: #10b981; box-shadow: 0 0 8px #10b981; }
|
| 298 |
+
|
| 299 |
+
#soap-panel .prose, #soap-panel p, #soap-panel li, #soap-panel strong {
|
| 300 |
+
color: #10131c !important;
|
| 301 |
+
}
|
| 302 |
+
#soap-panel { min-height: 340px; }
|
| 303 |
+
|
| 304 |
+
.timing-badges { display: flex; gap: 0.75rem; flex-wrap: wrap; }
|
| 305 |
+
.timing-badge {
|
| 306 |
+
flex: 1;
|
| 307 |
+
min-width: 150px;
|
| 308 |
+
background: #f2f4f9;
|
| 309 |
+
border: 1px solid #e3e7f0;
|
| 310 |
+
border-radius: 0.75rem;
|
| 311 |
+
padding: 0.85rem 1rem;
|
| 312 |
+
}
|
| 313 |
+
.timing-badge .label {
|
| 314 |
+
font-size: 0.72rem;
|
| 315 |
+
text-transform: uppercase;
|
| 316 |
+
letter-spacing: 0.08em;
|
| 317 |
+
color: #667085;
|
| 318 |
+
margin-bottom: 0.3rem;
|
| 319 |
+
}
|
| 320 |
+
.timing-badge .value {
|
| 321 |
+
font-family: 'Outfit', sans-serif;
|
| 322 |
+
font-size: 1.4rem;
|
| 323 |
+
font-weight: 600;
|
| 324 |
+
color: #10131c;
|
| 325 |
+
}
|
| 326 |
+
.timing-badge .value span { font-size: 0.95rem; color: #667085; font-weight: 500; }
|
| 327 |
+
"""
|
| 328 |
+
|
| 329 |
+
HEAD = """
|
| 330 |
+
<link rel="stylesheet" href="https://fonts.googleapis.com/css2?family=Outfit:wght@500;600;700;800&display=swap">
|
| 331 |
+
<script>
|
| 332 |
+
(() => {
|
| 333 |
+
const LIGHT = "#f6f7fb";
|
| 334 |
+
let painting = false;
|
| 335 |
+
const paint = () => {
|
| 336 |
+
if (painting) return;
|
| 337 |
+
painting = true;
|
| 338 |
+
try {
|
| 339 |
+
document.documentElement.classList.remove("dark");
|
| 340 |
+
document.body?.classList.remove("dark");
|
| 341 |
+
document.querySelectorAll(".dark").forEach((el) => el.classList.remove("dark"));
|
| 342 |
+
for (const el of [document.documentElement, document.body, document.querySelector("gradio-app")]) {
|
| 343 |
+
if (!el) continue;
|
| 344 |
+
el.style.setProperty("background", LIGHT, "important");
|
| 345 |
+
el.style.setProperty("background-color", LIGHT, "important");
|
| 346 |
+
el.style.setProperty("color-scheme", "light", "important");
|
| 347 |
+
}
|
| 348 |
+
} finally {
|
| 349 |
+
painting = false;
|
| 350 |
+
}
|
| 351 |
+
};
|
| 352 |
+
const url = new URL(window.location.href);
|
| 353 |
+
if (url.searchParams.get("__theme") !== "light") {
|
| 354 |
+
url.searchParams.set("__theme", "light");
|
| 355 |
+
window.history.replaceState({}, "", url);
|
| 356 |
+
}
|
| 357 |
+
paint();
|
| 358 |
+
document.addEventListener("DOMContentLoaded", paint);
|
| 359 |
+
new MutationObserver((mutations) => {
|
| 360 |
+
const needs = mutations.some((m) => {
|
| 361 |
+
const el = m.target;
|
| 362 |
+
return el.classList?.contains("dark") || (el.style && !String(el.style.background || "").includes(LIGHT));
|
| 363 |
+
});
|
| 364 |
+
if (needs) paint();
|
| 365 |
+
}).observe(document.documentElement, {
|
| 366 |
+
attributes: true,
|
| 367 |
+
attributeFilter: ["class", "style"],
|
| 368 |
+
subtree: true,
|
| 369 |
+
});
|
| 370 |
+
})();
|
| 371 |
+
</script>
|
| 372 |
+
"""
|
| 373 |
+
|
| 374 |
+
TOPBAR_HTML = """
|
| 375 |
+
<div id="top-bar">
|
| 376 |
+
<div id="brand"><span class="logo-dot"></span>MedScribe</div>
|
| 377 |
+
</div>
|
| 378 |
+
"""
|
| 379 |
+
|
| 380 |
+
HEADER_HTML = """
|
| 381 |
+
<div id="app-header">
|
| 382 |
+
<span class="eyebrow">MedASR + MedGemma 4B</span>
|
| 383 |
+
<h1>AI Medical Scribe</h1>
|
| 384 |
+
<p>Turn a raw clinical recording into a structured SOAP note.</p>
