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app.py

@@ -35,6 +35,8 @@ CSS = """
   --accent-deep: #0c4641;
   --accent-soft: #dbeee8;
   --accent-warm: #b8643d;
+  --accent-bright: #d06a3b;
+  --accent-bright-deep: #b25124;
   --accent-warm-soft: #f3e1d5;
   --line: #c6cdbf;
   --warning: #8a4b0f;
@@ -122,13 +124,6 @@ CSS = """
   margin-top: 0.45rem;
 }
 
-.panel-note {
-  border-left: 4px solid var(--accent);
-  background: rgba(19,90,82,0.06);
-  padding: 0.9rem 1rem;
-  border-radius: 12px;
-}
-
 .metric-strip {
   display: grid;
   grid-template-columns: repeat(3, minmax(0, 1fr));
@@ -140,7 +135,7 @@ CSS = """
   background: linear-gradient(180deg, rgba(255,255,255,0.92), rgba(248,244,236,0.9));
   padding: 0.8rem 0.9rem;
   border-radius: 18px;
-  min-height: 7.5rem;
+  min-height: 6.4rem;
   box-shadow: 0 8px 24px rgba(23,37,45,0.04);
 }
 
@@ -311,11 +306,32 @@ CSS = """
 
 .gradio-container input,
 .gradio-container textarea,
-.gradio-container select {
+.gradio-container select,
+.gradio-container [role="combobox"],
+.gradio-container [role="listbox"],
+.gradio-container [role="option"],
+.gradio-container .choices,
+.gradio-container .choices__inner,
+.gradio-container .choices__list,
+.gradio-container .choices__item {
   background: #fffdf8 !important;
   border: 1px solid #bfc8bf !important;
   border-radius: 14px !important;
   box-shadow: inset 0 1px 0 rgba(255,255,255,0.7) !important;
+  color: var(--ink) !important;
+}
+
+.gradio-container [role="listbox"],
+.gradio-container .choices__list,
+.gradio-container .choices__item {
+  background: #fffdf8 !important;
+  color: var(--ink) !important;
+}
+
+.gradio-container [role="option"][aria-selected="true"],
+.gradio-container .choices__item--selectable.is-highlighted {
+  background: #e7f0ed !important;
+  color: #0d3d38 !important;
 }
 
 .gradio-container input:focus,
@@ -336,14 +352,14 @@ CSS = """
 }
 
 .gradio-container button.primary {
-  background: linear-gradient(180deg, var(--accent), var(--accent-deep)) !important;
+  background: linear-gradient(180deg, var(--accent-bright), var(--accent-bright-deep)) !important;
   color: #f7fbfa !important;
   border: none !important;
-  box-shadow: 0 12px 24px rgba(22,91,85,0.18) !important;
+  box-shadow: 0 14px 26px rgba(184,100,61,0.24) !important;
 }
 
 .gradio-container button.secondary {
-  background: linear-gradient(180deg, #f3e3d6, #edd9ca) !important;
+  background: linear-gradient(180deg, #f6e7da, #f0ddcd) !important;
   color: var(--ink) !important;
   border: 1px solid #dbc4b4 !important;
 }
@@ -458,6 +474,9 @@ EXAMPLES = {
     },
 }
 
