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-former_processing_embedding_id,embedding_id,n_genes,dimension,dtype,npz_array_key,embeddings_npz,genes_tsv,metadata_json,status,modality,embedding_name,download_source,original_model_or_method,embedding_generated_by,model_checkpoint,pooling_strategy,license,file_size_bytes
-alphagenome_tss1mb_regulatory_tracksummary_pca256_v1_1,alphagenome_tss1mb_regulatory_tracksummary_pca256,20084,256,float32,embeddings,data/embeddings/alphagenome_tss1mb_regulatory_tracksummary_pca256/embeddings.npz,data/embeddings/alphagenome_tss1mb_regulatory_tracksummary_pca256/genes.tsv,data/embeddings/alphagenome_tss1mb_regulatory_tracksummary_pca256/metadata.json,processed_qc_passed,,AlphaGenome-TSS1Mb-regulatoryTrackSummary-PCA256-v1.1,,,,,,,19270344
-basenji2_tss_131kb_human_central3_v1_1,basenji2_tss_131kb_human_central3,20097,5313,float32,embeddings,data/embeddings/basenji2_tss_131kb_human_central3/embeddings.npz,data/embeddings/basenji2_tss_131kb_human_central3/genes.tsv,data/embeddings/basenji2_tss_131kb_human_central3/metadata.json,processed_qc_passed,regulatory DNA / Basenji2 TSS sequence model,Basenji2-TSS-131kb-human-central3-log1p-zscore-v1.1,,,,,,,389641898
-biobert_gene_protein_summary_v1_1,biobert_gene_protein_summary,19168,768,float32,embeddings,data/embeddings/biobert_gene_protein_summary/embeddings.npz,data/embeddings/biobert_gene_protein_summary/genes.tsv,data/embeddings/biobert_gene_protein_summary/metadata.json,,literature_text_gene_summary,BioBERT-GeneProteinSummary-v1.1,GenePT Zenodo v2 summaries,,Daniel locally,dmis-lab/biobert-base-cased-v1.2,"final hidden layer mean pooling over valid non-special, non-padding tokens",,54606212
-bioconceptvec_cbow_v1_1,bioconceptvec_cbow,17040,100,float32,embeddings,data/embeddings/bioconceptvec_cbow/embeddings.npz,data/embeddings/bioconceptvec_cbow/genes.tsv,data/embeddings/bioconceptvec_cbow/metadata.json,,biomedical_literature_text,BioConceptVec-CBOW-v1.1,,,,,,,6339061
-bioconceptvec_fasttext_v1_1,bioconceptvec_fasttext,17040,100,float32,embeddings,data/embeddings/bioconceptvec_fasttext/embeddings.npz,data/embeddings/bioconceptvec_fasttext/genes.tsv,data/embeddings/bioconceptvec_fasttext/metadata.json,,biomedical_literature_text,BioConceptVec-fastText-v1.1,,,,,,,6254929
-bioconceptvec_glove_v1_1,bioconceptvec_glove,17040,100,float32,embeddings,data/embeddings/bioconceptvec_glove/embeddings.npz,data/embeddings/bioconceptvec_glove/genes.tsv,data/embeddings/bioconceptvec_glove/metadata.json,,biomedical_literature_text,BioConceptVec-GloVe-v1.1,,,,,,,6350146
-bioconceptvec_skipgram_v1_1,bioconceptvec_skipgram,17040,100,float32,embeddings,data/embeddings/bioconceptvec_skipgram/embeddings.npz,data/embeddings/bioconceptvec_skipgram/genes.tsv,data/embeddings/bioconceptvec_skipgram/metadata.json,,biomedical_literature_text,BioConceptVec-SkipGram-v1.1,,,,,,,6335039
-cmap_gse106127_cgs_mean_landmark978_zscore_v1_1,cmap_gse106127_cgs_mean_landmark978_zscore,4070,978,float32,embeddings,data/embeddings/cmap_gse106127_cgs_mean_landmark978_zscore/embeddings.npz,data/embeddings/cmap_gse106127_cgs_mean_landmark978_zscore/genes.tsv,data/embeddings/cmap_gse106127_cgs_mean_landmark978_zscore/metadata.json,processed_qc_passed,perturbational transcriptomics / L1000 consensus genetic perturbation signatures,CMap-GSE106127-CGS-mean-landmark978-zscore-v1.1,,,,,,,14768959
-deepnf_string_v12_ppmi_svd_fusion_v1_1,deepnf_string_v12_ppmi_svd_fusion,19071,256,float32,embeddings,data/embeddings/deepnf_string_v12_ppmi_svd_fusion/embeddings.npz,data/embeddings/deepnf_string_v12_ppmi_svd_fusion/genes.tsv,data/embeddings/deepnf_string_v12_ppmi_svd_fusion/metadata.json,,STRING network multimodal sparse PPMI/SVD fusion,deepNF-STRING-v12-PPMI-SVD-fusion-v1.1,"STRING v12 human protein.links.detailed, protein.info, and protein.aliases files",deepNF: deep network fusion for protein function prediction,Daniel locally from STRING v12 channel networks,,,,18225284
