Spaces:
Sleeping
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Commit ·
1ff0d2d
1
Parent(s): 42e56c5
Medi-LLM: public demo
Browse files- app/demo/demo.py +284 -279
- app/utils/create_hf_space.py +9 -0
- app/utils/inference_utils.py +84 -6
- requirements-dev.txt +54 -0
- requirements.txt +16 -38
app/demo/demo.py
CHANGED
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@@ -70,7 +70,7 @@ def classify(role, mode, normalize_mode, emr_text, image, use_rollout):
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# Model caching
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if mode not in model_cache:
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model_cache[mode] = load_model(mode
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model = model_cache[mode]
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# Run prediction
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@@ -529,301 +529,306 @@ def reset_ui():
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custom_css =
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with gr.Blocks(css=custom_css) as demo:
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# Hidden State
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role_state = gr.State(value="User")
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mode_state = gr.State(value=DEFAULT_MODE)
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rollout_state = gr.State(value=False)
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normaliza_mode_state = gr.State(value="visual")
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inference_done = gr.State(value=False)
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# Role and Mode selection
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with gr.Row(equal_height=True):
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with gr.Column():
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role = gr.Radio(["User", "Doctor"], value="User", label="Select Role", info="Doctors see insights like Grad-CAM and token attention", elem_id="role_selector")
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mode = gr.Radio(["text", "image", "multimodal"], value=DEFAULT_MODE, label="Select Input Mode", info="Choose Diagnosis input type", elem_id="mode_selector")
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with gr.Column(visible=False) as normalize_mode_column:
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normalize_mode = gr.Radio(
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["visual", "probabilistic"],
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value="visual",
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label="Attention Normalization",
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info="Softmax sums to 1 (probabilistic). Visual uses gamma-boosted scaling for color clarity."
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)
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use_rollout = gr.Checkbox(
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label="Use attention rollout (CLS -> inputs)",
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value=False,
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info="Includes residuals and multiplies attention across layers. Slower but often more faithful."
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)
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normalize_mode.change(
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fn=lambda val: val,
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inputs=[normalize_mode],
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outputs=[normaliza_mode_state]
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)
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use_rollout.change(
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fn=lambda v: v,
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inputs=[use_rollout],
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outputs=[rollout_state]
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)
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elem_id="
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class_probs_json = gr.JSON(label="🔍 Class Probabilities", visible=True, elem_classes=["json-box"])
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with insights_tab:
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with gr.Tab("📷 Grad-CAM"):
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gradcam_img = gr.Image(visible=False, elem_classes=["gr-image-box"])
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with gr.Tab("🔬 Token Attention"):
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token_attention = gr.HighlightedText(
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visible=False,
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show_legend=False,
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color_map={
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"0.0": "#7aa2f7", # blue
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"0.25": "#80deea", # cyan
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"0.5": "#fbc02d", # yellow
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"0.75": "#ff8a65", # orange
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"1.0": "#f7768e", # red
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},
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elem_classes=["token-attn-box"]
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)
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top5_html = gr.HTML(value="", visible=False)
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<span style="font-size: 14px; color: #c0caf5;">1.0</span>
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</div>
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</div>
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""")
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with gr.Row():
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loading_msg = gr.Markdown(value="", visible=False, elem_classes=["loading-msg"])
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# Bind inference
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submit_btn.click(
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fn=show_loading_msg,
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outputs=[loading_msg]
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).then(
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fn=classify,
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inputs=[role_state, mode_state, normaliza_mode_state, emr_text, image, rollout_state],
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outputs=[
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result_box,
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gradcam_img,
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token_attention,
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top5_html,
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confidence_label,
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insights_tab,
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prediction_count_box,
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class_probs_json,
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]
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).then(
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fn=lambda: gr.update(value="", visible=False),
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outputs=[loading_msg]
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).then(
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fn=lambda: True,
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outputs=[inference_done]
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)
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inputs=[inference_done, role_state, mode_state, normalize_mode, emr_text, image, rollout_state],
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outputs=[
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result_box,
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gradcam_img,
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token_attention,
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top5_html,
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confidence_label,
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insights_tab,
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prediction_count_box,
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class_probs_json,
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]
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confidence_label,
