manylatents 0.1.5

Unified dimensionality reduction and neural network analysis framework

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        m a n y l a t e n t s

  one geometry, learned through many latents

---

install

uv add manylatents

Optional extras:

uv add manylatents[hf]         # HuggingFace trainer
uv add manylatents[torchdr]    # GPU-accelerated DR via TorchDR
uv add manylatents[jax]        # JAX backend (diffrax)
uv add manylatents[all]        # everything

pip also works

pip install manylatents

quickstart

# embed a swiss roll with UMAP
manylatents algorithms/latent=umap data=swissroll

# add metrics
manylatents algorithms/latent=umap data=swissroll \
  metrics=trustworthiness

# sweep algorithms
manylatents --multirun \
  algorithms/latent=umap,phate,tsne \
  data=swissroll metrics=trustworthiness

development install

git clone https://github.com/latent-reasoning-works/manylatents.git
cd manylatents && uv sync

from manylatents.api import run

result = run(data="swissroll", algorithm="pca", metrics=["trustworthiness"])

embeddings = result["embeddings"]   # (n, d) ndarray
scores     = result["scores"]       # {"trustworthiness": 0.95}

# chain: PCA 50d -> PHATE 2d
result2 = run(input_data=result["embeddings"], algorithm="phate")

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architecture

  CLI                         API
  manylatents ...             run(data=, algorithm=, ...)
       │                           │
       ▼                           ▼
  ┌─────────┐               ┌───────────┐
  │ main.py │               │  api.py   │
  │ Hydra   │               │ registries│
  └────┬────┘               └─────┬─────┘
       │    instantiate objects    │
       └──────────┬───────────────┘
                  ▼
        ┌──────────────────┐      ┌────────────────┐
        │  experiment.py   │─────►│  evaluate.py   │
        │  run_experiment()│      │  evaluate()    │
        │                  │      │  prewarm_cache │
        │  LatentModule    │      │  compute_knn   │
        │    fit/transform │      │  metric_fn(    │
        │  LightningModule │      │   cache=cache) │
        │    trainer.fit   │      └────────────────┘
        └──────────────────┘

Two base classes, one decision rule:

if the algorithm...	use	interface
has no training loop	LatentModule	fit(x) / transform(x)
trains with backprop	LightningModule	trainer.fit() / encode(x)

Both produce LatentOutputs — a dict keyed by "embeddings". All metrics receive a shared cache dict for deduplicated kNN and eigenvalue computation.

---

algorithms

17 algorithms -- 12 latent modules, 5 lightning modules

PCA, t-SNE, UMAP, PHATE, DiffusionMap, MDS, MultiscalePHATE, Merging, Classifier, Leiden, ReebGraph, SelectiveCorrection, Autoencoder, AANet, LatentODE, HF Trainer, Reconstruction AE.

neighborhood_size=k sweeps kNN uniformly across algorithms.

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metrics

20+ metrics across three evaluation contexts

Embedding fidelity (trustworthiness, continuity, kNN preservation), spectral analysis (affinity spectrum, spectral decay rate), topological features (persistent homology), and dataset properties (stratification).

All metrics share a cache dict for deduplicated kNN computation. List-valued parameters expand via flatten_and_unroll_metrics() -- one kNN computation covers the entire sweep.

Config pattern: metrics=<name> (each metric config has an at: field for evaluation context)

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data

6 synthetic manifolds + precomputed loader

Swiss roll, torus, saddle surface, gaussian blobs, DLA tree, and custom .npy/.npz files. Domain-specific datasets (genomics, single-cell) available via extensions.

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citing

If manylatents was useful in your research, a citation goes a long way:

@software{manylatents2026,
  title     = {manyLatents: Unified Dimensionality Reduction and Neural Network Analysis},
  author    = {Valdez C{\'o}rdova, C{\'e}sar Miguel and Scicluna, Matthew and Ni, Shuang},
  year      = {2026},
  url       = {https://github.com/latent-reasoning-works/manylatents},
  license   = {MIT}
}

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_{MIT License · Latent Reasoning Works}