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@@ -231,21 +231,21 @@ Finally, wait for the progress bar completed, and the fine-tuned model will be s
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To use a fine-tuned model for inference, please first download the desired models from [HuggingFace](https://huggingface.co/zhangtaolab) or [ModelScope](https://www.modelscope.cn/organization/zhangtaolab) to local or provide a model trained by yourself.
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* Here is the [finetune models list](docs/en/resources/finetune_models.md)
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* Here is the recommended models for different genomic tasks
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| Genomic task | Recommended model | Accuracy | F1 | AUROC | R2 | Link |
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| ------------------------------ | ------------------------- | -------- | ------ | ------ | ----- | ---- |
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| Core promoters | Plant DNAGPT 6mer | 0.8946 | 0.8961 | - | - | [Huggingface](https://huggingface.co/zhangtaolab/plant-dnagpt-6mer-promoter) / [Modelscope](https://modelscope.cn/models/zhangtaolab/plant-dnagpt-6mer-promoter) |
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| Sequence conservation | Plant DNAMamba 6mer | 0.9053 | 0.9055 | - | - | [Huggingface](https://huggingface.co/zhangtaolab/plant-dnamamba-6mer-conservation) / [Modelscope](https://modelscope.cn/models/zhangtaolab/plant-dnamamba-6mer-conservation) |
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| H3K27ac | Plant DNAMamba 6mer | 0.8135 | 0.8165 | - | - | [Huggingface](https://huggingface.co/zhangtaolab/plant-dnamamba-6mer-H3K27ac) / [Modelscope](https://modelscope.cn/models/zhangtaolab/plant-dnamamba-6mer-H3K27ac) |
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| H3K27me3 | Plant DNAMamba 4mer | 0.7757 | 0.7843 | - | - | [Huggingface](https://huggingface.co/zhangtaolab/plant-dnamamba-4mer-H3K27me3) / [Modelscope](https://modelscope.cn/models/zhangtaolab/plant-dnamamba-4mer-H3K27me3) |
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| H3K4me3 | Plant DNAMamba 5mer | 0.8996 | 0.8991 | - | - | [Huggingface](https://huggingface.co/zhangtaolab/plant-dnamamba-5mer-H3K4me3) / [Modelscope](https://modelscope.cn/models/zhangtaolab/plant-dnamamba-5mer-H3K4me3) |
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| lncRNAs | Plant DNAGemma 6mer | 0.8571 | 0.8821 | - | - | [Huggingface](https://huggingface.co/zhangtaolab/plant-dnagemma-6mer-lncRNAs) / [Modelscope](https://modelscope.cn/models/zhangtaolab/plant-dnagemma-6mer-lncRNAs) |
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| Open chromatin | Plant DNAMamba BPE | - | 0.6413 | 0.8177 | - | [Huggingface](https://huggingface.co/zhangtaolab/plant-dnamamba-BPE-open_chromatin) / [Modelscope](https://modelscope.cn/models/zhangtaolab/plant-dnamamba-BPE-open_chromatin) |
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| Promoter strength (leaf) | Plant NT singlebase | - | - | - | 0.768 | [Huggingface](https://huggingface.co/zhangtaolab/plant-nucleotide-transformer-singlebase-promoter_strength_leaf) / [Modelscope](https://modelscope.cn/models/zhangtaolab/plant-nucleotide-transformer-singlebase-promoter_strength_leaf) |
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| Promoter strength (protoplast) | Plant DNAGemma singlebase | - | - | - | 0.721 | [Huggingface](https://huggingface.co/zhangtaolab/plant-dnagemma-singlebase-promoter_strength_protoplast) / [Modelscope](https://modelscope.cn/models/zhangtaolab/plant-dnagemma-singlebase-promoter_strength_protoplast) |
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| Genomic task | Recommended model | Link |
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| ------------------------------ | ------------------------- | ---- |
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| Core promoters | Plant DNAGPT 6mer | [Huggingface](https://huggingface.co/zhangtaolab/plant-dnagpt-6mer-promoter) / [Modelscope](https://modelscope.cn/models/zhangtaolab/plant-dnagpt-6mer-promoter) |
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| Sequence conservation | Plant DNAMamba 6mer | [Huggingface](https://huggingface.co/zhangtaolab/plant-dnamamba-6mer-conservation) / [Modelscope](https://modelscope.cn/models/zhangtaolab/plant-dnamamba-6mer-conservation) |
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| H3K27ac | Plant DNAMamba 6mer | [Huggingface](https://huggingface.co/zhangtaolab/plant-dnamamba-6mer-H3K27ac) / [Modelscope](https://modelscope.cn/models/zhangtaolab/plant-dnamamba-6mer-H3K27ac) |
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| H3K27me3 | Plant DNAMamba 4mer | [Huggingface](https://huggingface.co/zhangtaolab/plant-dnamamba-4mer-H3K27me3) / [Modelscope](https://modelscope.cn/models/zhangtaolab/plant-dnamamba-4mer-H3K27me3) |
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| H3K4me3 | Plant DNAMamba 5mer | [Huggingface](https://huggingface.co/zhangtaolab/plant-dnamamba-5mer-H3K4me3) / [Modelscope](https://modelscope.cn/models/zhangtaolab/plant-dnamamba-5mer-H3K4me3) |
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| lncRNAs | Plant DNAGemma 6mer | [Huggingface](https://huggingface.co/zhangtaolab/plant-dnagemma-6mer-lncRNAs) / [Modelscope](https://modelscope.cn/models/zhangtaolab/plant-dnagemma-6mer-lncRNAs) |
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| Open chromatin | Plant DNAMamba BPE | [Huggingface](https://huggingface.co/zhangtaolab/plant-dnamamba-BPE-open_chromatin) / [Modelscope](https://modelscope.cn/models/zhangtaolab/plant-dnamamba-BPE-open_chromatin) |
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| Promoter strength (leaf) | Plant NT singlebase | [Huggingface](https://huggingface.co/zhangtaolab/plant-nucleotide-transformer-singlebase-promoter_strength_leaf) / [Modelscope](https://modelscope.cn/models/zhangtaolab/plant-nucleotide-transformer-singlebase-promoter_strength_leaf) |
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| Promoter strength (protoplast) | Plant DNAGemma singlebase | [Huggingface](https://huggingface.co/zhangtaolab/plant-dnagemma-singlebase-promoter_strength_protoplast) / [Modelscope](https://modelscope.cn/models/zhangtaolab/plant-dnagemma-singlebase-promoter_strength_protoplast) |
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* All the [finetune models list](docs/en/resources/finetune_models.md)
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We use Plant DNAGPT model as example to predict active core promoter in plants.
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