C1vy/haruka_v2_data

Haruka v2: preprocessed inputs and fitted outputs for the reproduction notebooks

Ready-to-fit AnnData files for every figure of Haruka v2 (code: https://github.com/C0nc/haruka_v2, branch v2, folder notebooks/). Each folder matches one notebook; with these files the notebook can start at the fit stage. fitted/ holds the same AnnData objects with the paper's default Haruka fit added (z, s, predicted neighbourhoods) for further analysis; the notebooks unpack them and reuse the fit instead of refitting (HARUKA_REFIT=1 refits).

hf download C1vy/haruka_v2_data --repo-type dataset --local-dir haruka_v2_data --exclude "fitted/*"   # inputs (~3.7 GB)
hf download C1vy/haruka_v2_data --repo-type dataset --local-dir haruka_v2_data --include "fitted/*"   # fitted (~5.8 GB)
hf download C1vy/haruka_v2_data 06_fibrosis/gse250346_unaffected_vs_all_fibrosis.h5ad --repo-type dataset --local-dir .

file	size	notebook	source / preprocessing
02_fig2_benchmark/mouse_brain_A8_paired.h5ad	31 MB	02_fig2_benchmark	aging coronal mouse-brain MERFISH section paired with a copy carrying 3 planted composition-shift domains (build_paired_sections.py, seed 20260815)
02_fig2_benchmark/mouse_brain_A9_paired.h5ad	32 MB	02_fig2_benchmark	aging coronal mouse-brain MERFISH section paired with a copy carrying 3 planted composition-shift domains (build_paired_sections.py, seed 20260815)
02_fig2_benchmark/mouse_brain_B17_paired.h5ad	38 MB	02_fig2_benchmark	aging coronal mouse-brain MERFISH section paired with a copy carrying 3 planted composition-shift domains (build_paired_sections.py, seed 20260815)
02_fig2_benchmark/mouse_brain_B3_paired.h5ad	31 MB	02_fig2_benchmark	aging coronal mouse-brain MERFISH section paired with a copy carrying 3 planted composition-shift domains (build_paired_sections.py, seed 20260815)
02_fig2_benchmark/mouse_brain_B5_paired.h5ad	36 MB	02_fig2_benchmark	aging coronal mouse-brain MERFISH section paired with a copy carrying 3 planted composition-shift domains (build_paired_sections.py, seed 20260815)
03_fig3_ad_plaque/ad_starmap.h5ad	56 MB	03_fig3_ad_plaque	STARmap PLUS AD mouse, 13 months, control vs disease (prepare_studies.py ad)
03_fig3_ad_plaque/codex_wholeslice_all7_no_oligo.h5ad	58 MB	03_fig3_ad_plaque	human AD CODEX whole slices, 4 AD / 3 control donors, 34 proteins, normalised (build_wholeslice.py)
03_fig3_ad_plaque/codex_wholeslice_ctl3VsCtl14.h5ad	26 MB	03_fig3_ad_plaque	arm-swap control: Ctl-3 relabelled disease vs Ctl-1/4 (build_ctl3_vs_ctl14.py)
03_fig3_ad_plaque/codex_abeta_objects.tar.gz	2 MB	03_fig3_ad_plaque	CODEX-CNS amyloid-beta plaque objects (position, class, intensities) for the 4 AD donors and Ctl-3, from the original release; extracted into the repository
04_exercise/exercise_old_full.h5ad	1,064 MB	04_exercise	Sun et al. aging/exercise brain MERFISH, old control vs old exercise, 594,896 cells x 300 genes (prepare_exercise.py)
05_petracer/petracer_M2-1_lineage.h5ad	293 MB	05_petracer	PEtracer M2-1: non-tumour control vs malignant cells in tumours, lineage columns for evaluation only (build_m2_tumour_vs_normal.py + build_m2_lineage.py)
06_fibrosis/gse250346_unaffected_vs_all_fibrosis.h5ad	291 MB	06_fibrosis	GSE250346 lung Xenium, unaffected vs fibrosis, 1.63 M cells x 343 genes (export_gse250346_unaffected_vs_fibrosis.R + build_h5ad.py)
06_fibrosis/he_annot_matched.csv.gz	22 MB	06_fibrosis	GSE250346 H&E region annotations matched to cells (match_he_annotations.py)
07_kras/mouselung_kras_xenium_clean_noC3.h5ad	1,731 MB	07_kras	KRAS inhibitor (MRTX1133) mouse lung Xenium 5K, 920,681 cells; X log-normalised, raw counts in layers["counts"]

Fitted AnnData (fitted/)

The input AnnData plus the default Haruka v2 fit used in the figures, matched cell by cell:

key	content
obsm['X_haruka_z']	background latent z (32-d), shared by control and condition cells
obsm['X_haruka_s']	salient latent s (32-d). The decoder sets s = 0 for control cells, so analyse s on condition cells only
obsm['haruka_D_z0'], obsm['haruka_D_zs']	predicted composition of the k = 20 spatial neighbours from [z, 0] and [z, s]
obsm['haruka_salient_shift']	D([z,s]) − D([z,0]): what the condition changed in the cell's neighbourhood
obsm['haruka_null_shift_0..2']	the same with s shuffled across cells (exercise, KRAS)
obsm['haruka_M_z0'], obsm['haruka_M_shift']	Fig. 2/3 only: predicted per-type neighbour mean expression (16-d SVD per type) and its salient shift
obs['haruka_condition_arm'], obs['haruka_in_fit']	condition-arm cells; cells included in the fit
uns['haruka']	composition column names (cell types), condition key/value, all fit arguments (JSON)

