---
language: en
license: apache-2.0
tags:
  - bioasq
  - biomedical
  - reranking
  - information-retrieval
---

# BioASQ Phase A Reranker Models

Fine-tuned rerankers for biomedical document retrieval, trained on BioASQ data.
All models are cross-encoders fine-tuned from publicly available base models.

## Loading a model

```python
from transformers import AutoTokenizer, AutoModelForSequenceClassification

subfolder = "nvidia-llama-nemotron-rerank-1b-v2-E2-S4-Mmulti_neg_pairwise-Linfonce-FullData"
tokenizer = AutoTokenizer.from_pretrained("IEETA/BioASQ-14B", subfolder=subfolder)
model = AutoModelForSequenceClassification.from_pretrained("IEETA/BioASQ-14B", subfolder=subfolder)
```

For nvidia/llama-nemotron variants, also copy `llama_bidirectional_model.py` from the subfolder
and pass `trust_remote_code=True`.

---

## outputs-E5-Pairwise — Shifter sampler, 5 epochs, pairwise

| Model | Path | map-bioasq@10 |
|---|---|---|
| nvidia/llama-nemotron-rerank-1b-v2 | `nvidia-llama-nemotron-rerank-1b-v2-E5-Pairwise` | 0.9970 |
| BAAI/bge-reranker-v2-m3 | `BAAI-bge-reranker-v2-m3-E5-Pairwise` | 0.6824 |
| BAAI/bge-reranker-base | `BAAI-bge-reranker-base-E5-Pairwise` | 0.6686 |
| nboost/pt-biobert-base-msmarco | `nboost-pt-biobert-base-msmarco-E5-Pairwise` | 0.6608 |
| cross-encoder/ms-marco-MiniLM-L-6-v2 | `cross-encoder-ms-marco-MiniLM-L-6-v2-E5-Pairwise` | 0.6373 |
| ncbi/MedCPT-Cross-Encoder | `ncbi-MedCPT-Cross-Encoder-E5-Pairwise` | 0.6404 |
| michiyasunaga/BioLinkBERT-base | `michiyasunaga-BioLinkBERT-base-E5-Pairwise` | 0.6403 |
| monologg/biobert_v1.1_pubmed | `monologg-biobert_v1.1_pubmed-E5-Pairwise` | 0.6346 |
| microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext | `microsoft-BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext-E5-Pairwise` | 0.6291 |
| pritamdeka/S-PubMedBert-MS-MARCO | `pritamdeka-S-PubMedBert-MS-MARCO-E5-Pairwise` | 0.5985 |
| allenai/specter2_base | `allenai-specter2_base-E5-Pairwise` | 0.5912 |
| dmis-lab/biobert-base-cased-v1.2 | `dmis-lab-biobert-base-cased-v1.2-E5-Pairwise` | 0.5848 |
| cross-encoder/ms-marco-electra-base | `cross-encoder-ms-marco-electra-base-E5-Pairwise` | 0.5654 |
| emilyalsentzer/Bio_ClinicalBERT | `emilyalsentzer-Bio_ClinicalBERT-E5-Pairwise` | 0.4587 |
| cambridgeltl/SapBERT-from-PubMedBERT-fulltext | `cambridgeltl-SapBERT-from-PubMedBERT-fulltext-E5-Pairwise` | 0.2594 |

---

## outputs — Experiments

| Model | Characteristics | Path | map-bioasq@10 |
|---|---|---|---|
| nvidia/llama-nemotron-rerank-1b-v2 | E2-S4, multi_neg_pairwise, InfoNCE, FullData | `nvidia-llama-nemotron-rerank-1b-v2-E2-S4-Mmulti_neg_pairwise-Linfonce-FullData` | 0.9995 |
| nvidia/llama-nemotron-rerank-1b-v2 | E2, pairwise (13B1+13B2) | `nvidia-llama-nemotron-rerank-1b-v2_llama-E2-Pairwise` | 0.9970 |
| BAAI/bge-reranker-v2-m3 | E2-S1, pairwise, FullData, shifter | `BAAI-bge-reranker-v2-m3-E2-S1-Mpairwise-FullDataTrue` | 0.6705 |
| BAAI/bge-reranker-base | E2-S1, pairwise, FullData, shifter | `BAAI-bge-reranker-base-E2-S1-Mpairwise-FullDataTrue` | 0.6489 |
| nboost/pt-biobert-base-msmarco | E2-S1, pairwise, FullData, shifter | `nboost-pt-biobert-base-msmarco-E2-S1-Mpairwise-FullDataTrue` | 0.6274 |
| ncbi/MedCPT-Cross-Encoder | E2-S1, pairwise, FullData, shifter | `ncbi-MedCPT-Cross-Encoder-E2-S1-Mpairwise-FullDataTrue` | 0.6251 |
| michiyasunaga/BioLinkBERT-base | E2-S1, pairwise, FullData, shifter | `michiyasunaga-BioLinkBERT-base-E2-S1-Mpairwise-FullDataTrue` | 0.6178 |
| microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext | E2-S1, pairwise, FullData, shifter | `microsoft-BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext-E2-S1-Mpairwise-FullDataTrue` | 0.6153 |
| cross-encoder/ms-marco-MiniLM-L-6-v2 | E3-S8, multi_neg_pairwise | `cross-encoder-ms-marco-MiniLM-L-6-v2-E3-S8-Mmulti_neg_pairwise` | 0.6098 |
| monologg/biobert_v1.1_pubmed | E2-S1, pairwise, FullData, shifter | `monologg-biobert_v1.1_pubmed-E2-S1-Mpairwise-FullDataTrue` | 0.6053 |
| cross-encoder/ms-marco-MiniLM-L-6-v2 | E2-S1, pairwise, FullData, shifter | `cross-encoder-ms-marco-MiniLM-L-6-v2-E2-S1-Mpairwise-FullDataTrue` | 0.5944 |
| pritamdeka/S-PubMedBert-MS-MARCO | E2-S1, pairwise, FullData, shifter | `pritamdeka-S-PubMedBert-MS-MARCO-E2-S1-Mpairwise-FullDataTrue` | 0.5839 |
| michiyasunaga/BioLinkBERT-large | E2-S1, pairwise, FullData, shifter | `michiyasunaga-BioLinkBERT-large-E2-S1-Mpairwise-FullDataTrue` | 0.5781 |
| ncbi/MedCPT-Cross-Encoder | E3-S1, pairwise, FullData, shifter | `ncbi-MedCPT-Cross-Encoder-E3-S1-Mpairwise-FullDataTrue` | 0.5766 |