-deepsea_tss_1kb_epigenomic_probs_v1_1,deepsea_tss_1kb_epigenomic_probs,20097,919,float32,embeddings,data/embeddings/deepsea_tss_1kb_epigenomic_probs/embeddings.npz,data/embeddings/deepsea_tss_1kb_epigenomic_probs/genes.tsv,data/embeddings/deepsea_tss_1kb_epigenomic_probs/metadata.json,processed_qc_passed,regulatory DNA / promoter-TSS sequence model,DeepSEA-TSS-1kb-epigenomic-probabilities-zscore-v1.1,,,,,,,66380222
-depmap_crispr_gene_effect_pca256_v1_1,depmap_crispr_gene_effect_pca256,18562,256,float32,embeddings,data/embeddings/depmap_crispr_gene_effect_pca256/embeddings.npz,data/embeddings/depmap_crispr_gene_effect_pca256/genes.tsv,data/embeddings/depmap_crispr_gene_effect_pca256/metadata.json,processed_qc_passed,functional genomics / CRISPR dependency,DepMap-CRISPRGeneEffect-PCA256-v1.1,,,,,,,17729467
-dnabert2_117m_cds_v1_1,dnabert2_117m_cds,20085,768,float32,embeddings,data/embeddings/dnabert2_117m_cds/embeddings.npz,data/embeddings/dnabert2_117m_cds/genes.tsv,data/embeddings/dnabert2_117m_cds/metadata.json,processed_qc_passed,,dnabert2_117m_cds_v1_1,,,,,"Mean pooling over final-layer non-special token embeddings. Long CDS sequences split into nucleotide chunks, then length-weighted mean of chunk-level embeddings.",,57063502
-enformer_tss_393kb_human_central3_v1_1,enformer_tss_393kb_human_central3,20097,5313,float32,embeddings,data/embeddings/enformer_tss_393kb_human_central3/embeddings.npz,data/embeddings/enformer_tss_393kb_human_central3/genes.tsv,data/embeddings/enformer_tss_393kb_human_central3/metadata.json,processed_qc_passed,regulatory DNA / long-range TSS sequence model,Enformer-TSS-393kb-human-central3-log1p-zscore-v1.1,,,,,,,390033274
-esm2_v1_1,esm2,18690,1280,float32,embeddings,data/embeddings/esm2/embeddings.npz,data/embeddings/esm2/genes.tsv,data/embeddings/esm2/metadata.json,,protein_sequence,ESM2-v1.1,,,,,,,88766138
-frogs_archs4_256_v1_1,frogs_archs4_256,16265,256,float32,embeddings,data/embeddings/frogs_archs4_256/embeddings.npz,data/embeddings/frogs_archs4_256/genes.tsv,data/embeddings/frogs_archs4_256/metadata.json,processed_qc_passed,,frogs_archs4_256_v1_1,,,,,,,15433953
-gene2vec_v1_1,gene2vec,17916,200,float32,embeddings,data/embeddings/gene2vec/embeddings.npz,data/embeddings/gene2vec/genes.tsv,data/embeddings/gene2vec/metadata.json,,coexpression_expression,Gene2Vec-v1.1,,,,,,,13292179
-genecompass_base_gene_token_v1_1,genecompass_base_gene_token,16578,768,float32,embeddings,data/embeddings/genecompass_base_gene_token/embeddings.npz,data/embeddings/genecompass_base_gene_token/genes.tsv,data/embeddings/genecompass_base_gene_token/metadata.json,processed_qc_passed,gene expression single-cell foundation model / knowledge-informed gene-token embedding,genecompass_base_gene_token_v1_1,official GeneCompass ScienceDB checkpoint linked from official GitHub README,"GeneCompass Base, 12-layer knowledge-informed cross-species foundation model",Daniel locally by extracting checkpoint embedding weights; no training or inference,,none; static learned token embedding weight extracted directly from checkpoint,,47272177
-geneformer_v2_316m_v1_1,geneformer_v2_316m,20007,1152,float32,embeddings,data/embeddings/geneformer_v2_316m/embeddings.npz,data/embeddings/geneformer_v2_316m/genes.tsv,data/embeddings/geneformer_v2_316m/metadata.json,,single_cell_expression_foundation_model,Geneformer-V2-316M-v1.1,Official ctheodoris/Geneformer Hugging Face repository,,Extracted locally from official Geneformer model input gene-token embedding layer,,,,85511948
-genept_ada_v1_1_conservative,genept_ada_conservative,19099,1536,float32,embeddings,data/embeddings/genept_ada_conservative/embeddings.npz,data/embeddings/genept_ada_conservative/genes.tsv,data/embeddings/genept_ada_conservative/metadata.json,,biomedical_literature_text,GenePT-ADA-v1.1-conservative,,,,,,,98626668
