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PlantHelixSeek-H3K4me3
zhangtaolab/PlantHelixSeek-H3K4me3
PlantHelixSeek-H3K4me3 is a text classification model from zhangtaolab. Use it when you need a label for a piece of text. It is set up for transformers. The card lists the license as cc-by-nc-4.0.
Fine-tuned checkpoint of PlantHelixSeek (470M parameters) for binary classification of H3K4me3.
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At a glance
- Task
- Text Classification
- Library
- transformers
- License
- cc-by-nc-4.0
- Model type
- HelixSeek
- Access
- Public
- Created
- Jul 19, 2026
- Updated
- Nov 5, 2026
- SHA
- 64c68168
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Base models
Model card
From the Hugging Face model README
PlantHelixSeek-H3K4me3
Fine-tuned checkpoint of PlantHelixSeek (470M parameters) for binary classification of H3K4me3.
Task
- Type: binary classification of H3K4me3
- Label: 0 = no mark, 1 = mark present
- Input length: up to 2,000 bp
- Dataset: plant-multi-species-histone-modifications
Dataset and splits
The checkpoint uses the released train.csv, dev.csv and test.csv splits of plant-multi-species-histone-modifications (81,920 / 10,240 / 10,240 sequences). The source of the dataset is described on its dataset card.
Training
| Setting | Value |
|---|---|
| Base model | PlantHelixSeek-470M |
| Epochs | 3 |
| Learning rate | 2e-5 |
| Per-device batch size | 1 |
| Gradient accumulation | 16 |
| Effective batch size | 16 |
| Warm-up ratio | 0.1 |
| Weight decay | 0.01 |
| Scheduler | linear |
| Optimizer | AdamW (fused) |
| Precision | bf16 |
| Gradient clipping | 1.0 |
| Seed | 42 |
| Hardware | one NVIDIA GPU |
| Training loss | 0.207 |
| Training time | 3.6 h |
Held-out validation metrics
Metrics on the held-out dev.csv split (the split used for checkpoint selection).
| Metric | Value |
|---|---|
| f1 | 0.910 |
| AUROC | 0.970 |
| AUPRC | 0.972 |
| mcc | 0.821 |
| accuracy | 0.910 |
Usage
from transformers import AutoModelForSequenceClassification, AutoTokenizer
model = AutoModelForSequenceClassification.from_pretrained(
"zhangtaolab/PlantHelixSeek-H3K4me3", trust_remote_code=True
)
tokenizer = AutoTokenizer.from_pretrained(
"zhangtaolab/PlantHelixSeek-H3K4me3", trust_remote_code=True
)
Always pass trust_remote_code=True; the HelixSeek architecture is registered through the Hugging Face auto_map mechanism.
Citation
Wu Y, He Y, Chen L, Liu Y, Wang T, Zhao H, Zhang Y, Zhang T. PlantHelixSeek learns transferable genome representations that capture conserved genome grammar for functional interpretation across plant species. Molecular Plant, 2026. Manuscript MOLECULAR-PLANT-D-26-00999 (DOI to be assigned).
Dataset source: Liu et al., Molecular Plant 2025.
License
CC-BY-NC 4.0 (research use; contact the authors for commercial licensing).
- Task
- Text Classification
- Library
- transformers
- Type
- HelixSeek
- License
- cc-by-nc-4.0
- Created
- Jul 19, 2026
- Updated
- Nov 5, 2026