Leagein/BioXArena-Data-Public

BioXArena Data Public

This directory is the public data package for BioXArena.

Based on the current folder contents, it contains:

• 9 domains
• 76 task folders
• 76 public/description.md files
• 76 public/sample_submission.csv files

Each task follows the same top-level layout:

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

Within each task, the public/ directory typically includes:

• Task description: description.md
• Sample submission template: sample_submission.csv
• Training data: train.csv / train.jsonl.gz / train_*.npz / ...
• Test data: test.csv / test.jsonl.gz / test_*.npz / ...
• Modality-specific assets: image folders, sequence files, sparse matrices, h5ad, structure files, or other task-specific resources

The exact file set varies by task. Some tasks are primarily table-based, while others also include microscopy images, molecular structures, single-cell matrices, genomic sequence files, or other multimodal resources stored under the same public/ directory.

Download From Hugging Face

This package is intended to be distributed on Hugging Face at:

• https://huggingface.co/datasets/Leagein/BioXArena-Data-Public

Users can download and extract it like this:

wget "https://huggingface.co/datasets/Leagein/BioXArena-Data-Public/resolve/main/BioXArena-Data-Public.tar.gz" -O BioXArena-Data-Public.tar.gz
tar -xzf BioXArena-Data-Public.tar.gz

You can also use huggingface-cli:

huggingface-cli download Leagein/BioXArena-Data-Public BioXArena-Data-Public.tar.gz --repo-type dataset --local-dir .
tar -xzf BioXArena-Data-Public.tar.gz

Domain Summary

Domain	# Tasks
chemical-biology	8
imaging	8
network-biology	8
perturbation-dynamics	8
phenotype-disease	8
sequence	10
single-cell	10
structure	8
text-integrated	8

Task Catalog

Chemical Biology

Task Folder	Task Title	Task Type	Evaluation Metric	Description
bace1-binding-affinity	DTI BindingDB BACE1 — Binding Affinity Regression	Regression	Pearson Correlation	Predict the binding affinity of small molecules against Beta-secretase 1 (BACE1).
cell-painting-perturbation	Cell Painting Compound Perturbation Matching	Classification	Accuracy	Predict which compound perturbation was applied to cells based on multi-channel Cell Painting morphological profiles.
cyp-inhibition-multi-label	CYP Enzyme Inhibition Multi-Label Prediction	Multi-label classification	Macro ROC-AUC	Predict whether small molecules inhibit each of five major cytochrome P450 (CYP) enzymes.
egfr-binding-affinity	DTI BindingDB EGFR — Binding Affinity Regression	Regression	Pearson Correlation	Predict the binding affinity of small molecules against Epidermal Growth Factor Receptor (EGFR).
gpcr-binding-multi-class	GPCR Binding Multi-Class Classification	Multi-class classification	Macro F1	Classify small molecules by the class of G protein-coupled receptor (GPCR) they bind to.
herg-binding-affinity	DTI BindingDB hERG — Binding Affinity Regression	Regression	Pearson Correlation	Predict the binding affinity of small molecules against the hERG (human Ether-à-go-go-Related Gene) potassium channel.
kinase-selectivity-multi-label	Kinase Selectivity Multi-Label Prediction	Multi-label classification	Macro ROC-AUC	Predict the inhibition activity of small molecules against a panel of eight clinically relevant kinases.
tox21-sr-are	Tox21 SR-ARE — Oxidative Stress Toxicity Prediction	Binary classification	ROC-AUC	Predict whether a small molecule activates the Antioxidant Response Element (ARE) signaling pathway, as measured in the Tox21 stress response (SR) panel.

