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Add BEND 2.0 dataset card and verified benchmark assets

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BEND2.bib ADDED
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+ @misc{bjerregaard2026benchmarking,
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+ title = {{BEND 2.0}: Benchmarking the Capabilities Needed to Design {DNA}},
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+ author = {Bjerregaard, Andreas and Brilli, Dionysia Danai and
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+ DeVries, Rachael and Antoniadis, Panagiotis and Li, Yan and
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+ Krogh, Anders and Boomsma, Wouter and Winther, Ole and
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+ Marin, Frederikke Isa},
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+ year = {2026},
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+ url = {https://huggingface.co/datasets/yhsure/BEND2}
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+ }
FILES.md ADDED
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+ # File guide
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+
3
+ All data files are under `data/`. They are byte-identical to the source assets
4
+ used by the BEND 2.0 evaluation package at revision
5
+ `bca34753d2993f6f23c7de25cc41fb8523656bbd`.
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+
7
+ The files have different schemas. Download them individually with
8
+ `hf_hub_download`, or together with `snapshot_download`. The dataset viewer
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+ provides separate previews of the five Parquet tables; its `data` split is only
10
+ a display grouping. Use each task's stored assignments and evaluation rules.
11
+
12
+ ## Source archives
13
+
14
+ | File | Size | Contents |
15
+ | --- | ---: | --- |
16
+ | `opensplice.tsv.gz` | 425.5 MB | Unchanged OpenSplice version-5 experimental table. BEND prepares 590,104 variants in 466 genes, retaining reference and variant sequences, measured effects, uncertainties and gene identifiers. |
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+ | `siraj.zip` | 93.3 MB | Unchanged Siraj saturation-mutagenesis archive. BEND prepares 340,584 mutation/cell records in 128 elements; pairing HepG2 and K562 gives 170,292 cell contrasts. |
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+ | `hg38.2bit` | 835.4 MB | Unchanged UCSC hg38 reference genome, used to extract the long GTEx sequence windows. |
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+
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+ The archives are inputs to the benchmark's preparation code. They are not a
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+ single training table. Preserve the original filenames when using
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+ `BEND2_ASSET_DIR`.
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+
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+ ## Atlas
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+
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+ | File | Contents |
27
+ | --- | --- |
28
+ | `atlas-population.parquet` | 7,684 rows: 4,223 training, 1,023 validation, 2,411 candidate and 27 excluded sequences. Columns include `id`, `sequence`, `family_id`, `population`, `split`, `eligible_calibration` and `program_annotations`. All sequences are 145 bases. |
29
+ | `atlas-programs.csv` | Sixteen activity patterns, with `program`, `on_cells` and `off_cells`. Cell names are separated by `\|`. |
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+ | `atlas-source-activities.parquet` | Two measured activities in each of twelve cells for the 5,246 fitting sequences. |
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+ | `atlas-candidate-activities.parquet` | The corresponding measurements for the 2,411 candidates, kept separately from fitting data. |
32
+
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+ The activity columns start with `r1_` and `r2_`; `id` joins them to the sequence
34
+ table. Pandas reads `id` as the index, while Arrow exposes it as a column.
35
+ Activities are float64 values calculated from UMI-deduplicated RNA and DNA counts,
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+ with a pseudocount of 0.5 and normalization to the median of 35 negative controls.
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+ No measurement values were changed for this mirror.
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+
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+ Sequences belonging to families that overlap the candidates are excluded from
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+ fitting. The 27 excluded rows are retained in the population table to document
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+ that separation. BEND uses 7,657 sequences in total.
42
+
43
+ ## Sequence-prior panel
44
+
45
+ `prior-panel.parquet` contains 1,536 fixed-strand, 1,200-base GRCh38 windows:
46
+ 1,024 for baseline fitting and 512 for evaluation, separated by genomic blocks.
47
+ Columns include sequence, genomic coordinates, `reference_base`,
48
+ `recovery_position` and `split`. The hidden position is index 600 in zero-based
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+ coordinates.
