speciesLM k6, metazoa, upstream

added_tokens.json

@@ -0,0 +1,496 @@
+{
+  "acanthaster_planci_gca001949145v1": 4101,
+  "acanthochromis_polyacanthus": 4102,
+  "accipiter_nisus": 4103,
+  "acromyrmex_echinatior_gca000204515v1rs": 4104,
+  "acropora_millepora_gca013753865v1": 4105,
+  "actinia_equina_gca011057435": 4106,
+  "actinia_tenebrosa_gca009602425v1": 4107,
+  "acyrthosiphon_pisum": 4108,
+  "adineta_vaga": 4109,
+  "aedes_aegypti_lvpagwg": 4110,
+  "aedes_albopictus": 4111,
+  "agrilus_planipennis_gca000699045v2": 4112,
+  "ailuropoda_melanoleuca": 4113,
+  "amazona_collaria": 4114,
+  "amphibalanus_amphitrite_gca019059575v1": 4115,
+  "amphilophus_citrinellus": 4116,
+  "amphimedon_queenslandica": 4117,
+  "amphiprion_ocellaris": 4118,
+  "amphiprion_percula": 4119,
+  "amyelois_transitella_gca001186105v1rs": 4120,
+  "anabas_testudineus": 4121,
+  "anas_platyrhynchos": 4122,
+  "anas_zonorhyncha": 4123,
+  "anneissia_japonica_gca011630105v1": 4124,
+  "anolis_carolinensis": 4125,
+  "anopheles_albimanus": 4126,
+  "anopheles_arabiensis": 4127,
+  "anopheles_atroparvus_gca914969975": 4128,
+  "anopheles_christyi": 4129,
+  "anopheles_coluzzii_ngousso": 4130,
+  "anopheles_culicifacies": 4131,
+  "anopheles_darlingi": 4132,
+  "anopheles_dirus": 4133,
+  "anopheles_epiroticus": 4134,
+  "anopheles_farauti": 4135,
+  "anopheles_funestus": 4136,
+  "anopheles_gambiae": 4137,
+  "anopheles_maculatus": 4138,
+  "anopheles_melas": 4139,
+  "anopheles_merus": 4140,
+  "anopheles_minimus": 4141,
+  "anopheles_quadriannulatus": 4142,
+  "anopheles_sinensis_china": 4143,
+  "anopheles_stephensi": 4144,
+  "anoplophora_glabripennis": 4145,
+  "anser_brachyrhynchus": 4146,
+  "anser_cygnoides": 4147,
+  "anthonomus_grandis_gca022605725v3rs": 4148,
+  "aotus_nancymaae": 4149,
+  "aphidius_gifuensis_gca014905175v1": 4150,
+  "apis_dorsata_gca000469605v1rs": 4151,
+  "apis_florea_gca000184785v2rs": 4152,
+  "apis_mellifera": 4153,
+  "aplysia_californica_gca000002075v2": 4154,
+  "apteryx_haastii": 4155,
+  "apteryx_owenii": 4156,
+  "apteryx_rowi": 4157,
+  "aquila_chrysaetos_chrysaetos": 4158,
+  "ascaris_suum": 4159,
+  "astatotilapia_calliptera": 4160,
+  "asterias_rubens_gca902459465v3": 4161,
+  "astyanax_mexicanus": 4162,
+  "athalia_rosae_gca917208135v1": 4163,
+  "athene_cunicularia": 4164,
+  "atta_cephalotes": 4165,
+  "bactrocera_dorsalis_gca000789215v2": 4166,
+  "bactrocera_latifrons_gca001853355v1": 4167,
+  "bactrocera_tryoni_gca016617805v2": 4168,
+  "balaenoptera_musculus": 4169,
+  "belgica_antarctica": 4170,
+  "bemisia_tabaci_ssa3nig": 4171,
+  "betta_splendens": 4172,
+  "bicyclus_anynana_gca900239965v1rs": 4173,
+  "biomphalaria_glabrata": 4174,
+  "bison_bison_bison": 4175,
+  "bombus_impatiens": 4176,
+  "bombus_terrestris_gca910591885v2": 4177,
+  "bombyx_mandarina_gca003987935v1rs": 4178,
+  "bombyx_mori": 4179,
+  "bos_grunniens": 4180,
+  "bos_indicus_hybrid": 4181,
+  "bos_mutus": 4182,
+  "bos_taurus_hybrid": 4183,
+  "branchiostoma_lanceolatum": 4184,
+  "brugia_malayi": 4185,
+  "bubo_bubo": 4186,
+  "buteo_japonicus": 4187,
+  "caenorhabditis_brenneri": 4188,
+  "caenorhabditis_briggsae": 4189,
+  "caenorhabditis_elegans": 4190,
+  "caenorhabditis_japonica": 4191,
+  "caenorhabditis_remanei": 4192,
+  "cairina_moschata_domestica": 4193,
+  "calidris_pugnax": 4194,
+  "calidris_pygmaea": 4195,
+  "callithrix_jacchus": 4196,
+  "callorhinchus_milii": 4197,
+  "camarhynchus_parvulus": 4198,
+  "camelus_dromedarius": 4199,
+  "camponotus_floridanus_gca003227725v1rs": 4200,
+  "canis_lupus_familiarisgsd": 4201,
+  "capitella_teleta": 4202,
+  "capra_hircus": 4203,
+  "carassius_auratus": 4204,
+  "carlito_syrichta": 4205,
+  "castor_canadensis": 4206,
+  "catagonus_wagneri": 4207,
+  "catharus_ustulatus": 4208,
+  "cavia_aperea": 4209,
+  "cavia_porcellus": 4210,
+  "cebus_imitator": 4211,
+  "centruroides_sculpturatus_gca000671375v2": 4212,
+  "ceratitis_capitata_gca000347755v4": 4213,
+  "cercocebus_atys": 4214,
+  "cervus_hanglu_yarkandensis": 4215,
+  "chelonoidis_abingdonii": 4216,
+  "chelonus_insularis_gca013357705v1rs": 4217,
+  "chelydra_serpentina": 4218,
+  "chinchilla_lanigera": 4219,
+  "chlorocebus_sabaeus": 4220,
+  "choloepus_hoffmanni": 4221,
+  "chrysemys_picta_bellii": 4222,
+  "chrysolophus_pictus": 4223,
+  "cimex_lectularius": 4224,
+  "ciona_intestinalis": 4225,
+  "ciona_savignyi": 4226,
+  "clupea_harengus": 4227,
+  "clytia_hemisphaerica_gca902728285": 4228,
+  "colobus_angolensis_palliatus": 4229,
+  "copidosoma_floridanum_gca000648655v2": 4230,
+  "corvus_moneduloides": 4231,
+  "cotesia_glomerata_gca020080835v1": 4232,
+  "cottoperca_gobio": 4233,
+  "coturnix_japonica": 4234,
+  "crassostrea_gigas": 4235,
+  "crassostrea_virginica_gca002022765v4": 4236,
+  "cricetulus_griseus_picr": 4237,
+  "crocodylus_porosus": 4238,
+  "culex_quinquefasciatus_gca015732765v1": 4239,
+  "culicoides_sonorensis": 4240,
+  "cyanistes_caeruleus": 4241,
+  "cyclopterus_lumpus": 4242,
+  "cynoglossus_semilaevis": 4243,
+  "cyprinodon_variegatus": 4244,
+  "cyprinus_carpio_carpio": 4245,
+  "danaus_plexippus": 4246,
+  "danio_rerio": 4247,
+  "daphnia_magna_gca020631705v2": 4248,
+  "daphnia_pulex": 4249,
+  "daphnia_pulicaria_gca021234035v2rs": 4250,
+  "dasypus_novemcinctus": 4251,
+  "delphinapterus_leucas": 4252,