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insights_tab,
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prediction_count_box,
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class_probs_json
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download_btn.click(
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fn=export_csv,
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inputs=[filename_input, role_state],
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outputs=[
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csv_output,
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csv_output,
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export_status_box
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).then(
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fn=blink_box_effect,
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inputs=[csv_output],
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outputs=[csv_output]
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).then(
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fn=disable_filename_input,
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outputs=[filename_input]
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)
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confirm_clear_btn.click(
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fn=clear_confirmed,
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inputs=[role_state],
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outputs=[
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prediction_count_box, # reset prediction count
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confirm_box, # show success message
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csv_output, # hide CSV output file
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filename_input # re-enable input box
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]
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).then(
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fn=lambda: gr.update(visible=False), # Hide confirm button
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outputs=[confirm_clear_btn]
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).then(
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fn=reset_confirm_box,
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outputs=[confirm_box]
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fn=reset_ui,
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outputs=[
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emr_text, # 1
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image, # 2
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max_file_note, # 3
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result_box, # 4
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gradcam_img, # 5
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token_attention, # 6
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top5_html, # 7
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confidence_label, # 8
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insights_tab, # 9
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class_probs_json, # 10
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role_state, # 11
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mode_state, # 12
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normaliza_mode_state, # 13
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role, # 14 (radio)
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mode, # 15 (radio)
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normalize_mode, # 16 (radio)
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normalize_mode_column, # 17 (column visibility)
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use_rollout, # 18
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rollout_state, # 19
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loading_msg, # 20
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inference_done, # 21
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export_status_box # 22
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]
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)
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if __name__ == "__main__":
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demo.launch()
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# Model caching
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if mode not in model_cache:
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model_cache[mode] = load_model(mode)
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model = model_cache[mode]
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# Run prediction
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)
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def build_ui():
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# Load CSS safely (don't crash if file is missing on remote)
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style_path = Path(__file__).resolve().parent / "style.css"
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custom_css = style_path.read_text(encoding="utf-8") if style_path.exists() else ""
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with gr.Blocks(css=custom_css) as demo:
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# ----- Header -----
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gr.Markdown("<h2 class='centered'>🩺 Medi-LLM: Clinical Triage Assistant 🩻</h2>")
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gr.Markdown("<p class='centered'>Upload a chest X-ray and/or enter EMR text to get a triage level prediction.</p>")
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gr.HTML(
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"""
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<div class='welcome-banner' style="background-color: #24283b; border-left: 4px solid #7aa2f7; padding: 16px; border-radius: 8px; margin-bottom: 16px;">
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<h3 style="margin-top: 0; color: #c0caf5;">👋 Welcome to Medi-LLM</h3>
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<p style="color: #a9b1d6; line-height: 1.6;">
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This AI assistant helps triage patients using <strong>EMR text</strong> and <strong>chest X-rays</strong>.<br>
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📝 Enter EMR notes, 📷 upload a chest X-ray, or use both for a multimodal diagnosis.<br>
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👩⚕️ Select <strong>Doctor</strong> mode to view insights like Grad-CAM heatmaps and token-level attention.<br>
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💾 Save your results for later by exporting them to a CSV file.
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</p>
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</div>
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"""
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# ----- Hidden State -----
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role_state = gr.State(value="User")
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mode_state = gr.State(value=DEFAULT_MODE)
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rollout_state = gr.State(value=False)
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normaliza_mode_state = gr.State(value="visual")
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inference_done = gr.State(value=False)
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|
| 562 |
+
# ----- Role and Mode selection -----
|
| 563 |
+
with gr.Row(equal_height=True):
|
| 564 |
+
with gr.Column():
|
| 565 |
+
role = gr.Radio(["User", "Doctor"], value="User", label="Select Role", info="Doctors see insights like Grad-CAM and token attention", elem_id="role_selector")
|
| 566 |
+
mode = gr.Radio(["text", "image", "multimodal"], value=DEFAULT_MODE, label="Select Input Mode", info="Choose Diagnosis input type", elem_id="mode_selector")
|
| 567 |
+
with gr.Column(visible=False) as normalize_mode_column:
|
| 568 |
+
normalize_mode = gr.Radio(
|
| 569 |
+
["visual", "probabilistic"],
|
| 570 |
+
value="visual",
|
| 571 |
+
label="Attention Normalization",
|
| 572 |
+
info="Softmax sums to 1 (probabilistic). Visual uses gamma-boosted scaling for color clarity."
|
| 573 |
+
)
|
| 574 |
+
use_rollout = gr.Checkbox(
|
| 575 |
+
label="Use attention rollout (CLS -> inputs)",
|
| 576 |
+
value=False,
|
| 577 |
+
info="Includes residuals and multiplies attention across layers. Slower but often more faithful."
