Datasets:

fabricioslv
/

omnimind-hic-multispecies

text stringlengths 3.25k 3.25k
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0.0024 0.0031 0.0028 0.0023 0.0033 0.0027 0.0024 0.0037 0.0026 0.0021 0.0033 0.0041 0.0039 0.0034 0.0031 0.0036 0.0033 0.0041 0.0036 0.0042 0.0037 0.0035 0.0043 0.0044 0.0049 0.0037 0.0045 0.0040 0.0050 0.0043 0.0049 0.0055 0.0051 0.0055 0.0056 0.0057 0.0056 0.0054 0.0068 0.0067 0.0072 0.0094 0.0083 0.0096 0.0098 0.011...
0.0026 0.0022 0.0025 0.0026 0.0024 0.0029 0.0024 0.0034 0.0030 0.0026 0.0025 0.0028 0.0034 0.0028 0.0024 0.0036 0.0036 0.0037 0.0033 0.0033 0.0038 0.0034 0.0034 0.0048 0.0045 0.0043 0.0040 0.0041 0.0038 0.0043 0.0053 0.0047 0.0052 0.0056 0.0048 0.0046 0.0052 0.0056 0.0059 0.0063 0.0077 0.0086 0.0079 0.0087 0.0087 0.011...
0.0028 0.0027 0.0024 0.0029 0.0028 0.0027 0.0021 0.0029 0.0031 0.0035 0.0029 0.0027 0.0027 0.0032 0.0033 0.0038 0.0033 0.0028 0.0031 0.0036 0.0029 0.0039 0.0038 0.0037 0.0042 0.0041 0.0038 0.0051 0.0039 0.0055 0.0048 0.0064 0.0054 0.0060 0.0064 0.0049 0.0043 0.0054 0.0070 0.0068 0.0068 0.0082 0.0079 0.0093 0.0088 0.008...
0.0028 0.0023 0.0028 0.0029 0.0035 0.0032 0.0023 0.0028 0.0029 0.0026 0.0037 0.0032 0.0022 0.0037 0.0034 0.0033 0.0045 0.0031 0.0035 0.0036 0.0033 0.0040 0.0031 0.0036 0.0040 0.0052 0.0053 0.0046 0.0052 0.0034 0.0057 0.0053 0.0055 0.0064 0.0057 0.0074 0.0073 0.0061 0.0053 0.0073 0.0076 0.0057 0.0079 0.0078 0.0077 0.006...
0.0020 0.0030 0.0022 0.0028 0.0026 0.0028 0.0020 0.0024 0.0029 0.0024 0.0031 0.0029 0.0034 0.0032 0.0034 0.0038 0.0035 0.0039 0.0032 0.0032 0.0032 0.0033 0.0036 0.0037 0.0038 0.0039 0.0042 0.0034 0.0042 0.0047 0.0047 0.0052 0.0051 0.0067 0.0060 0.0047 0.0050 0.0063 0.0070 0.0080 0.0060 0.0071 0.0065 0.0064 0.0066 0.006...
0.0020 0.0024 0.0024 0.0032 0.0026 0.0023 0.0021 0.0031 0.0029 0.0034 0.0035 0.0025 0.0030 0.0030 0.0027 0.0033 0.0028 0.0036 0.0031 0.0027 0.0028 0.0034 0.0033 0.0043 0.0039 0.0042 0.0040 0.0037 0.0032 0.0045 0.0043 0.0061 0.0043 0.0060 0.0053 0.0042 0.0062 0.0043 0.0059 0.0060 0.0061 0.0066 0.0055 0.0062 0.0060 0.006...
0.0022 0.0022 0.0020 0.0028 0.0034 0.0023 0.0030 0.0026 0.0033 0.0025 0.0032 0.0026 0.0033 0.0031 0.0024 0.0037 0.0024 0.0025 0.0032 0.0029 0.0028 0.0037 0.0034 0.0035 0.0039 0.0037 0.0038 0.0035 0.0047 0.0043 0.0047 0.0051 0.0053 0.0054 0.0056 0.0055 0.0055 0.0055 0.0065 0.0054 0.0068 0.0044 0.0052 0.0059 0.0054 0.006...
0.0026 0.0027 0.0025 0.0034 0.0025 0.0027 0.0027 0.0028 0.0031 0.0027 0.0022 0.0029 0.0024 0.0030 0.0029 0.0030 0.0036 0.0032 0.0035 0.0032 0.0027 0.0032 0.0029 0.0035 0.0045 0.0040 0.0041 0.0040 0.0042 0.0037 0.0048 0.0053 0.0046 0.0053 0.0039 0.0043 0.0049 0.0047 0.0056 0.0043 0.0061 0.0070 0.0071 0.0054 0.0049 0.005...
0.0030 0.0026 0.0026 0.0024 0.0018 0.0027 0.0027 0.0027 0.0031 0.0027 0.0033 0.0024 0.0028 0.0028 0.0033 0.0026 0.0033 0.0031 0.0029 0.0030 0.0030 0.0040 0.0024 0.0033 0.0043 0.0042 0.0047 0.0046 0.0051 0.0033 0.0045 0.0042 0.0051 0.0053 0.0042 0.0056 0.0042 0.0055 0.0044 0.0051 0.0060 0.0046 0.0055 0.0063 0.0057 0.005...
0.0016 0.0025 0.0027 0.0026 0.0027 0.0024 0.0023 0.0030 0.0025 0.0040 0.0027 0.0023 0.0025 0.0029 0.0026 0.0035 0.0028 0.0034 0.0021 0.0029 0.0025 0.0026 0.0028 0.0030 0.0034 0.0047 0.0036 0.0042 0.0035 0.0038 0.0040 0.0046 0.0039 0.0051 0.0047 0.0047 0.0046 0.0050 0.0049 0.0048 0.0050 0.0057 0.0050 0.0060 0.0049 0.004...
0.0025 0.0029 0.0026 0.0022 0.0021 0.0025 0.0023 0.0024 0.0025 0.0031 0.0033 0.0023 0.0027 0.0022 0.0025 0.0027 0.0025 0.0023 0.0033 0.0023 0.0023 0.0034 0.0027 0.0032 0.0028 0.0032 0.0034 0.0034 0.0029 0.0039 0.0027 0.0038 0.0038 0.0044 0.0041 0.0032 0.0042 0.0043 0.0043 0.0043 0.0049 0.0050 0.0043 0.0044 0.0038 0.005...

