Upload 48 files

yangheng/.gitattributes

@@ -0,0 +1,55 @@
+*.7z filter=lfs diff=lfs merge=lfs -text
+*.arrow filter=lfs diff=lfs merge=lfs -text
+*.bin filter=lfs diff=lfs merge=lfs -text
+*.bz2 filter=lfs diff=lfs merge=lfs -text
+*.ckpt filter=lfs diff=lfs merge=lfs -text
+*.ftz filter=lfs diff=lfs merge=lfs -text
+*.gz filter=lfs diff=lfs merge=lfs -text
+*.h5 filter=lfs diff=lfs merge=lfs -text
+*.joblib filter=lfs diff=lfs merge=lfs -text
+*.lfs.* filter=lfs diff=lfs merge=lfs -text
+*.lz4 filter=lfs diff=lfs merge=lfs -text
+*.mlmodel filter=lfs diff=lfs merge=lfs -text
+*.model filter=lfs diff=lfs merge=lfs -text
+*.msgpack filter=lfs diff=lfs merge=lfs -text
+*.npy filter=lfs diff=lfs merge=lfs -text
+*.npz filter=lfs diff=lfs merge=lfs -text
+*.onnx filter=lfs diff=lfs merge=lfs -text
+*.ot filter=lfs diff=lfs merge=lfs -text
+*.parquet filter=lfs diff=lfs merge=lfs -text
+*.pb filter=lfs diff=lfs merge=lfs -text
+*.pickle filter=lfs diff=lfs merge=lfs -text
+*.pkl filter=lfs diff=lfs merge=lfs -text
+*.pt filter=lfs diff=lfs merge=lfs -text
+*.pth filter=lfs diff=lfs merge=lfs -text
+*.rar filter=lfs diff=lfs merge=lfs -text
+*.safetensors filter=lfs diff=lfs merge=lfs -text
+saved_model/**/* filter=lfs diff=lfs merge=lfs -text
+*.tar.* filter=lfs diff=lfs merge=lfs -text
+*.tar filter=lfs diff=lfs merge=lfs -text
+*.tflite filter=lfs diff=lfs merge=lfs -text
+*.tgz filter=lfs diff=lfs merge=lfs -text
+*.wasm filter=lfs diff=lfs merge=lfs -text
+*.xz filter=lfs diff=lfs merge=lfs -text
+*.zip filter=lfs diff=lfs merge=lfs -text
+*.zst filter=lfs diff=lfs merge=lfs -text
+*tfevents* filter=lfs diff=lfs merge=lfs -text
+# Audio files - uncompressed
+*.pcm filter=lfs diff=lfs merge=lfs -text
+*.sam filter=lfs diff=lfs merge=lfs -text
+*.raw filter=lfs diff=lfs merge=lfs -text
+# Audio files - compressed
+*.aac filter=lfs diff=lfs merge=lfs -text
+*.flac filter=lfs diff=lfs merge=lfs -text
+*.mp3 filter=lfs diff=lfs merge=lfs -text
+*.ogg filter=lfs diff=lfs merge=lfs -text
+*.wav filter=lfs diff=lfs merge=lfs -text
+# Image files - uncompressed
+*.bmp filter=lfs diff=lfs merge=lfs -text
+*.gif filter=lfs diff=lfs merge=lfs -text
+*.png filter=lfs diff=lfs merge=lfs -text
+*.tiff filter=lfs diff=lfs merge=lfs -text
+# Image files - compressed
+*.jpg filter=lfs diff=lfs merge=lfs -text
+*.jpeg filter=lfs diff=lfs merge=lfs -text
+*.webp filter=lfs diff=lfs merge=lfs -text

yangheng/GB/3UTRBERT.json

@@ -0,0 +1,48 @@
+{
+   "config":{
+      "model":"multimolecule/utrbert-4mer",
+      "model_args":"pretrained=multimolecule/utrbert-4mer,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"k-mers", "# of Params":"86M", "Pretraining Data":"20,362 Sequences", "Species":"Multi-Species", "Nucleic Acid":"mRNA 3'UTR"},
+      "model_dtype":"bfloat16",
+      "model_name":"multimolecule/utrbert-4mer",
+      "model_sha":"main"
+   },
+   "results":{
+      "DEM":{
+         "F1":0.8950
+      },
+      "DOW":{
+         "F1":0.9022
+      },
+      "DRE":{
+         "F1":0.7435
+      },
+      "DME":{
+         "F1":0.8014
+      },
+      "HCE":{
+         "F1":0.7023
+      },
+      "HEE":{
+         "F1":0.7633
+      },
+      "HRE":{
+         "F1":0.9847
+      },
+      "HNP":{
+         "F1":0.8249
+      },
+      "HOR":{
+         "F1":0.6678
+      }
+   }
+}

yangheng/GB/Caduceus.json

@@ -0,0 +1,48 @@
+{
+   "config":{
+      "model":"kuleshov-group/caduceus-ps_seqlen-131k_d_model-256_n_layer-16",
+      "model_args":"pretrained= kuleshov-group/caduceus-ps_seqlen-131k_d_model-256_n_layer-16,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"SNT", "# of Params":"7.73M", "Pretraining Data":"35 billion nucleotide base pairs", "Species":"Human", "Nucleic Acid":"DNA"},
+      "model_dtype":"bfloat16",
+      "model_name":"kuleshov-group/caduceus-ps_seqlen-131k_d_model-256_n_layer-16",
+      "model_sha":"main"
+   },
+   "results":{
+      "DEM":{
+         "F1":0.9213
+      },
+      "DOW":{
+         "F1":0.9474
+      },
+      "DRE":{
+         "F1":0.7203
+      },
+      "DME":{
+         "F1":0.7561
+      },
+      "HCE":{
+         "F1":0.7020
+      },
+      "HEE":{
+         "F1":0.7647
+      },
+      "HRE":{
+         "F1":0.7916
+      },
+      "HNP":{
+         "F1":0.8436
+      },
+      "HOR":{
+         "F1":0.6317
+      }
+   }
+}

yangheng/GB/DNABERT-2-117M.json

@@ -0,0 +1,48 @@
+{
+   "config":{
+      "model":"zhihan1996/DNABERT-2-117M",
+      "model_args":"pretrained=zhihan1996/DNABERT-2-117M,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"BPE", "# of Params":"117M", "Pretraining Data":"32.49B Tokens", "Species":"Human + 135 Species", "Nucleic Acid":"DNA"},
+      "model_dtype":"bfloat16",
+      "model_name":"zhihan1996/DNABERT-2-117M",
+      "model_sha":"main"
+   },
+   "results":{
+      "DEM":{
+         "F1":0.9267
+      },
+      "DOW":{
+         "F1":0.9517
+      },
+      "DRE":{
+         "F1":0.4377
+      },
+      "DME":{
+         "F1":0.7721
+      },
+      "HCE":{
+         "F1":0.7558
+      },
+      "HEE":{
+         "F1":0.8066
+      },
+      "HRE":{
+         "F1":0.7814
+      },
+      "HNP":{
+         "F1":0.8580
+      },
+      "HOR":{
+         "F1":0.6803
+      }
+   }
+}