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+
51
+ `prior-query-seeds.json` stores the two masking seeds per evaluation window used
52
+ by the NTv3 paper-prior adapter. It contains no sequences, hidden bases or
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+ measurement outcomes. These reference-genome sequences may have appeared in
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+ model pretraining.
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+
56
+ ## Additional Siraj measurements
57
+
58
+ `siraj-numeric-reference.npz` preserves exact float64 values for all 340,584
59
+ mutation/cell records. Its arrays are `record_id_bytes`, `columns` and `values`;
60
+ the numeric columns are `y_ref`, `y_alt`, `delta_y` and `sigma`.
61
+
62
+ `siraj_selective.parquet` contains 181,458 mutation and no-edit identifiers with
63
+ columns `ID`, `truth_hepg2` and `truth_k562`. These effects average the per-repeat
64
+ `log2((RNA + 0.5) / (DNA + 0.5))` difference from the unmutated parent across
65
+ five repeats. They are separate from the posterior effect estimates in the
66
+ Siraj archive. The cell-selective task uses 167,958 eligible substitutions
67
+ across 127 loci; the table also retains the identifiers needed for preparation.
68
+
69
+ ## GTEx
70
+
71
+ `gtex-targets.npz` contains `truth` (19,282 genes × 51 tissues), `gene_ids`,
72
+ `tissues`, and training, validation and test index arrays. Targets are
73
+ `log1p(TPM)` from the public GTEx v10 median-expression summary.
74
+
75
+ `gtex-genes.tsv` records gene identifiers and GENCODE v39 transcription-start
76
+ coordinates for reference-forward 131,072-base hg38 windows. It preserves the
77
+ target matrix's row order.
78
+
79
+ There are 12,146 training and 1,350 validation genes. The stored test set has
80
+ 5,786 genes; the four exclusions listed in `assets.json` leave the same
81
+ 5,782-gene evaluation set used in the paper. They lack complete predictions in
82
+ the paper's common model/reference comparison.
83
+
84
+ These are frozen GTEx v10 files and do not necessarily reflect the most current
85
+ or accurate data from the GTEx Portal. They contain public aggregate expression
86
+ only. No individual donor records or genotypes are included.
87
+
88
+ ## Provenance and checksums
89
+
90
+ - `assets.json` is an unchanged copy of the benchmark's source manifest. Its
91
+ `distribution: bundled` entries describe how the Python package ships those
92
+ assets, rather than their location in this Hugging Face repository.
93
+ - `checksums.json` lists the local `data/` paths, byte counts and SHA-256 values
94
+ for this release. The original MD5 checksums remain in `assets.json` where used
95
+ by the benchmark.
96
+ - `LICENSE.md` maps files to their source terms and acknowledgements.
97
+
98
+ The checksum manifest identifies file contents independently of the download
99
+ host. Rehosting does not change candidate sets, fold assignments, measurements
100
+ or scoring.
LICENSE.md ADDED
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+ # Data sources and terms
2
+
3
+ This collection contains data from several sources. Each file retains the terms
4
+ listed below; this notice does not replace those terms. The BEND 2.0 software
5
+ license does not apply to third-party data.
6
+
7
+ The three larger source files (`opensplice.tsv.gz`, `siraj.zip` and `hg38.2bit`)
8
+ are unchanged copies. The remaining files are benchmark selections, prepared
9
+ measurements or BEND 2.0 metadata. Their preparation is described in [FILES.md](FILES.md)
10
+ and the original [asset manifest](assets.json).