+DEFAULT_EXAMPLE_NAME = "JAK2 cell assay"
+DEFAULT_EXAMPLE = EXAMPLES[DEFAULT_EXAMPLE_NAME]
+
 
 def _parse_smiles_text(value: str | None) -> list[str]:
     if not value:
@@ -715,19 +734,19 @@ with gr.Blocks(title="BioAssayAlign Compatibility Explorer", analytics_enabled=F
 <div id="hero">
   <div class="hero-grid">
     <div>
-      <div class="eyebrow">BioAssayAlign · assay-conditioned molecule ranking</div>
-      <div class="hero-title">Triage a candidate library against an assay concept</div>
+      <div class="eyebrow">BioAssayAlign · assay-conditioned compound ranking</div>
+      <div class="hero-title">Rank a compound list against one assay definition</div>
       <div class="hero-copy">
-        Write the assay the way a scientist would describe it, submit candidate SMILES, and get a ranked shortlist from the current BioAssayAlign compatibility model.
-        The output is designed for practical prioritization, not generic search.
+        Define an assay in structured scientific terms, submit a candidate molecule set, and obtain a within-list ranking from the current BioAssayAlign compatibility model.
+        The output is intended for shortlist prioritization, retrospective analysis, and assay-conditioned compound triage.
       </div>
     </div>
     <div class="hero-side">
-      <div class="hero-side-title">What this Space is good at</div>
+      <div class="hero-side-title">Operational scope</div>
       <ul class="hero-list">
-        <li>ranking a shortlist for one assay at a time</li>
-        <li>comparing molecules relative to the same submitted list</li>
-        <li>surfacing invalid or malformed SMILES immediately</li>
+        <li>Single-assay compound ranking with explicit assay metadata</li>
+        <li>Relative prioritization within the submitted molecule set</li>
+        <li>Immediate rejection of malformed or non-parseable SMILES</li>
       </ul>
     </div>
   </div>
@@ -736,21 +755,13 @@ with gr.Blocks(title="BioAssayAlign Compatibility Explorer", analytics_enabled=F
     )
 