yangheng/GB/HyenaDNA.json

@@ -0,0 +1,48 @@
+{
+   "config":{
+      "model":"LongSafari/hyenadna-large-1m-seqlen-hf",
+      "model_args":"pretrained=LongSafari/hyenadna-large-1m-seqlen-hf,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"SNT", "# of Params":"47M", "Pretraining Data":"~3.2B Tokens", "Species":"Human", "Nucleic Acid":"DNA"},
+      "model_dtype":"bfloat16",
+      "model_name":"LongSafari/hyenadna-large-1m-seqlen-hf",
+      "model_sha":"main"
+   },
+   "results":{
+      "DEM":{
+         "F1":0.8821
+      },
+      "DOW":{
+         "F1":0.9413
+      },
+      "DRE":{
+         "F1":0.7011
+      },
+      "DME":{
+         "F1":0.7644
+      },
+      "HCE":{
+         "F1":0.7038
+      },
+      "HEE":{
+         "F1":0.7958
+      },
+      "HRE":{
+         "F1":0.9633
+      },
+      "HNP":{
+         "F1":0.8599
+      },
+      "HOR":{
+         "F1":0.6703
+      }
+   }
+}

yangheng/GB/NT-V2-100M.json

@@ -0,0 +1,48 @@
+{
+   "config":{
+      "model":"InstaDeepAI/nucleotide-transformer-v2-100m-multi-species",
+      "model_args":"pretrained=InstaDeepAI/nucleotide-transformer-v2-100m-multi-species,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"k-mers", "# of Params":"96M", "Pretraining Data":"300B Tokens", "Species":"Human + 850 Species", "Nucleic Acid":"DNA"},
+      "model_dtype":"bfloat16",
+      "model_name":"InstaDeepAI/nucleotide-transformer-v2-100m-multi-species",
+      "model_sha":"main"
+   },
+   "results":{
+      "DEM":{
+         "F1":0.9166
+      },
+      "DOW":{
+         "F1":0.9432
+      },
+      "DRE":{
+         "F1":0.7820
+      },
+      "DME":{
+         "F1":0.8172
+      },
+      "HCE":{
+         "F1":0.7198
+      },
+      "HEE":{
+         "F1":0.7985
+      },
+      "HRE":{
+         "F1":0.9330
+      },
+      "HNP":{
+         "F1":0.8530
+      },
+      "HOR":{
+         "F1":0.6853
+      }
+   }
+}

yangheng/GB/OmniGenome186M.json

@@ -0,0 +1,48 @@
+{
+   "config":{
+      "model":"yangheng/omnigenome-186M",
+      "model_args":"pretrained=yangheng/omnigenome-186M,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"SNT", "# of Params":"186M", "Pretraining Data":"54.2B Tokens", "Species":"1124 Plant Species", "Nucleic Acid":"mRNA, CDS, UTR"},
+      "model_dtype":"bfloat16",
+      "model_name":"yangheng/omnigenome-186M",
+      "model_sha":"main"
+   },
+   "results":{
+      "DEM":{
+         "F1":0.9416
+      },
+      "DOW":{
+         "F1":0.9349
+      },
+      "DRE":{
+         "F1":0.7717
+      },
+      "DME":{
+         "F1":0.8034
+      },
+      "HCE":{
+         "F1":0.7351
+      },
+      "HEE":{
+         "F1":0.8223
+      },
+      "HRE":{
+         "F1":0.9566
+      },
+      "HNP":{
+         "F1":0.8787
+      },
+      "HOR":{
+         "F1":0.6897
+      }
+   }
+}

yangheng/GB/SpliceBERT.json

@@ -0,0 +1,48 @@
+{
+   "config":{
+      "model":"multimolecule/splicebert",
+      "model_args":"pretrained=multimolecule/splicebert,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"SNT", "# of Params":"19.7M", "Pretraining Data":"65 billion nucleotides", "Species":"Multi-Species", "Nucleic Acid":"mRNA"},
+      "model_dtype":"bfloat16",
+      "model_name":"multimolecule/splicebert",
+      "model_sha":"main"
+   },
+   "results":{
+      "DEM":{
+         "F1":0.9472
+      },
+      "DOW":{
+         "F1":0.9642
+      },
+      "DRE":{
+         "F1":0.7229
+      },
+      "DME":{
+         "F1":0.7470
+      },
+      "HCE":{
+         "F1":0.7350
+      },
+      "HEE":{
+         "F1":0.7960
+      },
+      "HRE":{
+         "F1":0.9523
+      },
+      "HNP":{
+         "F1":0.8957
+      },
+      "HOR":{
+         "F1":0.6889
+      }
+   }
+}

yangheng/GUE/3UTRBERT.json

@@ -0,0 +1,42 @@
+{
+   "config":{
+      "model":"multimolecule/utrbert-4mer",
+      "model_args":"pretrained=multimolecule/utrbert-4mer,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"k-mers", "# of Params":"86M", "Pretraining Data":"20,362 Sequences", "Species":"Multi-Species", "Nucleic Acid":"mRNA 3'UTR"},
+      "model_dtype":"bfloat16",
+      "model_name":"multimolecule/utrbert-4mer",
+      "model_sha":"main"
+   },
+   "results":{
+      "Yeast EMP":{
+         "F1":0.7189
+      },
+      "Mouse TF-M":{
+         "F1":0.7146
+      },
+      "Virus CVC":{
+         "F1":0.6871
+      },
+      "Human TF-H":{
+         "F1":0.7485
+      },
+      "Human PD":{
+         "F1":0.8237
+      },
+      "Human CPD":{
+         "F1":0.9051
+      },
+      "Human SSP":{
+         "F1":0.8195
+      }
+   }
+}

yangheng/GUE/Caduceus.json

@@ -0,0 +1,42 @@
+{
+   "config":{
+      "model":"kuleshov-group/caduceus-ps_seqlen-131k_d_model-256_n_layer-16",
+      "model_args":"pretrained= kuleshov-group/caduceus-ps_seqlen-131k_d_model-256_n_layer-16,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"SNT", "# of Params":"7.73M", "Pretraining Data":"35 billion nucleotide base pairs", "Species":"Human", "Nucleic Acid":"DNA"},
+      "model_dtype":"bfloat16",
+      "model_name":"kuleshov-group/caduceus-ps_seqlen-131k_d_model-256_n_layer-16",
+      "model_sha":"main"
+   },
+   "results":{
+      "Yeast EMP":{
+         "F1":0.7349
+      },
+      "Mouse TF-M":{
+         "F1":0.7818
+      },
+      "Virus CVC":{
+         "F1":0.4909
+      },
+      "Human TF-H":{
+         "F1":0.7956
+      },
+      "Human PD":{
+         "F1":0.8913
+      },
+      "Human CPD":{
+         "F1":0.8509
+      },
+      "Human SSP":{
+         "F1":0.8182
+      }
+   }
+}