11
+
12
+ | Files under `data/` | Source and applicable terms |
13
+ | --- | --- |
14
+ | `opensplice.tsv.gz` | OpenSplice experimental master table, [Figshare version 5](https://doi.org/10.6084/m9.figshare.32337414.v5). [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/). |
15
+ | `siraj.zip`, `siraj-numeric-reference.npz`, `siraj_selective.parquet` | Siraj et al., *Functional dissection of complex and molecular trait variants at single nucleotide resolution*, [Zenodo 15297965](https://doi.org/10.5281/zenodo.15297965). [CC BY-NC 4.0](https://creativecommons.org/licenses/by-nc/4.0/). |
16
+ | `atlas-population.parquet`, `atlas-programs.csv`, `atlas-source-activities.parquet`, `atlas-candidate-activities.parquet` | Castillo-Hair et al., *Programming human cell type-specific gene expression via an atlas of AI-designed enhancers*, [Zenodo 17410822](https://doi.org/10.5281/zenodo.17410822). [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/). |
17
+ | `hg38.2bit`, `prior-panel.parquet` | Genome Reference Consortium GRCh38, distributed by UCSC. [Assembly-specific use and distribution terms](https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/README.txt) and [UCSC data terms](https://www.genome.ucsc.edu/license/). |
18
+ | `gtex-targets.npz` | GTEx v10 public median-expression summary, under the [GTEx Portal data license](https://gtexportal.org/home/license). |
19
+ | `gtex-genes.tsv` | GTEx's GENCODE v39 gene annotation. [GENCODE data access and attribution](https://www.gencodegenes.org/pages/data_access.html), [EMBL-EBI terms](https://www.ebi.ac.uk/about/terms-of-use/) and [GTEx terms](https://gtexportal.org/home/license). |
20
+ | `prior-query-seeds.json` | BEND 2.0 reproducibility metadata, under the project [MIT license](licenses/MIT.txt). |
21
+
22
+ ## Attribution and changes
23
+
24
+ CC BY 4.0 permits sharing and adaptation with attribution, a license link and an
25
+ indication of changes. CC BY-NC 4.0 provides those permissions for noncommercial
26
+ purposes. Rehosting the Siraj files here does not grant commercial-use rights.
27
+ Retain the original source credits and notices with redistributed copies.
28
+
29
+ **Siraj and ENCODE.** The cell-selective measurements were derived from ENCODE
30
+ files [ENCFF769XOF](https://www.encodeproject.org/files/ENCFF769XOF/) and
31
+ [ENCFF526SMM](https://www.encodeproject.org/files/ENCFF526SMM/), produced by Ryan
32
+ Tewhey's laboratory. We acknowledge the ENCODE Consortium and the producing
33
+ laboratory. Follow [ENCODE's attribution guidance](https://www.encodeproject.org/help/citing-encode/)
34
+ and [data-use policy](https://www.encodeproject.org/about/data-use-policy/).
35
+ The combined Siraj-derived table retains the Siraj release's noncommercial terms.
36
+
37
+ **GTEx.** We acknowledge the GTEx Project and GTEx Portal as the source of the
38
+ public expression summaries. The GTEx files are a frozen BEND 2.0 subset of
39
+ **GTEx v10** and do not necessarily reflect the most current or accurate data
40
+ available from the GTEx Portal. They contain public aggregate expression, not
41
+ individual-level genotype or donor data. No endorsement by GTEx is implied.
42
+ The exact input URLs are recorded in `assets.json`:
43
+
44
+ - [GTEx v10 median TPM](https://storage.googleapis.com/adult-gtex/bulk-gex/v10/rna-seq/GTEx_Analysis_v10_RNASeQCv2.4.2_gene_median_tpm.gct.gz)
45
+ - [GENCODE v39 annotation distributed with GTEx v10](https://storage.googleapis.com/adult-gtex/references/v10/reference-tables/gencode.v39.GRCh38.genes.gtf)
46
+
47
+ **Reference genome.** We acknowledge the Genome Reference Consortium and UCSC
48
+ Genome Browser. This release contains GRCh38 reference sequence and fixed
49
+ benchmark windows, not personal genomes. The download-directory README records
50
+ the assembly's upstream use and distribution terms.
51
+
52
+ The dataset title, preparation and benchmark organization do not imply endorsement
53
+ by any of the original data producers. Please cite the original studies as well
54
+ as BEND 2.0 when using their data.
