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Open-weight model · Text classification

bionerd-re

by Joshy Alphonse joshyalphonse/bionerd-re

bionerd-re is an open-weight model for text classification from Joshy Alphonse, released under MIT License. It has 109M parameters and a 512-token context. At 16-bit it needs about 0.3 GB of GPU memory, which fits on 1x MI300X from $1.85 an hour, at the lowest prices in the SAVRN Index. It draws 55 downloads a month.

BioNERD's own typed relation-extraction model "C": microsoft/BiomedNLP-BiomedBERT-base-uncased-abstract-fulltext (MIT) fine-tuned on the BioRED Train split (public domain) as an entity-marker sequence classifier. No accuracy is claimed here.

Parameters109M
Context512
Weights1.6 GB
Licensemit
AccessOpen weights
Monthly Downloads55

Runs On

What it takes to serve bionerd-re (109M parameters): the memory its weights need at each precision, and the cheapest way to rent enough data-center GPUs to hold them.

PrecisionWeightsMemory neededCheapest setupPer hourAlso fits
16-bit 0.2 GB 0.3 GB 1x MI300X (192 GB)
Vultr
$1.85 1x H100 $1.99 · 1x MI325X $2.00
8-bit 0.1 GB 0.1 GB 1x MI300X (192 GB)
Vultr
$1.85 1x H100 $1.99 · 1x MI325X $2.00
4-bit 0.1 GB 0.1 GB 1x MI300X (192 GB)
Vultr
$1.85 1x H100 $1.99 · 1x MI325X $2.00

Memory is the weights at that precision plus 20% for the runtime and a short context; a long context needs more. Prices are the lowest on-demand hourly rates in the SAVRN Index, read Oct 9, 2026.

bionerd-re on every accelerator the SAVRN Index prices, at every precision

Model Card

By Joshy Alphonse, published under mit, revision 94503c5b79f7.

BioNERD's own typed relation-extraction model "C": microsoft/BiomedNLP-BiomedBERT-base-uncased-abstract-fulltext (MIT) fine-tuned on the BioRED Train split (public domain) as an entity-marker sequence classifier. No accuracy is claimed here. BioNERD shows its measured labels in the app's model catalog, each tied to this exact artefact.

Read Joshy Alphonse's full model card

bionerd-re — C (BiomedBERT, BioRED typed relations)

BioNERD's own typed relation-extraction model "C": microsoft/BiomedNLP-BiomedBERT-base-uncased-abstract-fulltext (MIT) fine-tuned on the BioRED Train split (public domain) as an entity-marker sequence classifier.

  • Input: text with [E1] … [/E1] and [E2] … [/E2] around the two arguments (the four marker tokens are in the tokenizer).
  • Labels: 0 = None, then BioRED's eight types in this order: Association, Positive_Correlation, Negative_Correlation, Bind, Cotreatment, Comparison, Drug_Interaction, Conversion.
  • Training: seed 13, lr 2e-5, batch 16, up to 5 epochs, max length 512, 2 negatives per positive; the best epoch on BioRED Dev typed F1 was kept.

No accuracy is claimed here. BioNERD shows its measured labels in the app's model catalog, each tied to this exact artefact.

File sha256
config.json 6ac24d941178b632550aa2cb2c81594b9c88463bea01c32c5712064afbb23732
model.safetensors 7a96681585571fa82910d3e547bd71ff83eb5285c0859a37ae272116bbcca598
tokenizer_config.json 8b1605c818426817b2b46a1dbf23e834c7fc893a1a04cbda394382d719cb553a
tokenizer.json 8c801ddf1fd1e9591578b90b7e3fa2bc895d80af941ae967f1f1869ea75aaca4

Configuration

Architecture
BertForSequenceClassification
Context length (tokens)
512
Layers
12
Hidden size
768
Feed-forward size
3,072
Attention heads
12
Vocabulary size
30,526
Model type
bert

Identity and Version

Repository
joshyalphonse/bionerd-re
Publisher
Joshy Alphonse
Task
Text classification
Modality
Text
Library
transformers
Parameters
109M parameters
Languages
Not stated by the source
Revision
94503c5b79f76ae2e5115a1c76d1a116489494a6
First published
2026-10-04
Last updated
2026-10-09

Files and Weights

30 files, 1.6 GB in total. The weights are 5 files totalling 1.6 GB in gguf, safetensors.

