Reference

The reference documents curated public package surfaces, not every internal module. Source code and tests are authoritative when examples disagree.

Fast import paths

Use the root package for the main workflow objects:

from phylognn import (
    GATBiLSTMNet,
    TemporalBiLSTMEncoder,
    Trainer,
    TrainingConfig,
    TreeFeatureEngineer,
    TreeToGraphConverter,
    __version__,
)

Reference areas

Data

Feature engineering and tree-to-graph conversion APIs.

Models

Public model classes and shared model base behavior.

Training

Trainer, configuration, datasets, metrics, TOML helpers, and tracking.

Tree I/O

Optional DendroPy-backed file reading and conversion helpers.

Utilities

Small public utility helpers.

• Data Reference
• Models Reference
• Training Reference
• Tree I/O Reference
• Utilities Reference

Public coverage

The reference covers root exports, phylognn.data, phylognn.models, phylognn.training, optional phylognn.io, and phylognn.utils. Low-level model layers and private helpers are omitted unless they are intentionally exposed by a curated public facade.