README.md ADDED
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+ ---
2
+ pretty_name: BEND 2.0
3
+ license: other
4
+ license_name: bend2-source-specific
5
+ license_link: LICENSE.md
6
+ tags:
7
+ - biology
8
+ - genomics
9
+ - dna
10
+ - benchmark
11
+ - sequence-design
12
+ - bend2
13
+ configs:
14
+ - config_name: atlas_sequences
15
+ default: true
16
+ data_files:
17
+ - split: data
18
+ path: data/atlas-population.parquet
19
+ - config_name: atlas_source_activity
20
+ data_files:
21
+ - split: data
22
+ path: data/atlas-source-activities.parquet
23
+ - config_name: atlas_candidate_activity
24
+ data_files:
25
+ - split: data
26
+ path: data/atlas-candidate-activities.parquet
27
+ - config_name: sequence_prior
28
+ data_files:
29
+ - split: data
30
+ path: data/prior-panel.parquet
31
+ - config_name: siraj_cell_activity
32
+ data_files:
33
+ - split: data
34
+ path: data/siraj_selective.parquet
35
+ ---
36
+
37
+ ![BEND 2.0 — Benchmarking the capabilities needed to design DNA](media/readme-banner.png)
38
+
39
+ We built BEND 2.0 to test whether genomic models can guide the design of DNA. Across eight tasks, we examine how they predict sequence function, account for cell type and genetic background, and choose sequences that produce a desired response.
40
+
41
+ <picture>
42
+ <source media="(prefers-color-scheme: dark)" srcset="media/capabilities-wide-dark.svg">
43
+ <img src="media/capabilities-wide-light.svg" alt="Five capabilities: sequence priors, functional prediction, biological context, genetic interactions and genomic design.">
44
+ </picture>
45
+
46
+ This repository contains the data used by the benchmark: fixed sequence panels, prepared measurements and unchanged copies of the larger source files. Download only what you need, or keep the complete **1.39 GB** release locally.
47
+
48
+ [Browse files](https://huggingface.co/datasets/yhsure/BEND2/tree/main/data) · [File guide](FILES.md) · [Source terms](LICENSE.md) · [Citation](#citation)
49
+
50
+ ## Start with the enhancer sequences
51
+
52
+ Atlas contains 7,657 sequences used by BEND 2.0. Models learn from 5,246 sequences, then choose among 2,411 candidates to produce a desired pattern of activity across twelve cell types.
53
+
54
+ ```python
55
+ import pyarrow.compute as pc
56
+ import pyarrow.parquet as pq
57
+ from huggingface_hub import hf_hub_download
58
+
59
+ path = hf_hub_download(
60
+ "yhsure/BEND2",
61
+ "data/atlas-population.parquet",
62
+ repo_type="dataset",
63
+ revision="v1.0",
64
+ )
65
+ sequences = pq.read_table(path)
66
+ candidates = sequences.filter(
67
+ pc.equal(sequences["split"], "candidate")
68
+ ).select(["id", "sequence"])
69
+ ```
70
+
71
+ The table keeps the training, validation and candidate assignments, plus 27 excluded sequences for traceability. The two [activity tables](FILES.md#atlas) contain the measured responses. The viewer above shows each table separately; its `data` label is not a training split.
72
+
73
+ <details>
74
+ <summary><strong>Download the full release or use it with BEND 2.0</strong></summary>
75
+
76
+ Install `huggingface_hub` to download files; the example above also uses `pyarrow`.
77
+
78
+ ```python
79
+ from huggingface_hub import snapshot_download
80
+
81
+ snapshot_download(
82
+ "yhsure/BEND2",
83
+ repo_type="dataset",
84
+ revision="v1.0",
85
+ local_dir="bend2-data",
86
+ allow_patterns=["data/*", "assets.json", "checksums.json", "LICENSE.md"],
87
+ )
88
+ ```
89
+
90
+ If you already have the BEND 2.0 evaluation package, point it to this local copy:
91
+
92
+ ```bash
93
+ export BEND2_ASSET_DIR="$PWD/bend2-data/data"
94
+ bend2 run my_model.py --tasks siraj --output results/my-model
95
+ ```
96
+
97
+ The package checks the files against its existing manifest. Its small bundled datasets are unchanged. Model weights and embeddings are separate from this data release.
