mbzuai-ai4bio/BioXArena-Pro-Public

BioXArena-Pro Public

Public data package of BioXArena-Pro (release v5.1.1, 2026-10-21): 64 harder biology tasks in 8 domains, 8 tasks per domain. Each task folder contains public/description.md (task, data construction, split, metric and rules), public/sample_submission.csv, the training and test inputs, and any modality-specific assets. Test labels are not included; they are in the access-controlled repository mbzuai-ai4bio/BioXArena-Pro-Private.

Every task was audited for label leakage, shortcuts and description errors before release; the per-task description.md records the data version and what changed. Scores obtained on earlier internal versions are not comparable with this release.

Changes in v5.1.1 (2026-10-21)

A final check of all 64 tasks found two tasks whose test information could be turned into score; both were fixed:

• phenotype-disease/covid-nb-hospitalization-forecast (data v5.1): the test set now has two forecast origins (weeks 76 and 103; 100 records) instead of four. With origins 9 weeks apart, a later origin's record allowed the earlier origin's target-week rates to be reconstructed. Same records and labels for the kept origins.
• single-cell-spatial/gastrulation-xl-kinetic-state (v5.2.1, description only): a sentence that stated the stages of the test-only embryo pools was removed. Data unchanged.

Description corrections without data changes (removed test-set counts or corrected numbers and wording): boom-xl-csd, tdc-xl-dti-binding-affinity, pring-xl-cross-species-ppi, lnctard-xl-relation, cellverse-xl-cta, tahoe-xl-single-cell, clinvar-nb-disease-variant-effect, skempi-xl-ppi-ddg, asep-xl-epitope, subcell-xl-localization, calcium-nb-neuron-segmentation, medmnist3d-xl-decathlon.

Layout

BioXArena-Pro-Data-Public/
└── <domain>/
    └── <task>/
        └── public/
            ├── description.md
            ├── sample_submission.csv
            ├── training data
            ├── test data
            └── modality-specific assets

Download

Full package (extracts to BioXArena-Pro-Data-Public/<domain>/<task>/public/):

hf download mbzuai-ai4bio/BioXArena-Pro-Public BioXArena-Pro-Data-Public.tar.gz --repo-type dataset --local-dir .
tar -xzf BioXArena-Pro-Data-Public.tar.gz

Size: 101.73 GB (sha256 72bef86dc7c0e6dffd09affb3aec33b7af20590dbda400042b2c58788c76f0a9).

One archive per domain under Data-Public-by-Domain/ (each extracts to <domain>/<task>/public/); Data-Public-by-Domain/MANIFEST.txt lists the tasks and checksums.

Archive	Size	# Tasks	Tasks Included
Data-Public-by-Domain/chemical-biology-8tasks-all.tar.gz	305.54 MB	8	All 8 chemical-biology tasks
Data-Public-by-Domain/imaging-8tasks-all.tar.gz	57.63 GB	8	All 8 imaging tasks
Data-Public-by-Domain/network-biology-8tasks-all.tar.gz	3.69 GB	8	All 8 network-biology tasks
Data-Public-by-Domain/perturbation-8tasks-all.tar.gz	852.27 MB	8	All 8 perturbation tasks
Data-Public-by-Domain/phenotype-disease-8tasks-all.tar.gz	313.71 MB	8	All 8 phenotype-disease tasks
Data-Public-by-Domain/sequence-genomics-8tasks-all.tar.gz	7.25 GB	8	All 8 sequence-genomics tasks
Data-Public-by-Domain/single-cell-spatial-8tasks-all.tar.gz	3.81 GB	8	All 8 single-cell-spatial tasks
Data-Public-by-Domain/structure-8tasks-all.tar.gz	27.87 GB	8	All 8 structure tasks