+  "dendroctonus_ponderosae_gca000355655v1": 4253,
+  "dendronephthya_gigantea_gca004324835v1": 4254,
+  "denticeps_clupeoides": 4255,
+  "dermacentor_andersoni_gca023375885v2rs": 4256,
+  "dermacentor_silvarum_gca013339745v1": 4257,
+  "dermatophagoides_pteronyssinus_gca001901225v2": 4258,
+  "diabrotica_virgifera_gca917563875v2rs": 4259,
+  "dicentrarchus_labrax": 4260,
+  "dimorphilus_gyrociliatus_gca904063045v1": 4261,
+  "dinothrombium_tinctorium": 4262,
+  "dipodomys_ordii": 4263,
+  "diuraphis_noxia_gca001186385v1": 4264,
+  "dromaius_novaehollandiae": 4265,
+  "drosophila_ananassae": 4266,
+  "drosophila_erecta": 4267,
+  "drosophila_grimshawi": 4268,
+  "drosophila_melanogaster": 4269,
+  "drosophila_mojavensis": 4270,
+  "drosophila_persimilis": 4271,
+  "drosophila_pseudoobscura": 4272,
+  "drosophila_sechellia": 4273,
+  "drosophila_simulans": 4274,
+  "drosophila_virilis": 4275,
+  "drosophila_willistoni": 4276,
+  "drosophila_yakuba": 4277,
+  "dufourea_novaeangliae_gca001272555v1rs": 4278,
+  "echeneis_naucrates": 4279,
+  "echinococcus_granulosus_gca000524195v1rs": 4280,
+  "echinops_telfairi": 4281,
+  "electrophorus_electricus": 4282,
+  "eptatretus_burgeri": 4283,
+  "equus_asinus": 4284,
+  "equus_caballus": 4285,
+  "erinaceus_europaeus": 4286,
+  "erpetoichthys_calabaricus": 4287,
+  "erythrura_gouldiae": 4288,
+  "esox_lucius": 4289,
+  "eufriesea_mexicana_gca001483705v1rs": 4290,
+  "eurytemora_affinis_gca000591075v2": 4291,
+  "exaiptasia_diaphana_gca001417965v1": 4292,
+  "falco_tinnunculus": 4293,
+  "felis_catus": 4294,
+  "ficedula_albicollis": 4295,
+  "folsomia_candida": 4296,
+  "fukomys_damarensis": 4297,
+  "fundulus_heteroclitus": 4298,
+  "gadus_morhua": 4299,
+  "galendromus_occidentalis_gca000255335v2rs": 4300,
+  "galleria_mellonella_gca003640425v2rs": 4301,
+  "gallus_gallus_gca000002315v5": 4302,
+  "gambusia_affinis": 4303,
+  "gasterosteus_aculeatus": 4304,
+  "geospiza_fortis": 4305,
+  "gigantopelta_aegis_gca016097555v1": 4306,
+  "glossina_austeni": 4307,
+  "glossina_brevipalpis": 4308,
+  "glossina_fuscipes": 4309,
+  "glossina_morsitans": 4310,
+  "glossina_pallidipes": 4311,
+  "glossina_palpalis": 4312,
+  "gopherus_agassizii": 4313,
+  "gopherus_evgoodei": 4314,
+  "gorilla_gorilla": 4315,
+  "gouania_willdenowi": 4316,
+  "habropoda_laboriosa_gca001263275v1rs": 4317,
+  "haemaphysalis_longicornis_gca013339765v1": 4318,
+  "haliotis_rubra_gca003918875v1rs": 4319,
+  "haliotis_rufescens_gca023055435v1rs": 4320,
+  "haplochromis_burtoni": 4321,
+  "harpegnathos_saltator_gca003227715v2rs": 4322,
+  "heliconius_melpomene": 4323,
+  "helicoverpa_armigera_gca023701775v1rs": 4324,
+  "helicoverpa_zea_gca022581195v1rs": 4325,
+  "helobdella_robusta": 4326,
+  "hermetia_illucens_gca905115235v1": 4327,
+  "heterocephalus_glaber_male": 4328,
+  "hippocampus_comes": 4329,
+  "hofstenia_miamia": 4330,
+  "homalodisca_vitripennis_gca021130785v2rs": 4331,
+  "homarus_americanus_gca018991925v1": 4332,
+  "homo_sapiens": 4333,
+  "hucho_hucho": 4334,
+  "hyalella_azteca_gca000764305v2": 4335,
+  "hyalomma_asiaticum_gca013339685v1": 4336,
+  "hydra_vulgaris_gca022113875v1rs": 4337,
+  "hymenolepis_microstoma": 4338,
+  "hypsibius_exemplaris_gca002082055v1": 4339,
+  "ictalurus_punctatus": 4340,
+  "ictidomys_tridecemlineatus": 4341,
+  "ixodes_persulcatus_gca013358835v1": 4342,
+  "ixodes_scapularis_gca016920785v2": 4343,
+  "jaculus_jaculus": 4344,
+  "junco_hyemalis": 4345,
+  "kryptolebias_marmoratus": 4346,
+  "labrus_bergylta": 4347,
+  "larimichthys_crocea": 4348,
+  "lates_calcarifer": 4349,
+  "laticauda_laticaudata": 4350,
+  "latimeria_chalumnae": 4351,
+  "leguminivora_glycinivorella_gca023078275v1rs": 4352,
+  "lepeophtheirus_salmonis_gca016086655v3rs": 4353,
+  "lepidothrix_coronata": 4354,
+  "lepisosteus_oculatus": 4355,
+  "leptinotarsa_decemlineata_gca000500325v2": 4356,
+  "leptobrachium_leishanense": 4357,
+  "leptotrombidium_deliense": 4358,
+  "limulus_polyphemus_gca000517525v1": 4359,
+  "linepithema_humile_gca000217595v1rs": 4360,
+  "lingula_anatina": 4361,
+  "loa_loa": 4362,
+  "lonchura_striata_domestica": 4363,
+  "lottia_gigantea": 4364,
+  "loxodonta_africana": 4365,
+  "lucilia_cuprina_gca022045245v1rs": 4366,
+  "lutzomyia_longipalpis": 4367,
+  "lynx_canadensis": 4368,
+  "lytechinus_variegatus_gca018143015v1": 4369,
+  "macaca_fascicularis": 4370,
+  "macaca_mulatta": 4371,
+  "macaca_nemestrina": 4372,
+  "malurus_cyaneus_samueli": 4373,
+  "manacus_vitellinus": 4374,
+  "mandrillus_leucophaeus": 4375,
+  "manduca_sexta_gca014839805v1rs": 4376,
+  "marmota_marmota_marmota": 4377,
+  "mastacembelus_armatus": 4378,
+  "mayetiola_destructor": 4379,
+  "maylandia_zebra": 4380,
+  "megachile_rotundata_gca000220905v1rs": 4381,
+  "megaselia_scalaris": 4382,
+  "meleagris_gallopavo": 4383,
+  "melitaea_cinxia_gca905220565v1": 4384,
+  "melopsittacus_undulatus": 4385,
+  "mercenaria_mercenaria_gca014805675v2": 4386,
+  "meriones_unguiculatus": 4387,
+  "mesocricetus_auratus": 4388,
+  "microcebus_murinus": 4389,
+  "microtus_ochrogaster": 4390,
+  "mizuhopecten_yessoensis_gca002113885v2": 4391,
+  "mnemiopsis_leidyi": 4392,
+  "mola_mola": 4393,
+  "monodelphis_domestica": 4394,
+  "monodon_monoceros": 4395,
+  "monomorium_pharaonis_gca013373865v2": 4396,
+  "monopterus_albus": 4397,