Imaging

Task Folder	Task Title	Task Type	Evaluation Metric	Description
amos-organ-segmentation	AMOS: Abdominal Multi-Organ Segmentation	Segmentation	Mean Dice Score	Segment 15 abdominal organs from 3D CT and MRI volumes.
drug-moa-prediction	Drug MOA Prediction	Multi-class classification	Macro F1	Predict the mechanism of action (MOA) of compounds from fluorescence microscopy images of drug-treated MCF-7 breast cancer cells.
labelfree-cell-counting	Label-Free Cell Counting	Regression	Spearman Rank Correlation	Predict the number of cells in label-free phase contrast microscopy images from the LIVECell dataset.
lung-nodule-malignancy	Lung Nodule Malignancy Prediction (LIDC-IDRI)	Multi-class classification	Accuracy	Predict the malignancy level of lung nodules from 3D CT image crops combined with radiologist-annotated semantic features and patient demographics.
mitochondria-counting	Mitochondria Instance Counting in Electron Microscopy (MitoEM)	Regression	MAE	Predict the number of mitochondria instances in electron microscopy (EM) image patches from human and rat brain tissue.
nucleus-type-classification	Nucleus Type Classification	Multi-class classification	Macro F1	Predict the dominant nucleus type in H&E-stained histopathology image patches from the PanNuke dataset.
skin-lesion-diagnosis	Skin Lesion Diagnosis (HAM10000)	Multi-class classification	Accuracy	Classify dermatoscopic images of skin lesions into 7 diagnostic categories using both the image and clinical metadata.
virtual-staining	Virtual Staining — IHC Positive Ratio Prediction	Regression	Spearman Rank Correlation	Predict the immunohistochemistry (IHC) positive tissue fraction from H&E-stained histopathology images.

Network Biology

Task Folder	Task Title	Task Type	Evaluation Metric	Description
gene-disease-association	Gene-Disease Association Strength Prediction (DisGeNET)	Regression	Pearson Correlation	Predict the strength of association between a gene and a disease.
go-function-multi-label	GO Function Multi-Label Prediction	Multi-label classification	Macro ROC-AUC	Predict Gene Ontology (GO) biological process annotations for proteins.
metabolic-network-kegg	Metabolic Network Enzyme-Reaction Prediction (KEGG)	Binary classification	ROC-AUC	Predict whether an enzyme catalyzes a given biochemical reaction in the KEGG metabolic network.
pathway-membership-reactome	Pathway Membership Classification (Reactome)	Multi-class classification	Accuracy	Predict the Reactome pathway category that a protein belongs to.
ppi-prediction-string	Protein-Protein Interaction Prediction (STRING)	Binary classification	ROC-AUC	Predict whether two proteins physically or functionally interact based on their sequences and network topology features.
protein-complex-corum	Protein Complex Classification (CORUM)	Multi-class classification	Accuracy	Predict the protein complex category a protein belongs to from the CORUM database.
synthetic-lethality-prediction	Synthetic Lethality Prediction	Binary classification	ROC-AUC	Predict whether a pair of genes exhibits synthetic lethality, where simultaneous loss of both genes leads to cell death while loss of either gene alone is viable.
tf-regulatory-prediction	TF Regulatory Network Prediction (ENCODE)	Binary classification	ROC-AUC	Predict transcription factor (TF) to target gene regulatory relationships using ENCODE-derived features.

Perturbation Dynamics

Task Folder	Task Title	Task Type	Evaluation Metric	Description
cancer-drug-sensitivity	Cancer Drug Sensitivity	Regression	Spearman Rank Correlation	Predict the sensitivity of cancer cell lines to drug compounds, measured as the natural log of the half-maximal inhibitory concentration (ln_ic50).
crispr-perturbation-prediction	CRISPR Perturbation Prediction	Multi-output regression	Mean Pearson Correlation	Predict the transcriptional response to CRISPR genetic perturbations.
drug-transcriptional-response	Drug Transcriptional Response	Multi-output regression	Mean Pearson Correlation	Predict the transcriptional response of cells to drug perturbations at specific doses and in specific cell lines.
eccite-multimodal-perturbation	ECCITE-seq Multimodal CRISPR Perturbation Response	Multi-output regression	Mean Pearson Correlation	Predict how a CRISPR perturbation changes both RNA and protein expression in single cells.
gene-regulatory-network-inference	Gene Regulatory Network Inference	Edge prediction	AUPRC	Infer gene regulatory edges from single-cell expression data and pseudotime information.
multi-timepoint-perturbation	Multi-Timepoint Perturbation	Multi-output regression	Mean Pearson Correlation	Predict time-resolved transcriptional responses to drug perturbations.
rna-velocity-cell-transition	RNA Velocity Cell Transition	Multi-output regression	Mean Pearson Correlation	Predict unspliced RNA counts from spliced RNA counts for individual cells.
spear-atac-perturbation	Spear-ATAC Chromatin Accessibility Perturbation Response	Multi-output regression	Mean Pearson Correlation	Predict how CRISPR perturbations alter chromatin accessibility profiles in single cells.

