README.md

---
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

```bash
pip install -r requirements.txt
python example_usage.py
```

## Python usage

```python
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.