yangheng/GUE/DNABERT-2-117M.json

@@ -0,0 +1,42 @@
+{
+   "config":{
+      "model":"zhihan1996/DNABERT-2-117M",
+      "model_args":"pretrained=zhihan1996/DNABERT-2-117M,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"BPE", "# of Params":"117M", "Pretraining Data":"32.49B Tokens", "Species":"Human + 135 Species", "Nucleic Acid":"DNA"},
+      "model_dtype":"bfloat16",
+      "model_name":"zhihan1996/DNABERT-2-117M",
+      "model_sha":"main"
+   },
+   "results":{
+      "Yeast EMP":{
+         "F1":0.7585
+      },
+      "Mouse TF-M":{
+         "F1":0.8623
+      },
+      "Virus CVC":{
+         "F1":0.6890
+      },
+      "Human TF-H":{
+         "F1":0.8180
+      },
+      "Human PD":{
+         "F1":0.9017
+      },
+      "Human CPD":{
+         "F1":0.8257
+      },
+      "Human SSP":{
+         "F1":0.8521
+      }
+   }
+}

yangheng/GUE/HyenaDNA.json

@@ -0,0 +1,42 @@
+{
+   "config":{
+      "model":"LongSafari/hyenadna-large-1m-seqlen-hf",
+      "model_args":"pretrained=LongSafari/hyenadna-large-1m-seqlen-hf,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"SNT", "# of Params":"47M", "Pretraining Data":"~3.2B Tokens", "Species":"Human", "Nucleic Acid":"DNA"},
+      "model_dtype":"bfloat16",
+      "model_name":"LongSafari/hyenadna-large-1m-seqlen-hf",
+      "model_sha":"main"
+   },
+   "results":{
+      "Yeast EMP":{
+         "F1":0.7308
+      },
+      "Mouse TF-M":{
+         "F1":0.7344
+      },
+      "Virus CVC":{
+         "F1":0.6637
+      },
+      "Human TF-H":{
+         "F1":0.7762
+      },
+      "Human PD":{
+         "F1":0.9119
+      },
+      "Human CPD":{
+         "F1":0.8431
+      },
+      "Human SSP":{
+         "F1":0.8334
+      }
+   }
+}

yangheng/GUE/NT-V2-100M.json

@@ -0,0 +1,42 @@
+{
+   "config":{
+      "model":"InstaDeepAI/nucleotide-transformer-v2-100m-multi-species",
+      "model_args":"pretrained=InstaDeepAI/nucleotide-transformer-v2-100m-multi-species,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"k-mers", "# of Params":"96M", "Pretraining Data":"300B Tokens", "Species":"Human + 850 Species", "Nucleic Acid":"DNA"},
+      "model_dtype":"bfloat16",
+      "model_name":"InstaDeepAI/nucleotide-transformer-v2-100m-multi-species",
+      "model_sha":"main"
+   },
+   "results":{
+      "Yeast EMP":{
+         "F1":0.7493
+      },
+      "Mouse TF-M":{
+         "F1":0.7810
+      },
+      "Virus CVC":{
+         "F1":0.5923
+      },
+      "Human TF-H":{
+         "F1":0.7912
+      },
+      "Human PD":{
+         "F1":0.9087
+      },
+      "Human CPD":{
+         "F1":0.8470
+      },
+      "Human SSP":{
+         "F1":0.8413
+      }
+   }
+}

yangheng/GUE/OmniGenome186M.json

@@ -0,0 +1,42 @@
+{
+   "config":{
+      "model":"yangheng/omnigenome-186M",
+      "model_args":"pretrained=yangheng/omnigenome-186M,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"SNT", "# of Params":"186M", "Pretraining Data":"54.2B Tokens", "Species":"1124 Plant Species", "Nucleic Acid":"mRNA, CDS, UTR"},
+      "model_dtype":"bfloat16",
+      "model_name":"yangheng/omnigenome-186M",
+      "model_sha":"main"
+   },
+   "results":{
+      "Yeast EMP":{
+         "F1":0.7851
+      },
+      "Mouse TF-M":{
+         "F1":0.8472
+      },
+      "Virus CVC":{
+         "F1":0.7472
+      },
+      "Human TF-H":{
+         "F1":0.8173
+      },
+      "Human PD":{
+         "F1":0.9004
+      },
+      "Human CPD":{
+         "F1":0.8522
+      },
+      "Human SSP":{
+         "F1":0.9039
+      }
+   }
+}

yangheng/GUE/SpliceBERT.json

@@ -0,0 +1,42 @@
+{
+   "config":{
+      "model":"multimolecule/splicebert",
+      "model_args":"pretrained=multimolecule/splicebert,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"SNT", "# of Params":"19.7M", "Pretraining Data":"65 billion nucleotides", "Species":"Multi-Species", "Nucleic Acid":"mRNA"},
+      "model_dtype":"bfloat16",
+      "model_name":"multimolecule/splicebert",
+      "model_sha":"main"
+   },
+   "results":{
+      "Yeast EMP":{
+         "F1":0.7766
+      },
+      "Mouse TF-M":{
+         "F1":0.8497
+      },
+      "Virus CVC":{
+         "F1":0.5624
+      },
+      "Human TF-H":{
+         "F1":0.8277
+      },
+      "Human PD":{
+         "F1":0.9224
+      },
+      "Human CPD":{
+         "F1":0.8396
+      },
+      "Human SSP":{
+         "F1":0.9381
+      }
+   }
+}

yangheng/PGB/3UTRBERT.json

@@ -0,0 +1,45 @@
+{
+   "config":{
+      "model":"multimolecule/utrbert-4mer",
+      "model_args":"pretrained=multimolecule/utrbert-4mer,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"k-mers", "# of Params":"86M", "Pretraining Data":"20,362 Sequences", "Species":"Multi-Species", "Nucleic Acid":"mRNA 3'UTR"},
+      "model_dtype":"bfloat16",
+      "model_name":"multimolecule/utrbert-4mer",
+      "model_sha":"main"
+   },
+"results":{
+      "PolyA":{
+         "F1":0.7648
+      },
+      "LncRNA":{
+         "F1":0.7075
+      },
+      "Chrom Acc":{
+         "F1":0.6371
+      },
+      "Prom Str":{
+         "RMSE":1.04
+      },
+      "Term Str":{
+         "RMSE":0.36
+      },
+      "Splice":{
+         "F1":0.9444
+      },
+      "Gene Exp":{
+         "RMSE":14.87
+      },
+      "Enhancer":{
+         "F1":0.7167
+      }
+   }
+}

