README.md

metadata

title: BacterialIdentifierShowcase
emoji: 🐨
colorFrom: red
colorTo: pink
sdk: gradio
sdk_version: 6.14.0
python_version: '3.13'
app_file: app.py
pinned: false
license: apache-2.0

PhenotypeClassifier Complete Package

PhenotypeClassifier is a phenotype-based bacterial genus prediction tool.

This package includes:

• phenotype_tinytransformer_v1_temperature_scaled.pt — calibrated TinyTransformer model
• phenotype_inference.py — reusable inference module
• phenotype_next_tests.py — model-based next-test recommender
• phenotype_reference_distributions.json — compact phenotype distribution reference
• example_usage.py — simple example script
• requirements.txt — dependencies

What it does

Given structured phenotype fields, it predicts likely bacterial genus and returns:

• Top genus
• Ranked genera
• Confidence
• Distinctness
• Missing fields
• Discriminatory next-test recommendations
• Confirmation next-test recommendations

Run example

pip install -r requirements.txt
python example_usage.py

Python usage

from phenotype_inference import PhenotypeClassifier
from phenotype_next_tests import PhenotypeNextTestRecommender

classifier = PhenotypeClassifier('phenotype_tinytransformer_v1_temperature_scaled.pt')
recommender = PhenotypeNextTestRecommender(classifier, 'phenotype_reference_distributions.json')

features = {
    'Gram Stain': 'Negative',
    'Shape': 'Rods',
    'Catalase': 'Positive',
    'Oxidase': 'Positive',
}

prediction = classifier.predict(features)
recommendations = recommender.recommend(features)

Important limitation

This is a phenotype-based genus prediction tool. It is not a confirmed laboratory identification, not a diagnostic result, and should not replace validated microbiology workflows.