import anndata as ad
a = ad.read_h5ad('fitted/07_kras/mouselung_kras_xenium_clean_noC3_haruka_fitted.h5ad')
cond = a.obs['haruka_condition_arm'].to_numpy()
z, s = a.obsm['X_haruka_z'][cond], a.obsm['X_haruka_s'][cond]
shift = a.obsm['haruka_salient_shift'][cond]        # columns: a.uns['haruka']['composition_columns']

file	size	fit
fitted/02_fig2_benchmark/mouse_brain_A8_paired_haruka_fitted.h5ad	238 MB	Fig. 2 simulation, λ = 10 default fit (Poisson likelihood)
fitted/02_fig2_benchmark/mouse_brain_A9_paired_haruka_fitted.h5ad	259 MB	Fig. 2 simulation, λ = 10 default fit (Poisson likelihood)
fitted/02_fig2_benchmark/mouse_brain_B17_paired_haruka_fitted.h5ad	302 MB	Fig. 2 simulation, λ = 10 default fit (Poisson likelihood)
fitted/02_fig2_benchmark/mouse_brain_B3_paired_haruka_fitted.h5ad	275 MB	Fig. 2 simulation, λ = 10 default fit (Poisson likelihood)
fitted/02_fig2_benchmark/mouse_brain_B5_paired_haruka_fitted.h5ad	297 MB	Fig. 2 simulation, λ = 10 default fit (Poisson likelihood)
fitted/03_fig3_ad_plaque/ad_haruka_fitted.h5ad	104 MB	Fig. 3 default fit
fitted/03_fig3_ad_plaque/codex_wholeslice_all7_no_oligo_haruka_fitted.h5ad	175 MB	Fig. 3 default fit
fitted/03_fig3_ad_plaque/codex_wholeslice_ctl3VsCtl14_haruka_fitted.h5ad	70 MB	Fig. 3 default fit
fitted/04_exercise/exercise_old_full_haruka_fitted.h5ad	570 MB	exercise default fit (+ 3 shuffled-s nulls)
fitted/05_petracer/petracer_M2-1_lineage_haruka_fitted.h5ad	336 MB	PEtracer default fit
fitted/06_fibrosis/gse250346_unaffected_vs_all_fibrosis_haruka_fitted.h5ad	1,465 MB	lung fibrosis default fit
fitted/07_kras/mouselung_kras_xenium_clean_noC3_haruka_fitted.h5ad	2,434 MB	KRAS default fit (+ 3 shuffled-s nulls)

Fit time per dataset (one H200; neighbourhood-target construction + 150 epochs): Fig. 2 sections ~3 min each, STARmap 15 min, CODEX 1.5-3.5 min, PEtracer 10 min, exercise 48 min, KRAS 1.6 h, lung fibrosis 6.8 h.

Saved baseline results (baselines/)

The notebooks reproduce the Haruka results only; the comparison methods are not refitted by default. Their saved results are extracted into the repository instead (RUN_BASELINE=1 refits them):

file	size	contents
baselines/02_fig2_benchmark_baselines.tar.gz	2 MB	Fig. 2: scVI / ContrastiveVI / expression + CellCharter scores per section, composition controls, CINEMA-OT rows, B5 map cache
baselines/03_fig3_ad_plaque_baselines.tar.gz	3 MB	Fig. 3: scVI latent (32-d) for STARmap AD
baselines/05_petracer_baselines.tar.gz	10 MB	PEtracer: scVI latent (32-d)

SHA-256

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da857a27c0ccd9560e3062b4f06ff3fc539ab9defd0f83edcbeea630534109b7  02_fig2_benchmark/mouse_brain_B17_paired.h5ad
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9b9e5bbd203c46e2abd59747b7956c7aefde5b0397d25dec2f6abde78f631fb0  03_fig3_ad_plaque/codex_wholeslice_ctl3VsCtl14.h5ad
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37a1e0ce3801fe9238dcc394ea2f1c3e055296d689c400f8e19f5133c5770bae  fitted/03_fig3_ad_plaque/ad_haruka_fitted.h5ad
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f6914465455282f0ca2d50621c2891d1e5044b2d5636152f43f7e4ed710d662e  fitted/04_exercise/exercise_old_full_haruka_fitted.h5ad
de2b6fef2365ff4b3392d3cb038f7231ee9a7d375df801c10f9d1dd535654af8  fitted/05_petracer/petracer_M2-1_lineage_haruka_fitted.h5ad
bc54a42a3fdb7f383436e3e5a8037262617b0b7d02cacce0ead641fdd982debc  fitted/06_fibrosis/gse250346_unaffected_vs_all_fibrosis_haruka_fitted.h5ad
4912d39272b3ada1281a0b26b93668d7554c814118c5da6a4282c20736b9a2ee  fitted/07_kras/mouselung_kras_xenium_clean_noC3_haruka_fitted.h5ad
d2b58ed6b6454ad467dc64a6aed41cba3693c5af01290be4e6ccccd51955c241  baselines/02_fig2_benchmark_baselines.tar.gz
0a1a2ea2e75f4e5d2d24bdc8cfc195070fcaff1007d07d462030950325080d7b  baselines/03_fig3_ad_plaque_baselines.tar.gz
c686adeab993ad4b9576c1fbde57111a18e3cd0c6a1f62053f47ffe377a9f270  baselines/05_petracer_baselines.tar.gz

Licences follow the original data releases (GEO GSE250346, STARmap PLUS, CODEX-CNS, PEtracer, Sun et al.); the KRAS Xenium data are shared by the data owners for reproduction of this work.