Tasks

Domain	Task	Title
chemical-biology	boom-xl-csd	BOOM-XL-CSD: Out-of-Distribution Molecular Property Prediction
chemical-biology	chemixhub-xl-conductivity	CheMixHub-XL Conductivity: Mixture Ionic Conductivity
chemical-biology	drugcomb-xl-multiomics-synergy	DrugComb-XL: Synergy of New Compounds in NCI-60 Combination Screens
chemical-biology	kano-molecular-property-prediction	Molecular Property Prediction (KANO benchmark suite)
chemical-biology	massspecgym-xl-msms-retrieval	MassSpecGym-XL: Molecule Retrieval from Tandem Mass Spectra
chemical-biology	solubility-xl	Solubility-XL: Aqueous Solubility Prediction
chemical-biology	tdc-xl-dti-binding-affinity	TDC-XL-DTI-Binding-Affinity: Drug–Target Affinity Prediction
chemical-biology	uspto-nb-reaction-product	Organic Reaction Product Prediction on New Substrates (USPTO-480k)
imaging	calcium-nb-neuron-segmentation	Neuron Segmentation from Simulated and Real Two-Photon Calcium Imaging
imaging	cryocrab-xl-quality	CryoCRAB-XL: Cryo-EM Micrograph Quality (CTF Fit Resolution) Regression
imaging	drugclass-xl-if	DrugClass-XL: Drug-Treatment Classification in a New Screen
imaging	mammovqa-xl-external	MammoVQA-XL: Mammography Visual Question Answering
imaging	medmnist3d-xl-decathlon	MedMNIST3D-XL: Classification Under an Unknown Acquisition Shift (five sources)
imaging	microscopy-instance-segmentation	Microscopy Instance Segmentation
imaging	rocov2-xl-retrieval	ROCOv2-XL: Matching a Radiology Image to Its Caption Among Concept-Similar Candidates
imaging	subcell-xl-localization	SubCell-XL: Subcellular Localization of Tagged Proteins from Microscopy Crops
network-biology	causalbench-xl-grn	CausalBench-XL: Which Perturbations Move a Gene
network-biology	lnctard-xl-relation	LncTarD-XL: Relation-Conditioned Target Ranking
network-biology	music-xl-seccomplex	MuSIC-XL-SECComplex: Protein Co-Complex Discovery from SEC-MS
network-biology	ppi-nb-cross-species	Protein-Protein Interaction Prediction
network-biology	pring-xl-cross-species-ppi	PRING-XL: Cross-Species Protein-Protein Interaction Prediction
network-biology	scigym-xl-sbml	SciGym-XL: Completing Partial Pathway Models of Unseen Pathways (SBML)
network-biology	swissprot-nb-protein-function	Protein Function Prediction from Sequence
network-biology	synlethdb-xl-sl	SynLethDB-XL: Synthetic-Lethal Partner Ranking
perturbation	cellverse-xl-cta	CellVerse-XL: annotate an MS cohort with a healthy-control reference
perturbation	cpjump-xl-genetic-matching	CPJUMP-XL: Cold-Target Compound-to-Gene Matching from Cell Painting
perturbation	gdsc-xl-lineage-holdout-response	GDSC-XL: Drug Response in Cancer Lineages Not Seen in Training
perturbation	perturbench-xl-response	PerturBench-XL: Context-Specific Perturbation Response
perturbation	scgenescope-xl-treatment	scGeneScope-XL: Single-Cell Treatment Classification
perturbation	sciplex-xl-distribution	sci-Plex-XL: Transcriptional Response of Active Drugs in Unseen Drug × Cell-Line Pairs
perturbation	tahoe-xl-single-cell	Tahoe-100M: drug response of a new cell line from its baseline profile
perturbation	xatlas-orion-xl-perturb	X-Atlas/Orion-XL: Transcriptional Response to the Knock-down of an Unseen Gene
phenotype-disease	clinvar-nb-disease-variant-effect	Disease-Specific Variant Effect Prediction
phenotype-disease	covid-nb-hospitalization-forecast	COVID-19 Hospitalization Trend Forecasting (multi-origin)
phenotype-disease	cptac-pan-xl-protein-imputation	CPTAC-Pan-XL: External Protein Imputation
phenotype-disease	gutcrc-xl-cross-cohort-detection	GutCRC-XL: Detecting Colorectal Cancer from Stool Metagenomes in Unseen Cohorts
phenotype-disease	msk-met-xl-tumor-origin	MSK-MET-XL: Assay-Generation-OOD Tumor Origin