|
| 578 |
+
)
|
| 579 |
+
|
| 580 |
+
# ----- Inputs -----
|
| 581 |
+
with gr.Row():
|
| 582 |
+
with gr.Column(scale=3, elem_id="text_col"):
|
| 583 |
+
emr_text, image, max_file_note = render_inputs(DEFAULT_MODE)
|
| 584 |
+
|
| 585 |
+
# ----- Actions -----
|
| 586 |
+
with gr.Row():
|
| 587 |
+
submit_btn = gr.Button(
|
| 588 |
+
"🔍 Run Inference",
|
| 589 |
+
elem_id="inference_btn"
|
| 590 |
+
)
|
| 591 |
+
reset_btn = gr.Button(
|
| 592 |
+
"↩️ Reset",
|
| 593 |
+
elem_id="reset_btn"
|
| 594 |
+
)
|
| 595 |
|
| 596 |
+
# ----- Outputs -----
|
| 597 |
+
with gr.Column(elem_classes=["output-box"]):
|
| 598 |
+
result_box = gr.Textbox(label="🧪 Triage Prediction", interactive=False)
|
| 599 |
+
confidence_label = gr.Label(label="📊 Confidence", visible=False)
|
| 600 |
+
prediction_count_box = gr.Textbox(value="Predictions: 0", interactive=False, label="🧮 Count", elem_id="prediction_count_box")
|
| 601 |
+
insights_tab = gr.Tabs(visible=False)
|
| 602 |
+
class_probs_json = gr.JSON(label="🔍 Class Probabilities", visible=True, elem_classes=["json-box"])
|
| 603 |
+
with insights_tab:
|
| 604 |
+
with gr.Tab("📷 Grad-CAM"):
|
| 605 |
+
gradcam_img = gr.Image(visible=False, elem_classes=["gr-image-box"])
|
| 606 |
+
with gr.Tab("🔬 Token Attention"):
|
| 607 |
+
token_attention = gr.HighlightedText(
|
| 608 |
+
visible=False,
|
| 609 |
+
show_legend=False,
|
| 610 |
+
color_map={
|
| 611 |
+
"0.0": "#7aa2f7", # blue
|
| 612 |
+
"0.25": "#80deea", # cyan
|
| 613 |
+
"0.5": "#fbc02d", # yellow
|
| 614 |
+
"0.75": "#ff8a65", # orange
|
| 615 |
+
"1.0": "#f7768e", # red
|
| 616 |
+
},
|
| 617 |
+
elem_classes=["token-attn-box"]
|
| 618 |
+
)
|
| 619 |
+
top5_html = gr.HTML(value="", visible=False)
|
| 620 |
+
|
| 621 |
+
inject_tooltips()
|
| 622 |
+
|
| 623 |
+
gr.HTML("""
|
| 624 |
+
<div class="attention-legend">
|
| 625 |
+
<div style="display: flex; align-items: center; gap: 8px;">
|
| 626 |
+
<span style="font-size: 14px; color: #c0caf5;">0.0</span>
|
| 627 |
+
<div class="attention-gradient-bar"></div>
|
| 628 |
+
<span style="font-size: 14px; color: #c0caf5;">1.0</span>
|
| 629 |
+
</div>
|
| 630 |
+
</div>
|
| 631 |
+
""")
|
| 632 |
+
|
| 633 |
+
with gr.Row():
|
| 634 |
+
loading_msg = gr.Markdown(value="", visible=False, elem_classes=["loading-msg"])
|
| 635 |
+
|
| 636 |
+
# ----- Inference Wiring -----
|
| 637 |
+
submit_btn.click(
|
| 638 |
+
fn=show_loading_msg,
|
| 639 |
+
outputs=[loading_msg]
|
| 640 |
+
).then(
|
| 641 |
+
fn=classify,
|
| 642 |
+
inputs=[role_state, mode_state, normaliza_mode_state, emr_text, image, rollout_state],
|
| 643 |
+
outputs=[
|
| 644 |
+
result_box,
|
| 645 |
+
gradcam_img,
|
| 646 |
+
token_attention,
|
| 647 |
+
top5_html,
|
| 648 |
+
confidence_label,
|
| 649 |
+
insights_tab,
|
| 650 |
+
prediction_count_box,
|
| 651 |
+
class_probs_json,
|
| 652 |
+
]
|
| 653 |
+
).then(
|
| 654 |
+
fn=lambda: gr.update(value="", visible=False),
|
| 655 |
+
outputs=[loading_msg]
|
| 656 |
+
).then(
|
| 657 |
+
fn=lambda: True,
|
| 658 |
+
outputs=[inference_done]
|
| 659 |
)
|
| 660 |
+
|
| 661 |
+
# ----- Role/Mode/Param Change Wiring -----
|
| 662 |
+
role.change(
|
| 663 |
+
fn=update_role_state,
|
| 664 |
+
inputs=[role],
|
| 665 |
+
outputs=[role_state, normalize_mode_column, insights_tab, token_attention, gradcam_img, use_rollout, top5_html]
|
| 666 |
)
|
| 667 |
|
| 668 |
+
# Input Updates
|
| 669 |
+
mode.change(
|
| 670 |
+
fn=lambda m: (*render_inputs(m), m),