     with gr.Row():
-        with gr.Column(scale=5):
-            gr.HTML(
-                """
-<div class="panel-note">
-Use structured assay fields when possible. Missing fields are allowed, but species, readout, format, and target metadata usually improve ranking quality.
-</div>
-"""
-            )
-        with gr.Column(scale=4):
+        with gr.Column(scale=9):
             gr.HTML(
                 f"""
 <div class="metric-strip">
-  <div class="metric-card"><span>Default model</span><strong>{MODEL_REPO_ID}</strong></div>
-  <div class="metric-card"><span>Use the output for</span><strong>ranking, not probability</strong></div>
-  <div class="metric-card"><span>Interactive cap</span><strong>{MAX_INPUT_SMILES} molecules</strong></div>
+  <div class="metric-card"><span>Model</span><strong>Qwen3-Embedding-0.6B compatibility scorer</strong></div>
+  <div class="metric-card"><span>Input contract</span><strong>1 assay definition + up to {MAX_INPUT_SMILES} candidate SMILES</strong></div>
+  <div class="metric-card"><span>Score semantics</span><strong>Use rank and relative score within the submitted list</strong></div>
 </div>
 """
             )
@@ -758,9 +769,9 @@ Use structured assay fields when possible. Missing fields are allowed, but speci
     gr.HTML(
         """
 <div class="guide-grid">
-  <div class="guide-card"><strong>1. Describe the assay</strong>Use normal lab language. Add UniProt, readout, format, and organism when known.</div>
-  <div class="guide-card"><strong>2. Load candidate chemistry</strong>Paste one SMILES per line or upload a CSV with a <code>smiles</code> column.</div>
-  <div class="guide-card"><strong>3. Interpret list-relative rank</strong>Read <em>priority</em> and <em>relative score</em> first. Treat raw score as a debug signal only.</div>
+  <div class="guide-card"><strong>1. Specify the assay</strong>Include target, readout, organism, and format when known. Missing fields are allowed but reduce context.</div>
+  <div class="guide-card"><strong>2. Provide a candidate set</strong>Paste one SMILES per line or upload a CSV with a <code>smiles</code> column.</div>
+  <div class="guide-card"><strong>3. Read the output scientifically</strong>Use rank and relative score for shortlist decisions. Raw model score is an internal compatibility logit.</div>
 </div>
 """
     )
@@ -773,29 +784,29 @@ Use structured assay fields when possible. Missing fields are allowed, but speci
 <div class="pane-header">
   <div>
     <div class="pane-kicker">Assay definition</div>
-    <div class="pane-title">Describe the biological question</div>
+    <div class="pane-title">Define the assay context</div>
   </div>
 </div>
-<div class="pane-copy">The model performs best when the assay text is concrete and metadata is explicit. Missing fields are allowed.</div>
+<div class="pane-copy">The model performs best when the assay description is concrete and metadata fields are explicit. This form is preloaded with a live example.</div>
 <div class="helper-row">
-  <div class="helper-chip"><strong>Use plain lab language</strong>Focus on readout, target, cell system, or assay format.</div>
-  <div class="helper-chip"><strong>Add UniProt when known</strong>Target identifiers usually sharpen the rank order.</div>
-  <div class="helper-chip"><strong>One assay at a time</strong>Scores are meant to compare molecules within the same submitted list.</div>
+  <div class="helper-chip"><strong>Describe the protocol signal</strong>State the readout, assay system, target biology, and measurement context.</div>
+  <div class="helper-chip"><strong>Use target identifiers</strong>UniProt IDs often improve separation between plausible and implausible candidates.</div>
+  <div class="helper-chip"><strong>Interpret scores locally</strong>Ranking is meaningful within the submitted library, not across unrelated runs.</div>
 </div>
 """
                 )
-                example_name = gr.Dropdown(choices=list(EXAMPLES.keys()), value="JAK2 cell assay", label="Live example")
-                gr.HTML("<div class='examples-note'>Examples run against the live model. They are not screenshots or mocked outputs.</div>")
-                load_example_btn = gr.Button("Load live example", variant="secondary")
-                assay_title = gr.Textbox(label="Assay title")
-                description = gr.Textbox(label="Description", lines=6, placeholder="Describe the assay in practical lab language.")
+                example_name = gr.Dropdown(choices=list(EXAMPLES.keys()), value=DEFAULT_EXAMPLE_NAME, label="Example assay")
+                gr.HTML("<div class='examples-note'>The form is initialized with a live JAK2 example. Selecting another example will overwrite the current fields.</div>")
+                load_example_btn = gr.Button("Replace with selected example", variant="secondary")
+                assay_title = gr.Textbox(label="Assay title", value=DEFAULT_EXAMPLE["title"])
+                description = gr.Textbox(label="Description", value=DEFAULT_EXAMPLE["description"], lines=6, placeholder="Describe the assay in practical lab language.")
                 with gr.Row():
-                    organism = gr.Textbox(label="Organism", placeholder="Homo sapiens")
-                    readout = gr.Textbox(label="Readout", placeholder="binding / fluorescence / luminescence")
+                    organism = gr.Textbox(label="Organism", value=DEFAULT_EXAMPLE["organism"], placeholder="Homo sapiens")
+                    readout = gr.Textbox(label="Readout", value=DEFAULT_EXAMPLE["readout"], placeholder="binding / fluorescence / luminescence")
                 with gr.Row():
-                    assay_format = gr.Textbox(label="Assay format", placeholder="biochemical / cell-based")
-                    assay_type = gr.Textbox(label="Assay type", placeholder="binding / inhibition / activation")
-                target_uniprot = gr.Textbox(label="Target UniProt IDs", placeholder="Q06187, P52333")
+                    assay_format = gr.Textbox(label="Assay format", value=DEFAULT_EXAMPLE["assay_format"], placeholder="biochemical / cell-based")
+                    assay_type = gr.Textbox(label="Assay type", value=DEFAULT_EXAMPLE["assay_type"], placeholder="binding / inhibition / activation")
+                target_uniprot = gr.Textbox(label="Target UniProt IDs", value=DEFAULT_EXAMPLE["target_uniprot"], placeholder="Q06187, P52333")
 
