LICENSE
README.md
pyproject.toml
dgeb/__init__.py
dgeb/cli.py
dgeb/dgeb.py
dgeb/eval_utils.py
dgeb/evaluators.py
dgeb/modality.py
dgeb/models.py
dgeb.egg-info/PKG-INFO
dgeb.egg-info/SOURCES.txt
dgeb.egg-info/dependency_links.txt
dgeb.egg-info/entry_points.txt
dgeb.egg-info/requires.txt
dgeb.egg-info/top_level.txt
dgeb/tasks/__init__.py
dgeb/tasks/bigene_mining_tasks.py
dgeb/tasks/classification_tasks.py
dgeb/tasks/clustering_tasks.py
dgeb/tasks/eds_tasks.py
dgeb/tasks/pair_classification_tasks.py
dgeb/tasks/retrieval_tasks.py
dgeb/tasks/tasks.py
leaderboard/submissions/esm2_t12_35M_UR50D/MIBIG_protein_classification.json
leaderboard/submissions/esm2_t12_35M_UR50D/arch_retrieval.json
leaderboard/submissions/esm2_t12_35M_UR50D/bacarch_bigene.json
leaderboard/submissions/esm2_t12_35M_UR50D/convergent_enzymes_classification.json
leaderboard/submissions/esm2_t12_35M_UR50D/cyano_operonic_pair.json
leaderboard/submissions/esm2_t12_35M_UR50D/ec_classification.json
leaderboard/submissions/esm2_t12_35M_UR50D/ecoli_operonic_pair.json
leaderboard/submissions/esm2_t12_35M_UR50D/euk_retrieval.json
leaderboard/submissions/esm2_t12_35M_UR50D/fefe_phylogeny.json
leaderboard/submissions/esm2_t12_35M_UR50D/modac_paralogy_bigene.json
leaderboard/submissions/esm2_t12_35M_UR50D/mopb_clustering.json
leaderboard/submissions/esm2_t12_35M_UR50D/rpob_arch_phylogeny.json
leaderboard/submissions/esm2_t12_35M_UR50D/rpob_bac_phylogeny.json
leaderboard/submissions/esm2_t12_35M_UR50D/vibrio_operonic_pair.json
leaderboard/submissions/esm2_t30_150M_UR50D/MIBIG_protein_classification.json
leaderboard/submissions/esm2_t30_150M_UR50D/arch_retrieval.json
leaderboard/submissions/esm2_t30_150M_UR50D/bacarch_bigene.json
leaderboard/submissions/esm2_t30_150M_UR50D/convergent_enzymes_classification.json
leaderboard/submissions/esm2_t30_150M_UR50D/cyano_operonic_pair.json
leaderboard/submissions/esm2_t30_150M_UR50D/ec_classification.json
leaderboard/submissions/esm2_t30_150M_UR50D/ecoli_operonic_pair.json
leaderboard/submissions/esm2_t30_150M_UR50D/euk_retrieval.json
leaderboard/submissions/esm2_t30_150M_UR50D/fefe_phylogeny.json
leaderboard/submissions/esm2_t30_150M_UR50D/modac_paralogy_bigene.json
leaderboard/submissions/esm2_t30_150M_UR50D/mopb_clustering.json
leaderboard/submissions/esm2_t30_150M_UR50D/rpob_arch_phylogeny.json
leaderboard/submissions/esm2_t30_150M_UR50D/rpob_bac_phylogeny.json
leaderboard/submissions/esm2_t30_150M_UR50D/vibrio_operonic_pair.json
leaderboard/submissions/esm2_t33_650M_UR50D/MIBIG_protein_classification.json
leaderboard/submissions/esm2_t33_650M_UR50D/arch_retrieval.json
leaderboard/submissions/esm2_t33_650M_UR50D/bacarch_bigene.json
leaderboard/submissions/esm2_t33_650M_UR50D/convergent_enzymes_classification.json
leaderboard/submissions/esm2_t33_650M_UR50D/cyano_operonic_pair.json
leaderboard/submissions/esm2_t33_650M_UR50D/ec_classification.json
leaderboard/submissions/esm2_t33_650M_UR50D/ecoli_operonic_pair.json
leaderboard/submissions/esm2_t33_650M_UR50D/euk_retrieval.json
leaderboard/submissions/esm2_t33_650M_UR50D/fefe_phylogeny.json
leaderboard/submissions/esm2_t33_650M_UR50D/modac_paralogy_bigene.json
