Valentyn Bezshapkin
Rename DeepCNN-MERGED_cellular_component_model_params.json to DeepCNN-MERGED_cc_model_params.json
bd2ad72
| { | |
| "num_filters": [ | |
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| "dropout": 0.3, | |
| "l2_reg": 0.0002, | |
| "lr": 0.0002, | |
| "epochs": 60, | |
| "batch_size": 64, | |
| "pad_len": null, | |
| "ontology": "cc", | |
| "model_name": "./trained_models/DeepCNN-MERGED_cellular_component", | |
| "lm_model_name": null, | |
| "train_tfrecord_fn": "/mnt/ceph/users/vgligorijevic/ContactMaps/DeepFRI2.0_TFRecords/*_GO_train", | |
| "valid_tfrecord_fn": "/mnt/ceph/users/vgligorijevic/ContactMaps/DeepFRI2.0_TFRecords/*_GO_valid", | |
| "annot_fn": "/mnt/ceph/users/vgligorijevic/ContactMaps/DeepFRI2.0_data/nrPDB-GO_annot.tsv", | |
| "test_list": "/mnt/ceph/users/vgligorijevic/ContactMaps/DeepFRI2.0_data/nrPDB-GO_test.csv", | |
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| ], | |
| "gonames": [ | |
| "coated vesicle membrane", | |
| "host intracellular region", | |
| "preribosome, small subunit precursor", | |
| "microbody", | |
| "light-harvesting complex", | |
| "site of DNA damage", | |
| "adherens junction", | |
| "organelle membrane", | |
| "midbody", | |
| "phosphopyruvate hydratase complex", | |
| "bacterial-type flagellum filament", | |
| "spindle pole", | |
| "rough endoplasmic reticulum membrane", | |
| "external side of plasma membrane", | |
| "respiratory chain complex", | |
| "ATPase complex", | |
| "spliceosomal complex", | |
| "actin-based cell projection", | |
| "nuclear protein-containing complex", | |
| "ribonucleoprotein granule", | |
| "cyclin-dependent protein kinase holoenzyme complex", | |
| "inner mitochondrial membrane protein complex", | |
| "SWI/SNF complex", | |
| "proteasome accessory complex", | |
| "CCR4-NOT core complex", | |
| "Set1C/COMPASS complex", | |
| "protein-DNA complex", | |
| "nuclear lumen", | |
| "sarcomere", | |
| "icosahedral viral capsid", | |
| "I band", | |
| "organelle inner membrane", | |
| "SWI/SNF superfamily-type complex", | |
| "clathrin coat", | |
| "spliceosomal tri-snRNP complex", | |
| "postsynapse", | |
| "contractile fiber", | |
| "mitochondrial respiratory chain complex I", | |
| "cytoplasmic stress granule", | |
| "external encapsulating structure", | |
| "storage vacuole", | |
| "virion part", | |
| "organelle envelope", | |
| "cell division site", | |
| "proton-transporting two-sector ATPase complex, catalytic domain", | |
| "other organism cell", | |
| "calcium channel complex", | |
| "recycling endosome membrane", | |
| "preribosome", | |
| "actin cytoskeleton", | |
| "endosome", | |
| "DNA repair complex", | |
| "receptor complex", | |
| "U5 snRNP", | |
| "proteasome regulatory particle", | |
| "ruffle membrane", | |
| "late endosome", | |
| "cell projection membrane", | |
| "secretory granule", | |
| "plasma membrane raft", | |
| "microvillus", | |
| "potassium channel complex", | |
| "signal recognition particle", | |
| "post-mRNA release spliceosomal complex", | |
| "chloroplast envelope", | |
| "Sm-like protein family complex", | |
| "histone deacetylase complex", | |
| "spindle", | |
| "spindle microtubule", | |
| "intracellular protein-containing complex", | |
| "ATPase dependent transmembrane transport complex", | |
| "histone acetyltransferase complex", | |
| "prespliceosome", | |
| "apical part of cell", | |
| "myofibril", | |
| "catalytic complex", | |
| "RNA polymerase complex", | |