+  "moschus_moschiferus": 4398,
+  "mus_caroli": 4399,
+  "mus_musculus": 4400,
+  "mus_pahari": 4401,
+  "mus_spicilegus": 4402,
+  "mus_spretus": 4403,
+  "musca_domestica": 4404,
+  "mustela_putorius_furo": 4405,
+  "myotis_lucifugus": 4406,
+  "myripristis_murdjan": 4407,
+  "naja_naja": 4408,
+  "nannospalax_galili": 4409,
+  "nasonia_vitripennis": 4410,
+  "necator_americanus": 4411,
+  "nematostella_vectensis": 4412,
+  "neodiprion_lecontei_gca021901455v1rs": 4413,
+  "neodiprion_pinetum_gca021155775v1rs": 4414,
+  "neogobius_melanostomus": 4415,
+  "neolamprologus_brichardi": 4416,
+  "neovison_vison": 4417,
+  "nilaparvata_lugens_gca014356525v1rs": 4418,
+  "nomascus_leucogenys": 4419,
+  "notamacropus_eugenii": 4420,
+  "notechis_scutatus": 4421,
+  "nothobranchius_furzeri": 4422,
+  "nothoprocta_perdicaria": 4423,
+  "numida_meleagris": 4424,
+  "ochotona_princeps": 4425,
+  "octodon_degus": 4426,
+  "octopus_bimaculoides": 4427,
+  "octopus_sinensis_gca006345805v1": 4428,
+  "onchocerca_volvulus": 4429,
+  "oncorhynchus_kisutch": 4430,
+  "oncorhynchus_mykiss": 4431,
+  "oncorhynchus_tshawytscha": 4432,
+  "onthophagus_taurus_gca000648695v2": 4433,
+  "ooceraea_biroi_gca003672135v1": 4434,
+  "orbicella_faveolata_gca002042975v1": 4435,
+  "orchesella_cincta": 4436,
+  "oreochromis_aureus": 4437,
+  "oreochromis_niloticus": 4438,
+  "ornithorhynchus_anatinus": 4439,
+  "orussus_abietinus_gca000612105v2": 4440,
+  "oryctolagus_cuniculus": 4441,
+  "oryzias_javanicus": 4442,
+  "oryzias_latipes": 4443,
+  "oryzias_melastigma": 4444,
+  "oryzias_sinensis": 4445,
+  "otolemur_garnettii": 4446,
+  "otus_sunia": 4447,
+  "ovis_aries_rambouillet": 4448,
+  "owenia_fusiformis_gca903813345v1": 4449,
+  "pan_paniscus": 4450,
+  "pan_troglodytes": 4451,
+  "panthera_leo": 4452,
+  "panthera_pardus": 4453,
+  "panthera_tigris_altaica": 4454,
+  "papio_anubis": 4455,
+  "parambassis_ranga": 4456,
+  "paramormyrops_kingsleyae": 4457,
+  "parasteatoda_tepidariorum_gca000365465v3": 4458,
+  "parus_major": 4459,
+  "patiria_miniata_gca015706575v1": 4460,
+  "pavo_cristatus": 4461,
+  "pectinophora_gossypiella_gca024362695v1rs": 4462,
+  "pediculus_humanus": 4463,
+  "pelodiscus_sinensis": 4464,
+  "pelusios_castaneus": 4465,
+  "penaeus_chinensis_gca019202785v2rs": 4466,
+  "penaeus_japonicus_gca017312705v1": 4467,
+  "penaeus_monodon_gca015228065v1": 4468,
+  "penaeus_vannamei_gca003789085v1": 4469,
+  "periophthalmus_magnuspinnatus": 4470,
+  "peromyscus_maniculatus_bairdii": 4471,
+  "petromyzon_marinus": 4472,
+  "phascolarctos_cinereus": 4473,
+  "phasianus_colchicus": 4474,
+  "phlebotomus_papatasi": 4475,
+  "phlebotomus_perniciosus_gca918844115v2": 4476,
+  "phocoena_sinus": 4477,
+  "physeter_catodon": 4478,
+  "piliocolobus_tephrosceles": 4479,
+  "pocillopora_damicornis_gca003704095v1": 4480,
+  "podarcis_muralis": 4481,
+  "poecilia_formosa": 4482,
+  "poecilia_latipinna": 4483,
+  "poecilia_mexicana": 4484,
+  "poecilia_reticulata": 4485,
+  "pogona_vitticeps": 4486,
+  "pogonomyrmex_barbatus_gca000187915v1rs": 4487,
+  "polistes_canadensis_gca001313835v1rs": 4488,
+  "polistes_dominula_gca001465965v1rs": 4489,
+  "polistes_fuscatus_gca010416935v1rs": 4490,
+  "pollicipes_pollicipes_gca011947565v2": 4491,
+  "pomacea_canaliculata_gca003073045v1": 4492,
+  "pomphorhynchus_laevis_gca012934845v2gb": 4493,
+  "pongo_abelii": 4494,
+  "portunus_trituberculatus_gca017591435v1": 4495,
+  "priapulus_caudatus_gca000485595v2": 4496,
+  "pristionchus_pacificus": 4497,
+  "procambarus_clarkii_gca020424385v2": 4498,
+  "procavia_capensis": 4499,
+  "prolemur_simus": 4500,
+  "propithecus_coquereli": 4501,
+  "pseudonaja_textilis": 4502,
+  "pteropus_vampyrus": 4503,
+  "pundamilia_nyererei": 4504,
+  "pygocentrus_nattereri": 4505,
+  "rattus_norvegicus_wkybbb": 4506,
+  "rhagoletis_pomonella_gca013731165v1": 4507,
+  "rhinolophus_ferrumequinum": 4508,
+  "rhinopithecus_bieti": 4509,
+  "rhinopithecus_roxellana": 4510,
+  "rhipicephalus_microplus_gca013339725v1": 4511,
+  "rhipicephalus_sanguineus_gca013339695v1": 4512,
+  "rhodnius_prolixus": 4513,
+  "rhopalosiphum_maidis_gca003676215v3": 4514,
+  "saccharomyces_cerevisiae": 4515,
+  "saccoglossus_kowalevskii_gca000003605v1": 4516,
+  "saimiri_boliviensis_boliviensis": 4517,
+  "salarias_fasciatus": 4518,
+  "salmo_salar": 4519,
+  "salmo_trutta": 4520,
+  "salvator_merianae": 4521,
+  "sander_lucioperca": 4522,
+  "sarcophilus_harrisii": 4523,
+  "sarcoptes_scabiei": 4524,
+  "schistocerca_americana_gca021461395v2rs": 4525,
+  "schistosoma_haematobium_gca000699445v2rs": 4526,
+  "schistosoma_mansoni": 4527,
+  "sciurus_vulgaris": 4528,
+  "scleropages_formosus": 4529,
+  "scophthalmus_maximus": 4530,
+  "serinus_canaria": 4531,
+  "seriola_dumerili": 4532,
+  "seriola_lalandi_dorsalis": 4533,
+  "sinocyclocheilus_anshuiensis": 4534,
+  "sinocyclocheilus_grahami": 4535,
+  "sinocyclocheilus_rhinocerous": 4536,
+  "sipha_flava_gca003268045v1": 4537,
+  "sitophilus_oryzae_gca002938485v2rs": 4538,
+  "solenopsis_invicta": 4539,
+  "sorex_araneus": 4540,
+  "sparus_aurata": 4541,
+  "spermophilus_dauricus": 4542,
+  "sphaeramia_orbicularis": 4543,
+  "sphenodon_punctatus": 4544,
+  "stachyris_ruficeps": 4545,
+  "stegastes_partitus": 4546,
+  "stegodyphus_dumicola_gca010614865v2rs": 4547,
+  "stegodyphus_mimosarum": 4548,
