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Challenge

Pediatric Rapid WGS Decision Agent using Google ADK and o3

Rapid whole-genome sequencing in pediatric ICU settings demands immediate, high-confidence clinical phenotype mapping. Developers will build a Google ADK agent powered by o3 to cross-reference patient HPO terms with pediatric rWGS variant files, generating rapid diagnostic candidate rankings within a 30-second processing window.

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Challenge brief

What you are building

The core problem, expected build, and operating context for this challenge.

Develop an automated pediatric rWGS diagnostic tool using Google ADK and o3 reasoning model to match HPO terms with genomic variants.

Delivery guide

How work is evaluated

Evaluation

Evaluates candidate gene ranking recall, HPO match accuracy, and rapid processing execution speed.

Datasets

Shared data for this challenge

Review public datasets and any private uploads tied to your build.

Evaluation rubric

How submissions are scored

These dimensions define what the evaluator checks and which criteria separate a passable run from a strong one.

Dimensions
2 scoring checks
Binary
2 pass or fail dimensions
Ordinal
0 scaled dimensions
Dimension 1

top_gene_correctness

Validates that SCN1A is identified as the primary candidate gene.

Binary check

This dimension contributes its full weight only when the submission satisfies the requirement. Partial credit is not awarded.

Dimension 2

top_1_recall

Recall of true causal gene at position 1. • target: 0.95 • range: 0-1

Binary check

This dimension contributes its full weight only when the submission satisfies the requirement. Partial credit is not awarded.

Learning goals

What you should walk away with

  • Configure Google Agent Development Kit (ADK) agent with o3 model reasoning.

  • Parse Human Phenotype Ontology (HPO) terms from clinical ICU unstructured notes.

  • Cross-match HPO codes against whole-genome variant call format (VCF) data.

  • Generate prioritized candidate gene rankings for rare pediatric diseases.

Resources and assets

Reference links and supporting material

Dataset notes

Pediatric clinical vignettes with associated anonymized rWGS variant files and verified diagnoses.

How this agent runs

Evaluates candidate gene ranking recall, HPO match accuracy, and rapid processing execution speed.

Challenge input

JSON containing clinical HPO terms and candidate VCF variant list.

Google ADK

Provides robust structure for building complex multi-step agents.

o3

Delivers advanced multi-step logic needed for complex phenotype-genotype mapping.

Evaluated output

JSON containing top 3 ranked candidate genes and matched phenotype justifications.

Checks for
  • Validates that SCN1A is identified as the primary candidate gene.
  • Recall of true causal gene at position 1. • target: 0.95 • range: 0-1
Proof of success
  • Benchmark: Rare Disease Diagnostics Benchmark
  • Top 1 Recall target: 0.95
  • 1 public reference case
Runtime evidence
  • Python execution harness
  • Python sandbox (unavailable on Versalist)
View technical recipe

Configured tools

Action Space
  • Google · Optional
  • Google ADK · Optional
Policy Serving
  • o3 · Required

Evaluation contract

  • top_gene_correctness · Weight 1
  • top_1_recall · Weight 1

Recipe state

This is a preview. The configuration can change before the evaluation recipe is locked.

Frequently Asked Questions about Pediatric Rapid WGS Decision Agent using Google ADK and o3