|
| 671 |
+
inputs=[mode],
|
| 672 |
+
outputs=[emr_text, image, max_file_note, mode_state]
|
| 673 |
+
)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 674 |
|
| 675 |
+
normalize_mode.change(
|
| 676 |
+
fn=lambda val: val,
|
| 677 |
+
inputs=[normalize_mode],
|
| 678 |
+
outputs=[normaliza_mode_state]
|
| 679 |
+
)
|
| 680 |
|
| 681 |
+
use_rollout.change(
|
| 682 |
+
fn=lambda v: v,
|
| 683 |
+
inputs=[use_rollout],
|
| 684 |
+
outputs=[rollout_state]
|
| 685 |
+
)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 686 |
|
| 687 |
+
normalize_mode.change(
|
| 688 |
+
fn=rerun_if_done,
|
| 689 |
+
inputs=[inference_done, role_state, mode_state, normalize_mode, emr_text, image, rollout_state],
|
| 690 |
+
outputs=[
|
| 691 |
+
result_box,
|
| 692 |
+
gradcam_img,
|
| 693 |
+
token_attention,
|
| 694 |
+
top5_html,
|
| 695 |
+
confidence_label,
|
| 696 |
+
insights_tab,
|
| 697 |
+
prediction_count_box,
|
| 698 |
+
class_probs_json,
|
| 699 |
+
]
|
| 700 |
+
)
|
| 701 |
|
| 702 |
+
use_rollout.change(
|
| 703 |
+
fn=rerun_if_done,
|
| 704 |
+
inputs=[inference_done, role_state, mode_state, normalize_mode, emr_text, image, rollout_state],
|
| 705 |
+
outputs=[
|
| 706 |
+
result_box,
|
| 707 |
+
gradcam_img,
|
| 708 |
+
token_attention,
|
| 709 |
+
top5_html,
|
| 710 |
+
confidence_label,
|
| 711 |
+
insights_tab,
|
| 712 |
+
prediction_count_box,
|
| 713 |
+
class_probs_json
|
| 714 |
+
]
|
| 715 |
+
)
|
| 716 |
|
| 717 |
+
# ----- CSV Export & Log Controls -----
|
| 718 |
+
gr.Markdown("### 📁 Export Prediction Log")
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 719 |
|
| 720 |
+
with gr.Row(equal_height=True):
|
| 721 |
+
with gr.Column(scale=3):
|
| 722 |
+
filename_input = gr.Textbox(
|
| 723 |
+
label="CSV filename (optional)",
|
| 724 |
+
placeholder="e.g., triage_results.csv",
|
| 725 |
+
info="Set filename as needed or leave blank for auto-naming",
|
| 726 |
+
elem_id="csv_filename"
|
| 727 |
+
)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 728 |
|
| 729 |
+
export_status_box = gr.Textbox(
|
| 730 |
+
value="",
|
| 731 |
+
visible=False,
|
| 732 |
+
interactive=False,
|
| 733 |
+
label="",
|
| 734 |
+
elem_id="export_status"
|
| 735 |
+
)
|
| 736 |
|
| 737 |
+
with gr.Column(scale=4):
|
| 738 |
+
gr.Markdown(
|
| 739 |
+
"📑 **Summary**\n\nDownload your triage results for clinical review or research.",
|
| 740 |
+
elem_classes="centered"
|
| 741 |
+
)
|
| 742 |
+
with gr.Row():
|
| 743 |
+
with gr.Column(scale=1, min_width=200):
|
| 744 |
+
download_btn = gr.Button("💾 Export CSV", elem_id="export_button")
|
| 745 |
+
with gr.Column(scale=1, min_width=200):
|
| 746 |
+
clear_btn = gr.Button("🗑️ Clear Logs", elem_id="clear_button")
|
| 747 |
+
confirm_clear_btn = gr.Button("✅ Confirm Clear", visible=False, elem_id="confirm_button")
|
| 748 |
+
confirm_box = gr.Textbox(label="Status", interactive=False, visible=False, elem_id="confirm_box")
|
| 749 |
+
|
| 750 |
+
with gr.Column(scale=3):
|
| 751 |
+
csv_output = gr.File(label="📂 Download Link", elem_id="download_box")
|
| 752 |
+
|
| 753 |
+
download_btn.click(
|
| 754 |
+
fn=export_csv,
|
| 755 |
+
inputs=[filename_input, role_state],
|
| 756 |
+
outputs=[
|
| 757 |
+
csv_output,
|
| 758 |
+
csv_output,
|
| 759 |
+
export_status_box
|
| 760 |
+
]
|
| 761 |
+
).then(
|
| 762 |
+
fn=blink_box_effect,
|
| 763 |
+
inputs=[csv_output],
|
| 764 |
+
outputs=[csv_output]
|
| 765 |
+
).then(
|
| 766 |
+