yangheng/PGB/Agro-NT.json

@@ -0,0 +1,45 @@
+{
+   "config":{
+      "model":"InstaDeepAI/agro-nucleotide-transformer-1b",
+      "model_args":"pretrained=InstaDeepAI/agro-nucleotide-transformer-1b,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"k-mers", "# of Params":"985M", "Pretraining Data":"472.5B Tokens", "Species":"48 Edible Plants", "Nucleic Acid":"DNA"},
+      "model_dtype":"bfloat16",
+      "model_name":"InstaDeepAI/agro-nucleotide-transformer-1b",
+      "model_sha":"main"
+   },
+"results":{
+      "PolyA":{
+         "F1":0.7889
+      },
+      "LncRNA":{
+         "F1":0.6724
+      },
+      "Chrom Acc":{
+         "F1":0.6327
+      },
+      "Prom Str":{
+         "RMSE":0.94
+      },
+      "Term Str":{
+         "RMSE":0.78
+      },
+      "Splice":{
+         "F1":0.8845
+      },
+      "Gene Exp":{
+         "RMSE":15.56
+      },
+      "Enhancer":{
+         "F1":0.6283
+      }
+   }
+}

yangheng/PGB/CDSBERT.json

@@ -0,0 +1,45 @@
+{
+   "config":{
+      "model":"GleghornLab/cdsBERT",
+      "model_args":"pretrained=GleghornLab/cdsBERT,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"SNT", "# of Params":"420M", "Pretraining Data":"4M Sequences", "Species":"4,069 RNA families", "Nucleic Acid":"CDS"},
+      "model_dtype":"bfloat16",
+      "model_name":"GleghornLab/cdsBERT",
+      "model_sha":"main"
+   },
+   "results":{
+      "PolyA":{
+         "F1":0.3972
+      },
+      "LncRNA":{
+         "F1":0.3306
+      },
+      "Chrom Acc":{
+         "F1":0.4895
+      },
+      "Prom Str":{
+         "RMSE":2.19
+      },
+      "Term Str":{
+         "RMSE":0.59
+      },
+      "Splice":{
+         "F1":0.5220
+      },
+      "Gene Exp":{
+         "RMSE":14.77
+      },
+      "Enhancer":{
+         "F1":0.3393
+      }
+   }
+}

yangheng/PGB/Caduceus.json

@@ -0,0 +1,45 @@
+{
+   "config":{
+      "model":"kuleshov-group/caduceus-ps_seqlen-131k_d_model-256_n_layer-16",
+      "model_args":"pretrained= kuleshov-group/caduceus-ps_seqlen-131k_d_model-256_n_layer-16,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"SNT", "# of Params":"7.73M", "Pretraining Data":"35 billion nucleotide base pairs", "Species":"Human", "Nucleic Acid":"DNA"},
+      "model_dtype":"bfloat16",
+      "model_name":"kuleshov-group/caduceus-ps_seqlen-131k_d_model-256_n_layer-16",
+      "model_sha":"main"
+   },
+   "results":{
+      "PolyA":{
+         "F1":0.7089
+      },
+      "LncRNA":{
+         "F1":0.6840
+      },
+      "Chrom Acc":{
+         "F1":0.6453
+      },
+      "Prom Str":{
+         "RMSE":0.91
+      },
+      "Term Str":{
+         "RMSE":0.26
+      },
+      "Splice":{
+         "F1":0.7951
+      },
+      "Gene Exp":{
+         "RMSE":14.72
+      },
+      "Enhancer":{
+         "F1":0.6083
+      }
+   }
+}

yangheng/PGB/DNABERT-2-117M.json

@@ -0,0 +1,45 @@
+{
+   "config":{
+      "model":"zhihan1996/DNABERT-2-117M",
+      "model_args":"pretrained=zhihan1996/DNABERT-2-117M,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"BPE", "# of Params":"117M", "Pretraining Data":"32.49B Tokens", "Species":"Human + 135 Species", "Nucleic Acid":"DNA"},
+      "model_dtype":"bfloat16",
+      "model_name":"zhihan1996/DNABERT-2-117M",
+      "model_sha":"main"
+   },
+   "results":{
+      "PolyA":{
+         "F1":0.4135
+      },
+      "LncRNA":{
+         "F1":0.7255
+      },
+      "Chrom Acc":{
+         "F1":0.6149
+      },
+      "Prom Str":{
+         "RMSE":0.99
+      },
+      "Term Str":{
+         "RMSE":0.24
+      },
+      "Splice":{
+         "F1":0.4534
+      },
+      "Gene Exp":{
+         "RMSE":14.78
+      },
+      "Enhancer":{
+         "F1":0.3640
+      }
+   }
+}

yangheng/PGB/HyenaDNA.json

@@ -0,0 +1,45 @@
+{
+   "config":{
+      "model":"LongSafari/hyenadna-large-1m-seqlen-hf",
+      "model_args":"pretrained=LongSafari/hyenadna-large-1m-seqlen-hf,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"SNT", "# of Params":"47M", "Pretraining Data":"~3.2B Tokens", "Species":"Human", "Nucleic Acid":"DNA"},
+      "model_dtype":"bfloat16",
+      "model_name":"LongSafari/hyenadna-large-1m-seqlen-hf",
+      "model_sha":"main"
+   },
+   "results":{
+      "PolyA":{
+         "F1":0.8311
+      },
+      "LncRNA":{
+         "F1":0.5821
+      },
+      "Chrom Acc":{
+         "F1":0.5220
+      },
+      "Prom Str":{
+         "RMSE":0.88
+      },
+      "Term Str":{
+         "RMSE":0.26
+      },
+      "Splice":{
+         "F1":0.9028
+      },
+      "Gene Exp":{
+         "RMSE":14.76
+      },
+      "Enhancer":{
+         "F1":0.6617
+      }
+   }
+}