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Hi-C Contact Maps for Multi-Species Topological Analysis

Description

This dataset contains real Hi-C chromatin conformation contact maps for 4 species, sourced from NCBI GEO. It was assembled to corroborate topological data analysis (TDA) performed on nucleotide-transformer genomic embeddings in the OmniMind Dodecatíad v3 publication pack.

Species and Provenance

Species	GEO Accession	Format	Resolution	Samples	Size
Escherichia coli	GSE293552	matrix.txt.gz	10 kb	6	~1.2 MB
Saccharomyces cerevisiae	GSE278899	.cool.gz	1 kb	2	~15 MB
Caenorhabditis elegans	GSE199721	.cool.gz	2 kb	2	~171 MB
Homo sapiens (GM12878)	GSE318239	.mcool	multi-res	1	~2.4 GB

Directory Structure

hic_dataset/
├── ecoli/           # 6 Hi-C matrices (465×465, 10kb bins)
├── yeast/           # 2 .cool files (whole-genome S288c, 1kb)
├── celegans/        # 2 .cool files (N2, 2kb)
└── human/           # 1 .mcool (GM12878, multi-resolution)

Usage

# E. coli matrices (plain text, space-separated)
import gzip, numpy as np
with gzip.open('ecoli/GSM8885042_cWX2200_24H_Azure_10percent_Sau3AI_rep1-10k.matrix.txt.gz', 'rt') as f:
    matrix = np.array([[float(x) for x in line.split()] for line in f])

# Yeast/C. elegans .cool files
import cooler
c = cooler.Cooler('yeast/GSE278899_AP57_S288c_DSB_chr3_rDNA_normal_q20_v312_1kb.cool.gz')
matrix = c.matrix(balance=False)[:]

# Human .mcool (multi-resolution)
c = cooler.Cooler('human/GSE318239_GM12878_Direct_CAD-C_S_M_merged_igdiag1.mcool::resolutions/10000000')
matrix = c.matrix(balance=False)[:]

TDA Results Summary

Persistent homology (H0, H1) computed via ripser with maxdim=1 on inverse-contact distance matrices.

Species	Hi-C H1 features	Hi-C H1 entropy	Embedding H1 features	Embedding H1 entropy
E. coli	429–817	5.42–6.42	140	4.63
S. cerevisiae	256–386	5.07–5.79	113	4.46
C. elegans	2	0.69	52	3.55
H. sapiens	90	1.71	121	4.46

Key finding: C. elegans has the simplest chromatin topology (fewest H1 loops) in both Hi-C and embedding TDA — qualitatively consistent.

Limitations

maxdim=1 only (H2 too computationally expensive for 465+ bins)
Different resolutions across species (10kb to 1Mb effective)
Inverse-contact distance introduces epsilon artifacts for zero-contact bins
Embedding TDA uses euclidean distance in 512D space; Hi-C TDA uses inverse contact frequency
Not proof of equivalence — qualitative corroboration only

Citation

If you use this dataset, please cite the original GEO publications:

E. coli: GSE293552 (2025)
S. cerevisiae: GSE278899 (2025)
C. elegans: GSE199721 (2022)
H. sapiens: GSE318239 (2026)

License

CC-BY-4.0 (data sourced from NCBI GEO, which is public domain)

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