fn=disable_filename_input,
|
| 767 |
+
outputs=[filename_input]
|
| 768 |
+
)
|
| 769 |
|
| 770 |
+
clear_btn.click(
|
| 771 |
+
fn=lambda: (
|
| 772 |
+
confirm_clear(),
|
| 773 |
+
gr.Button(visible=True),
|
| 774 |
+
),
|
| 775 |
+
outputs=[confirm_box, confirm_clear_btn]
|
| 776 |
+
)
|
| 777 |
|
| 778 |
+
confirm_clear_btn.click(
|
| 779 |
+
fn=clear_confirmed,
|
| 780 |
+
inputs=[role_state],
|
| 781 |
+
outputs=[
|
| 782 |
+
prediction_count_box, # reset prediction count
|
| 783 |
+
confirm_box, # show success message
|
| 784 |
+
csv_output, # hide CSV output file
|
| 785 |
+
filename_input # re-enable input box
|
| 786 |
+
]
|
| 787 |
+
).then(
|
| 788 |
+
fn=lambda: gr.update(visible=False), # Hide confirm button
|
| 789 |
+
outputs=[confirm_clear_btn]
|
| 790 |
+
).then(
|
| 791 |
+
fn=reset_confirm_box,
|
| 792 |
+
outputs=[confirm_box]
|
| 793 |
+
)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 794 |
|
| 795 |
+
# ----- Reset Wiring -----
|
| 796 |
+
reset_btn.click(
|
| 797 |
+
fn=reset_ui,
|
| 798 |
+
outputs=[
|
| 799 |
+
emr_text, # 1
|
| 800 |
+
image, # 2
|
| 801 |
+
max_file_note, # 3
|
| 802 |
+
result_box, # 4
|
| 803 |
+
gradcam_img, # 5
|
| 804 |
+
token_attention, # 6
|
| 805 |
+
top5_html, # 7
|
| 806 |
+
confidence_label, # 8
|
| 807 |
+
insights_tab, # 9
|
| 808 |
+
class_probs_json, # 10
|
| 809 |
+
role_state, # 11
|
| 810 |
+
mode_state, # 12
|
| 811 |
+
normaliza_mode_state, # 13
|
| 812 |
+
role, # 14 (radio)
|
| 813 |
+
mode, # 15 (radio)
|
| 814 |
+
normalize_mode, # 16 (radio)
|
| 815 |
+
normalize_mode_column, # 17 (column visibility)
|
| 816 |
+
use_rollout, # 18
|
| 817 |
+
rollout_state, # 19
|
| 818 |
+
loading_msg, # 20
|
| 819 |
+
inference_done, # 21
|
| 820 |
+
export_status_box # 22
|
| 821 |
+
]
|
| 822 |
+
)
|
| 823 |
+
return demo
|
| 824 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 825 |
|
| 826 |
+
# Expose for Spaces & imports
|
| 827 |
+
demo = build_ui()
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 828 |
|
| 829 |
if __name__ == "__main__":
|
| 830 |
+
demo.launch(
|
| 831 |
+
server_name=os.getenv("GRADIO_SERVER_NAME", "127.0.0.1"),
|
| 832 |
+
server_port=int(os.getenv("GRADIO_SERVER_PORT", "7860")),
|
| 833 |
+
show_error=True,
|
| 834 |
+
)
|
|
|
app/utils/create_hf_space.py
ADDED
|
@@ -0,0 +1,9 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
from huggingface_hub import HfApi
|
| 2 |
+
HfApi().create_repo(
|
| 3 |
+
repo_id="Preetham22/medi-llm",
|
| 4 |
+
repo_type="space",
|
| 5 |
+
space_sdk="gradio",
|
| 6 |
+
exist_ok=True,
|
| 7 |
+
)
|
| 8 |
+
|
| 9 |
+
print("✅ Space ready: Preetham22/medi-llm")
|
app/utils/inference_utils.py
CHANGED
|
@@ -1,3 +1,4 @@
|
|
|
|
|
| 1 |
import sys
|
| 2 |
import torch
|
| 3 |
import yaml
|
|
@@ -5,6 +6,7 @@ import numpy as np
|
|
| 5 |
from pathlib import Path
|
| 6 |
from transformers import AutoTokenizer
|
| 7 |
from torchvision import transforms
|
|
|
|
| 8 |
|
| 9 |
ROOT_DIR = Path(__file__).resolve().parent.parent.parent
|
| 10 |
sys.path.append(str(ROOT_DIR))
|
|
@@ -12,10 +14,42 @@ sys.path.append(str(ROOT_DIR))
|
|
| 12 |
from src.multimodal_model import MediLLMModel
|
| 13 |
from app.utils.gradcam_utils import register_hooks, generate_gradcam
|
| 14 |
|
| 15 |
-
|
|
|
|
|
|
|
| 16 |
DEVICE = torch.device("cuda" if torch.cuda.is_available() else "cpu")
|
| 17 |
|
| 18 |
-
#
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 19 |
inv_map = {0: "low", 1: "medium", 2: "high"}