-genept_model3_gene_protein_v1_1_conservative,genept_model3_gene_protein_conservative,19103,3072,float32,embeddings,data/embeddings/genept_model3_gene_protein_conservative/embeddings.npz,data/embeddings/genept_model3_gene_protein_conservative/genes.tsv,data/embeddings/genept_model3_gene_protein_conservative/metadata.json,,biomedical_literature_text_plus_protein_sequence_text,GenePT-Model3-GeneProtein-v1.1-conservative,,,,,,,189551495
-gtex_tissue_median_log1p_zscore_v1_1,gtex_tissue_median_log1p_zscore,19353,68,float32,embeddings,data/embeddings/gtex_tissue_median_log1p_zscore/embeddings.npz,data/embeddings/gtex_tissue_median_log1p_zscore/genes.tsv,data/embeddings/gtex_tissue_median_log1p_zscore/metadata.json,processed_qc_passed,bulk RNA expression / normal tissue expression,GTEx-tissue-median-log1p-zscore-v1.1,,,,,,,4485371
-helix_mrna_full_transcript_v1_1,helix_mrna_full_transcript,19976,256,float32,embeddings,data/embeddings/helix_mrna_full_transcript/embeddings.npz,data/embeddings/helix_mrna_full_transcript/genes.tsv,data/embeddings/helix_mrna_full_transcript/metadata.json,processed_qc_passed,mRNA language model / mature transcript sequence,helix_mrna_full_transcript_v1_1,official HuggingFace model repository,Helix-mRNA,Daniel locally by model inference,helical-ai/helix-mRNA,"final token embeddings from official Helix wrapper, mean pooled over non-special sequence tokens; long transcripts chunked and token-count weighted",,19474797
-hetionet_nonppi_biomedical_context_tfidf_svd256_v1_1,hetionet_nonppi_biomedical_context_tfidf_svd256,18787,256,float32,embeddings,data/embeddings/hetionet_nonppi_biomedical_context_tfidf_svd256/embeddings.npz,data/embeddings/hetionet_nonppi_biomedical_context_tfidf_svd256/genes.tsv,data/embeddings/hetionet_nonppi_biomedical_context_tfidf_svd256/metadata.json,processed_qc_passed,heterogeneous biomedical knowledge graph / non-PPI gene context,Hetionet-nonPPI-biomedical-context-TFIDF-SVD256-v1.1,,,,,,,17704572
-hpa_normal_ihc_tissue_level_zscore_v1_1,hpa_normal_ihc_tissue_level_zscore,13420,59,float32,embeddings,data/embeddings/hpa_normal_ihc_tissue_level_zscore/embeddings.npz,data/embeddings/hpa_normal_ihc_tissue_level_zscore/genes.tsv,data/embeddings/hpa_normal_ihc_tissue_level_zscore/metadata.json,processed_qc_passed,protein expression / normal tissue immunohistochemistry,HPA-normal-IHC-tissue-level-zscore-v1.1,,,,,,,251036
-hpa_subcellular_location_multihot_zscore_v1_1,hpa_subcellular_location_multihot_zscore,13581,50,float32,embeddings,data/embeddings/hpa_subcellular_location_multihot_zscore/embeddings.npz,data/embeddings/hpa_subcellular_location_multihot_zscore/genes.tsv,data/embeddings/hpa_subcellular_location_multihot_zscore/metadata.json,processed_qc_passed,protein subcellular localization,HPA-subcellular-location-multihot-zscore-v1.1,,,,,,,38386
-hyenadna_medium_160k_cds_v1_1,hyenadna_medium_160k_cds,20085,256,float32,embeddings,data/embeddings/hyenadna_medium_160k_cds/embeddings.npz,data/embeddings/hyenadna_medium_160k_cds/genes.tsv,data/embeddings/hyenadna_medium_160k_cds/metadata.json,processed_qc_passed,DNA language model / canonical CDS sequence,hyenadna_medium_160k_cds_v1_1,official HuggingFace repository LongSafari/hyenadna-medium-160k-seqlen-hf,HyenaDNA medium 160k sequence-length checkpoint,Daniel locally by model inference,,final hidden-state mean pooling over non-special nucleotide tokens; long CDS split into chunks and token-count weighted,,18551316
-mahi_all_contexts_mean_v1_1,mahi_all_contexts_mean,18918,3666,float32,embeddings,data/embeddings/mahi_all_contexts_mean/embeddings.npz,data/embeddings/mahi_all_contexts_mean/genes.tsv,data/embeddings/mahi_all_contexts_mean/metadata.json,processed_qc_passed,,mahi_all_contexts_mean_v1_1,,,,,mean across all non-global tissue/cell contexts per Entrez gene,,245994508
-mahi_global_v1_1,mahi_global,18918,3666,float32,embeddings,data/embeddings/mahi_global/embeddings.npz,data/embeddings/mahi_global/genes.tsv,data/embeddings/mahi_global/metadata.json,processed_qc_passed,,mahi_global_v1_1,,,,,global context only,,167568851
