BIOSSES
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:
```python
import mteb
task = mteb.get_tasks(["BIOSSES"])
evaluator = mteb.MTEB(task)
model = mteb.get_model(YOUR_MODEL)
evaluator.run(model)
```
To learn more about how to run models on `mteb` task check out the [GitHub repitory](https://github.com/embeddings-benchmark/mteb).
## Citation
If you use this dataset, please cite the dataset as well as [mteb](https://github.com/embeddings-benchmark/mteb), as this dataset likely includes additional processing as a part of the [MMTEB Contribution](https://github.com/embeddings-benchmark/mteb/tree/main/docs/mmteb).
```bibtex
@article{10.1093/bioinformatics/btx238,
abstract = {{The amount of information available in textual format is rapidly increasing in the biomedical domain. Therefore, natural language processing (NLP) applications are becoming increasingly important to facilitate the retrieval and analysis of these data. Computing the semantic similarity between sentences is an important component in many NLP tasks including text retrieval and summarization. A number of approaches have been proposed for semantic sentence similarity estimation for generic English. However, our experiments showed that such approaches do not effectively cover biomedical knowledge and produce poor results for biomedical text.We propose several approaches for sentence-level semantic similarity computation in the biomedical domain, including string similarity measures and measures based on the distributed vector representations of sentences learned in an unsupervised manner from a large biomedical corpus. In addition, ontology-based approaches are presented that utilize general and domain-specific ontologies. Finally, a supervised regression based model is developed that effectively combines the different similarity computation metrics. A benchmark data set consisting of 100 sentence pairs from the biomedical literature is manually annotated by five human experts and used for evaluating the proposed methods.The experiments showed that the supervised semantic sentence similarity computation approach obtained the best performance (0.836 correlation with gold standard human annotations) and improved over the state-of-the-art domain-independent systems up to 42.6\\% in terms of the Pearson correlation metric.A web-based system for biomedical semantic sentence similarity computation, the source code, and the annotated benchmark data set are available at: http://tabilab.cmpe.boun.edu.tr/BIOSSES/.}},
author = {Soğancıoğlu, Gizem and Öztürk, Hakime and Özgür, Arzucan},
doi = {10.1093/bioinformatics/btx238},
eprint = {https://academic.oup.com/bioinformatics/article-pdf/33/14/i49/50315066/bioinformatics\_33\_14\_i49.pdf},
issn = {1367-4803},
journal = {Bioinformatics},
month = {07},
number = {14},
pages = {i49-i58},
title = {{BIOSSES: a semantic sentence similarity estimation system for the biomedical domain}},
url = {https://doi.org/10.1093/bioinformatics/btx238},
volume = {33},
year = {2017},
}
@article{enevoldsen2025mmtebmassivemultilingualtext,
title={MMTEB: Massive Multilingual Text Embedding Benchmark},
author={Kenneth Enevoldsen and Isaac Chung and Imene Kerboua and Márton Kardos and Ashwin Mathur and David Stap and Jay Gala and Wissam Siblini and Dominik Krzemiński and Genta Indra Winata and Saba Sturua and Saiteja Utpala and Mathieu Ciancone and Marion Schaeffer and Gabriel Sequeira and Diganta Misra and Shreeya Dhakal and Jonathan Rystrøm and Roman Solomatin and Ömer Çağatan and Akash Kundu and Martin Bernstorff and Shitao Xiao and Akshita Sukhlecha and Bhavish Pahwa and Rafał Poświata and Kranthi Kiran GV and Shawon Ashraf and Daniel Auras and Björn Plüster and Jan Philipp Harries and Loïc Magne and Isabelle Mohr and Mariya Hendriksen and Dawei Zhu and Hippolyte Gisserot-Boukhlef and Tom Aarsen and Jan Kostkan and Konrad Wojtasik and Taemin Lee and Marek Šuppa and Crystina Zhang and Roberta Rocca and Mohammed Hamdy and Andrianos Michail and John Yang and Manuel Faysse and Aleksei Vatolin and Nandan Thakur and Manan Dey and Dipam Vasani and Pranjal Chitale and Simone Tedeschi and Nguyen Tai and Artem Snegirev and Michael Günther and Mengzhou Xia and Weijia Shi and Xing Han Lù and Jordan Clive and Gayatri Krishnakumar and Anna Maksimova and Silvan Wehrli and Maria Tikhonova and Henil Panchal and Aleksandr Abramov and Malte Ostendorff and Zheng Liu and Simon Clematide and Lester James Miranda and Alena Fenogenova and Guangyu Song and Ruqiya Bin Safi and Wen-Ding Li and Alessia Borghini and Federico Cassano and Hongjin Su and Jimmy Lin and Howard Yen and Lasse Hansen and Sara Hooker and Chenghao Xiao and Vaibhav Adlakha and Orion Weller and Siva Reddy and Niklas Muennighoff},
publisher = {arXiv},
journal={arXiv preprint arXiv:2502.13595},
year={2025},
url={https://arxiv.org/abs/2502.13595},
doi = {10.48550/arXiv.2502.13595},
}
@article{muennighoff2022mteb,
author = {Muennighoff, Niklas and Tazi, Nouamane and Magne, Lo{\"\i}c and Reimers, Nils},
title = {MTEB: Massive Text Embedding Benchmark},
publisher = {arXiv},
journal={arXiv preprint arXiv:2210.07316},
year = {2022}
url = {https://arxiv.org/abs/2210.07316},
doi = {10.48550/ARXIV.2210.07316},
}
```
# Dataset Statistics