+  "stomoxys_calcitrans": 4549,
+  "strigamia_maritima": 4550,
+  "strigops_habroptila": 4551,
+  "strix_occidentalis_caurina": 4552,
+  "strongylocentrotus_purpuratus": 4553,
+  "strongyloides_ratti": 4554,
+  "struthio_camelus_australis": 4555,
+  "stylophora_pistillata_gca002571385v1": 4556,
+  "suricata_suricatta": 4557,
+  "sus_scrofa_usmarc": 4558,
+  "taeniopygia_guttata": 4559,
+  "takifugu_rubripes": 4560,
+  "teleopsis_dalmanni": 4561,
+  "terrapene_carolina_triunguis": 4562,
+  "tetranychus_urticae": 4563,
+  "tetraodon_nigroviridis": 4564,
+  "thelohanellus_kitauei": 4565,
+  "theropithecus_gelada": 4566,
+  "thrips_palmi_gca012932325v1rs": 4567,
+  "tigriopus_californicus_gca007210705": 4568,
+  "trialeurodes_vaporariorum_gca011764245": 4569,
+  "tribolium_castaneum": 4570,
+  "trichinella_spiralis": 4571,
+  "trichogramma_pretiosum_gca000599845v3": 4572,
+  "trichoplax_adhaerens": 4573,
+  "trichuris_muris": 4574,
+  "tupaia_belangeri": 4575,
+  "tursiops_truncatus": 4576,
+  "urocitellus_parryii": 4577,
+  "ursus_americanus": 4578,
+  "ursus_maritimus": 4579,
+  "ursus_thibetanus_thibetanus": 4580,
+  "varanus_komodoensis": 4581,
+  "varroa_destructor_gca002443255": 4582,
+  "venturia_canescens_gca019457755v1rs": 4583,
+  "vicugna_pacos": 4584,
+  "vombatus_ursinus": 4585,
+  "vulpes_vulpes": 4586,
+  "xenopus_tropicalis": 4587,
+  "xiphophorus_couchianus": 4588,
+  "xiphophorus_maculatus": 4589,
+  "zalophus_californianus": 4590,
+  "zerene_cesonia_gca012273895v2rs": 4591,
+  "zonotrichia_albicollis": 4592,
+  "zootermopsis_nevadensis": 4593,
+  "zosterops_lateralis_melanops": 4594
+}

config.json

@@ -0,0 +1,26 @@
+{
+  "_name_or_path": "/s/project/denovo-prosit/JohannesHingerl/BERTADN/final_models/huggingface_compatible/rotary_bert_huggingface",
+  "auto_map":
+      {"AutoModel": "modeling_rotarybert.RotaryBertModel",
+        "AutoModelForMaskedLM": "modeling_rotarybert.RotaryBertForMaskedLM"
+      },
+  "attention_probs_dropout_prob": 0.1,
+  "classifier_dropout": null,
+  "hidden_act": "gelu_new",
+  "hidden_dropout_prob": 0.1,
+  "hidden_size": 768,
+  "initializer_range": 0.02,
+  "intermediate_size": 3072,
+  "layer_norm_eps": 1e-12,
+  "max_position_embeddings": 8192,
+  "model_type": "bert",
+  "num_attention_heads": 12,
+  "num_hidden_layers": 12,
+  "pad_token_id": 0,
+  "position_embedding_type": "absolute",
+  "torch_dtype": "float32",
+  "transformers_version": "4.45.2",
+  "type_vocab_size": 2,
+  "use_cache": true,
+  "vocab_size": 4608
+}

generation_config.json

@@ -0,0 +1,5 @@
+{
+  "_from_model_config": true,
+  "pad_token_id": 0,
+  "transformers_version": "4.45.2"
+}

modeling_rotarybert.py

@@ -0,0 +1,162 @@
+import math
+from einops import rearrange, repeat
+from transformers.models.bert.modeling_bert import BertSelfAttention, BertAttention, BertLayer, BertEncoder, BertModel, BertForMaskedLM
+from typing import List, Optional, Tuple, Union
+from packaging import version
+import torch
+import torch.nn as nn
+
+def rotate_half(x, interleaved=False):
+    if not interleaved:
+        x1, x2 = x.chunk(2, dim=-1)
+        return torch.cat((-x2, x1), dim=-1)
+    else:
+        x1, x2 = x[..., ::2], x[..., 1::2]
+        return rearrange(torch.stack((-x2, x1), dim=-1), "... d two -> ... (d two)", two=2)
+
+
+def apply_rotary_emb_torch(x, cos, sin, interleaved=False):
+    """
+    x: (batch_size, seqlen, nheads, headdim)
+    cos, sin: (seqlen, rotary_dim / 2) or (batch_size, seqlen, rotary_dim / 2)
+    """
+    ro_dim = cos.shape[-1] * 2
+    assert ro_dim <= x.shape[-1]
+    cos = repeat(cos, "... d -> ... 1 (2 d)" if not interleaved else "... d -> ... 1 (d 2)")
+    sin = repeat(sin, "... d -> ... 1 (2 d)" if not interleaved else "... d -> ... 1 (d 2)")
+    return torch.cat(
+        [x[..., :ro_dim] * cos + rotate_half(x[..., :ro_dim], interleaved) * sin, x[..., ro_dim:]],
+        dim=-1,
+    )
+
+
+def generate_cos_sin(seqlen, rotary_dim, device, dtype):
+    inv_freq = 1.0 / (
+            10000.0
+            ** (torch.arange(0, rotary_dim, 2, device=device, dtype=torch.float32) / rotary_dim)
+        )
+    t = torch.arange(seqlen, device=device, dtype=torch.float32)
+    freqs = torch.outer(t, inv_freq)
+    cos = torch.cos(freqs).to(dtype)
+    sin = torch.sin(freqs).to(dtype)
+    return cos, sin
+
+# from transformers.models.roformer import RoFormerSinusoidalPositionalEmbedding
+
+
+class RotaryBertSdpaSelfAttention(BertSelfAttention):
+    def __init__(self, config, position_embedding_type=None):
+        super().__init__(config, position_embedding_type=position_embedding_type)
+        self.dropout_prob = config.attention_probs_dropout_prob
+        self.require_contiguous_qkv = False
+        # self.rotary_sinuses = RoFormerSinusoidalPositionalEmbedding(config.max_position_embeddings)
+
+    # Adapted from BertSelfAttention
+    def forward(
+        self,
+        hidden_states: torch.Tensor,
+        attention_mask = None,
+        head_mask = None,
+        encoder_hidden_states = None,
+        encoder_attention_mask = None,
+        past_key_value = None,
+        output_attentions = False,
+    ) -> Tuple[torch.Tensor]:
+        if output_attentions or head_mask is not None:
+            # TODO: Improve this warning with e.g. `model.config._attn_implementation = "manual"` once implemented.