-mashup_string_v1_1,mashup_string,16331,800,float32,embeddings,data/embeddings/mashup_string/embeddings.npz,data/embeddings/mashup_string/genes.tsv,data/embeddings/mashup_string/metadata.json,,network_ppi,Mashup-STRING-v1.1,,,,,,,47906054
-msa_transformer_depth1_uniprot_human_v1_1,msa_transformer_depth1_uniprot_human,19472,768,float32,embeddings,data/embeddings/msa_transformer_depth1_uniprot_human/embeddings.npz,data/embeddings/msa_transformer_depth1_uniprot_human/genes.tsv,data/embeddings/msa_transformer_depth1_uniprot_human/metadata.json,,protein_sequence_msa_transformer_depth1,MSATransformer-depth1-UniProt-human-v1.1,,MSA Transformer,Daniel locally,esm_msa1b_t12_100M_UR50S,mean residue representation from layer 12; long proteins split into non-overlapping windows and length-weighted mean pooled,,55476461
-newt_archs4_256_v1_1,newt_archs4_256,16265,256,float32,embeddings,data/embeddings/newt_archs4_256/embeddings.npz,data/embeddings/newt_archs4_256/genes.tsv,data/embeddings/newt_archs4_256/metadata.json,,multimodal functional/regulatory/co-expression/pathway gene embedding component from NEWT,NEWT-ARCHS4-256-v1.1,"Official NEWT Zenodo dataset release, DOI 10.5281/zenodo.19340318",NEWT component embedding,NEWT authors; processed locally into the project standard format,,,,15434849
-newt_cellnet_v1_1,newt_cellnet,17499,128,float32,embeddings,data/embeddings/newt_cellnet/embeddings.npz,data/embeddings/newt_cellnet/genes.tsv,data/embeddings/newt_cellnet/metadata.json,,multimodal functional/regulatory/co-expression/pathway gene embedding component from NEWT,NEWT-CellNet-v1.1,"Official NEWT Zenodo dataset release, DOI 10.5281/zenodo.19340318",NEWT component embedding,NEWT authors; processed locally into the project standard format,,,,8320324
-newt_go_256_v1_1,newt_go_256,13788,256,float32,embeddings,data/embeddings/newt_go_256/embeddings.npz,data/embeddings/newt_go_256/genes.tsv,data/embeddings/newt_go_256/metadata.json,,multimodal functional/regulatory/co-expression/pathway gene embedding component from NEWT,NEWT-GO-256-v1.1,"Official NEWT Zenodo dataset release, DOI 10.5281/zenodo.19340318",NEWT component embedding,NEWT authors; processed locally into the project standard format,,,,13109399
-newt_go_graph_v1_1,newt_go_graph,13788,256,float32,embeddings,data/embeddings/newt_go_graph/embeddings.npz,data/embeddings/newt_go_graph/genes.tsv,data/embeddings/newt_go_graph/metadata.json,,multimodal functional/regulatory/co-expression/pathway gene embedding component from NEWT,NEWT-GO-graph-v1.1,"Official NEWT Zenodo dataset release, DOI 10.5281/zenodo.19340318",NEWT component embedding,NEWT authors; processed locally into the project standard format,,,,13142698
-newt_msigdb_bundle_v1_1,newt_msigdb_bundle,15423,256,float32,embeddings,data/embeddings/newt_msigdb_bundle/embeddings.npz,data/embeddings/newt_msigdb_bundle/genes.tsv,data/embeddings/newt_msigdb_bundle/metadata.json,,multimodal functional/regulatory/co-expression/pathway gene embedding component from NEWT,NEWT-MSigDB-bundle-v1.1,"Official NEWT Zenodo dataset release, DOI 10.5281/zenodo.19340318",NEWT component embedding,NEWT authors; processed locally into the project standard format,,,,14773343
-node2vec_consensus_ppi_v1_1,node2vec_consensus_ppi,18356,128,float32,embeddings,data/embeddings/node2vec_consensus_ppi/embeddings.npz,data/embeddings/node2vec_consensus_ppi/genes.tsv,data/embeddings/node2vec_consensus_ppi/metadata.json,,PPI network embedding,Node2Vec-consensus-PPI-v1.1,ylaboratory/gene-embedding-benchmarks GitHub repository: src/other/preprocess_embedding/consensus.dat,node2vec: scalable feature learning for networks,Daniel locally from consensus.dat using reproducible random walks and Word2Vec skip-gram,,,,8710233
