Datasets:

TabBioMed
/

avida_htnfa_esm2

license: cc-by-4.0
pretty_name: avida_htnfa_esm2
task_categories:
  - tabular-classification
tags:
  - tabular
  - biomedical
  - benchmark
  - TabBioMed
  - proteomics
  - binary
size_categories:
  - 1K<n<10K
configs:
  - config_name: default
    data_files:
      - split: train
        path: data/train.parquet
      - split: validation
        path: data/val.parquet
      - split: test
        path: data/test.parquet

avida_htnfa_esm2

Part of TabBioMed (TabBioMed: A Large-Scale Benchmark for Biomedical Tabular Learning), a benchmark of 94 curated biomedical tabular datasets. Code, preprocessing and documentation: https://github.com/AI-sandbox/TabBioMed.

Binary classification: predict VHH nanobody binding to hTNFa. Single antigen — antigen features omitted. Features: mean-pooled ESM-2 (esm2_t12_35M_UR50D) embeddings of VHH sequence. Split: CD-HIT families (identity 0.8, coverage 0.8, on the VHH core without the constant leader and His-tag) assigned to train/val/test 70/15/15 by a label-balanced local search (partition sizes and val/test positive rates matched to the overall data); VHH families never span splits.

Domain	Task	Samples	Features	Classes
Proteomics	binary	5,580	480	2

Splits. Fixed train/val/test split (3910/835/835 rows).

Files

data/**.parquet: one row per sample. row_idx is the row index in the original TabBioMed array; f_<i>[_<name>] are the features (in order); target (or target_<j> for multi-target tasks) is the label. Categorical feature indices (0-based, among the features): []. Missing values are stored as nulls.
metadata.json: TabBioMed task metadata (task type, categorical indices, source, description).

from datasets import load_dataset
ds = load_dataset("TabBioMed/avida_htnfa_esm2")

A Croissant (1.1) description with Responsible-AI fields is distributed with the TabBioMed release.

Source and license

Source: COGNANO AVIDa datasets (HuggingFace: cognano/AVIDa-hIL6, cognano/AVIDa-hTNFa, cognano/AVIDa-SARS-CoV-2). VHH (nanobody) sequences with binary binding labels against antigen variants.

This derived dataset is distributed under CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/). Please also cite and respect the terms of the original source.

Citation

@inproceedings{tabbiomed2026,
  title     = {TabBioMed: A Large-Scale Benchmark for Biomedical Tabular Learning},
  author    = {Mateo Bernad{\'o}, Pau and Polapragada, Saivenkata Nagavyjayanthi and Bonet, David and Arbiol Rakuljic, Pol and Mogas Pladevall, Laia and Comajoan Cara, Mar{\c{c}}al and Gonzalez Ferrer, Jesus and Abante, Jordi and Mas Montserrat, Daniel and Haussler, David and Ioannidis, Alexander G.},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS), Evaluations and Datasets Track},
  year      = {2026}
}