98
+
99
+ </details>
100
+
101
+ ## Eight tasks
102
+
103
+ | Task | What is evaluated | Data |
104
+ | :--- | :--- | :--- |
105
+ | **Sequence prior** | Recovering a hidden DNA base | 512 GRCh38 windows |
106
+ | **Splicing effects** | Predicting how mutations change splicing | 590,104 variants in 466 genes · OpenSplice |
107
+ | **Cell differences** | Predicting how a mutation's effect differs between two cells | 170,292 substitutions in 128 elements · Siraj |
108
+ | **Tissue identification** | Identifying tissues from predicted expression profiles | 5,782 held-out genes, 51 tissues · GTEx |
109
+ | **Genetic interactions** | Predicting how a mutation's effect depends on the surrounding alleles | 68,026 paired mutations in 114 elements · Siraj |
110
+ | **Matching a response** | Choosing an edit with a similar effect to a reference edit | 331 targets in 110 elements · Siraj |
111
+ | **Cell-selective editing** | Increasing expression in one cell while limiting changes in another | 167,958 substitutions in 127 loci · Siraj |
112
+ | **Multi-cell design** | Choosing enhancers for a desired pattern of activity across cells | 16 patterns, 2,411 candidates · Atlas |
113
+
114
+ BEND 2.0 keeps related genes, elements or sequence families together when splitting data. Preserve these assignments when comparing models. See the [file guide](FILES.md) for the stored tables, measurements and exclusions.
115
+
116
+ ## Data sources
117
+
118
+ The original studies provide the experiments; BEND 2.0 provides the benchmark selections and prepared files. Please credit both. **Each source retains its own terms**, including Siraj's noncommercial restriction.
119
+
120
+ | Source | Release | Terms |
121
+ | :--- | :--- | :--- |
122
+ | **OpenSplice** | [Experimental master table, version 5](https://doi.org/10.6084/m9.figshare.32337414.v5) | CC BY 4.0 |
123
+ | **Siraj et al.** | [Saturation mutagenesis](https://doi.org/10.5281/zenodo.15297965) | CC BY-NC 4.0 |
124
+ | **Castillo-Hair et al.** | [Atlas of AI-designed enhancers](https://doi.org/10.5281/zenodo.17410822) | CC BY 4.0 |
125
+ | **GTEx** | [v10 public expression summaries](https://gtexportal.org/home/datasets) | [GTEx data terms](https://gtexportal.org/home/license) |
126
+ | **Genome Reference Consortium / UCSC** | [GRCh38 / hg38](https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/README.txt) | Reference assembly terms |
127
+
128
+ Cell-selective measurements also use ENCODE data from Ryan Tewhey's laboratory; gene coordinates use GENCODE v39. Full acknowledgements and file-specific terms are in [LICENSE.md](LICENSE.md).
129
+
130
+ The GTEx files are a frozen BEND 2.0 subset of **GTEx v10** and do not necessarily reflect the most current or accurate data available from the GTEx Portal. They contain public aggregate expression, not individual donor records or genotypes.
131
+
132
+ The original asset manifest is preserved in [assets.json](assets.json). [checksums.json](checksums.json) records the size and SHA-256 of every data file in this release.
133
+
134
+ ## Citation
135
+
136
+ If you use BEND 2.0, cite the benchmark and the original datasets used in your analysis.