Weights5 files · 1.6 GB
Configuration10 files · 27.4 KB
Tokenizer7 files · 1.9 MB
Documentation7 files · 24.7 KB
Repository1 file · 1.7 KB
Every file
FileTypeSizeSHA-256
bioredirect/bioredirect.safetensorsWeights440.7 MB 2c233a318c8c
biorex/model.safetensorsWeights433.2 MB 64526a02797f
lora-qwen3-8b/qwen3-8b-re-lora.ggufWeights87.3 MB 7842b213330b
lora-qwen36-27b/qwen3.6-27b-re-lora.ggufWeights216.2 MB 299cd7ec7711
model.safetensorsWeights438.0 MB 7a9668158557
bioredirect/added_tokens.jsonConfiguration1.4 KB —
bioredirect/bioredirect.jsonConfiguration604 B —
bioredirect/config.jsonConfiguration3.0 KB —
bioredirect/special_tokens_map.jsonConfiguration8.0 KB —
biorex/added_tokens.jsonConfiguration1.0 KB —
biorex/config.jsonConfiguration3.0 KB —
biorex/special_tokens_map.jsonConfiguration920 B —
config.jsonConfiguration1.1 KB —
lora-qwen3-8b/manifest.jsonConfiguration3.0 KB —
lora-qwen36-27b/manifest.jsonConfiguration5.3 KB —
README.mdDocumentation1.5 KB —
bioredirect/LICENSE-BioLinkBERT-Apache-2.0.txtDocumentation11.4 KB —
bioredirect/NOTICE.mdDocumentation2.8 KB —
biorex/LICENSE-BiomedBERT-MIT.txtDocumentation1.1 KB —
biorex/NOTICE.mdDocumentation3.8 KB —
lora-qwen3-8b/README.mdDocumentation1.6 KB —
lora-qwen36-27b/README.mdDocumentation2.5 KB —
.gitattributesRepository1.7 KB —
bioredirect/tokenizer_config.jsonTokenizer11.2 KB —
bioredirect/vocab.txtTokenizer254.0 KB —
biorex/tokenizer.jsonTokenizer686.5 KB —
biorex/tokenizer_config.jsonTokenizer1.2 KB —
biorex/vocab.txtTokenizer254.0 KB —
tokenizer.jsonTokenizer707.0 KB —
tokenizer_config.jsonTokenizer460 B —

License and Download

License
mit
Access
Open weights, no gate
Download size
1.6 GB
Download from Joshy Alphonse

Released by Joshy Alphonse through its official repository on Hugging Face. Read the license.

Built From

Memory Requirements

PrecisionWeights in memory
As published1.6 GB
16-bit0.2 GB
8-bit0.1 GB
4-bit0.1 GB

Weights only, from the published parameter count; the key-value cache and runtime add to this.

Questions About bionerd-re

How much GPU memory does bionerd-re need?

About 0.3 GB at 16-bit and 0.1 GB at 4-bit: the weights (109M parameters) plus a working margin. A long context needs more.

What is the cheapest GPU to run bionerd-re on?

At 16-bit, 1x MI300X from $1.85 an hour; at 4-bit, 1x MI300X from $1.85 an hour, at the lowest on-demand prices the SAVRN Index lists.

Can I use bionerd-re commercially?

Yes. bionerd-re is released under MIT License. The MIT License is a short permissive license. It permits commercial use, modification and redistribution, provided the copyright notice and permission notice are included.

What is bionerd-re's context length?

512 tokens, from the maximum position embeddings in its published configuration.

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