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{ "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 } }