leaderboard/submissions/esm2_t33_650M_UR50D/mopb_clustering.json
leaderboard/submissions/esm2_t33_650M_UR50D/rpob_arch_phylogeny.json
leaderboard/submissions/esm2_t33_650M_UR50D/rpob_bac_phylogeny.json
leaderboard/submissions/esm2_t33_650M_UR50D/vibrio_operonic_pair.json
leaderboard/submissions/esm2_t36_3B_UR50D/MIBIG_protein_classification.json
leaderboard/submissions/esm2_t36_3B_UR50D/arch_retrieval.json
leaderboard/submissions/esm2_t36_3B_UR50D/bacarch_bigene.json
leaderboard/submissions/esm2_t36_3B_UR50D/convergent_enzymes_classification.json
leaderboard/submissions/esm2_t36_3B_UR50D/cyano_operonic_pair.json
leaderboard/submissions/esm2_t36_3B_UR50D/ec_classification.json
leaderboard/submissions/esm2_t36_3B_UR50D/ecoli_operonic_pair.json
leaderboard/submissions/esm2_t36_3B_UR50D/euk_retrieval.json
leaderboard/submissions/esm2_t36_3B_UR50D/fefe_phylogeny.json
leaderboard/submissions/esm2_t36_3B_UR50D/modac_paralogy_bigene.json
leaderboard/submissions/esm2_t36_3B_UR50D/mopb_clustering.json
leaderboard/submissions/esm2_t36_3B_UR50D/rpob_arch_phylogeny.json
leaderboard/submissions/esm2_t36_3B_UR50D/rpob_bac_phylogeny.json
leaderboard/submissions/esm2_t36_3B_UR50D/vibrio_operonic_pair.json
leaderboard/submissions/esm2_t6_8M_UR50D/MIBIG_protein_classification.json
leaderboard/submissions/esm2_t6_8M_UR50D/arch_retrieval.json
leaderboard/submissions/esm2_t6_8M_UR50D/bacarch_bigene.json
leaderboard/submissions/esm2_t6_8M_UR50D/convergent_enzymes_classification.json
leaderboard/submissions/esm2_t6_8M_UR50D/cyano_operonic_pair.json
leaderboard/submissions/esm2_t6_8M_UR50D/ec_classification.json
leaderboard/submissions/esm2_t6_8M_UR50D/ecoli_operonic_pair.json
leaderboard/submissions/esm2_t6_8M_UR50D/euk_retrieval.json
leaderboard/submissions/esm2_t6_8M_UR50D/fefe_phylogeny.json
leaderboard/submissions/esm2_t6_8M_UR50D/modac_paralogy_bigene.json
leaderboard/submissions/esm2_t6_8M_UR50D/mopb_clustering.json
leaderboard/submissions/esm2_t6_8M_UR50D/rpob_arch_phylogeny.json
leaderboard/submissions/esm2_t6_8M_UR50D/rpob_bac_phylogeny.json
leaderboard/submissions/esm2_t6_8M_UR50D/vibrio_operonic_pair.json
leaderboard/submissions/esm3_sm_open_v1/MIBIG_protein_classification.json
leaderboard/submissions/esm3_sm_open_v1/arch_retrieval.json
leaderboard/submissions/esm3_sm_open_v1/bacarch_bigene.json
leaderboard/submissions/esm3_sm_open_v1/convergent_enzymes_classification.json
leaderboard/submissions/esm3_sm_open_v1/cyano_operonic_pair.json
leaderboard/submissions/esm3_sm_open_v1/ec_classification.json
leaderboard/submissions/esm3_sm_open_v1/ecoli_operonic_pair.json
leaderboard/submissions/esm3_sm_open_v1/euk_retrieval.json
leaderboard/submissions/esm3_sm_open_v1/fefe_phylogeny.json
leaderboard/submissions/esm3_sm_open_v1/modac_paralogy_bigene.json
leaderboard/submissions/esm3_sm_open_v1/mopb_clustering.json
leaderboard/submissions/esm3_sm_open_v1/rpob_arch_phylogeny.json
leaderboard/submissions/esm3_sm_open_v1/rpob_bac_phylogeny.json
leaderboard/submissions/esm3_sm_open_v1/vibrio_operonic_pair.json
leaderboard/submissions/evo-1-131k-base/MIBIG_dna_classification.json
