strnd 0.3.0

STRND: Graph reconstruction via Node2Vec (pecanpy) + UMAP

STRND

STRND = Spatio Topological Recovery by Network Discovery

• Feed an edge list (pandas DataFrame, NX, PyG, list of edges)
• Get back node coordinates in 2D or 3D (pandas DataFrame)

Install

pip install strnd

Minimal use

from strnd import get_strnd_positions_df

coords_df = get_strnd_positions_df(edge_df, dim=2)
# coords_df columns: node_ID, x, y

edge_df must have columns source, target (and optionally weight).

Example with Graph Generation + Quality Metrics

import numpy as np
from proxigraph.config import GraphConfig
from proxigraph.core import ProximityGraph
from PointQuality import QualityMetrics
from strnd import get_strnd_positions_df

np.random.seed(42)

# 1) create a graph
config = GraphConfig(dim=2, num_points=1000, L=1, point_mode="circle", proximity_mode="delaunay_corrected")
pg = ProximityGraph(config=config)
positions = pg.generate_positions()
edge_df = pg.get_edge_list(as_dataframe=True)

# 2) run STRND
rec_positions = get_strnd_positions_df(edge_df, dim=2)

# 3) quality
rec_positions_ordered = rec_positions.sort_values("node_ID")[["x","y"]].to_numpy()
qm = QualityMetrics(positions, rec_positions_ordered)
print(qm.evaluate_metrics(compute_distortion=False))

# 4) print head
print(rec_positions.head())

dependencies

• numpy
• pandas
• matplotlib
• pecanpy (node2vec)
• umap-learn
• (optional) proxigraph for the demo

Citation

If you use STRND in your work, please cite:

Core STRND paper

Fernández Bonet, D., & Hoffecker, I. T. (2023). Image recovery from unknown network mechanisms for DNA sequencing-based microscopy. Nanoscale, 15, 8153–8157. https://doi.org/10.1039/D2NR05435C

Related work

Dahlberg, S. K., Fernández Bonet, D., & Hoffecker, I. T. (2025). Hidden network preserved in Slide-tags data allows reference-free spatial reconstruction. Nature Communications. https://doi.org/10.1038/s41467-025-65295-w

Fernández Bonet, D., Blumenthal, J. I., Lang, S., Dahlberg, S. K., & Hoffecker, I. T. (2024). Spatial coherence of DNA barcode networks. bioRxiv. https://doi.org/10.1101/2024.05.12.593725