yangheng/PGB/NT-V2-100M.json

@@ -0,0 +1,45 @@
+{
+   "config":{
+      "model":"InstaDeepAI/nucleotide-transformer-v2-100m-multi-species",
+      "model_args":"pretrained=InstaDeepAI/nucleotide-transformer-v2-100m-multi-species,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"k-mers", "# of Params":"96M", "Pretraining Data":"300B Tokens", "Species":"Human + 850 Species", "Nucleic Acid":"DNA"},
+      "model_dtype":"bfloat16",
+      "model_name":"InstaDeepAI/nucleotide-transformer-v2-100m-multi-species",
+      "model_sha":"main"
+   },
+   "results":{
+      "PolyA":{
+         "F1":0.7126
+      },
+      "LncRNA":{
+         "F1":0.7308
+      },
+      "Chrom Acc":{
+         "F1":0.6571
+      },
+      "Prom Str":{
+         "RMSE":0.81
+      },
+      "Term Str":{
+         "RMSE":0.27
+      },
+      "Splice":{
+         "F1":0.9505
+      },
+      "Gene Exp":{
+         "RMSE":14.69
+      },
+      "Enhancer":{
+         "F1":0.7389
+      }
+   }
+}

yangheng/PGB/OmniGenome186M.json

@@ -0,0 +1,45 @@
+{
+   "config":{
+      "model":"yangheng/omnigenome-186M",
+      "model_args":"pretrained=yangheng/omnigenome-186M,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"SNT", "# of Params":"186M", "Pretraining Data":"54.2B Tokens", "Species":"1124 Plant Species", "Nucleic Acid":"mRNA, CDS, UTR"},
+      "model_dtype":"bfloat16",
+      "model_name":"yangheng/omnigenome-186M",
+      "model_sha":"main"
+   },
+   "results":{
+      "PolyA":{
+         "F1":0.8755
+      },
+      "LncRNA":{
+         "F1":0.7796
+      },
+      "Chrom Acc":{
+         "F1":0.6769
+      },
+      "Prom Str":{
+         "RMSE":0.59
+      },
+      "Term Str":{
+         "RMSE":0.18
+      },
+      "Splice":{
+         "F1":0.9841
+      },
+      "Gene Exp":{
+         "RMSE":14.71
+      },
+      "Enhancer":{
+         "F1":0.7977
+      }
+   }
+}

yangheng/PGB/RNA-BERT.json

@@ -0,0 +1,46 @@
+{
+   "config":{
+      "model":"multimolecule/rnabert",
+      "model_args":"pretrained=multimolecule/rnabert,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"SNT", "# of Params":"0.48M", "Pretraining Data":"76,237 human ncRNA sequences", "Species":"Human", "Nucleic Acid":"ncRNA"},
+      "model_dtype":"bfloat16",
+      "model_name":"multimolecule/rnabert",
+      "model_sha":"main"
+   },
+   "results":{
+      "PolyA":{
+         "F1":0.7854
+      },
+      "LncRNA":{
+         "F1":0.6199
+      },
+      "Chrom Acc":{
+         "F1":0.4894
+      },
+      "Prom Str":{
+         "RMSE":1.81
+      },
+      "Term Str":{
+         "RMSE":0.38
+      },
+      "Splice":{
+         "F1":0.9445
+      },
+      "Gene Exp":{
+         "RMSE":14.89
+      },
+      "Enhancer":{
+         "F1":0.5761
+      }
+
+   }
+}

yangheng/PGB/RNA-FM.json

@@ -0,0 +1,45 @@
+{
+   "config":{
+      "model":"multimolecule/rnafm",
+      "model_args":"pretrained=multimolecule/rnafm,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"SNT", "# of Params":"99.52M", "Pretraining Data":"23.7 million non-redundant RNA sequences", "Species":"Multi-Species", "Nucleic Acid":"ncRNA"},
+      "model_dtype":"bfloat16",
+      "model_name":"multimolecule/rnafm",
+      "model_sha":"main"
+   },
+   "results":{
+      "PolyA":{
+         "F1":0.8494
+      },
+      "LncRNA":{
+         "F1":0.6875
+      },
+      "Chrom Acc":{
+         "F1":0.5492
+      },
+      "Prom Str":{
+         "RMSE":0.95
+      },
+      "Term Str":{
+         "RMSE":0.27
+      },
+      "Splice":{
+         "F1":0.9595
+      },
+      "Gene Exp":{
+         "RMSE":14.83
+      },
+      "Enhancer":{
+         "F1":0.5714
+      }
+   }
+}

yangheng/PGB/RNA-MSM.json

@@ -0,0 +1,45 @@
+{
+   "config":{
+      "model":"multimolecule/rnamsm",
+      "model_args":"pretrained=multimolecule/rnamsm,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"SNT", "# of Params":"96.5M", "Pretraining Data":"3,932 RNA families", "Species":"Multi-Species", "Nucleic Acid":"RNA"},
+      "model_dtype":"bfloat16",
+      "model_name":"multimolecule/rnamsm",
+      "model_sha":"main"
+   },
+   "results":{
+      "PolyA":{
+         "F1":0.8425
+      },
+      "LncRNA":{
+         "F1":0.6749
+      },
+      "Chrom Acc":{
+         "F1":0.5352
+      },
+      "Prom Str":{
+         "RMSE":1.28
+      },
+      "Term Str":{
+         "RMSE":0.28
+      },
+      "Splice":{
+         "F1":0.9549
+      },
+      "Gene Exp":{
+         "RMSE":14.87
+      },
+      "Enhancer":{
+         "F1":0.6145
+      }
+   }
+}

yangheng/PGB/SpliceBERT.json

@@ -0,0 +1,45 @@
+{
+   "config":{
+      "model":"multimolecule/splicebert",
+      "model_args":"pretrained=multimolecule/splicebert,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"SNT", "# of Params":"19.7M", "Pretraining Data":"65 billion nucleotides", "Species":"Multi-Species", "Nucleic Acid":"mRNA"},
+      "model_dtype":"bfloat16",
+      "model_name":"multimolecule/splicebert",
+      "model_sha":"main"
+   },
+   "results":{
+      "PolyA":{
+         "F1":0.6523
+      },
+      "LncRNA":{
+         "F1":0.7188
+      },
+      "Chrom Acc":{
+         "F1":0.6362
+      },
+      "Prom Str":{
+         "RMSE":0.75
+      },
+      "Term Str":{
+         "RMSE":0.22
+      },
+      "Splice":{
+         "F1":0.9645
+      },
+      "Gene Exp":{
+         "RMSE":14.70
+      },
+      "Enhancer":{
+         "F1":0.6971
+      }
+   }
+}