-nt_v2_500m_multispecies_cds_v1_1,nt_v2_500m_multispecies_cds,20085,1024,float32,embeddings,data/embeddings/nt_v2_500m_multispecies_cds/embeddings.npz,data/embeddings/nt_v2_500m_multispecies_cds/genes.tsv,data/embeddings/nt_v2_500m_multispecies_cds/metadata.json,processed_qc_passed,DNA language model / CDS sequence,nt_v2_500m_multispecies_cds_v1_1,official HuggingFace model repository,Nucleotide Transformer v2,Daniel locally by model inference,InstaDeepAI/nucleotide-transformer-v2-500m-multi-species,"final hidden layer mean pooling over non-special, non-padding tokens; chunk-weighted by token count for long CDS",,76371728
-opa2vec_goa_human_v1_1,opa2vec_goa_human,18660,200,float32,embeddings,data/embeddings/opa2vec_goa_human/embeddings.npz,data/embeddings/opa2vec_goa_human/genes.tsv,data/embeddings/opa2vec_goa_human/metadata.json,,Gene Ontology / ontology-annotation semantic embedding,OPA2Vec-GOA-human-v1.1,Gene Ontology go-basic.obo and GOA human GAF,OPA2Vec,Daniel locally using an OPA2Vec-derived Python 3 workflow,,,,13852912
-orthrus_base_4track_full_transcript_v1_1,orthrus_base_4track_full_transcript,19976,256,float32,embeddings,data/embeddings/orthrus_base_4track_full_transcript/embeddings.npz,data/embeddings/orthrus_base_4track_full_transcript/genes.tsv,data/embeddings/orthrus_base_4track_full_transcript/metadata.json,processed_qc_passed,,orthrus_base_4track_full_transcript_v1_1,,,,,"Orthrus representation() sequence-level embedding. For transcripts longer than max_full_len, length-weighted mean of chunk-level Orthrus embeddings.",,18950246
-primekg_nonppi_biomedical_context_tfidf_svd256_v1_1,primekg_nonppi_biomedical_context_tfidf_svd256,19216,256,float32,embeddings,data/embeddings/primekg_nonppi_biomedical_context_tfidf_svd256/embeddings.npz,data/embeddings/primekg_nonppi_biomedical_context_tfidf_svd256/genes.tsv,data/embeddings/primekg_nonppi_biomedical_context_tfidf_svd256/metadata.json,processed_qc_passed,heterogeneous biomedical knowledge graph / non-PPI gene context,PrimeKG-nonPPI-biomedical-context-TFIDF-SVD256-v1.1,,,,,,,18076131
-probe_aac_v1_1,probe_aac,18873,20,float32,embeddings,data/embeddings/probe_aac/embeddings.npz,data/embeddings/probe_aac/genes.tsv,data/embeddings/probe_aac/metadata.json,,protein sequence / protein representation from PROBE human UniProt archive,probe_aac_v1_1,Official PROBE human_representation_vectors.tar.gz archive from Zenodo record 5795850 plus official HUBioDataLab/PROBE repository,AAC,PROBE authors / original PROBE human representation archive,,,,982437
-probe_albert_v1_1,probe_albert,18453,4096,float32,embeddings,data/embeddings/probe_albert/embeddings.npz,data/embeddings/probe_albert/genes.tsv,data/embeddings/probe_albert/metadata.json,,protein sequence / protein representation from PROBE human UniProt archive,probe_albert_v1_1,Official PROBE human_representation_vectors.tar.gz archive from Zenodo record 5795850 plus official HUBioDataLab/PROBE repository,ALBERT,PROBE authors / original PROBE human representation archive,,,,280084766
-probe_apaac_v1_1,probe_apaac,18871,80,float32,embeddings,data/embeddings/probe_apaac/embeddings.npz,data/embeddings/probe_apaac/genes.tsv,data/embeddings/probe_apaac/metadata.json,,protein sequence / protein representation from PROBE human UniProt archive,probe_apaac_v1_1,Official PROBE human_representation_vectors.tar.gz archive from Zenodo record 5795850 plus official HUBioDataLab/PROBE repository,APAAC,PROBE authors / original PROBE human representation archive,,,,5430243
-probe_bert_bfd_v1_1,probe_bert_bfd,18453,1024,float32,embeddings,data/embeddings/probe_bert_bfd/embeddings.npz,data/embeddings/probe_bert_bfd/genes.tsv,data/embeddings/probe_bert_bfd/metadata.json,,protein sequence / protein representation from PROBE human UniProt archive,probe_bert_bfd_v1_1,Official PROBE human_representation_vectors.tar.gz archive from Zenodo record 5795850 plus official HUBioDataLab/PROBE repository,BERT-BFD,PROBE authors / original PROBE human representation archive,,,,70423891