phenotype-disease	survpath-xl-multimodal	SurvPath-XL-Multimodal: TCGA survival from histology thumbnails + bulk RNA-seq
phenotype-disease	target-aml-xl-cytogenetics	TARGET-AML-XL: Protocol-OOD cytogenetic risk-group classification from clinical + multi-omics data
phenotype-disease	tcga-pancan-xl-multiomics-survival	TCGA-PanCan-XL: pan-cancer overall survival from three de-identified omics layers
sequence-genomics	aso-xl-knockdown-efficacy	ASO-XL: Antisense Oligonucleotide Knockdown Efficacy
sequence-genomics	cgbench-xl-variant	CGBench-XL: Clinical Variant Assertion from Variant Context
sequence-genomics	de-novo-peptide-sequencing-from-tandem-mass-spectrometry	De Novo Peptide Sequencing from Tandem Mass Spectrometry
sequence-genomics	deepstarr-nb-genomic-sequence	Genomic Sequence Prediction (14 instances)
sequence-genomics	escape-xl-amp-multilabel	ESCAPE-XL: multilabel antimicrobial-peptide classification
sequence-genomics	proteingym-xl-fitness	ProteinGym-XL: Region-Held-Out Mutation Fitness
sequence-genomics	sirna-xl-knockdown-efficacy	siRNA-XL: RNA Interference Knockdown Efficacy
sequence-genomics	yeast-nb-promoter-expression	Yeast Promoter Expression Prediction
single-cell-spatial	dlpfc-xl-spatial-domain	DLPFC-XL: Donor-OOD Spatial-Domain Annotation
single-cell-spatial	gastrulation-xl-kinetic-state	Gastrulation-XL: Developmental Stage and Cell Fate of Held-out Mouse Embryos
single-cell-spatial	hest-coad-xl-spatial-expression	HEST-COAD-XL: Patient-OOD Spatial Expression
single-cell-spatial	lung-cite-xl-cell-matching	CITE-XL: Cross-Protocol Cell Matching in Human PBMC CITE-seq
single-cell-spatial	openproblems-xl-rna-atac	OpenProblems-XL RNA-to-ATAC: Donor-OOD Chromatin Accessibility of Cell States
single-cell-spatial	openproblems-xl-rna-protein	OpenProblems-XL RNA-to-Protein: Donor-OOD CITE-seq Translation
single-cell-spatial	seqfish-xl-deconvolution	Hippocampus-XL: Spatial Deconvolution into 16 Cell Types
single-cell-spatial	tabula-sapiens-xl-ood-annotation	Tabula-Sapiens-XL: Donor-OOD Immune and Haematopoietic Cell Annotation
structure	asep-xl-epitope	Antibody-Specific Epitope Residues
structure	cath-nb-inverse-folding	Inverse Protein Folding (CATH 4.2 / 4.3, PDB2022)
structure	cpsea-xl-cyclic-peptide-affinity	Cyclic Peptide–Protein Binding Energy from Coarse Structure
structure	decoydb-xl-pose-classify	DecoyDB-XL-PoseClassify: Ranking Docked Poses Inside the Known Binding Site
structure	denoise-cryo-xl	DenoiseCryo-XL: Backbone Tracing and Residue Assignment in Experimental Cryo-EM Maps
structure	ppi-nb-interface-residues	Partner-specific protein-protein interface residue prediction
structure	psbench-xl-multimer-mqa	Quality Assessment of Predicted Protein-Complex Structures — Small Model Pools
structure	skempi-xl-ppi-ddg	Protein-protein binding free-energy change upon mutation (SKEMPI 2.0 ddG)

Scoring

Every grader returns a higher-is-better score in [0, 1]. Correlation and MCC metrics are reported as clip(r, 0, 1) (chance = 0); AUC, c-index, AP, F1, accuracy and MRR keep their native scale (for example chance = 0.5 for AUC). tahoe and sciplex are offset by the all-zero prediction, covid uses an RPS skill score. A task's public/description.md documents its inputs, split, metric and rules; the graders are in the BioXArena-Pro code release (tasks/<domain>/<task>/grade.py).

Licence

The packaging, splits, opaque identifiers and task descriptions are released under CC BY-NC 4.0. The underlying data come from public resources that keep their own licences and citation requirements; each task's public/description.md names its source.

Contact

MBZUAI AI4Bio (mbzuai-ai4bio on Hugging Face). Please report data problems in the repository's Community tab.