yangheng/README.md

@@ -0,0 +1,3 @@
+---
+license: mit
+---

yangheng/RGB/yangheng/3UTRBERT.json

@@ -0,0 +1,39 @@
+{
+   "config":{
+      "model":"multimolecule/utrbert-4mer",
+      "model_args":"pretrained=multimolecule/utrbert-4mer,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"k-mers", "# of Params":"86M", "Pretraining Data":"20,362 Sequences", "Species":"Multi-Species", "Nucleic Acid":"mRNA 3'UTR"},
+      "model_dtype":"bfloat16",
+      "model_name":"multimolecule/utrbert-4mer",
+      "model_sha":"main"
+   },
+   "results":{
+      "mRNA":{
+         "RMSE":0.7772
+      },
+      "SNMD":{
+         "AUC":0.5002
+      },
+      "SNMR":{
+         "F1":0.2401
+      },
+      "ArchiveII":{
+         "F1":0.7898
+      },
+      "bpRNA":{
+         "F1":0.5693
+      },
+      "RNAStralign":{
+         "F1":0.9203
+      }
+   }
+}

yangheng/RGB/yangheng/Agro-NT.json

@@ -0,0 +1,39 @@
+{
+   "config":{
+      "model":"InstaDeepAI/agro-nucleotide-transformer-1b",
+      "model_args":"pretrained=InstaDeepAI/agro-nucleotide-transformer-1b,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"k-mers", "# of Params":"985M", "Pretraining Data":"472.5B Tokens", "Species":"48 Edible Plants", "Nucleic Acid":"DNA"},
+      "model_dtype":"bfloat16",
+      "model_name":"InstaDeepAI/agro-nucleotide-transformer-1b",
+      "model_sha":"main"
+   },
+   "results":{
+      "mRNA":{
+         "RMSE":0.7830
+      },
+      "SNMD":{
+         "AUC":0.4999
+      },
+      "SNMR":{
+         "F1":0.2638
+      },
+      "ArchiveII":{
+         "F1":0.7013
+      },
+      "bpRNA":{
+         "F1":0.4871
+      },
+      "RNAStralign":{
+         "F1":0.7521
+      }
+   }
+}

yangheng/RGB/yangheng/CDSBERT.json

@@ -0,0 +1,39 @@
+{
+   "config":{
+      "model":"GleghornLab/cdsBERT",
+      "model_args":"pretrained=GleghornLab/cdsBERT,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"SNT", "# of Params":"420M", "Pretraining Data":"4M Sequences", "Species":"4,069 RNA families", "Nucleic Acid":"CDS"},
+      "model_dtype":"bfloat16",
+      "model_name":"GleghornLab/cdsBERT",
+      "model_sha":"main"
+   },
+   "results":{
+      "mRNA":{
+         "RMSE":0.7468
+      },
+      "SNMD":{
+         "AUC":0.5503
+      },
+      "SNMR":{
+         "F1":0.3616
+      },
+      "ArchiveII":{
+         "F1":0.8934
+      },
+      "bpRNA":{
+         "F1":0.7001
+      },
+      "RNAStralign":{
+         "F1":0.9715
+      }
+   }
+}

yangheng/RGB/yangheng/DNABERT-2-117M.json

@@ -0,0 +1,39 @@
+{
+   "config":{
+      "model":"zhihan1996/DNABERT-2-117M",
+      "model_args":"pretrained=zhihan1996/DNABERT-2-117M,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"BPE", "# of Params":"117M", "Pretraining Data":"32.49B Tokens", "Species":"Human + 135 Species", "Nucleic Acid":"DNA"},
+      "model_dtype":"bfloat16",
+      "model_name":"zhihan1996/DNABERT-2-117M",
+      "model_sha":"main"
+   },
+   "results":{
+      "mRNA":{
+         "RMSE":0.8158
+      },
+      "SNMD":{
+         "AUC":0.4994
+      },
+      "SNMR":{
+         "F1":0.1586
+      },
+      "ArchiveII":{
+         "F1":0.5982
+      },
+      "bpRNA":{
+         "F1":0.4340
+      },
+      "RNAStralign":{
+         "F1":0.6549
+      }
+   }
+}

yangheng/RGB/yangheng/HyenaDNA.json

@@ -0,0 +1,39 @@
+{
+   "config":{
+      "model":"LongSafari/hyenadna-large-1m-seqlen-hf",
+      "model_args":"pretrained=LongSafari/hyenadna-large-1m-seqlen-hf,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"SNT", "# of Params":"47M", "Pretraining Data":"~3.2B Tokens", "Species":"Human", "Nucleic Acid":"DNA"},
+      "model_dtype":"bfloat16",
+      "model_name":"LongSafari/hyenadna-large-1m-seqlen-hf",
+      "model_sha":"main"
+   },
+   "results":{
+      "mRNA":{
+         "RMSE":0.8056
+      },
+      "SNMD":{
+         "AUC":0.5332
+      },
+      "SNMR":{
+         "F1":0.3980
+      },
+      "ArchiveII":{
+         "F1":0.8423
+      },
+      "bpRNA":{
+         "F1":0.5662
+      },
+      "RNAStralign":{
+         "F1":0.9542
+      }
+   }
+}

yangheng/RGB/yangheng/NT-V2-100M.json

@@ -0,0 +1,39 @@
+{
+   "config":{
+      "model":"InstaDeepAI/nucleotide-transformer-v2-100m-multi-species",
+      "model_args":"pretrained=InstaDeepAI/nucleotide-transformer-v2-100m-multi-species,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"k-mers", "# of Params":"96M", "Pretraining Data":"300B Tokens", "Species":"Human + 850 Species", "Nucleic Acid":"DNA"},
+      "model_dtype":"bfloat16",
+      "model_name":"InstaDeepAI/nucleotide-transformer-v2-100m-multi-species",
+      "model_sha":"main"
+   },
+   "results":{
+      "mRNA":{
+         "RMSE":0.7826
+      },
+      "SNMD":{
+         "AUC":0.5049
+      },
+      "SNMR":{
+         "F1":0.2601
+      },
+      "ArchiveII":{
+         "F1":0.7990
+      },
+      "bpRNA":{
+         "F1":0.5660
+      },
+      "RNAStralign":{
+         "F1":0.9084
+      }
+   }
+}

yangheng/RGB/yangheng/OmniGenome186M.json

@@ -0,0 +1,39 @@
+{
+   "config":{
+      "model":"yangheng/omnigenome-186M",
+      "model_args":"pretrained=yangheng/omnigenome-186M,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"SNT", "# of Params":"186M", "Pretraining Data":"54.2B Tokens", "Species":"1124 Plant Species", "Nucleic Acid":"mRNA, CDS, UTR"},
+      "model_dtype":"bfloat16",
+      "model_name":"yangheng/omnigenome-186M",
+      "model_sha":"main"
+   },
+   "results":{
+      "mRNA":{
+         "RMSE":0.7164
+      },
+      "SNMD":{
+         "AUC":0.6381
+      },
+      "SNMR":{
+         "F1":0.4980
+      },
+      "ArchiveII":{
+         "F1":0.9520
+      },
+      "bpRNA":{
+         "F1":0.8248
+      },
+      "RNAStralign":{
+         "F1":0.9912
+      }
+   }
+}