-probe_bert_pfam_v1_1,probe_bert_pfam,18461,768,float32,embeddings,data/embeddings/probe_bert_pfam/embeddings.npz,data/embeddings/probe_bert_pfam/genes.tsv,data/embeddings/probe_bert_pfam/metadata.json,,protein sequence / protein representation from PROBE human UniProt archive,probe_bert_pfam_v1_1,Official PROBE human_representation_vectors.tar.gz archive from Zenodo record 5795850 plus official HUBioDataLab/PROBE repository,BERT-PFAM,PROBE authors / original PROBE human representation archive,,,,52703247
-probe_blast_v1_1,probe_blast,18873,20421,float32,embeddings,data/embeddings/probe_blast/embeddings.npz,data/embeddings/probe_blast/genes.tsv,data/embeddings/probe_blast/metadata.json,,protein sequence / protein representation from PROBE human UniProt archive,probe_blast_v1_1,Official PROBE human_representation_vectors.tar.gz archive from Zenodo record 5795850 plus official HUBioDataLab/PROBE repository,BLAST,PROBE authors / original PROBE human representation archive,,,,5517015
-probe_cpc_prot_v1_1,probe_cpc_prot,18453,512,float32,embeddings,data/embeddings/probe_cpc_prot/embeddings.npz,data/embeddings/probe_cpc_prot/genes.tsv,data/embeddings/probe_cpc_prot/metadata.json,,protein sequence / protein representation from PROBE human UniProt archive,probe_cpc_prot_v1_1,Official PROBE human_representation_vectors.tar.gz archive from Zenodo record 5795850 plus official HUBioDataLab/PROBE repository,CPC-PROT,PROBE authors / original PROBE human representation archive,,,,29870283
-probe_esmb1_v1_1,probe_esmb1,18453,1280,float32,embeddings,data/embeddings/probe_esmb1/embeddings.npz,data/embeddings/probe_esmb1/genes.tsv,data/embeddings/probe_esmb1/metadata.json,,protein sequence / protein representation from PROBE human UniProt archive,probe_esmb1_v1_1,Official PROBE human_representation_vectors.tar.gz archive from Zenodo record 5795850 plus official HUBioDataLab/PROBE repository,ESMB1,PROBE authors / original PROBE human representation archive,,,,87778870
-probe_gene2vec_uniprot_v1_1,probe_gene2vec_uniprot,17564,200,float32,embeddings,data/embeddings/probe_gene2vec_uniprot/embeddings.npz,data/embeddings/probe_gene2vec_uniprot/genes.tsv,data/embeddings/probe_gene2vec_uniprot/metadata.json,,protein sequence / protein representation from PROBE human UniProt archive,probe_gene2vec_uniprot_v1_1,Official PROBE human_representation_vectors.tar.gz archive from Zenodo record 5795850 plus official HUBioDataLab/PROBE repository,GENE2VEC,PROBE authors / original PROBE human representation archive,,,,13029054
-probe_hmmer_v1_1,probe_hmmer,18873,20421,float32,embeddings,data/embeddings/probe_hmmer/embeddings.npz,data/embeddings/probe_hmmer/genes.tsv,data/embeddings/probe_hmmer/metadata.json,,protein sequence / protein representation from PROBE human UniProt archive,probe_hmmer_v1_1,Official PROBE human_representation_vectors.tar.gz archive from Zenodo record 5795850 plus official HUBioDataLab/PROBE repository,HMMER,PROBE authors / original PROBE human representation archive,,,,18898149
-probe_ksep_v1_1,probe_ksep,18801,400,float32,embeddings,data/embeddings/probe_ksep/embeddings.npz,data/embeddings/probe_ksep/genes.tsv,data/embeddings/probe_ksep/metadata.json,,protein sequence / protein representation from PROBE human UniProt archive,probe_ksep_v1_1,Official PROBE human_representation_vectors.tar.gz archive from Zenodo record 5795850 plus official HUBioDataLab/PROBE repository,KSEP,PROBE authors / original PROBE human representation archive,,,,23775898
-probe_learned_vec_v1_1,probe_learned_vec,18873,64,float32,embeddings,data/embeddings/probe_learned_vec/embeddings.npz,data/embeddings/probe_learned_vec/genes.tsv,data/embeddings/probe_learned_vec/metadata.json,,protein sequence / protein representation from PROBE human UniProt archive,probe_learned_vec_v1_1,Official PROBE human_representation_vectors.tar.gz archive from Zenodo record 5795850 plus official HUBioDataLab/PROBE repository,LEARNED-VEC,PROBE authors / original PROBE human representation archive,,,,4489189
