@@ -231,21 +231,21 @@ Finally, wait for the progress bar completed, and the fine-tuned model will be s
231231
232232To 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.
233233
234- * Here is the [ finetune models list] ( docs/en/resources/finetune_models.md )
235-
236234* Here is the recommended models for different genomic tasks
237235
238- | Genomic task | Recommended model | Accuracy | F1 | AUROC | R2 | Link |
239- | ------------------------------ | ------------------------- | -------- | ------ | ------ | ----- | ---- |
240- | 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 ) |
241- | 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 ) |
242- | 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 ) |
243- | 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 ) |
244- | 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 ) |
245- | 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 ) |
246- | 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 ) |
247- | 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 ) |
248- | 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 ) |
236+ | Genomic task | Recommended model | Link |
237+ | ------------------------------ | ------------------------- | ---- |
238+ | Core promoters | Plant DNAGPT 6mer | [ Huggingface] ( https://huggingface.co/zhangtaolab/plant-dnagpt-6mer-promoter ) / [ Modelscope] ( https://modelscope.cn/models/zhangtaolab/plant-dnagpt-6mer-promoter ) |
239+ | Sequence conservation | Plant DNAMamba 6mer | [ Huggingface] ( https://huggingface.co/zhangtaolab/plant-dnamamba-6mer-conservation ) / [ Modelscope] ( https://modelscope.cn/models/zhangtaolab/plant-dnamamba-6mer-conservation ) |
240+ | H3K27ac | Plant DNAMamba 6mer | [ Huggingface] ( https://huggingface.co/zhangtaolab/plant-dnamamba-6mer-H3K27ac ) / [ Modelscope] ( https://modelscope.cn/models/zhangtaolab/plant-dnamamba-6mer-H3K27ac ) |
241+ | H3K27me3 | Plant DNAMamba 4mer | [ Huggingface] ( https://huggingface.co/zhangtaolab/plant-dnamamba-4mer-H3K27me3 ) / [ Modelscope] ( https://modelscope.cn/models/zhangtaolab/plant-dnamamba-4mer-H3K27me3 ) |
242+ | H3K4me3 | Plant DNAMamba 5mer | [ Huggingface] ( https://huggingface.co/zhangtaolab/plant-dnamamba-5mer-H3K4me3 ) / [ Modelscope] ( https://modelscope.cn/models/zhangtaolab/plant-dnamamba-5mer-H3K4me3 ) |
243+ | lncRNAs | Plant DNAGemma 6mer | [ Huggingface] ( https://huggingface.co/zhangtaolab/plant-dnagemma-6mer-lncRNAs ) / [ Modelscope] ( https://modelscope.cn/models/zhangtaolab/plant-dnagemma-6mer-lncRNAs ) |
244+ | 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 ) |
245+ | 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 ) |
246+ | 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 ) |
247+
248+ * All the [ finetune models list] ( docs/en/resources/finetune_models.md )
249249
250250We use Plant DNAGPT model as example to predict active core promoter in plants.
251251
0 commit comments