initial commit

app.py

@@ -0,0 +1,89 @@
+import os
+import gradio as gr
+from datasets import load_dataset
+from typing import Union, Dict, List, Optional
+import pandas as pd
+from smolagents import CodeAgent, HfApiModel, tool, GradioUI
+from opentelemetry import trace
+from opentelemetry.sdk.trace import TracerProvider
+from opentelemetry.sdk.trace.export import BatchSpanProcessor
+from opentelemetry.exporter.otlp.proto.http.trace_exporter import OTLPSpanExporter
+from openinference.instrumentation.smolagents import SmolagentsInstrumentor
+
+PHOENIX_API_KEY = os.getenv("PHOENIX_API_KEY")
+api_key = f"api_key={PHOENIX_API_KEY}"
+os.environ["OTEL_EXPORTER_OTLP_HEADERS"] = api_key
+os.environ["PHOENIX_CLIENT_HEADERS"] = api_key
+os.environ["PHOENIX_COLLECTOR_ENDPOINT"] = "https://app.phoenix.arize.com"
+
+endpoint = "https://app.phoenix.arize.com/v1/traces"
+trace_provider = TracerProvider()
+trace_provider.add_span_processor(BatchSpanProcessor(OTLPSpanExporter(endpoint)))
+SmolagentsInstrumentor().instrument(tracer_provider=trace_provider)
+
+examples = [
+    ["Validate whether FANCA interacts with PALB2 in homologous recombination repair using BioGRID and PubMed evidence."],
+    ["Show the evolution of TP53-MDM2 interaction evidence from 2018-2023, highlighting key supporting papers."],
+    ["Compare BRCA2 interaction networks between human and mouse homologs, marking conserved relationships."],
+    ["Identify synthetic lethal partners for BRCA1-deficient cancers with confidence > 0.9 and clinical trial associations."],
+    ["Find novel VHL interactors proposed in 2023 PubMed articles not yet in BioGRID."],
+    ["Visualize the ATM interaction network with nodes sized by betweenness centrality and colored by validation source."],
+    ["Explain the Fanconi Anemia pathway and show its core components with experimental validation status."],
+    ["Correlate TP53BP1 protein interactions with mRNA co-expression patterns in TCGA breast cancer data."],
+    ["Identify high-betweenness nodes in the KRAS interaction network with druggable protein products."],
+    ["List all interactions with conflicting evidence between BioGRID and STRING, sorted by confidence delta."],
+]
+
+class GradioUIWithExamples(GradioUI):
+    def __init__(self, agent, examples=None, **kwargs):
+        super().__init__(agent, **kwargs)
+        self.examples = examples
+
+    def build_interface(self):
+        with gr.Blocks() as demo:
+            gr.Markdown("## Biomedical Knowledge Graph")
+            gr.Markdown("""
+            An experimental knowledge graph platform that transforms fragmented biomedical data into insight.
+            """)
+
+            input_box = gr.Textbox(
+                label="Your Question",
+                placeholder="e.g., 'Find novel VHL interactors proposed in 2023 PubMed articles not yet in BioGRID.'"
+            )
+            output_box = gr.Textbox(
+                label="Analysis Results",
+                placeholder="Response will appear here...",
+                interactive=False,
+            )
+            submit_button = gr.Button("Submit")
+
+            submit_button.click(
+                self.agent.run,
+                inputs=input_box,
+                outputs=output_box,
+            )
+
+            if self.examples:
+                gr.Markdown("### Examples")
+                for example in self.examples:
+                    gr.Button(example[0]).click(
+                        lambda x=example[0]: x,
+                        inputs=[],
+                        outputs=input_box,
+                    )
+        return demo
+
+    def launch(self):
+        demo = self.build_interface()
+        demo.launch()
+
+model = HfApiModel()
+agent = CodeAgent(
+    tools=[],
+    model=model,
+    additional_authorized_imports=["gradio","pandas","numpy"],
+    add_base_tools=True
+)
+
+interface = GradioUIWithExamples(agent, examples=examples)
+interface.launch()