leaderboard/submissions/evo-1-131k-base/arch_16S_phylogeny.json
leaderboard/submissions/evo-1-131k-base/bac_16S_phylogeny.json
leaderboard/submissions/evo-1-131k-base/ec_dna_classification.json
leaderboard/submissions/evo-1-131k-base/ecoli_rna_clustering.json
leaderboard/submissions/evo-1-131k-base/euk_18S_phylogeny.json
leaderboard/submissions/evo-1-131k-base/rpob_arch_dna_phylogeny.json
leaderboard/submissions/evo-1-131k-base/rpob_bac_dna_phylogeny.json
leaderboard/submissions/evo-1-8k-base/MIBIG_dna_classification.json
leaderboard/submissions/evo-1-8k-base/arch_16S_phylogeny.json
leaderboard/submissions/evo-1-8k-base/bac_16S_phylogeny.json
leaderboard/submissions/evo-1-8k-base/ec_dna_classification.json
leaderboard/submissions/evo-1-8k-base/ecoli_rna_clustering.json
leaderboard/submissions/evo-1-8k-base/euk_18S_phylogeny.json
leaderboard/submissions/evo-1-8k-base/rpob_arch_dna_phylogeny.json
leaderboard/submissions/evo-1-8k-base/rpob_bac_dna_phylogeny.json
leaderboard/submissions/nucleotide-transformer-v2-100m-multi-species/MIBIG_dna_classification.json
leaderboard/submissions/nucleotide-transformer-v2-100m-multi-species/arch_16S_phylogeny.json
leaderboard/submissions/nucleotide-transformer-v2-100m-multi-species/bac_16S_phylogeny.json
leaderboard/submissions/nucleotide-transformer-v2-100m-multi-species/ec_dna_classification.json
leaderboard/submissions/nucleotide-transformer-v2-100m-multi-species/ecoli_rna_clustering.json
leaderboard/submissions/nucleotide-transformer-v2-100m-multi-species/euk_18S_phylogeny.json
leaderboard/submissions/nucleotide-transformer-v2-100m-multi-species/rpob_arch_dna_phylogeny.json
leaderboard/submissions/nucleotide-transformer-v2-100m-multi-species/rpob_bac_dna_phylogeny.json
leaderboard/submissions/nucleotide-transformer-v2-250m-multi-species/MIBIG_dna_classification.json
leaderboard/submissions/nucleotide-transformer-v2-250m-multi-species/arch_16S_phylogeny.json
leaderboard/submissions/nucleotide-transformer-v2-250m-multi-species/bac_16S_phylogeny.json
leaderboard/submissions/nucleotide-transformer-v2-250m-multi-species/ec_dna_classification.json
leaderboard/submissions/nucleotide-transformer-v2-250m-multi-species/ecoli_rna_clustering.json
leaderboard/submissions/nucleotide-transformer-v2-250m-multi-species/euk_18S_phylogeny.json
leaderboard/submissions/nucleotide-transformer-v2-250m-multi-species/rpob_arch_dna_phylogeny.json
leaderboard/submissions/nucleotide-transformer-v2-250m-multi-species/rpob_bac_dna_phylogeny.json
leaderboard/submissions/nucleotide-transformer-v2-500m-multi-species/MIBIG_dna_classification.json
leaderboard/submissions/nucleotide-transformer-v2-500m-multi-species/arch_16S_phylogeny.json
leaderboard/submissions/nucleotide-transformer-v2-500m-multi-species/bac_16S_phylogeny.json
leaderboard/submissions/nucleotide-transformer-v2-500m-multi-species/ec_dna_classification.json
leaderboard/submissions/nucleotide-transformer-v2-500m-multi-species/ecoli_rna_clustering.json
leaderboard/submissions/nucleotide-transformer-v2-500m-multi-species/euk_18S_phylogeny.json
leaderboard/submissions/nucleotide-transformer-v2-500m-multi-species/rpob_arch_dna_phylogeny.json
