config
dict | results
dict |
|---|---|
{
"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"
} | {
"mRNA": {
"RMSE": 0.7772
},
"SNMD": {
"AUC": 0.5002
},
"SNMR": {
"F1": 0.2401
},
"ArchiveII": {
"F1": 0.7898
},
"bpRNA": {
"F1": 0.5693
},
"RNAStralign": {
"F1": 0.9203
}
} |
{
"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"
} | {
"mRNA": {
"RMSE": 0.783
},
"SNMD": {
"AUC": 0.4999
},
"SNMR": {
"F1": 0.2638
},
"ArchiveII": {
"F1": 0.7013
},
"bpRNA": {
"F1": 0.4871
},
"RNAStralign": {
"F1": 0.7521
}
} |
{
"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"
} | {
"mRNA": {
"RMSE": 0.7468
},
"SNMD": {
"AUC": 0.5503
},
"SNMR": {
"F1": 0.3616
},
"ArchiveII": {
"F1": 0.8934
},
"bpRNA": {
"F1": 0.7001
},
"RNAStralign": {
"F1": 0.9715
}
} |
{
"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"
} | {
"mRNA": {
"RMSE": 0.8158
},
"SNMD": {
"AUC": 0.4994
},
"SNMR": {
"F1": 0.1586
},
"ArchiveII": {
"F1": 0.5982
},
"bpRNA": {
"F1": 0.434
},
"RNAStralign": {
"F1": 0.6549
}
} |
{
"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"
} | {
"mRNA": {
"RMSE": 0.8056
},
"SNMD": {
"AUC": 0.5332
},
"SNMR": {
"F1": 0.398
},
"ArchiveII": {
"F1": 0.8423
},
"bpRNA": {
"F1": 0.5662
},
"RNAStralign": {
"F1": 0.9542
}
} |
{
"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"
} | {
"mRNA": {
"RMSE": 0.7826
},
"SNMD": {
"AUC": 0.5049
},
"SNMR": {
"F1": 0.2601
},
"ArchiveII": {
"F1": 0.799
},
"bpRNA": {
"F1": 0.566
},
"RNAStralign": {
"F1": 0.9084
}
} |
{
"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"
} | {
"mRNA": {
"RMSE": 0.7164
},
"SNMD": {
"AUC": 0.6381
},
"SNMR": {
"F1": 0.498
},
"ArchiveII": {
"F1": 0.952
},
"bpRNA": {
"F1": 0.8248
},
"RNAStralign": {
"F1": 0.9912
}
} |
{
"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"
} | {
"mRNA": {
"RMSE": 0.734
},
"SNMD": {
"AUC": 0.5811
},
"SNMR": {
"F1": 0.4644
},
"ArchiveII": {
"F1": 0.8905
},
"bpRNA": {
"F1": 0.691
},
"RNAStralign": {
"F1": 0.9697
}
} |
{
"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"
} | {
"mRNA": {
"RMSE": 0.7191
},
"SNMD": {
"AUC": 0.6244
},
"SNMR": {
"F1": 0.4891
},
"ArchiveII": {
"F1": 0.9498
},
"bpRNA": {
"F1": 0.8234
},
"RNAStralign": {
"F1": 0.9901
}
} |
{
"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"
} | {
"mRNA": {
"RMSE": 0.7191
},
"SNMD": {
"AUC": 0.6244
},
"SNMR": {
"F1": 0.4891
},
"ArchiveII": {
"F1": 0.9498
},
"bpRNA": {
"F1": 0.8234
},
"RNAStralign": {
"F1": 0.9901
}
} |