Phenotype Disease

Task Folder	Task Title	Task Type	Evaluation Metric	Description
alzheimers-disease-staging	Alzheimer's Disease Staging	Multi-class classification	Accuracy	Predict the Alzheimer's disease neuropathological change (ADNC) stage from single-nucleus gene expression profiles.
autism-diagnosis	Autism Spectrum Disorder Diagnosis (ABIDE)	Binary classification	ROC-AUC	Predict autism spectrum disorder (ASD) diagnosis from brain imaging quality metrics and phenotypic data.
breast-cancer-subtype	Breast Cancer Molecular Subtype Classification (METABRIC)	Multi-class classification	Macro F1	Predict the molecular subtype of breast cancer from clinical features and gene expression profiles.
covid19-severity-classification	COVID-19 Severity Classification	Multi-class classification	Macro F1	Predict the clinical severity of COVID-19 patients from single-cell RNA sequencing data.
diabetes-readmission	Diabetes Hospital Readmission Prediction	Multi-class classification	Macro F1	Predict whether a diabetes patient will be readmitted to the hospital within 30 days, after 30 days, or not at all.
genotype-to-phenotype	Genotype to Phenotype — Gene Expression Prediction	Regression	Pearson Correlation	Predict gene expression levels from genotype principal components and transcriptomic context.
pan-cancer-survival-prediction	Pan-Cancer Survival Prediction	Survival regression	Concordance Index	Predict patient survival risk scores from clinical and molecular features across 33 TCGA cancer types.
spatial-immune-infiltration	Spatial Immune Infiltration Prediction	Multi-output regression	Pearson Correlation	Predict the expression levels of six key immune marker genes at each spatial spot in breast cancer tissue sections.

Sequence

Task Folder	Task Title	Task Type	Evaluation Metric	Description
gene-tissue-expression	Gene Tissue Expression Prediction	Regression	Pearson Correlation	Predict gene expression levels across human tissues.
isoform-expression	RNA Isoform Expression Prediction	Multi-output regression	Mean Spearman Correlation	Predict transcript isoform expression levels across 30 human tissues.
multi-tf-binding	Multi-TF Binding Prediction	Binary classification	ROC-AUC	Predict whether a transcription factor (TF) binds to a given genomic region in a specific cell type.
protein-protein-interaction	Protein-Protein Interaction Prediction	Binary classification	ROC-AUC	Predict whether two proteins physically interact based on their amino acid sequences.
regulatory-element-detection	Regulatory Element Detection	Multi-class classification	Macro F1	Classify candidate cis-regulatory elements (cCREs) into functional categories based on their genomic coordinates.
remote-homology-detection	Remote Homology Similarity Prediction	Regression	Spearman Rank Correlation	Predict the structural similarity (TM-score) between pairs of protein domains based on their sequences.
rna-protein-binding-affinity	RNA-Protein Binding Affinity Prediction	Regression	Spearman Rank Correlation	Predict the binding affinity score between RNA sequences and RNA-binding proteins (RBPs) from RBNS (RNA Bind-n-Seq) experiments.
rna-protein-binding-signal	RNA-Protein Binding Signal Prediction	Regression	Spearman Rank Correlation	Predict the continuous eCLIP binding signal score for RNA-protein interactions.
rna-reactivity-imputation	RNA Reactivity Imputation	Multi-output regression	Mean Per-Sample Pearson Correlation	Impute missing RNA chemical reactivity values from partially observed icSHAPE in-vivo probing data.
variant-effect-pathogenicity	Variant Effect Pathogenicity Prediction	Multi-class classification	Macro F1	Predict the clinical pathogenicity of single nucleotide variants (SNVs).