leaderboard/submissions/nucleotide-transformer-v2-500m-multi-species/rpob_bac_dna_phylogeny.json
leaderboard/submissions/nucleotide-transformer-v2-50m-multi-species/MIBIG_dna_classification.json
leaderboard/submissions/nucleotide-transformer-v2-50m-multi-species/arch_16S_phylogeny.json
leaderboard/submissions/nucleotide-transformer-v2-50m-multi-species/bac_16S_phylogeny.json
leaderboard/submissions/nucleotide-transformer-v2-50m-multi-species/ec_dna_classification.json
leaderboard/submissions/nucleotide-transformer-v2-50m-multi-species/ecoli_rna_clustering.json
leaderboard/submissions/nucleotide-transformer-v2-50m-multi-species/euk_18S_phylogeny.json
leaderboard/submissions/nucleotide-transformer-v2-50m-multi-species/rpob_arch_dna_phylogeny.json
leaderboard/submissions/nucleotide-transformer-v2-50m-multi-species/rpob_bac_dna_phylogeny.json
leaderboard/submissions/progen2-large/MIBIG_protein_classification.json
leaderboard/submissions/progen2-large/arch_retrieval.json
leaderboard/submissions/progen2-large/bacarch_bigene.json
leaderboard/submissions/progen2-large/convergent_enzymes_classification.json
leaderboard/submissions/progen2-large/cyano_operonic_pair.json
leaderboard/submissions/progen2-large/ec_classification.json
leaderboard/submissions/progen2-large/ecoli_operonic_pair.json
leaderboard/submissions/progen2-large/euk_retrieval.json
leaderboard/submissions/progen2-large/fefe_phylogeny.json
leaderboard/submissions/progen2-large/modac_paralogy_bigene.json
leaderboard/submissions/progen2-large/mopb_clustering.json
leaderboard/submissions/progen2-large/rpob_arch_phylogeny.json
leaderboard/submissions/progen2-large/rpob_bac_phylogeny.json
leaderboard/submissions/progen2-large/vibrio_operonic_pair.json
leaderboard/submissions/progen2-medium/MIBIG_protein_classification.json
leaderboard/submissions/progen2-medium/arch_retrieval.json
leaderboard/submissions/progen2-medium/bacarch_bigene.json
leaderboard/submissions/progen2-medium/convergent_enzymes_classification.json
leaderboard/submissions/progen2-medium/cyano_operonic_pair.json
leaderboard/submissions/progen2-medium/ec_classification.json
leaderboard/submissions/progen2-medium/ecoli_operonic_pair.json
leaderboard/submissions/progen2-medium/euk_retrieval.json
leaderboard/submissions/progen2-medium/fefe_phylogeny.json
leaderboard/submissions/progen2-medium/modac_paralogy_bigene.json
leaderboard/submissions/progen2-medium/mopb_clustering.json
leaderboard/submissions/progen2-medium/rpob_arch_phylogeny.json
leaderboard/submissions/progen2-medium/rpob_bac_phylogeny.json
leaderboard/submissions/progen2-medium/vibrio_operonic_pair.json
leaderboard/submissions/progen2-small/MIBIG_protein_classification.json
leaderboard/submissions/progen2-small/arch_retrieval.json
leaderboard/submissions/progen2-small/bacarch_bigene.json
leaderboard/submissions/progen2-small/convergent_enzymes_classification.json
leaderboard/submissions/progen2-small/cyano_operonic_pair.json
leaderboard/submissions/progen2-small/ec_classification.json
leaderboard/submissions/progen2-small/ecoli_operonic_pair.json
leaderboard/submissions/progen2-small/euk_retrieval.json