yangheng/RGB/yangheng/SpliceBERT.json

@@ -0,0 +1,39 @@
+{
+   "config":{
+      "model":"multimolecule/splicebert",
+      "model_args":"pretrained=multimolecule/splicebert,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"SNT", "# of Params":"19.7M", "Pretraining Data":"65 billion nucleotides", "Species":"Multi-Species", "Nucleic Acid":"mRNA"},
+      "model_dtype":"bfloat16",
+      "model_name":"multimolecule/splicebert",
+      "model_sha":"main"
+   },
+   "results":{
+      "mRNA":{
+         "RMSE":0.7340
+      },
+      "SNMD":{
+         "AUC":0.5811
+      },
+      "SNMR":{
+         "F1":0.4644
+      },
+      "ArchiveII":{
+         "F1":0.8905
+      },
+      "bpRNA":{
+         "F1":0.6910
+      },
+      "RNAStralign":{
+         "F1":0.9697
+      }
+   }
+}

yangheng/RGB/yangheng/results_OmniGenome-52M.json

@@ -0,0 +1,39 @@
+{
+   "config":{
+      "model":"yangheng/omnigenome-52M",
+      "model_args":"pretrained=yangheng/omnigenome-52M,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"SNT", "# of Params":"52M", "Pretraining Data":"54.2B Tokens", "Species":"1124 Plant Species", "Nucleic Acid":"mRNA, CDS, UTR"},
+      "model_dtype":"bfloat16",
+      "model_name":"yangheng/omnigenome-52M",
+      "model_sha":"main"
+   },
+   "results":{
+      "mRNA":{
+         "RMSE":0.7191
+      },
+      "SNMD":{
+         "AUC":0.6244
+      },
+      "SNMR":{
+         "F1":0.4891
+      },
+      "ArchiveII":{
+         "F1":0.9498
+      },
+      "bpRNA":{
+         "F1":0.8234
+      },
+      "RNAStralign":{
+         "F1":0.9901
+      }
+   }
+}

yangheng/yangheng/MODEL/3UTRBERT.json

@@ -0,0 +1,39 @@
+{
+   "config":{
+      "model":"multimolecule/utrbert-4mer",
+      "model_args":"pretrained=multimolecule/utrbert-4mer,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"k-mers", "# of Params":"86M", "Pretraining Data":"20,362 Sequences", "Species":"Multi-Species", "Nucleic Acid":"mRNA 3'UTR"},
+      "model_dtype":"bfloat16",
+      "model_name":"multimolecule/utrbert-4mer",
+      "model_sha":"main"
+   },
+   "results":{
+      "mRNA":{
+         "RMSE":0.7772
+      },
+      "SNMD":{
+         "AUC":0.5002
+      },
+      "SNMR":{
+         "F1":0.2401
+      },
+      "ArchiveII":{
+         "F1":0.7898
+      },
+      "bpRNA":{
+         "F1":0.5693
+      },
+      "RNAStralign":{
+         "F1":0.9203
+      }
+   }
+}

yangheng/yangheng/MODEL/Agro-NT.json

@@ -0,0 +1,39 @@
+{
+   "config":{
+      "model":"InstaDeepAI/agro-nucleotide-transformer-1b",
+      "model_args":"pretrained=InstaDeepAI/agro-nucleotide-transformer-1b,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"k-mers", "# of Params":"985M", "Pretraining Data":"472.5B Tokens", "Species":"48 Edible Plants", "Nucleic Acid":"DNA"},
+      "model_dtype":"bfloat16",
+      "model_name":"InstaDeepAI/agro-nucleotide-transformer-1b",
+      "model_sha":"main"
+   },
+   "results":{
+      "mRNA":{
+         "RMSE":0.7830
+      },
+      "SNMD":{
+         "AUC":0.4999
+      },
+      "SNMR":{
+         "F1":0.2638
+      },
+      "ArchiveII":{
+         "F1":0.7013
+      },
+      "bpRNA":{
+         "F1":0.4871
+      },
+      "RNAStralign":{
+         "F1":0.7521
+      }
+   }
+}

yangheng/yangheng/MODEL/CDSBERT.json

@@ -0,0 +1,39 @@
+{
+   "config":{
+      "model":"GleghornLab/cdsBERT",
+      "model_args":"pretrained=GleghornLab/cdsBERT,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"SNT", "# of Params":"420M", "Pretraining Data":"4M Sequences", "Species":"4,069 RNA families", "Nucleic Acid":"CDS"},
+      "model_dtype":"bfloat16",
+      "model_name":"GleghornLab/cdsBERT",
+      "model_sha":"main"
+   },
+   "results":{
+      "mRNA":{
+         "RMSE":0.7468
+      },
+      "SNMD":{
+         "AUC":0.5503
+      },
+      "SNMR":{
+         "F1":0.3616
+      },
+      "ArchiveII":{
+         "F1":0.8934
+      },
+      "bpRNA":{
+         "F1":0.7001
+      },
+      "RNAStralign":{
+         "F1":0.9715
+      }
+   }
+}

yangheng/yangheng/MODEL/DNABERT-2-117M.json

@@ -0,0 +1,39 @@
+{
+   "config":{
+      "model":"zhihan1996/DNABERT-2-117M",
+      "model_args":"pretrained=zhihan1996/DNABERT-2-117M,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"BPE", "# of Params":"117M", "Pretraining Data":"32.49B Tokens", "Species":"Human + 135 Species", "Nucleic Acid":"DNA"},
+      "model_dtype":"bfloat16",
+      "model_name":"zhihan1996/DNABERT-2-117M",
+      "model_sha":"main"
+   },
+   "results":{
+      "mRNA":{
+         "RMSE":0.8158
+      },
+      "SNMD":{
+         "AUC":0.4994
+      },
+      "SNMR":{
+         "F1":0.1586
+      },
+      "ArchiveII":{
+         "F1":0.5982
+      },
+      "bpRNA":{
+         "F1":0.4340
+      },
+      "RNAStralign":{
+         "F1":0.6549
+      }
+   }
+}

yangheng/yangheng/MODEL/HyenaDNA.json

@@ -0,0 +1,39 @@
+{
+   "config":{
+      "model":"LongSafari/hyenadna-large-1m-seqlen-hf",
+      "model_args":"pretrained=LongSafari/hyenadna-large-1m-seqlen-hf,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"SNT", "# of Params":"47M", "Pretraining Data":"~3.2B Tokens", "Species":"Human", "Nucleic Acid":"DNA"},
+      "model_dtype":"bfloat16",
+      "model_name":"LongSafari/hyenadna-large-1m-seqlen-hf",
+      "model_sha":"main"
+   },
+   "results":{
+      "mRNA":{
+         "RMSE":0.8056
+      },
+      "SNMD":{
+         "AUC":0.5332
+      },
+      "SNMR":{
+         "F1":0.3980
+      },
+      "ArchiveII":{
+         "F1":0.8423
+      },
+      "bpRNA":{
+         "F1":0.5662
+      },
+      "RNAStralign":{
+         "F1":0.9542
+      }
+   }
+}