| "Golgi-associated vesicle membrane", | |
| "clathrin-coated pit", | |
| "symplast", | |
| "protein acetyltransferase complex", | |
| "heterochromatin", | |
| "non-motile cilium", | |
| "transcription factor TFIID complex", | |
| "replisome", | |
| "lytic vacuole", | |
| "apoplast", | |
| "mitochondrial proton-transporting ATP synthase complex", | |
| "secretory vesicle", | |
| "precatalytic spliceosome", | |
| "mitochondrial inner membrane", | |
| "sarcolemma", | |
| "ciliary basal body", | |
| "cytosol", | |
| "tertiary granule", | |
| "mitochondrial proton-transporting ATP synthase complex, coupling factor F(o)", | |
| "mitochondrial matrix", | |
| "endoribonuclease complex", | |
| "outer membrane-bounded periplasmic space", | |
| "cytoplasmic vesicle lumen", | |
| "fibrillar center", | |
| "intracellular organelle lumen", | |
| "plasma membrane region", | |
| "myelin sheath", | |
| "mitochondrial large ribosomal subunit", | |
| "chromosomal region", | |
| "cullin-RING ubiquitin ligase complex", | |
| "lysosome", | |
| "proton-transporting ATP synthase complex, catalytic core F(1)", | |
| "intrinsic component of endoplasmic reticulum membrane", | |
| "U6 snRNP", | |
| "virus tail, baseplate", | |
| "MHC class I protein complex", | |
| "cell-cell junction", | |
| "nuclear DNA-directed RNA polymerase complex", | |
| "nucleosome", | |
| "integral component of mitochondrial membrane", | |
| "NADH dehydrogenase complex", | |
| "spliceosomal snRNP complex", | |
| "photosystem", | |
| "extracellular region", | |
| "COPI-coated vesicle membrane", | |
| "perinuclear region of cytoplasm", | |
| "intrinsic component of organelle membrane", | |
| "glutamatergic synapse", | |
| "synaptic vesicle", | |
| "photoreceptor cell cilium", | |
| "bounding membrane of organelle", | |
| "myosin complex", | |
| "RNA polymerase I complex", | |
| "immunoglobulin complex, circulating", | |
| "Ino80 complex", | |
| "telomerase holoenzyme complex", | |
| "endosome membrane", | |
| "centrosome", | |
| "supramolecular complex", | |
| "peroxisome", | |
| "nuclear envelope", | |
| "virion membrane", | |
| "outer membrane", | |
| "basolateral plasma membrane", | |
| "organelle subcompartment", | |
| "postsynaptic specialization", | |
| "respiratory chain complex I", | |
| "nucleolus", | |
| "SCF ubiquitin ligase complex", | |
| "ficolin-1-rich granule lumen", | |
| "blood microparticle", | |
| "cell tip", | |
| "transferase complex, transferring phosphorus-containing groups", | |
| "anchoring junction", | |
| "leading edge membrane", | |
| "microtubule cytoskeleton", | |
| "proton-transporting two-sector ATPase complex", | |
| "endoplasmic reticulum membrane", | |
| "synapse", | |
| "thylakoid", | |
| "ribonucleoside-diphosphate reductase complex", | |
| "plasma membrane bounded cell projection cytoplasm", | |
| "immunoglobulin complex", | |
| "sno(s)RNA-containing ribonucleoprotein complex", | |
| "Golgi membrane", | |
| "nuclear pore", | |
| "9+0 non-motile cilium", | |
| "polysomal ribosome", | |
| "mitochondrial small ribosomal subunit", | |
| "vesicle membrane", | |
| "organellar small ribosomal subunit", | |
| "viral nucleocapsid", | |
| "host cellular component", | |
| "Prp19 complex", | |
| "dendritic spine", | |
| "integrin complex", | |
| "endoplasmic reticulum protein-containing complex", | |
| "proton-transporting V-type ATPase complex", | |
| "chromosome", | |
| "P-body", | |
| "DNA helicase complex", | |