-probe_mut2vec_v1_1,probe_mut2vec,17445,300,float32,embeddings,data/embeddings/probe_mut2vec/embeddings.npz,data/embeddings/probe_mut2vec/genes.tsv,data/embeddings/probe_mut2vec/metadata.json,,protein sequence / protein representation from PROBE human UniProt archive,probe_mut2vec_v1_1,Official PROBE human_representation_vectors.tar.gz archive from Zenodo record 5795850 plus official HUBioDataLab/PROBE repository,MUT2VEC,PROBE authors / original PROBE human representation archive,,,,10844260
-probe_pfam_v1_1,probe_pfam,18873,6227,float32,embeddings,data/embeddings/probe_pfam/embeddings.npz,data/embeddings/probe_pfam/genes.tsv,data/embeddings/probe_pfam/metadata.json,,protein sequence / protein representation from PROBE human UniProt archive,probe_pfam_v1_1,Official PROBE human_representation_vectors.tar.gz archive from Zenodo record 5795850 plus official HUBioDataLab/PROBE repository,PFAM,PROBE authors / original PROBE human representation archive,,,,548968
-probe_protvec_v1_1,probe_protvec,18873,100,float32,embeddings,data/embeddings/probe_protvec/embeddings.npz,data/embeddings/probe_protvec/genes.tsv,data/embeddings/probe_protvec/metadata.json,,protein sequence / protein representation from PROBE human UniProt archive,probe_protvec_v1_1,Official PROBE human_representation_vectors.tar.gz archive from Zenodo record 5795850 plus official HUBioDataLab/PROBE repository,PROTVEC,PROBE authors / original PROBE human representation archive,,,,7066137
-probe_seqvec_v1_1,probe_seqvec,18873,1024,float32,embeddings,data/embeddings/probe_seqvec/embeddings.npz,data/embeddings/probe_seqvec/genes.tsv,data/embeddings/probe_seqvec/metadata.json,,protein sequence / protein representation from PROBE human UniProt archive,probe_seqvec_v1_1,Official PROBE human_representation_vectors.tar.gz archive from Zenodo record 5795850 plus official HUBioDataLab/PROBE repository,SEQVEC,PROBE authors / original PROBE human representation archive,,,,71841293
-probe_t5_v1_1,probe_t5,18453,1024,float32,embeddings,data/embeddings/probe_t5/embeddings.npz,data/embeddings/probe_t5/genes.tsv,data/embeddings/probe_t5/metadata.json,,protein sequence / protein representation from PROBE human UniProt archive,probe_t5_v1_1,Official PROBE human_representation_vectors.tar.gz archive from Zenodo record 5795850 plus official HUBioDataLab/PROBE repository,T5,PROBE authors / original PROBE human representation archive,,,,70153727
-probe_tcga_embedding_v1_1,probe_tcga_embedding,18221,50,float32,embeddings,data/embeddings/probe_tcga_embedding/embeddings.npz,data/embeddings/probe_tcga_embedding/genes.tsv,data/embeddings/probe_tcga_embedding/metadata.json,,protein sequence / protein representation from PROBE human UniProt archive,probe_tcga_embedding_v1_1,Official PROBE human_representation_vectors.tar.gz archive from Zenodo record 5795850 plus official HUBioDataLab/PROBE repository,TCGA-EMBEDDING,PROBE authors / original PROBE human representation archive,,,,3378621
-probe_unirep_v1_1,probe_unirep,18873,5700,float32,embeddings,data/embeddings/probe_unirep/embeddings.npz,data/embeddings/probe_unirep/genes.tsv,data/embeddings/probe_unirep/metadata.json,,protein sequence / protein representation from PROBE human UniProt archive,probe_unirep_v1_1,Official PROBE human_representation_vectors.tar.gz archive from Zenodo record 5795850 plus official HUBioDataLab/PROBE repository,UNIREP,PROBE authors / original PROBE human representation archive,,,,410932244
-probe_xlnet_v1_1,probe_xlnet,18453,1024,float32,embeddings,data/embeddings/probe_xlnet/embeddings.npz,data/embeddings/probe_xlnet/genes.tsv,data/embeddings/probe_xlnet/metadata.json,,protein sequence / protein representation from PROBE human UniProt archive,probe_xlnet_v1_1,Official PROBE human_representation_vectors.tar.gz archive from Zenodo record 5795850 plus official HUBioDataLab/PROBE repository,XLNET,PROBE authors / original PROBE human representation archive,,,,70519787