|
| 385 |
+
</div>
|
| 386 |
+
"""
|
| 387 |
+
|
| 388 |
+
|
| 389 |
+
def timing_html(transcription_s: float, generation_s: float) -> str:
|
| 390 |
+
total = transcription_s + generation_s
|
| 391 |
+
return f"""
|
| 392 |
+
<div class="timing-badges">
|
| 393 |
+
<div class="timing-badge">
|
| 394 |
+
<div class="label">Transcription</div>
|
| 395 |
+
<div class="value">{transcription_s:.2f}<span>s</span></div>
|
| 396 |
+
</div>
|
| 397 |
+
<div class="timing-badge">
|
| 398 |
+
<div class="label">SOAP Generation</div>
|
| 399 |
+
<div class="value">{generation_s:.2f}<span>s</span></div>
|
| 400 |
+
</div>
|
| 401 |
+
<div class="timing-badge">
|
| 402 |
+
<div class="label">Total</div>
|
| 403 |
+
<div class="value">{total:.2f}<span>s</span></div>
|
| 404 |
+
</div>
|
| 405 |
+
</div>
|
| 406 |
+
"""
|
| 407 |
+
|
| 408 |
+
|
| 409 |
+
def pick_sample(label):
|
| 410 |
+
return SAMPLES.get(label)
|
| 411 |
+
|
| 412 |
+
|
| 413 |
+
def run(audio_file):
|
| 414 |
+
if audio_file is None:
|
| 415 |
+
return (
|
| 416 |
+
"No audio file selected.",
|
| 417 |
+
"*Select an audio file and click Run.*",
|
| 418 |
+
timing_html(0, 0),
|
| 419 |
+
)
|
| 420 |
+
|
| 421 |
+
result = run_pipeline(audio_file)
|
| 422 |
+
return (
|
| 423 |
+
result.transcript,
|
| 424 |
+
result.soap_note,
|
| 425 |
+
timing_html(result.transcription_seconds, result.generation_seconds),
|
| 426 |
+
)
|
| 427 |
+
|
| 428 |
+
|
| 429 |
+
with gr.Blocks(title="AI Medical Scribe") as demo:
|
| 430 |
+
gr.HTML(TOPBAR_HTML)
|
| 431 |
+
gr.HTML(HEADER_HTML)
|
| 432 |
+
|
| 433 |
+
with gr.Column(elem_classes=["card"], elem_id="sample-panel"):
|
| 434 |
+
gr.HTML(
|
| 435 |
+
'<div class="panel-title"><span class="dot dot-blue"></span>Choose a sample recording</div>'
|
| 436 |
+
)
|
| 437 |
+
sample_picker = gr.Radio(
|
| 438 |
+
choices=list(SAMPLES.keys()),
|
| 439 |
+
value=None,
|
| 440 |
+
show_label=False,
|
| 441 |
+
elem_id="sample-radio",
|
| 442 |
+
)
|
| 443 |
+
|
| 444 |
+
with gr.Column(elem_id="control-row"):
|
| 445 |
+
audio_input = gr.Audio(
|
| 446 |
+
label="Audio recording",
|
| 447 |
+
sources=["upload"],
|
| 448 |
+
type="filepath",
|
| 449 |
+
elem_id="audio-upload",
|
| 450 |
+
)
|
| 451 |
+
with gr.Row(elem_id="run-row"):
|
| 452 |
+
run_button = gr.Button(
|
| 453 |
+
"Run pipeline", variant="primary", elem_id="run-btn", size="lg"
|
| 454 |
+
)
|
| 455 |
+
|
| 456 |
+
with gr.Row():
|
| 457 |
+
with gr.Column(elem_classes=["card"], elem_id="transcript-panel"):
|
| 458 |
+
gr.HTML(
|
| 459 |
+
'<div class="panel-title"><span class="dot dot-blue"></span>MedASR Transcript</div>'
|
| 460 |
+
)
|
| 461 |
+
transcript_output = gr.Textbox(
|
| 462 |
+
show_label=False,
|
| 463 |
+
lines=15,
|
| 464 |
+
container=False,
|
| 465 |
+
placeholder="Transcript will appear here…",
|
| 466 |
+
)
|
| 467 |
+
with gr.Column(elem_classes=["card"], elem_id="soap-panel"):
|
| 468 |
+
gr.HTML(
|
| 469 |
+
'<div class="panel-title"><span class="dot dot-violet"></span>SOAP Note — MedGemma 4B</div>'
|
| 470 |
+
)
|
| 471 |
+
soap_output = gr.Markdown("*SOAP note will appear here…*")
|
| 472 |
+
|
| 473 |
+
with gr.Column(elem_classes=["card"], elem_id="timing-panel"):
|
| 474 |
+
gr.HTML(
|
| 475 |
+
'<div class="panel-title"><span class="dot dot-emerald"></span>Step Timing</div>'
|
| 476 |
+
)
|
| 477 |
+
timing_output = gr.HTML(timing_html(0, 0))
