Viharikvs/aadimodeldataset

Aadi Training Data

Raw and processed genomics data used to train Aadi, a 404M-parameter plant-DNA foundation model by UrbanKisaan Inc. This repository holds the inputs behind two stages: self-supervised pretraining of the shared frozen trunk on 49 plant genomes, and supervised RNA-seq + ATAC coverage training for maize and Arabidopsis.

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Contents

Component	Size	Files	What it is
ssl_corpus/	70 GB	49 genomes	Genome FASTA for self-supervised trunk pretraining (Ensembl Plants r56; AgroNT breadth corpus + one extra)
maize_b73_v5/	393 GB	~226	Maize (B73 NAM 5.0) RNA-seq + ATAC: raw reads, alignments, coverage, indices
arabidopsis_tair10/	173 GB	~424	Arabidopsis (TAIR10) RNA-seq + ATAC: raw reads, alignments, coverage, indices
Total	~686 GB	~754

Directory layout

.
├── ssl_corpus/                     49 plant-genome FASTAs + .fai + agront_corpus_species.txt
│   ├── zea_mays.fa, oryza_sativa.fa, triticum_aestivum.fa, ...
│   └── agront_corpus_species.txt   the species manifest
├── maize_b73_v5/
│   ├── fastq/                      raw paired-end reads (.fastq.gz)
│   ├── rna_bam/                    STAR RNA-seq alignments (*_Aligned.sortedByCoord.out.bam + .bai)
│   ├── atac_bam/                   bowtie2 ATAC alignments (atac_*.bam + .bai)
│   ├── bigwig/                     per-base CPM coverage tracks (.bw)
│   ├── indices/                    STAR / bowtie2 genome indices
│   ├── reference/                  Zm-B73-REFERENCE-NAM-5.0 genome (.fa) + annotation (.gtf/.gff3)
│   ├── metadata/                   sample manifests
│   └── logs/                       alignment logs
└── arabidopsis_tair10/             same subfolder structure, TAIR10

Provenance

• SSL corpus: 49 plant genomes from Ensembl Plants release 56 — the AgroNT 48-species breadth set plus one additional genome. Species manifest: ssl_corpus/agront_corpus_species.txt.
• Reference genomes:
  • Maize — Zea_mays.Zm-B73-REFERENCE-NAM-5.0, Ensembl Plants r61 (FASTA + GTF + GFF3).
  • Arabidopsis — Arabidopsis_thaliana.TAIR10, Ensembl Plants r56 (FASTA + GTF).
• Reads: public RNA-seq and ATAC-seq runs from ENA/SRA (accessions preserved in filenames, e.g. RNA ERR2273051, ATAC SRR4000469; maize ATAC SRR28817197, etc.). RNA aligned with STAR, ATAC with bowtie2; per-base coverage computed as CPM and stored as bigWig.

The full acquisition and preprocessing pipeline is scripted in the Aadi repo under scripts/data_pipeline/ (fetch_agront_corpus.sh, maize_align_and_bigwig.py).

Relationship to the model

The frozen trunk and per-task adapters trained on this data live in Viharikvs/aadimodel. ssl_corpus/ produced the shared 404M trunk; the maize and Arabidopsis coverage data produced the supervised heads and the cross-species transfer results.

License

Proprietary — Copyright (c) 2026 UrbanKisaan Inc. All rights reserved. The underlying genome assemblies and sequencing runs are publicly available from Ensembl Plants and ENA/SRA under their respective terms; the curation, processing, and assembly of this collection are proprietary.