|
| 20 |
|
| 21 |
# Tokenizer and image transform
|
|
@@ -27,22 +61,63 @@ image_transform = transforms.Compose([
|
|
| 27 |
])
|
| 28 |
|
| 29 |
|
| 30 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 31 |
with open(config_path, "r") as f:
|
| 32 |
-
|
|
|
|
|
|
|
|
|
|
| 33 |
|
|
|
|
| 34 |
model = MediLLMModel(
|
| 35 |
mode=mode,
|
| 36 |
dropout=config["dropout"],
|
| 37 |
hidden_dim=config["hidden_dim"]
|
| 38 |
)
|
| 39 |
-
|
| 40 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 41 |
model.to(DEVICE)
|
| 42 |
model.eval()
|
| 43 |
return model
|
| 44 |
|
| 45 |
|
|
|
|
|
|
|
|
|
|
| 46 |
def attention_rollout(attentions, last_k=4, residual_alpha=0.5):
|
| 47 |
"""
|
| 48 |
attentions_tuple: tuple/list of layer attentions; each is (B,H,S,S)
|
|
@@ -139,6 +214,9 @@ def _normalize_for_display_wordlevel(attn_scores, normalize_mode="visual", tempe
|
|
| 139 |
return attn_array0, labels
|
| 140 |
|
| 141 |
|
|
|
|
|
|
|
|
|
|
| 142 |
def predict(
|
| 143 |
model,
|
| 144 |
mode,
|
|
|
|
| 1 |
+
import os
|
| 2 |
import sys
|
| 3 |
import torch
|
| 4 |
import yaml
|
|
|
|
| 6 |
from pathlib import Path
|
| 7 |
from transformers import AutoTokenizer
|
| 8 |
from torchvision import transforms
|
| 9 |
+
from huggingface_hub import hf_hub_download
|
| 10 |
|
| 11 |
ROOT_DIR = Path(__file__).resolve().parent.parent.parent
|
| 12 |
sys.path.append(str(ROOT_DIR))
|
|
|
|
| 14 |
from src.multimodal_model import MediLLMModel
|
| 15 |
from app.utils.gradcam_utils import register_hooks, generate_gradcam
|
| 16 |
|
| 17 |
+
# --------------------
|
| 18 |
+
# Runtime / Hub config
|
| 19 |
+
# --------------------
|
| 20 |
DEVICE = torch.device("cuda" if torch.cuda.is_available() else "cpu")
|
| 21 |
|
| 22 |
+
# Map modes -> filenames in HF model repo
|
| 23 |
+
HF_MODEL_REPO = os.getenv("HF_MODEL_REPO", "Preetham22/medi-llm-weights")
|
| 24 |
+
HF_WEIGHTS_REV = os.getenv("HF_WEIGHTS_REV", None) # optional (commit/tag/branch)
|
| 25 |
+
FILENAMES = {
|
| 26 |
+
"text": "medi_llm_state_dict_text.pth",
|
| 27 |
+
"image": "medi_llm_state_dict_image.pth",
|
| 28 |
+
"multimodal": "medi_llm_state_dict_multimodal.pth"
|
| 29 |
+
}
|
| 30 |
+
|
| 31 |
+
|
| 32 |
+
def resolve_weights_path(mode: str) -> str:
|
| 33 |
+
"""Download (or reuse cached) weights for the given mode from HF Hub."""
|
| 34 |
+
if mode not in FILENAMES:
|
| 35 |
+
raise ValueError(f"Unknown mode '{mode}'. Expected one of {list(FILENAMES)}.")
|
| 36 |
+
filename = FILENAMES[mode]
|
| 37 |
+
try:
|
| 38 |
+
return hf_hub_download(
|
| 39 |
+
repo_id=HF_MODEL_REPO,
|
| 40 |
+
filename=filename,
|
| 41 |
+
revision=HF_WEIGHTS_REV # can be None
|
| 42 |
+
)
|
| 43 |
+
except Exception as e:
|
| 44 |
+
raise RuntimeError(
|
| 45 |
+
f"Failed to fetch weights '{filename}' from repo '{HF_MODEL_REPO}'."
|
| 46 |
+
f"Set HF_MODEL_REPO or check filenames. Original error: {e}"
|
| 47 |
+
)
|
| 48 |
+
|
| 49 |
+
|
| 50 |
+
# ----------------------
|
| 51 |
+
# Labels / preprocessing
|
| 52 |
+
# ----------------------
|
| 53 |
inv_map = {0: "low", 1: "medium", 2: "high"}
|
| 54 |
|
| 55 |
# Tokenizer and image transform
|
|
|
|
| 61 |
])
|
| 62 |
|
| 63 |
|
| 64 |
+
# ----------------------
|
| 65 |
+
# Model load
|
| 66 |
+
# ----------------------
|
| 67 |
+
def _safe_torch_load(path: str, map_location: torch.device):
|
| 68 |
+
"""
|
| 69 |
+
Prefer weights_only=True (newer Pytorch), but fall back if not supported.