leaderboard/submissions/progen2-small/fefe_phylogeny.json
leaderboard/submissions/progen2-small/modac_paralogy_bigene.json
leaderboard/submissions/progen2-small/mopb_clustering.json
leaderboard/submissions/progen2-small/rpob_arch_phylogeny.json
leaderboard/submissions/progen2-small/rpob_bac_phylogeny.json
leaderboard/submissions/progen2-small/vibrio_operonic_pair.json
leaderboard/submissions/progen2-xlarge/MIBIG_protein_classification.json
leaderboard/submissions/progen2-xlarge/arch_retrieval.json
leaderboard/submissions/progen2-xlarge/bacarch_bigene.json
leaderboard/submissions/progen2-xlarge/convergent_enzymes_classification.json
leaderboard/submissions/progen2-xlarge/cyano_operonic_pair.json
leaderboard/submissions/progen2-xlarge/ec_classification.json
leaderboard/submissions/progen2-xlarge/ecoli_operonic_pair.json
leaderboard/submissions/progen2-xlarge/euk_retrieval.json
leaderboard/submissions/progen2-xlarge/fefe_phylogeny.json
leaderboard/submissions/progen2-xlarge/modac_paralogy_bigene.json
leaderboard/submissions/progen2-xlarge/mopb_clustering.json
leaderboard/submissions/progen2-xlarge/rpob_arch_phylogeny.json
leaderboard/submissions/progen2-xlarge/rpob_bac_phylogeny.json
leaderboard/submissions/progen2-xlarge/vibrio_operonic_pair.json
leaderboard/submissions/prot_t5_xl_bfd/MIBIG_protein_classification.json
leaderboard/submissions/prot_t5_xl_bfd/arch_retrieval.json
leaderboard/submissions/prot_t5_xl_bfd/bacarch_bigene.json
leaderboard/submissions/prot_t5_xl_bfd/convergent_enzymes_classification.json
leaderboard/submissions/prot_t5_xl_bfd/cyano_operonic_pair.json
leaderboard/submissions/prot_t5_xl_bfd/ec_classification.json
leaderboard/submissions/prot_t5_xl_bfd/ecoli_operonic_pair.json
leaderboard/submissions/prot_t5_xl_bfd/euk_retrieval.json
leaderboard/submissions/prot_t5_xl_bfd/fefe_phylogeny.json
leaderboard/submissions/prot_t5_xl_bfd/modac_paralogy_bigene.json
leaderboard/submissions/prot_t5_xl_bfd/mopb_clustering.json
leaderboard/submissions/prot_t5_xl_bfd/rpob_arch_phylogeny.json
leaderboard/submissions/prot_t5_xl_bfd/rpob_bac_phylogeny.json
leaderboard/submissions/prot_t5_xl_bfd/vibrio_operonic_pair.json
leaderboard/submissions/prot_t5_xl_uniref50/MIBIG_protein_classification.json
leaderboard/submissions/prot_t5_xl_uniref50/arch_retrieval.json
leaderboard/submissions/prot_t5_xl_uniref50/bacarch_bigene.json
leaderboard/submissions/prot_t5_xl_uniref50/convergent_enzymes_classification.json
leaderboard/submissions/prot_t5_xl_uniref50/cyano_operonic_pair.json
leaderboard/submissions/prot_t5_xl_uniref50/ec_classification.json
leaderboard/submissions/prot_t5_xl_uniref50/ecoli_operonic_pair.json
leaderboard/submissions/prot_t5_xl_uniref50/euk_retrieval.json
leaderboard/submissions/prot_t5_xl_uniref50/fefe_phylogeny.json
leaderboard/submissions/prot_t5_xl_uniref50/modac_paralogy_bigene.json
leaderboard/submissions/prot_t5_xl_uniref50/mopb_clustering.json
leaderboard/submissions/prot_t5_xl_uniref50/rpob_arch_phylogeny.json
leaderboard/submissions/prot_t5_xl_uniref50/rpob_bac_phylogeny.json
leaderboard/submissions/prot_t5_xl_uniref50/vibrio_operonic_pair.json
scripts/eval_all_models.py
scripts/plot_benchmarks.py