|
| 478 |
+
|
| 479 |
+
# Picking a sample loads it into the player (so it can be listened to
|
| 480 |
+
# immediately); the player's own .change then kicks off the pipeline,
|
| 481 |
+
# so transcription/generation run while playback is already available.
|
| 482 |
+
sample_picker.change(fn=pick_sample, inputs=[sample_picker], outputs=[audio_input])
|
| 483 |
+
audio_input.change(
|
| 484 |
+
fn=run,
|
| 485 |
+
inputs=[audio_input],
|
| 486 |
+
outputs=[transcript_output, soap_output, timing_output],
|
| 487 |
+
)
|
| 488 |
+
run_button.click(
|
| 489 |
+
fn=run,
|
| 490 |
+
inputs=[audio_input],
|
| 491 |
+
outputs=[transcript_output, soap_output, timing_output],
|
| 492 |
+
)
|
| 493 |
+
|
| 494 |
+
if __name__ == "__main__":
|
| 495 |
+
demo.launch(
|
| 496 |
+
css=CUSTOM_CSS,
|
| 497 |
+
head=HEAD,
|
| 498 |
+
footer_links=[],
|
| 499 |
+
)
|
llm.py
ADDED
|
@@ -0,0 +1,118 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
"""Audio -> MedASR transcript -> MedGemma 4B SOAP note pipeline."""
|
| 2 |
+
|
| 3 |
+
import os
|
| 4 |
+
import time
|
| 5 |
+
from dataclasses import dataclass
|
| 6 |
+
|
| 7 |
+
import spaces
|
| 8 |
+
import torch
|
| 9 |
+
from transformers import AutoModelForImageTextToText, AutoProcessor, pipeline
|
| 10 |
+
|
| 11 |
+
ASR_MODEL_ID = os.environ.get("MEDASR_MODEL_ID", "google/medasr")
|
| 12 |
+
LLM_MODEL_ID = os.environ.get("MEDGEMMA_MODEL_ID", "google/medgemma-4b-it")
|
| 13 |
+
|
| 14 |
+
SYSTEM_PROMPT = (
|
| 15 |
+
"You are a clinical documentation engine. Convert the transcript into a "
|
| 16 |
+
"SOAP note (Subjective, Objective, Assessment, Plan). Infer which "
|
| 17 |
+
"statements come from the doctor versus the patient based on context "
|
| 18 |
+
"(questions, clinical observations vs. symptom descriptions). Do not "
|
| 19 |
+
"fabricate any detail not present in the transcript. If speaker "
|
| 20 |
+
"attribution is unclear, mark it as unclear rather than guessing "
|
| 21 |
+
"confidently."
|
| 22 |
+
)
|
| 23 |
+
|
| 24 |
+
_asr_pipe = None
|
| 25 |
+
_llm_model = None
|
| 26 |
+
_llm_processor = None
|
| 27 |
+
|
| 28 |
+
|
| 29 |
+
def _device_and_dtype():
|
| 30 |
+
if torch.cuda.is_available():
|
| 31 |
+
return "cuda", torch.bfloat16
|
| 32 |
+
if torch.backends.mps.is_available():
|
| 33 |
+
return "mps", torch.float16
|
| 34 |
+
return "cpu", torch.float32
|
| 35 |
+
|
| 36 |
+
|
| 37 |
+
def get_asr_pipeline():
|
| 38 |
+
global _asr_pipe
|
| 39 |
+
if _asr_pipe is None:
|
| 40 |
+
device, dtype = _device_and_dtype()
|
| 41 |
+
_asr_pipe = pipeline(
|
| 42 |
+
"automatic-speech-recognition",
|
| 43 |
+
model=ASR_MODEL_ID,
|
| 44 |
+
device=device,
|
| 45 |
+
dtype=dtype,
|
| 46 |
+
)
|
| 47 |
+
return _asr_pipe
|
| 48 |
+
|
| 49 |
+
|
| 50 |
+
def get_llm():
|
| 51 |
+
global _llm_model, _llm_processor
|
| 52 |
+
if _llm_model is None:
|
| 53 |
+
device, dtype = _device_and_dtype()
|
| 54 |
+
_llm_model = AutoModelForImageTextToText.from_pretrained(
|
| 55 |
+
LLM_MODEL_ID, dtype=dtype, device_map=device
|
| 56 |
+
)
|
| 57 |
+
_llm_processor = AutoProcessor.from_pretrained(LLM_MODEL_ID)
|
| 58 |
+
return _llm_model, _llm_processor
|
| 59 |
+
|
| 60 |
+
|
| 61 |
+
def transcribe(audio_path: str) -> str:
|
| 62 |
+
"""Transcribe an audio file to text using MedASR, chunked for long audio."""
