bio
Datasets
All datasets matching “bio”CVPR-BiomedSegFMThis repository contains the BiomedSegFM dataset, a crucial resource for the CVPR 2025 Competition: Foundation Models for 3D Biomedical Image Segmentation.
Foundation Models for Interactive 3D Biomedical Image Segmentation (Homepage)
Foundation Models for Text-guided 3D Biomedical Image Segmentation (Homepage)
CVPR 2025 Competition: Foundation Models for 3D Biomedical Image Segmentation
Highly recommend watching the webinar recording to learn about the task settings and… See the full description on the dataset page: https://huggingface.co/datasets/junma/CVPR-BiomedSegFM.BioMysteryBench-preview
BioMysteryBench (preview)
A 5-problem preview of BioMysteryBench,
a bioinformatics research benchmark created by Anthropic. Each problem
provides anonymized biological data files and asks a question that requires
real analysis to answer — the source dataset cannot be looked up.
v11 (2026-07): preview refreshed — hb022 and hb053 were removed from the
benchmark; hb024 and hb035 replace them here. See CHANGELOG.md.
Contents
problems.csv / problems.parquet — one row… See the full description on the dataset page: https://huggingface.co/datasets/Anthropic/BioMysteryBench-preview.biosses-sts
BIOSSES
An MTEB dataset
Massive Text Embedding Benchmark
Biomedical Semantic Similarity Estimation.
Task category
t2t
Domains
Medical
Reference
https://tabilab.cmpe.boun.edu.tr/BIOSSES/DataSet.html
How to evaluate on this task
You can evaluate an embedding model on this dataset using the following code:
import mteb
task = mteb.get_tasks(["BIOSSES"])
evaluator = mteb.MTEB(task)
model = mteb.get_model(YOUR_MODEL)
evaluator.run(model)
To learn more… See the full description on the dataset page: https://huggingface.co/datasets/mteb/biosses-sts.bio-mqm-datasetThis dataset is compiled from the official Amazon repository (all respective licensing applies).
It contains system translations, multiple references, and their quality evaluation on the MQM scale. It accompanies the ACL 2024 paper Fine-Tuned Machine Translation Metrics Struggle in Unseen Domains.
Watch a brief 4 minutes-long video.
Abstract: We introduce a new, extensive multidimensional quality metrics (MQM) annotated dataset covering 11 language pairs in the biomedical domain. We use this… See the full description on the dataset page: https://huggingface.co/datasets/zouhar/bio-mqm-dataset.BioMysteryBench-full
BioMysteryBench (full set)
90 mystery-bioinformatics problems. Each problem provides anonymized
biological data files and asks a question that requires real analysis
(alignment, expression, variant calling, motif discovery, structure, etc.)
to answer — the source dataset cannot be looked up.
v11 (2026-07): 9 problems removed and 24 problems edited after an
answer-key audit — see CHANGELOG.md.
Contents
problems.csv / problems.parquet — one row per problem:
id —… See the full description on the dataset page: https://huggingface.co/datasets/Anthropic/BioMysteryBench-full.biomedica_webdataset_24M
Dataset Card for Dataset Name
Arxiv: Arxiv
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Website: Biomedica
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Training instructions: OpenCLIP
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Tutorial: Google Colab
BIOMEDICA Dataset is a large-scale, deep-learning-ready biomedical dataset containing over 24M imagecaption pairs and 30M image-references from 6M unique open-source articles. Each… See the full description on the dataset page: https://huggingface.co/datasets/BIOMEDICA/biomedica_webdataset_24M.