+            logger.warning_once(
+                "BertSdpaSelfAttention is used but `torch.nn.functional.scaled_dot_product_attention` does not support "
+                "non-absolute `position_embedding_type` or `output_attentions=True` or `head_mask`. Falling back to "
+                "the manual attention implementation, but specifying the manual implementation will be required from "
+                "Transformers version v5.0.0 onwards. This warning can be removed using the argument "
+                '`attn_implementation="eager"` when loading the model.'
+            )
+            
+
+        bsz, tgt_len, _ = hidden_states.size()
+
+        query_layer = self.query(hidden_states)
+
+
+        is_cross_attention = encoder_hidden_states is not None
+
+        current_states = encoder_hidden_states if is_cross_attention else hidden_states
+        attention_mask = encoder_attention_mask if is_cross_attention else attention_mask
+
+        # Check `seq_length` of `past_key_value` == `len(current_states)` to support prefix tuning
+
+        key_layer = self.key(current_states)
+        value_layer = self.value(current_states)
+
+        
+        query_layer = self.transpose_for_scores(query_layer)
+        key_layer = self.transpose_for_scores(key_layer)
+        value_layer = self.transpose_for_scores(value_layer)
+        
+
+
+        query_layer, key_layer = query_layer.permute(0,2,1,3), key_layer.permute(0,2,1,3)
+
+
+        cos, sin = generate_cos_sin(query_layer.shape[1], query_layer.shape[-1], device = query_layer.device, dtype = torch.float32)
+
+
+        query_layer, key_layer = apply_rotary_emb_torch(query_layer, cos, sin), apply_rotary_emb_torch(key_layer, cos, sin)
+
+        query_layer, key_layer = query_layer.permute(0,2,1,3), key_layer.permute(0,2,1,3)
+        
+        
+        # SDPA with memory-efficient backend is broken in torch==2.1.2 when using non-contiguous inputs and a custom
+        # attn_mask, so we need to call `.contiguous()` here. This was fixed in torch==2.2.0.
+        # Reference: https://github.com/pytorch/pytorch/issues/112577
+        if self.require_contiguous_qkv and query_layer.device.type == "cuda" and attention_mask is not None:
+            query_layer = query_layer.contiguous()
+            key_layer = key_layer.contiguous()
+            value_layer = value_layer.contiguous()
+
+
+        is_causal = (
+            True if self.is_decoder and not is_cross_attention and attention_mask is None and tgt_len > 1 else False
+        )
+        attn_output = torch.nn.functional.scaled_dot_product_attention(
+            query_layer,
+            key_layer,
+            value_layer,
+            attn_mask=attention_mask,
+            dropout_p=self.dropout_prob if self.training else 0.0,
+            is_causal=is_causal,
+        )
+
+        attn_output = attn_output.transpose(1, 2)
+        attn_output = attn_output.reshape(bsz, tgt_len, self.all_head_size)
+
+        outputs = (attn_output,)
+        if self.is_decoder:
+            outputs = outputs + (past_key_value,)
+        return outputs
+
+
+class RotaryBertAttention(BertAttention):
+    def __init__(self, config):
+        super().__init__(config)
+        self.self = RotaryBertSdpaSelfAttention(config)
+
+class RotaryBertLayer(BertLayer):
+    def __init__(self, config):
+        super().__init__(config)
+        self.attention = RotaryBertAttention(config)
+
+class RotaryBertEncoder(BertEncoder):
+    def __init__(self, config):
+        super().__init__(config)
+        self.layer = nn.ModuleList([RotaryBertLayer(config) for _ in range(config.num_hidden_layers)])
+
+class RotaryBertModel(BertModel):
+    def __init__(self, config):
+        super().__init__(config)
+        self.encoder = RotaryBertEncoder(config)
+    
+class RotaryBertForMaskedLM(BertForMaskedLM):
+    def __init__(self, config):
+        super().__init__(config)
+        self.bert = RotaryBertModel(config)

pytorch_model.bin

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:78bb502f89c7f13649c5787f672f045618affb36ec0d70bdca90c972877ba64c
+size 398592581

special_tokens_map.json

@@ -0,0 +1,503 @@
+{
+  "additional_special_tokens": [
+    "acanthaster_planci_gca001949145v1",
+    "acanthochromis_polyacanthus",
+    "accipiter_nisus",
+    "acromyrmex_echinatior_gca000204515v1rs",
+    "acropora_millepora_gca013753865v1",
+    "actinia_equina_gca011057435",
+    "actinia_tenebrosa_gca009602425v1",
+    "acyrthosiphon_pisum",
+    "adineta_vaga",
+    "aedes_aegypti_lvpagwg",
+    "aedes_albopictus",
+    "agrilus_planipennis_gca000699045v2",
+    "ailuropoda_melanoleuca",
+    "amazona_collaria",
+    "amphibalanus_amphitrite_gca019059575v1",
+    "amphilophus_citrinellus",
+    "amphimedon_queenslandica",
+    "amphiprion_ocellaris",
+    "amphiprion_percula",
+    "amyelois_transitella_gca001186105v1rs",
+    "anabas_testudineus",
+    "anas_platyrhynchos",
+    "anas_zonorhyncha",
+    "anneissia_japonica_gca011630105v1",
+    "anolis_carolinensis",
+    "anopheles_albimanus",
+    "anopheles_arabiensis",
+    "anopheles_atroparvus_gca914969975",
+    "anopheles_christyi",