|
| 63 |
+
pipe = get_asr_pipeline()
|
| 64 |
+
result = pipe(audio_path, chunk_length_s=20, stride_length_s=2)
|
| 65 |
+
return result["text"].strip()
|
| 66 |
+
|
| 67 |
+
|
| 68 |
+
def generate_soap_note(transcript: str) -> str:
|
| 69 |
+
model, processor = get_llm()
|
| 70 |
+
messages = [
|
| 71 |
+
{"role": "system", "content": [{"type": "text", "text": SYSTEM_PROMPT}]},
|
| 72 |
+
{"role": "user", "content": [{"type": "text", "text": transcript}]},
|
| 73 |
+
]
|
| 74 |
+
inputs = processor.apply_chat_template(
|
| 75 |
+
messages,
|
| 76 |
+
add_generation_prompt=True,
|
| 77 |
+
tokenize=True,
|
| 78 |
+
return_dict=True,
|
| 79 |
+
return_tensors="pt",
|
| 80 |
+
).to(model.device)
|
| 81 |
+
|
| 82 |
+
input_len = inputs["input_ids"].shape[-1]
|
| 83 |
+
|
| 84 |
+
with torch.inference_mode():
|
| 85 |
+
generated_ids = model.generate(
|
| 86 |
+
**inputs,
|
| 87 |
+
max_new_tokens=1024,
|
| 88 |
+
do_sample=False,
|
| 89 |
+
repetition_penalty=1.3,
|
| 90 |
+
)
|
| 91 |
+
|
| 92 |
+
new_tokens = generated_ids[0][input_len:]
|
| 93 |
+
return processor.decode(new_tokens, skip_special_tokens=True).strip()
|
| 94 |
+
|
| 95 |
+
|
| 96 |
+
@dataclass
|
| 97 |
+
class PipelineResult:
|
| 98 |
+
transcript: str
|
| 99 |
+
soap_note: str
|
| 100 |
+
transcription_seconds: float
|
| 101 |
+
generation_seconds: float
|
| 102 |
+
|
| 103 |
+
|
| 104 |
+
@spaces.GPU(duration=120)
|
| 105 |
+
def run_pipeline(audio_path: str) -> PipelineResult:
|
| 106 |
+
t0 = time.perf_counter()
|
| 107 |
+
transcript = transcribe(audio_path)
|
| 108 |
+
t1 = time.perf_counter()
|
| 109 |
+
|
| 110 |
+
soap_note = generate_soap_note(transcript)
|
| 111 |
+
t2 = time.perf_counter()
|
| 112 |
+
|
| 113 |
+
return PipelineResult(
|
| 114 |
+
transcript=transcript,
|
| 115 |
+
soap_note=soap_note,
|
| 116 |
+
transcription_seconds=t1 - t0,
|
| 117 |
+
generation_seconds=t2 - t1,
|
| 118 |
+
)
|
requirements.txt
ADDED
|
@@ -0,0 +1,11 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
torch==2.13.0
|
| 2 |
+
torchaudio==2.11.0
|
| 3 |
+
transformers==5.14.1
|
| 4 |
+
accelerate==1.14.0
|
| 5 |
+
soundfile==0.14.0
|
| 6 |
+
librosa==0.11.0
|
| 7 |
+
huggingface_hub==1.24.0
|
| 8 |
+
gradio==6.20.0
|
| 9 |
+
spaces
|
| 10 |
+
sentencepiece
|
| 11 |
+
pillow
|
test_audio/.DS_Store
ADDED
|
Binary file (6.15 kB). View file
|
|
|
test_audio/clips/D0420-S1-T01_clip.wav
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:3aca81a6750e0e091fa7daec5a3046513f8fdded0dcf4b3cbef45ef86b841434
|
| 3 |
+
size 2880154
|
test_audio/clips/D0420-S2-T01_clip.wav
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:0b990a7cf8d577e73ab47cd5580f95ab053feee176fad7dc54b007f1def38b97
|
| 3 |
+
size 2880154
|
test_audio/clips/D0420-S3-T01_clip.wav
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:163265a5609dd0aec3c322786b5296275166350e708523b2ac9c3e44ae08a797
|
| 3 |
+
size 2880154
|