yangheng/yangheng/MODEL/NT-V2-100M.json

@@ -0,0 +1,39 @@
+{
+   "config":{
+      "model":"InstaDeepAI/nucleotide-transformer-v2-100m-multi-species",
+      "model_args":"pretrained=InstaDeepAI/nucleotide-transformer-v2-100m-multi-species,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"k-mers", "# of Params":"96M", "Pretraining Data":"300B Tokens", "Species":"Human + 850 Species", "Nucleic Acid":"DNA"},
+      "model_dtype":"bfloat16",
+      "model_name":"InstaDeepAI/nucleotide-transformer-v2-100m-multi-species",
+      "model_sha":"main"
+   },
+   "results":{
+      "mRNA":{
+         "RMSE":0.7826
+      },
+      "SNMD":{
+         "AUC":0.5049
+      },
+      "SNMR":{
+         "F1":0.2601
+      },
+      "ArchiveII":{
+         "F1":0.7990
+      },
+      "bpRNA":{
+         "F1":0.5660
+      },
+      "RNAStralign":{
+         "F1":0.9084
+      }
+   }
+}

yangheng/yangheng/MODEL/OmniGenome186M.json

@@ -0,0 +1,39 @@
+{
+   "config":{
+      "model":"yangheng/omnigenome-186M",
+      "model_args":"pretrained=yangheng/omnigenome-186M,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"SNT", "# of Params":"186M", "Pretraining Data":"54.2B Tokens", "Species":"1124 Plant Species", "Nucleic Acid":"mRNA, CDS, UTR"},
+      "model_dtype":"bfloat16",
+      "model_name":"yangheng/omnigenome-186M",
+      "model_sha":"main"
+   },
+   "results":{
+      "mRNA":{
+         "RMSE":0.7164
+      },
+      "SNMD":{
+         "AUC":0.6381
+      },
+      "SNMR":{
+         "F1":0.4980
+      },
+      "ArchiveII":{
+         "F1":0.9520
+      },
+      "bpRNA":{
+         "F1":0.8248
+      },
+      "RNAStralign":{
+         "F1":0.9912
+      }
+   }
+}

yangheng/yangheng/MODEL/SpliceBERT.json

@@ -0,0 +1,39 @@
+{
+   "config":{
+      "model":"multimolecule/splicebert",
+      "model_args":"pretrained=multimolecule/splicebert,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"SNT", "# of Params":"19.7M", "Pretraining Data":"65 billion nucleotides", "Species":"Multi-Species", "Nucleic Acid":"mRNA"},
+      "model_dtype":"bfloat16",
+      "model_name":"multimolecule/splicebert",
+      "model_sha":"main"
+   },
+   "results":{
+      "mRNA":{
+         "RMSE":0.7340
+      },
+      "SNMD":{
+         "AUC":0.5811
+      },
+      "SNMR":{
+         "F1":0.4644
+      },
+      "ArchiveII":{
+         "F1":0.8905
+      },
+      "bpRNA":{
+         "F1":0.6910
+      },
+      "RNAStralign":{
+         "F1":0.9697
+      }
+   }
+}

yangheng/yangheng/MODEL/results_OmniGenome-52M.json

@@ -0,0 +1,39 @@
+{
+   "config":{
+      "model":"yangheng/omnigenome-52M",
+      "model_args":"pretrained=yangheng/omnigenome-52M,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"SNT", "# of Params":"52M", "Pretraining Data":"54.2B Tokens", "Species":"1124 Plant Species", "Nucleic Acid":"mRNA, CDS, UTR"},
+      "model_dtype":"bfloat16",
+      "model_name":"yangheng/omnigenome-52M",
+      "model_sha":"main"
+   },
+   "results":{
+      "mRNA":{
+         "RMSE":0.7191
+      },
+      "SNMD":{
+         "AUC":0.6244
+      },
+      "SNMR":{
+         "F1":0.4891
+      },
+      "ArchiveII":{
+         "F1":0.9498
+      },
+      "bpRNA":{
+         "F1":0.8234
+      },
+      "RNAStralign":{
+         "F1":0.9901
+      }
+   }
+}

yangheng/yangheng/OmniGenome/OmniGenome186MResults

@@ -0,0 +1,39 @@
+{
+   "config":{
+      "model":"omnigenome-186M",
+      "model_args":"pretrained=yangheng/OmniGenome-186M,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"SNT", "# of Params":"186M", "Pretraining Data":"54.2B Tokens", "Species":"1124 Plant Species", "Nucleic Acid":"mRNA, CDS, UTR"},
+      "model_dtype":"bfloat16",
+      "model_name":"OmniGenome-52M",
+      "model_sha":"main"
+   },
+   "results":{
+      "mRNA":{
+         "RMSE":0.7164
+      },
+      "SNMD":{
+         "AUC":63.81
+      },
+      "SNMR":{
+         "F1":49.80
+      },
+      "ArchiveII":{
+         "F1":95.20
+      },
+      "bpRNA":{
+         "F1":82.48
+      },
+      "RNAStralign":{
+         "F1":99.12
+      }
+   }
+}

yangheng/yangheng/OmniGenome/OmniGenomeResults.json

@@ -0,0 +1,39 @@
+{
+   "config":{
+      "model":"omnigenome-52M",
+      "model_args":"pretrained=yangheng/OmniGenome-52M,revision=main,dtype=bfloat16",
+      "num_fewshot":0,
+      "batch_size":1,
+      "batch_sizes":[
+         
+      ],
+      "device":"cpu",
+      "no_cache":true,
+      "limit":20,
+      "bootstrap_iters":100000,
+      "description_dict":{"Tokenization":"SNT", "# of Params":"52M", "Pretraining Data":"54.2B Tokens", "Species":"1124 Plant Species", "Nucleic Acid":"mRNA, CDS, UTR"},
+      "model_dtype":"bfloat16",
+      "model_name":"OmniGenome-52M",
+      "model_sha":"main"
+   },
+   "results":{
+      "mRNA":{
+         "RMSE":0.7191
+      },
+      "SNMD":{
+         "AUC":0.6244
+      },
+      "SNMR":{
+         "F1":0.4891
+      },
+      "ArchiveII":{
+         "F1":0.9498
+      },
+      "bpRNA":{
+         "F1":0.8234
+      },
+      "RNAStralign":{
+         "F1":0.9901
+      }
+   }
+}