+    "anopheles_coluzzii_ngousso",
+    "anopheles_culicifacies",
+    "anopheles_darlingi",
+    "anopheles_dirus",
+    "anopheles_epiroticus",
+    "anopheles_farauti",
+    "anopheles_funestus",
+    "anopheles_gambiae",
+    "anopheles_maculatus",
+    "anopheles_melas",
+    "anopheles_merus",
+    "anopheles_minimus",
+    "anopheles_quadriannulatus",
+    "anopheles_sinensis_china",
+    "anopheles_stephensi",
+    "anoplophora_glabripennis",
+    "anser_brachyrhynchus",
+    "anser_cygnoides",
+    "anthonomus_grandis_gca022605725v3rs",
+    "aotus_nancymaae",
+    "aphidius_gifuensis_gca014905175v1",
+    "apis_dorsata_gca000469605v1rs",
+    "apis_florea_gca000184785v2rs",
+    "apis_mellifera",
+    "aplysia_californica_gca000002075v2",
+    "apteryx_haastii",
+    "apteryx_owenii",
+    "apteryx_rowi",
+    "aquila_chrysaetos_chrysaetos",
+    "ascaris_suum",
+    "astatotilapia_calliptera",
+    "asterias_rubens_gca902459465v3",
+    "astyanax_mexicanus",
+    "athalia_rosae_gca917208135v1",
+    "athene_cunicularia",
+    "atta_cephalotes",
+    "bactrocera_dorsalis_gca000789215v2",
+    "bactrocera_latifrons_gca001853355v1",
+    "bactrocera_tryoni_gca016617805v2",
+    "balaenoptera_musculus",
+    "belgica_antarctica",
+    "bemisia_tabaci_ssa3nig",
+    "betta_splendens",
+    "bicyclus_anynana_gca900239965v1rs",
+    "biomphalaria_glabrata",
+    "bison_bison_bison",
+    "bombus_impatiens",
+    "bombus_terrestris_gca910591885v2",
+    "bombyx_mandarina_gca003987935v1rs",
+    "bombyx_mori",
+    "bos_grunniens",
+    "bos_indicus_hybrid",
+    "bos_mutus",
+    "bos_taurus_hybrid",
+    "branchiostoma_lanceolatum",
+    "brugia_malayi",
+    "bubo_bubo",
+    "buteo_japonicus",
+    "caenorhabditis_brenneri",
+    "caenorhabditis_briggsae",
+    "caenorhabditis_elegans",
+    "caenorhabditis_japonica",
+    "caenorhabditis_remanei",
+    "cairina_moschata_domestica",
+    "calidris_pugnax",
+    "calidris_pygmaea",
+    "callithrix_jacchus",
+    "callorhinchus_milii",
+    "camarhynchus_parvulus",
+    "camelus_dromedarius",
+    "camponotus_floridanus_gca003227725v1rs",
+    "canis_lupus_familiarisgsd",
+    "capitella_teleta",
+    "capra_hircus",
+    "carassius_auratus",
+    "carlito_syrichta",
+    "castor_canadensis",
+    "catagonus_wagneri",
+    "catharus_ustulatus",
+    "cavia_aperea",
+    "cavia_porcellus",
+    "cebus_imitator",
+    "centruroides_sculpturatus_gca000671375v2",
+    "ceratitis_capitata_gca000347755v4",
+    "cercocebus_atys",
+    "cervus_hanglu_yarkandensis",
+    "chelonoidis_abingdonii",
+    "chelonus_insularis_gca013357705v1rs",
+    "chelydra_serpentina",
+    "chinchilla_lanigera",
+    "chlorocebus_sabaeus",
+    "choloepus_hoffmanni",
+    "chrysemys_picta_bellii",
+    "chrysolophus_pictus",
+    "cimex_lectularius",
+    "ciona_intestinalis",
+    "ciona_savignyi",
+    "clupea_harengus",
+    "clytia_hemisphaerica_gca902728285",
+    "colobus_angolensis_palliatus",
+    "copidosoma_floridanum_gca000648655v2",
+    "corvus_moneduloides",
+    "cotesia_glomerata_gca020080835v1",
+    "cottoperca_gobio",
+    "coturnix_japonica",
+    "crassostrea_gigas",
+    "crassostrea_virginica_gca002022765v4",
+    "cricetulus_griseus_picr",
+    "crocodylus_porosus",
+    "culex_quinquefasciatus_gca015732765v1",
+    "culicoides_sonorensis",
+    "cyanistes_caeruleus",
+    "cyclopterus_lumpus",
+    "cynoglossus_semilaevis",
+    "cyprinodon_variegatus",
+    "cyprinus_carpio_carpio",
+    "danaus_plexippus",
+    "danio_rerio",
+    "daphnia_magna_gca020631705v2",
+    "daphnia_pulex",
+    "daphnia_pulicaria_gca021234035v2rs",
+    "dasypus_novemcinctus",
+    "delphinapterus_leucas",
+    "dendroctonus_ponderosae_gca000355655v1",
+    "dendronephthya_gigantea_gca004324835v1",
+    "denticeps_clupeoides",
+    "dermacentor_andersoni_gca023375885v2rs",
+    "dermacentor_silvarum_gca013339745v1",
+    "dermatophagoides_pteronyssinus_gca001901225v2",
+    "diabrotica_virgifera_gca917563875v2rs",
+    "dicentrarchus_labrax",
+    "dimorphilus_gyrociliatus_gca904063045v1",
+    "dinothrombium_tinctorium",
+    "dipodomys_ordii",
+    "diuraphis_noxia_gca001186385v1",
+    "dromaius_novaehollandiae",
+    "drosophila_ananassae",
+    "drosophila_erecta",
+    "drosophila_grimshawi",
+    "drosophila_melanogaster",
+    "drosophila_mojavensis",
+    "drosophila_persimilis",
+    "drosophila_pseudoobscura",
+    "drosophila_sechellia",
+    "drosophila_simulans",
+    "drosophila_virilis",
+    "drosophila_willistoni",
+    "drosophila_yakuba",
+    "dufourea_novaeangliae_gca001272555v1rs",
+    "echeneis_naucrates",
+    "echinococcus_granulosus_gca000524195v1rs",
+    "echinops_telfairi",
+    "electrophorus_electricus",
+    "eptatretus_burgeri",
+    "equus_asinus",
+    "equus_caballus",
+    "erinaceus_europaeus",
+    "erpetoichthys_calabaricus",
+    "erythrura_gouldiae",
+    "esox_lucius",
+    "eufriesea_mexicana_gca001483705v1rs",
+    "eurytemora_affinis_gca000591075v2",
+    "exaiptasia_diaphana_gca001417965v1",
+    "falco_tinnunculus",
+    "felis_catus",
+    "ficedula_albicollis",
+    "folsomia_candida",