-pubmedbert_gene_protein_summary_v1_1,pubmedbert_gene_protein_summary,19168,768,float32,embeddings,data/embeddings/pubmedbert_gene_protein_summary/embeddings.npz,data/embeddings/pubmedbert_gene_protein_summary/genes.tsv,data/embeddings/pubmedbert_gene_protein_summary/metadata.json,,literature_text_gene_summary,PubMedBERT-GeneProteinSummary-v1.1,GenePT Zenodo v2 summaries,,Daniel locally,microsoft/BiomedNLP-BiomedBERT-base-uncased-abstract-fulltext,"final hidden layer mean pooling over valid non-special, non-padding tokens",,54786752
-rnafm_full_transcript_v1_1,rnafm_full_transcript,19976,640,float32,embeddings,data/embeddings/rnafm_full_transcript/embeddings.npz,data/embeddings/rnafm_full_transcript/genes.tsv,data/embeddings/rnafm_full_transcript/metadata.json,processed_qc_passed,,rnafm_full_transcript_v1_1,,,,/local/home/dtabares/data/raw_embeddings/rnafm_full_transcript_v1_1/hf_model/RNA-FM_pretrained.pth,Final layer 12 mean token pooling over real RNA tokens only; BOS/EOS excluded; long transcripts split into chunks and chunk means length-weighted,,47521441
-scfoundation_gene_pos_v1_1,scfoundation_gene_pos,19062,768,float32,embeddings,data/embeddings/scfoundation_gene_pos/embeddings.npz,data/embeddings/scfoundation_gene_pos/genes.tsv,data/embeddings/scfoundation_gene_pos/metadata.json,,single_cell_expression_foundation_model / learned gene identity-position embedding,scFoundation-gene-pos-v1.1,Official scFoundation GitHub repository and official SharePoint checkpoint linked from the repository,scFoundation / xTrimoGene,Extracted locally from official scFoundation gene sub-checkpoint model.pos_emb.weight,,,,54234742
-scgpt_pancancer_v1_1,scgpt_pancancer,19071,512,float32,embeddings,data/embeddings/scgpt_pancancer/embeddings.npz,data/embeddings/scgpt_pancancer/genes.tsv,data/embeddings/scgpt_pancancer/metadata.json,processed_qc_passed,,scgpt_pancancer_v1_1,,,,,,,36187165
-scgpt_whole_human_v1_1,scgpt_whole_human,19280,512,float32,embeddings,data/embeddings/scgpt_whole_human/embeddings.npz,data/embeddings/scgpt_whole_human/genes.tsv,data/embeddings/scgpt_whole_human/metadata.json,,single_cell_expression_foundation_model,scGPT-whole-human-v1.1,Official scGPT whole-human Google Drive checkpoint linked from the scGPT project,,Extracted locally from official scGPT whole-human model input gene-token embedding layer,,,,36573474
-scprint_medium_v1_5_gene_v1_1,scprint_medium_v1_5_gene,19995,256,float32,embeddings,data/embeddings/scprint_medium_v1_5_gene/embeddings.npz,data/embeddings/scprint_medium_v1_5_gene/genes.tsv,data/embeddings/scprint_medium_v1_5_gene/metadata.json,,single_cell_expression_foundation_model / learned gene-token embedding,scPRINT-medium-v1.5-gene-v1.1,Official scPRINT HuggingFace repository jkobject/scPRINT,scPRINT,Extracted locally from official scPRINT medium-v1.5 checkpoint,,,,18989317
-spliceai_canonical_splice_site_profile_v1_1,spliceai_canonical_splice_site_profile,20097,606,float32,embeddings,data/embeddings/spliceai_canonical_splice_site_profile/embeddings.npz,data/embeddings/spliceai_canonical_splice_site_profile/genes.tsv,data/embeddings/spliceai_canonical_splice_site_profile/metadata.json,processed_qc_passed,splicing sequence model / canonical transcript splice-site profiles,SpliceAI-canonical-splice-site-profile-zscore-v1.1,,,,,,,41717181
-uce_33l_v1_1,uce_33l,19082,1280,float32,embeddings,data/embeddings/uce_33l/embeddings.npz,data/embeddings/uce_33l/genes.tsv,data/embeddings/uce_33l/metadata.json,,single_cell_expression_foundation_model / protein-informed gene-token embedding,UCE-33L-v1.1,Official UCE GitHub repository plus official Figshare model files,Universal Cell Embeddings (UCE),Extracted locally from official UCE all_tokens and 33-layer checkpoint gene encoder,,,,89725640