|
| 70 |
+
"""
|
| 71 |
+
try:
|
| 72 |
+
return torch.load(path, map_location=map_location, weights_only=True) # PyTorch >= 2.2/2.3
|
| 73 |
+
except TypeError:
|
| 74 |
+
return torch.load(path, map_location=map_location)
|
| 75 |
+
|
| 76 |
+
|
| 77 |
+
def load_model(mode: str, config_path: str = str(Path("config/config.yaml").resolve())):
|
| 78 |
+
"""
|
| 79 |
+
Load MediLLMModel for the given mode and populate weights from HF Hub.
|
| 80 |
+
Expects config/config.yaml with keys per mode (dropout, hidden_dim).
|
| 81 |
+
"""
|
| 82 |
with open(config_path, "r") as f:
|
| 83 |
+
cfg_all = yaml.safe_load(f)
|
| 84 |
+
if mode not in cfg_all:
|
| 85 |
+
raise KeyError(f"Mode '{mode}' not found in {config_path}. Keys: {list(cfg_all.keys())}")
|
| 86 |
+
config = cfg_all[mode]
|
| 87 |
|
| 88 |
+
# Build model
|
| 89 |
model = MediLLMModel(
|
| 90 |
mode=mode,
|
| 91 |
dropout=config["dropout"],
|
| 92 |
hidden_dim=config["hidden_dim"]
|
| 93 |
)
|
| 94 |
+
|
| 95 |
+
# Download weights & load
|
| 96 |
+
weights_path = resolve_weights_path(mode)
|
| 97 |
+
state = _safe_torch_load(weights_path, map_location=DEVICE)
|
| 98 |
+
|
| 99 |
+
# Sometimes checkpoints save as {'state_dict': ...}
|
| 100 |
+
if isinstance(state, dict) and "state_dict" in state:
|
| 101 |
+
state = state["state_dict"]
|
| 102 |
+
|
| 103 |
+
try:
|
| 104 |
+
model.load_state_dict(state) # strict by default
|
| 105 |
+
except RuntimeError as e:
|
| 106 |
+
# allow non-strict if minor mismatches (buffer names)
|
| 107 |
+
try:
|
| 108 |
+
model.load_state_dict(state, strict=False)
|
| 109 |
+
print(f"⚠️ Loaded with strict=False due to: {e}")
|
| 110 |
+
except Exception:
|
| 111 |
+
raise
|
| 112 |
+
|
| 113 |
model.to(DEVICE)
|
| 114 |
model.eval()
|
| 115 |
return model
|
| 116 |
|
| 117 |
|
| 118 |
+
# -----------------------
|
| 119 |
+
# Attention rollout utils
|
| 120 |
+
# -----------------------
|
| 121 |
def attention_rollout(attentions, last_k=4, residual_alpha=0.5):
|
| 122 |
"""
|
| 123 |
attentions_tuple: tuple/list of layer attentions; each is (B,H,S,S)