+    "fukomys_damarensis",
+    "fundulus_heteroclitus",
+    "gadus_morhua",
+    "galendromus_occidentalis_gca000255335v2rs",
+    "galleria_mellonella_gca003640425v2rs",
+    "gallus_gallus_gca000002315v5",
+    "gambusia_affinis",
+    "gasterosteus_aculeatus",
+    "geospiza_fortis",
+    "gigantopelta_aegis_gca016097555v1",
+    "glossina_austeni",
+    "glossina_brevipalpis",
+    "glossina_fuscipes",
+    "glossina_morsitans",
+    "glossina_pallidipes",
+    "glossina_palpalis",
+    "gopherus_agassizii",
+    "gopherus_evgoodei",
+    "gorilla_gorilla",
+    "gouania_willdenowi",
+    "habropoda_laboriosa_gca001263275v1rs",
+    "haemaphysalis_longicornis_gca013339765v1",
+    "haliotis_rubra_gca003918875v1rs",
+    "haliotis_rufescens_gca023055435v1rs",
+    "haplochromis_burtoni",
+    "harpegnathos_saltator_gca003227715v2rs",
+    "heliconius_melpomene",
+    "helicoverpa_armigera_gca023701775v1rs",
+    "helicoverpa_zea_gca022581195v1rs",
+    "helobdella_robusta",
+    "hermetia_illucens_gca905115235v1",
+    "heterocephalus_glaber_male",
+    "hippocampus_comes",
+    "hofstenia_miamia",
+    "homalodisca_vitripennis_gca021130785v2rs",
+    "homarus_americanus_gca018991925v1",
+    "homo_sapiens",
+    "hucho_hucho",
+    "hyalella_azteca_gca000764305v2",
+    "hyalomma_asiaticum_gca013339685v1",
+    "hydra_vulgaris_gca022113875v1rs",
+    "hymenolepis_microstoma",
+    "hypsibius_exemplaris_gca002082055v1",
+    "ictalurus_punctatus",
+    "ictidomys_tridecemlineatus",
+    "ixodes_persulcatus_gca013358835v1",
+    "ixodes_scapularis_gca016920785v2",
+    "jaculus_jaculus",
+    "junco_hyemalis",
+    "kryptolebias_marmoratus",
+    "labrus_bergylta",
+    "larimichthys_crocea",
+    "lates_calcarifer",
+    "laticauda_laticaudata",
+    "latimeria_chalumnae",
+    "leguminivora_glycinivorella_gca023078275v1rs",
+    "lepeophtheirus_salmonis_gca016086655v3rs",
+    "lepidothrix_coronata",
+    "lepisosteus_oculatus",
+    "leptinotarsa_decemlineata_gca000500325v2",
+    "leptobrachium_leishanense",
+    "leptotrombidium_deliense",
+    "limulus_polyphemus_gca000517525v1",
+    "linepithema_humile_gca000217595v1rs",
+    "lingula_anatina",
+    "loa_loa",
+    "lonchura_striata_domestica",
+    "lottia_gigantea",
+    "loxodonta_africana",
+    "lucilia_cuprina_gca022045245v1rs",
+    "lutzomyia_longipalpis",
+    "lynx_canadensis",
+    "lytechinus_variegatus_gca018143015v1",
+    "macaca_fascicularis",
+    "macaca_mulatta",
+    "macaca_nemestrina",
+    "malurus_cyaneus_samueli",
+    "manacus_vitellinus",
+    "mandrillus_leucophaeus",
+    "manduca_sexta_gca014839805v1rs",
+    "marmota_marmota_marmota",
+    "mastacembelus_armatus",
+    "mayetiola_destructor",
+    "maylandia_zebra",
+    "megachile_rotundata_gca000220905v1rs",
+    "megaselia_scalaris",
+    "meleagris_gallopavo",
+    "melitaea_cinxia_gca905220565v1",
+    "melopsittacus_undulatus",
+    "mercenaria_mercenaria_gca014805675v2",
+    "meriones_unguiculatus",
+    "mesocricetus_auratus",
+    "microcebus_murinus",
+    "microtus_ochrogaster",
+    "mizuhopecten_yessoensis_gca002113885v2",
+    "mnemiopsis_leidyi",
+    "mola_mola",
+    "monodelphis_domestica",
+    "monodon_monoceros",
+    "monomorium_pharaonis_gca013373865v2",
+    "monopterus_albus",
+    "moschus_moschiferus",
+    "mus_caroli",
+    "mus_musculus",
+    "mus_pahari",
+    "mus_spicilegus",
+    "mus_spretus",
+    "musca_domestica",
+    "mustela_putorius_furo",
+    "myotis_lucifugus",
+    "myripristis_murdjan",
+    "naja_naja",
+    "nannospalax_galili",
+    "nasonia_vitripennis",
+    "necator_americanus",
+    "nematostella_vectensis",
+    "neodiprion_lecontei_gca021901455v1rs",
+    "neodiprion_pinetum_gca021155775v1rs",
+    "neogobius_melanostomus",
+    "neolamprologus_brichardi",
+    "neovison_vison",
+    "nilaparvata_lugens_gca014356525v1rs",
+    "nomascus_leucogenys",
+    "notamacropus_eugenii",
+    "notechis_scutatus",
+    "nothobranchius_furzeri",
+    "nothoprocta_perdicaria",
+    "numida_meleagris",
+    "ochotona_princeps",
+    "octodon_degus",
+    "octopus_bimaculoides",
+    "octopus_sinensis_gca006345805v1",
+    "onchocerca_volvulus",
+    "oncorhynchus_kisutch",
+    "oncorhynchus_mykiss",
+    "oncorhynchus_tshawytscha",
+    "onthophagus_taurus_gca000648695v2",
+    "ooceraea_biroi_gca003672135v1",
+    "orbicella_faveolata_gca002042975v1",
+    "orchesella_cincta",
+    "oreochromis_aureus",
+    "oreochromis_niloticus",
+    "ornithorhynchus_anatinus",
+    "orussus_abietinus_gca000612105v2",
+    "oryctolagus_cuniculus",
+    "oryzias_javanicus",
+    "oryzias_latipes",
+    "oryzias_melastigma",
+    "oryzias_sinensis",
+    "otolemur_garnettii",
+    "otus_sunia",
+    "ovis_aries_rambouillet",
+    "owenia_fusiformis_gca903813345v1",
+    "pan_paniscus",
+    "pan_troglodytes",
+    "panthera_leo",
+    "panthera_pardus",
+    "panthera_tigris_altaica",
+    "papio_anubis",
+    "parambassis_ranga",
+    "paramormyrops_kingsleyae",
+    "parasteatoda_tepidariorum_gca000365465v3",
+    "parus_major",
+    "patiria_miniata_gca015706575v1",
+    "pavo_cristatus",