             with gr.Column(scale=5, elem_classes="pane"):
                 gr.HTML(
@@ -803,22 +814,23 @@ Use structured assay fields when possible. Missing fields are allowed, but speci
 <div class="pane-header">
   <div>
     <div class="pane-kicker">Candidate set</div>
-    <div class="pane-title">Submit the molecules you care about</div>
+    <div class="pane-title">Submit the candidate molecules</div>
   </div>
 </div>
-<div class="pane-copy">The model ranks molecules relative to this exact submitted list. For interactive use, keep the batch moderate and chemically sensible.</div>
+<div class="pane-copy">The model ranks compounds relative to this exact submitted set. Use parent or cleaned molecules when possible.</div>
 """
                 )
                 smiles_text = gr.Textbox(
                     label="Candidate SMILES",
+                    value=DEFAULT_EXAMPLE["smiles"],
                     lines=14,
                     placeholder="Paste one candidate molecule per line. Example: CCO",
                 )
                 upload_file = gr.File(label="Upload CSV / TXT / SMI", file_count="single", file_types=[".csv", ".txt", ".smi", ".smiles"])
                 top_k = gr.Slider(label="Top-K rows to display", minimum=5, maximum=200, step=5, value=DEFAULT_TOP_K)
-                gr.HTML("<div class='section-note'>Tip: prefer parent or neutralized molecules, one SMILES per row, and avoid obvious salts or malformed fragments.</div>")
+                gr.HTML("<div class='section-note'>Use one SMILES per row. Invalid or non-standardizable structures are flagged separately and excluded from ranking.</div>")
                 with gr.Row(elem_classes="action-row"):
-                    run_btn = gr.Button("Run ranking", variant="primary")
+                    run_btn = gr.Button("Run assay-conditioned ranking", variant="primary")
                     clear_btn = gr.ClearButton(value="Clear inputs", components=[assay_title, description, organism, readout, assay_format, assay_type, target_uniprot, smiles_text, upload_file])
 
         gr.HTML(
@@ -827,13 +839,13 @@ Use structured assay fields when possible. Missing fields are allowed, but speci
   <div class="pane-header">
     <div>
       <div class="pane-kicker">Output</div>
-      <div class="pane-title">Interpret the shortlist</div>
+      <div class="pane-title">Interpret the ranked shortlist</div>
     </div>
   </div>
   <div class="explain-grid">
-    <div class="explain-card"><strong>Priority</strong>High-level triage label for the submitted list. Start here.</div>
-    <div class="explain-card"><strong>Relative score</strong>0–100 scale within your submitted list only. It is not calibrated across unrelated lists.</div>
-    <div class="explain-card"><strong>Raw model score</strong>Useful for debugging or exporting, but not the first thing a scientist should read.</div>
+    <div class="explain-card"><strong>Priority band</strong>Use this as the first-pass triage signal when scanning the ranked list.</div>
+    <div class="explain-card"><strong>Relative score</strong>0–100 scale computed within the submitted list only. It is not calibrated across separate runs.</div>
+    <div class="explain-card"><strong>Model score</strong>Internal compatibility logit from the scorer head. Useful for export or debugging, not for direct biological interpretation.</div>
   </div>
 </div>
 """
@@ -863,17 +875,17 @@ Use structured assay fields when possible. Missing fields are allowed, but speci
   <div class="pane-header">
     <div>
       <div class="pane-kicker">Practical guidance</div>
-      <div class="pane-title">How to use this interface well</div>
+      <div class="pane-title">Operating guidance</div>
     </div>
   </div>
   <div class="explain-grid">
-    <div class="explain-card"><strong>Write the assay like a scientist</strong>Use concrete descriptions, not keywords alone. If the assay is target-defined, add UniProt.</div>
-    <div class="explain-card"><strong>Use clean candidate input</strong>Prefer parent or neutralized molecules. Upload a CSV with a <code>smiles</code> column if you have a larger list.</div>
-    <div class="explain-card"><strong>Interpret results as triage</strong>Use priority and relative score first. Treat the raw model score as an internal ranking value, not a probability.</div>
+    <div class="explain-card"><strong>Encode the assay explicitly</strong>Use full scientific language rather than keywords alone. Include target and readout when available.</div>
+    <div class="explain-card"><strong>Provide chemically reasonable candidates</strong>Prefer parent or neutralized structures. Upload a CSV with a <code>smiles</code> column for larger lists.</div>
+    <div class="explain-card"><strong>Use the output as a ranking signal</strong>Priority and relative score are the intended decision aids. Model score is not a calibrated success probability.</div>
   </div>
   <div class="footer-note" style="margin-top: 1rem;">
-    This Space is tuned for shortlist ranking. It is not a generative chemistry tool, not a medicinal chemistry oracle, and not a wet-lab substitute.
-    If you need a larger workflow, export the CSV and pass the ranked list into your own screening pipeline.
+    This Space is intended for assay-conditioned shortlist ranking. It is not a generative chemistry system and it does not replace confirmatory screening.
+    Export the ranked CSV if you want to continue downstream analysis in your own workflow.
   </div>
 </div>
 """