|
|
|
|
| 214 |
return attn_array0, labels
|
| 215 |
|
| 216 |
|
| 217 |
+
# ------------------
|
| 218 |
+
# Prediction
|
| 219 |
+
# ------------------
|
| 220 |
def predict(
|
| 221 |
model,
|
| 222 |
mode,
|
requirements-dev.txt
ADDED
|
@@ -0,0 +1,54 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
# (Bring in everything you listed, with safer caps)
|
| 2 |
+
|
| 3 |
+
# PyTorch stack (match minor versions!)
|
| 4 |
+
torch>=2.2,<2.4
|
| 5 |
+
torchvision>=0.17,<0.19
|
| 6 |
+
torchaudio>=2.2,<2.4
|
| 7 |
+
|
| 8 |
+
# Transformers & NLP
|
| 9 |
+
transformers>=4.41,<4.46
|
| 10 |
+
datasets>=2.19,<2.21
|
| 11 |
+
accelerate>=0.28,<0.31
|
| 12 |
+
peft>=0.11,<0.13
|
| 13 |
+
tokenizers>=0.15 # usually pulled by transformers, but explicit helps
|
| 14 |
+
safetensors>=0.4.3
|
| 15 |
+
huggingface_hub>=0.24,<0.26
|
| 16 |
+
# If you ever use T5/ALBERT etc., add:
|
| 17 |
+
# sentencepiece>=0.1.99
|
| 18 |
+
|
| 19 |
+
# Vision models
|
| 20 |
+
timm>=0.9.7,<1.0
|
| 21 |
+
opencv-python-headless>=4.8
|
| 22 |
+
Pillow>=10.0,<11
|
| 23 |
+
|
| 24 |
+
# Optimization / tracking
|
| 25 |
+
optuna>=3.5,<4
|
| 26 |
+
wandb>=0.16.6,<0.18
|
| 27 |
+
|
| 28 |
+
# Eval / viz
|
| 29 |
+
scikit-learn>=1.3,<1.6
|
| 30 |
+
matplotlib>=3.8,<3.9
|
| 31 |
+
seaborn>=0.13,<0.14
|
| 32 |
+
tqdm>=4.66,<5
|
| 33 |
+
|
| 34 |
+
# Data processing
|
| 35 |
+
pandas>=2.2,<2.3
|
| 36 |
+
numpy>=1.26,<2.2
|
| 37 |
+
pyyaml>=6.0
|
| 38 |
+
scipy>=1.11,<1.14 # sklearn relies on it; make it explicit to avoid surprises
|
| 39 |
+
|
| 40 |
+
# Optional deployment (FastAPI)
|
| 41 |
+
fastapi>=0.110,<0.114
|
| 42 |
+
pydantic>=2.5,<3
|
| 43 |
+
uvicorn>=0.27,<0.31
|
| 44 |
+
python-multipart>=0.0.6
|
| 45 |
+
# Optional perf:
|
| 46 |
+
json>=3.9
|
| 47 |
+
|
| 48 |
+
# Linting & testing
|
| 49 |
+
pytest>=7.4,<9
|
| 50 |
+
pytest-cov>=4.1,<5
|
| 51 |
+
pre-commit>=3.5,<4
|
| 52 |
+
flake8>=6.1,<7
|
| 53 |
+
# Optional modern linter:
|
| 54 |
+
ruff>=0.4,<0.7
|
requirements.txt
CHANGED
|
@@ -1,41 +1,19 @@
|
|
| 1 |
-
# Core
|
| 2 |
-
torch>=2.
|
| 3 |
-
torchvision>=0.
|
| 4 |
-
torchaudio
|
| 5 |
|
| 6 |
-
#
|
| 7 |
-
|
| 8 |
-
|
| 9 |
-
|
| 10 |
-
peft>=0.9.0
|
| 11 |
|
| 12 |
-
#
|
| 13 |
-
opencv-python>=4.8
|
| 14 |
-
Pillow>=10.0
|
| 15 |
-
|
| 16 |
-
|
| 17 |
-
|
| 18 |
-
|
| 19 |
-
|
| 20 |
-
|
| 21 |
-
# Evaluation and visualization
|
| 22 |
-
scikit-learn>=1.3.0
|
| 23 |
-
matplotlib>=3.8.0
|
| 24 |
-
seaborn>=0.13.0
|
| 25 |
-
tqdm>=4.65.0
|
| 26 |
-
|
| 27 |
-
# Data processing
|
| 28 |
-
pandas>=2.1.0
|
| 29 |
-
numpy>=1.25.0
|
| 30 |
pyyaml>=6.0
|
| 31 |
-
|
| 32 |
-
# FastAPI for deployment
|
| 33 |
-
fastapi>=0.100.0
|
| 34 |
-
uvicorn>=0.27.0
|
| 35 |
-
python-multipart>0.0.6
|
| 36 |
-
|
| 37 |
-
# Linting and testing
|
| 38 |
-
pytest>=7.4.0
|
| 39 |
-
pytest-cov>=4.1
|
| 40 |
-
pre-commit>=3.5.0
|
| 41 |
-
flake8>=6.1.0
|
|
|
|
| 1 |
+
# Core runtime (CPU)
|
| 2 |
+
torch>=2.2,<2.4
|
| 3 |
+
torchvision>=0.17,<0.19
|
| 4 |
+
# torchaudio not needed for this app; add if you really use it
|
| 5 |
|
| 6 |
+
# UI + model fetch
|
| 7 |
+
gradio>=3.45.2,<3.47
|
| 8 |
+
huggingface_hub>=0.24,<0.26
|
| 9 |
+
safetensors>=0.4.3
|
|
|
|
| 10 |
|
| 11 |
+
# Image / utils
|
| 12 |
+
opencv-python-headless>=4.8
|
| 13 |
+
Pillow>=10.0,<11
|
| 14 |
+
pandas>=2.2,<2.3
|
| 15 |
+
numpy>=1.26,<2.2
|
| 16 |
+
scikit-learn>=1.3,<1.6
|
| 17 |
+
tqdm>=4.66,<5
|
| 18 |
+
matplotlib>=3.8,<3.9
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 19 |
pyyaml>=6.0
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|