137
+
138
+ ```bibtex
139
+ @misc{bjerregaard2026benchmarking,
140
+ title = {{BEND 2.0}: Benchmarking the Capabilities Needed to Design {DNA}},
141
+ author = {Bjerregaard, Andreas and Brilli, Dionysia Danai and
142
+ DeVries, Rachael and Antoniadis, Panagiotis and Li, Yan and
143
+ Krogh, Anders and Boomsma, Wouter and Winther, Ole and
144
+ Marin, Frederikke Isa},
145
+ year = {2026},
146
+ url = {https://huggingface.co/datasets/yhsure/BEND2}
147
+ }
148
+ ```
149
+
150
+ [Download .bib](BEND2.bib)
assets.json ADDED
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1
+ {
2
+ "version": 1,
3
+ "sources": {
4
+ "opensplice": {
5
+ "title": "OpenSplice experimental master table, version 5",
6
+ "doi": "10.6084/m9.figshare.32337414.v5",
7
+ "license": "CC-BY-4.0"
8
+ },
9
+ "siraj": {
10
+ "title": "Functional dissection of complex and molecular trait variants at single nucleotide resolution",
11
+ "doi": "10.5281/zenodo.15297965",
12
+ "license": "CC-BY-NC-4.0",
13
+ "selective_outcome_provenance": {
14
+ "encode_files": [
15
+ "ENCFF769XOF",
16
+ "ENCFF526SMM"
17
+ ],
18
+ "estimator_sha256": "508bcf73961ced6a53b948e87440cd4b49b55a7aa6c9abefafd99a257e88ca42",
19
+ "protocol_seal_sha256": "a0441d12727376ae07e0a372067ecb6a6b94c24d5700f15b6e96e971164b854d"
20
+ }
21
+ },
22
+ "atlas": {
23
+ "title": "Programming human cell type-specific gene expression via an atlas of AI-designed enhancers",
24
+ "doi": "10.5281/zenodo.17410822",
25
+ "license": "CC-BY-4.0",
26
+ "upstream_processed_table_sha256": "7472bdeb0a2233bdff2ad6c3deed6b8ddf32b2c6f5f8202ad26c8f75838ec943"
27
+ },
28
+ "prior": {
29
+ "title": "Frozen BEND 2.0 GRCh38 sequence-prior panel",
30
+ "url": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/README.txt",
31
+ "license": "Human reference assembly; retain upstream attribution"
32
+ },
33
+ "genome": {
34
+ "title": "UCSC GRCh38/hg38 reference genome, 2015-04-30",
35
+ "url": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/README.txt",
36
+ "license": "Human reference assembly; retain upstream attribution"
37
+ },
38
+ "gtex": {
39
+ "title": "Frozen BEND 2.0 GTEx tissue expression targets and gene split",
40
+ "url": "https://gtexportal.org/home/datasets",
41
+ "license": "GTEx public summary-data terms; see data documentation",
42
+ "raw_summary_url": "https://storage.googleapis.com/adult-gtex/bulk-gex/v10/rna-seq/GTEx_Analysis_v10_RNASeQCv2.4.2_gene_median_tpm.gct.gz",
43
+ "gene_model_url": "https://storage.googleapis.com/adult-gtex/references/v10/reference-tables/gencode.v39.GRCh38.genes.gtf"
44
+ }
45
+ },
46
+ "files": {
47
+ "prior-panel.parquet": {
48
+ "bytes": 944867,
49
+ "sha256": "d4a07c4bcb98c4f5a3f94a6d82a3dfd5e01b3b5baedfc5efa075fe75e3f871f1",
50
+ "source": "prior",
51
+ "distribution": "bundled",
52
+ "provenance_url": "https://raw.githubusercontent.com/yhsure/genomic-bending/ea617f8d6f48532c299977427b1c9f34b216a1fc/src/bend2/resources/prior-panel.parquet",
53
+ "protocol": "1,024 baseline-training and 512 evaluation windows; 1,200 bases; recovery position 600; seed 20260910; 1 Mb genomic block separation."
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Git LFS Details

  • SHA256: 50f3b6d772f3b76d4fdc4c4d47480629f5a44571cebb3f7069a7f686172ae692
  • Pointer size: 131 Bytes
  • Size of remote file: 494 kB