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app.py

@@ -820,7 +820,10 @@ def run_ranking(
     ]
     summary = _build_summary(assay_text, valid_rows, invalid_rows, warning)
     csv_path = _results_to_csv(valid_rows, invalid_rows)
-    return summary, assay_text, pd.DataFrame(display_rows), pd.DataFrame(invalid_display), csv_path
+    invalid_frame = pd.DataFrame(invalid_display) if invalid_display else pd.DataFrame(columns=["input_smiles", "error"])
+    invalid_title = gr.update(visible=bool(invalid_display))
+    invalid_table = gr.update(value=invalid_frame, visible=bool(invalid_display))
+    return summary, assay_text, pd.DataFrame(display_rows), invalid_title, invalid_table, csv_path
 
 
 def load_example(example_name: str):
@@ -936,8 +939,8 @@ with gr.Blocks(title="BioAssayAlign Compatibility Explorer", analytics_enabled=F
             assay_preview = gr.Textbox(lines=12, label="Model-facing assay text")
         gr.HTML("<div class='section-note'><strong>Ranked candidates</strong></div>")
         ranked_df = gr.Dataframe(label=None, show_label=False, interactive=False, wrap=True, elem_classes="result-frame")
-        gr.HTML("<div class='section-note'><strong>Rejected inputs</strong></div>")
-        invalid_df = gr.Dataframe(label=None, show_label=False, interactive=False, wrap=True, elem_classes="result-frame")
+        invalid_title = gr.HTML("<div class='section-note'><strong>Rejected inputs</strong></div>", visible=False)
+        invalid_df = gr.Dataframe(label=None, show_label=False, interactive=False, wrap=True, elem_classes="result-frame", visible=False)
         download_file = gr.File(label="Export CSV", elem_classes="result-file")
 
         load_example_btn.click(
@@ -948,7 +951,7 @@ with gr.Blocks(title="BioAssayAlign Compatibility Explorer", analytics_enabled=F
         run_btn.click(
             run_ranking,
             inputs=[assay_title, description, organism, readout, assay_format, assay_type, target_uniprot, smiles_text, upload_file, top_k],
-            outputs=[summary, assay_preview, ranked_df, invalid_df, download_file],
+            outputs=[summary, assay_preview, ranked_df, invalid_title, invalid_df, download_file],
         )
 
 if __name__ == "__main__":