+    "pectinophora_gossypiella_gca024362695v1rs",
+    "pediculus_humanus",
+    "pelodiscus_sinensis",
+    "pelusios_castaneus",
+    "penaeus_chinensis_gca019202785v2rs",
+    "penaeus_japonicus_gca017312705v1",
+    "penaeus_monodon_gca015228065v1",
+    "penaeus_vannamei_gca003789085v1",
+    "periophthalmus_magnuspinnatus",
+    "peromyscus_maniculatus_bairdii",
+    "petromyzon_marinus",
+    "phascolarctos_cinereus",
+    "phasianus_colchicus",
+    "phlebotomus_papatasi",
+    "phlebotomus_perniciosus_gca918844115v2",
+    "phocoena_sinus",
+    "physeter_catodon",
+    "piliocolobus_tephrosceles",
+    "pocillopora_damicornis_gca003704095v1",
+    "podarcis_muralis",
+    "poecilia_formosa",
+    "poecilia_latipinna",
+    "poecilia_mexicana",
+    "poecilia_reticulata",
+    "pogona_vitticeps",
+    "pogonomyrmex_barbatus_gca000187915v1rs",
+    "polistes_canadensis_gca001313835v1rs",
+    "polistes_dominula_gca001465965v1rs",
+    "polistes_fuscatus_gca010416935v1rs",
+    "pollicipes_pollicipes_gca011947565v2",
+    "pomacea_canaliculata_gca003073045v1",
+    "pomphorhynchus_laevis_gca012934845v2gb",
+    "pongo_abelii",
+    "portunus_trituberculatus_gca017591435v1",
+    "priapulus_caudatus_gca000485595v2",
+    "pristionchus_pacificus",
+    "procambarus_clarkii_gca020424385v2",
+    "procavia_capensis",
+    "prolemur_simus",
+    "propithecus_coquereli",
+    "pseudonaja_textilis",
+    "pteropus_vampyrus",
+    "pundamilia_nyererei",
+    "pygocentrus_nattereri",
+    "rattus_norvegicus_wkybbb",
+    "rhagoletis_pomonella_gca013731165v1",
+    "rhinolophus_ferrumequinum",
+    "rhinopithecus_bieti",
+    "rhinopithecus_roxellana",
+    "rhipicephalus_microplus_gca013339725v1",
+    "rhipicephalus_sanguineus_gca013339695v1",
+    "rhodnius_prolixus",
+    "rhopalosiphum_maidis_gca003676215v3",
+    "saccharomyces_cerevisiae",
+    "saccoglossus_kowalevskii_gca000003605v1",
+    "saimiri_boliviensis_boliviensis",
+    "salarias_fasciatus",
+    "salmo_salar",
+    "salmo_trutta",
+    "salvator_merianae",
+    "sander_lucioperca",
+    "sarcophilus_harrisii",
+    "sarcoptes_scabiei",
+    "schistocerca_americana_gca021461395v2rs",
+    "schistosoma_haematobium_gca000699445v2rs",
+    "schistosoma_mansoni",
+    "sciurus_vulgaris",
+    "scleropages_formosus",
+    "scophthalmus_maximus",
+    "serinus_canaria",
+    "seriola_dumerili",
+    "seriola_lalandi_dorsalis",
+    "sinocyclocheilus_anshuiensis",
+    "sinocyclocheilus_grahami",
+    "sinocyclocheilus_rhinocerous",
+    "sipha_flava_gca003268045v1",
+    "sitophilus_oryzae_gca002938485v2rs",
+    "solenopsis_invicta",
+    "sorex_araneus",
+    "sparus_aurata",
+    "spermophilus_dauricus",
+    "sphaeramia_orbicularis",
+    "sphenodon_punctatus",
+    "stachyris_ruficeps",
+    "stegastes_partitus",
+    "stegodyphus_dumicola_gca010614865v2rs",
+    "stegodyphus_mimosarum",
+    "stomoxys_calcitrans",
+    "strigamia_maritima",
+    "strigops_habroptila",
+    "strix_occidentalis_caurina",
+    "strongylocentrotus_purpuratus",
+    "strongyloides_ratti",
+    "struthio_camelus_australis",
+    "stylophora_pistillata_gca002571385v1",
+    "suricata_suricatta",
+    "sus_scrofa_usmarc",
+    "taeniopygia_guttata",
+    "takifugu_rubripes",
+    "teleopsis_dalmanni",
+    "terrapene_carolina_triunguis",
+    "tetranychus_urticae",
+    "tetraodon_nigroviridis",
+    "thelohanellus_kitauei",
+    "theropithecus_gelada",
+    "thrips_palmi_gca012932325v1rs",
+    "tigriopus_californicus_gca007210705",
+    "trialeurodes_vaporariorum_gca011764245",
+    "tribolium_castaneum",
+    "trichinella_spiralis",
+    "trichogramma_pretiosum_gca000599845v3",
+    "trichoplax_adhaerens",
+    "trichuris_muris",
+    "tupaia_belangeri",
+    "tursiops_truncatus",
+    "urocitellus_parryii",
+    "ursus_americanus",
+    "ursus_maritimus",
+    "ursus_thibetanus_thibetanus",
+    "varanus_komodoensis",
+    "varroa_destructor_gca002443255",
+    "venturia_canescens_gca019457755v1rs",
+    "vicugna_pacos",
+    "vombatus_ursinus",
+    "vulpes_vulpes",
+    "xenopus_tropicalis",
+    "xiphophorus_couchianus",
+    "xiphophorus_maculatus",
+    "zalophus_californianus",
+    "zerene_cesonia_gca012273895v2rs",
+    "zonotrichia_albicollis",
+    "zootermopsis_nevadensis",
+    "zosterops_lateralis_melanops"
+  ],
+  "cls_token": "[CLS]",
+  "mask_token": "[MASK]",
+  "pad_token": "[PAD]",
+  "sep_token": "[SEP]",
+  "unk_token": "[UNK]"
+}

tokenizer_config.json

@@ -0,0 +1,17 @@
+{
+  "cls_token": "[CLS]",
+  "do_basic_tokenize": true,
+  "do_lower_case": false,
+  "mask_token": "[MASK]",
+  "max_len": 512,
+  "model_max_length": 2048,
+  "name_or_path": "/data/ouga/home/ag_gagneur/hingerl/BERTADN/preprocessing/tokenizer_upstream_metazoa",
+  "never_split": null,
+  "pad_token": "[PAD]",
+  "sep_token": "[SEP]",
+  "special_tokens_map_file": "/data/ouga/home/ag_gagneur/hingerl/.cache/huggingface/hub/models--zhihan1996--DNA_bert_6/snapshots/a79a8fd96ad172f964a4dbef3f4d7545a5034baa/special_tokens_map.json",
+  "strip_accents": null,
+  "tokenize_chinese_chars": true,
+  "tokenizer_class": "BertTokenizer",
+  "unk_token": "[UNK]"
+}