Single Cell

Task Folder	Task Title	Task Type	Evaluation Metric	Description
batch-integration	Cross-Batch Cell Type Classification	Multi-class classification	Accuracy	Predict cell types for single cells from unseen batches.
cell-type-from-expression	Cell Type Prediction from Expression	Multi-class classification	Accuracy	Predict cell types from single-cell gene expression profiles in a tissue microenvironment context.
chromatin-to-expression	Chromatin to Gene Expression Prediction	Multi-output regression	Pearson Correlation	Predict gene expression (RNA) from chromatin accessibility (ATAC-seq) data at single-cell resolution.
cite-seq-protein-prediction	CITE-seq Protein Level Prediction	Multi-output regression	Pearson Correlation	Predict surface protein abundance (ADT counts) from gene expression (RNA) and protein amino acid sequences.
cross-modality-cell-matching	Cross-Modality Cell Matching	Matching	Accuracy	Match cells across two single-cell modalities: scRNA-seq (gene expression) and scATAC-seq (chromatin accessibility).
cross-modality-cell-type	Cross-Modality Cell Type Classification	Multi-class classification	Macro F1	Predict cell types from multi-modal single-cell data (CITE-seq).
developmental-stage-prediction	Developmental Stage Prediction	Multi-class classification	Accuracy	Predict the developmental stage of retinal cells after correcting for batch effects across different experimental conditions.
gene-expression-denoising	Gene Expression Denoising	Multi-output regression	Mean Pearson Correlation	Denoise single-cell RNA sequencing count data by recovering true gene expression levels from noisy, dropout-affected measurements.
label-projection	Cell Type Label Projection	Multi-class classification	Accuracy	Predict cell type labels for unseen cells using a labeled reference dataset.
rna-to-protein-prediction	RNA to Protein Level Prediction	Multi-output regression	Mean Pearson Correlation	Predict surface protein (ADT) levels from RNA gene expression.

Structure

Task Folder	Task Title	Task Type	Evaluation Metric	Description
complex-structure-evaluation	Complex Structure Evaluation	Regression	Spearman Correlation	Predict the quality of computationally modeled protein complex structures.
enzyme-commission-prediction	Enzyme Commission Prediction	Multi-class classification	Macro F1	Predict the primary Enzyme Commission (EC) class of a protein based on its sequence and structural features.
protein-binding-site-detection	Protein Binding Site Detection	Binary classification	AUPRC	Predict whether a protein chain has high binding-site density.
protein-fold-classification	Protein Fold Classification	Multi-class classification	Accuracy	Predict the structural fold class of a protein domain.
protein-ligand-binding-affinity	Protein-Ligand Binding Affinity	Regression	Pearson Correlation	Predict the binding affinity (pK value) of protein-ligand complexes.
protein-protein-interface	Protein-Protein Interface	Regression	Pearson Correlation	Predict the fraction of interface residues in a protein-protein complex.
protein-stability-change	Protein Stability Change	Regression	Spearman Correlation	Predict the change in thermodynamic stability (ddG) caused by single amino acid mutations in proteins.
protein-structure-prediction	Protein 3D Structure Prediction	Structure prediction	TM-score	Predict the 3D structure of a protein from its amino acid sequence.

Text Integrated

Task Folder	Task Title	Task Type	Evaluation Metric	Description
biomedical-figure-vqa	Biomedical Figure Visual Question Answering (PMC-VQA)	Multiple-choice VQA	Accuracy	Answer multiple-choice questions about biomedical figures extracted from PubMed Central (PMC) scientific articles.
dna-enzyme-function	DNA Enzyme Function Classification (BioTalk)	Multi-class classification	Accuracy	Predict the Enzyme Commission (EC) class for a gene given its DNA nucleotide sequence and contextual information.
ecg-signal-qa	ECG Signal Question Answering (ECG-QA)	Open-ended QA	Accuracy	Answer clinical questions about 12-lead electrocardiogram (ECG) recordings.
gene-expression-classification	Gene Expression Classification (CellWhisperer)	Binary classification	ROC-AUC	Determine whether a text description correctly matches a gene expression profile.
medical-vqa	Medical Visual Question Answering (SLAKE)	Open-ended VQA	Accuracy	Answer open-ended clinical questions about medical radiology images.
molecule-qa	Molecule Question Answering (MoleculeQA)	Multiple-choice QA	Accuracy	Answer multiple-choice questions about molecules given their SMILES (Simplified Molecular-Input Line-Entry System) representation.
pathology-vqa	Pathology Visual Question Answering (PathVQA)	Open-ended VQA	Accuracy	Answer questions about pathology images.
protein-function-matching	Protein-Function Text Matching (SwissProtCLAP)	Binary classification	ROC-AUC	Determine whether a protein amino acid sequence matches a given functional text description.

How To Use

1. Choose a task under a domain.
2. Open that task's public/ directory.
3. Read public/description.md first.
4. Load the task-specific public inputs from the same public/ directory.
5. Generate predictions following public/sample_submission.csv.

Notes

• Public artifacts are heterogeneous across tasks. Depending on the task, public/ may contain tables, images, compressed arrays, single-cell objects, sequence files, or other modality-specific assets.
• The exact input and output expectations are task-specific, so description.md is the authoritative entry point for each task.