| "axoneme", | |
| "photosystem I", | |
| "pore complex", | |
| "mitochondrial ribosome", | |
| "mRNA cleavage factor complex", | |
| "cytoplasmic region", | |
| "postsynaptic membrane", | |
| "viral envelope", | |
| "MLL1/2 complex", | |
| "condensed nuclear chromosome", | |
| "primary lysosome", | |
| "secretory granule lumen", | |
| "neuron projection cytoplasm", | |
| "cell pole", | |
| "mitochondrial respiratory chain complex IV", | |
| "cytosolic large ribosomal subunit", | |
| "small ribosomal subunit", | |
| "polysome", | |
| "cytoplasmic side of plasma membrane", | |
| "mitochondrial outer membrane", | |
| "cytosolic proteasome complex", | |
| "ion channel complex", | |
| "nuclear ubiquitin ligase complex", | |
| "organelle envelope lumen", | |
| "proteasome regulatory particle, base subcomplex", | |
| "phycobilisome", | |
| "type II protein secretion system complex", | |
| "mitochondrial respirasome", | |
| "transcription factor TFIIH holo complex", | |
| "glycosome", | |
| "condensed chromosome kinetochore", | |
| "CMG complex", | |
| "ficolin-1-rich granule", | |
| "ciliary plasm", | |
| "membrane-enclosed lumen", | |
| "early endosome", | |
| "intrinsic component of membrane", | |
| "mitochondrial protein-containing complex", | |
| "dendritic tree", | |
| "endopeptidase complex", | |
| "chromosome, telomeric region", | |
| "photosynthetic membrane", | |
| "vesicle", | |
| "chloroplast", | |
| "microbody membrane", | |
| "phagophore assembly site", | |
| "peroxisomal membrane", | |
| "azurophil granule lumen", | |
| "host intracellular organelle", | |
| "virion", | |
| "cell leading edge", | |
| "anchored component of plasma membrane", | |
| "platelet alpha granule", | |
| "membrane coat", | |
| "host cell", | |
| "mitochondrial respiratory chain complex III", | |
| "polymeric cytoskeletal fiber", | |
| "respiratory chain complex III", | |
| "recycling endosome", | |
| "anaphase-promoting complex", | |
| "endodeoxyribonuclease complex", | |
| "RNA polymerase III complex", | |
| "small nuclear ribonucleoprotein complex", | |
| "nuclear body", | |
| "plastid envelope", | |
| "MHC protein complex", | |
| "plastid thylakoid", | |
| "catalytic step 1 spliceosome", | |
| "proton-transporting ATP synthase complex, coupling factor F(o)", | |
| "peptidase complex", | |
| "transport vesicle membrane", | |
| "side of membrane", | |
| "SAGA-type complex", | |
| "extrinsic component of cytoplasmic side of plasma membrane", | |
| "SLIK (SAGA-like) complex", | |
| "U2-type catalytic step 2 spliceosome", | |
| "kinetochore", | |
| "sarcoplasm", | |
| "acetyltransferase complex", | |
| "photosystem II oxygen evolving complex", | |
| "secretory granule membrane", | |
| "host cell nucleus", | |
| "plasma membrane signaling receptor complex", | |
| "eukaryotic translation initiation factor 3 complex", | |
| "mediator complex", | |
| "integral component of membrane", | |
| "stereocilium", | |
| "ATP-binding cassette (ABC) transporter complex", | |
| "membrane raft", | |
| "MLL1 complex", | |
| "phagocytic vesicle membrane", | |
| "other organism part", | |
| "serine/threonine protein kinase complex", | |
| "coated vesicle", | |
| "chaperone complex", | |
| "peroxisomal matrix", | |
| "protein complex involved in cell adhesion", | |
| "host cell cytoplasm", | |
| "apical plasma membrane", | |
| "envelope", | |
| "melanosome", | |
| "ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing", | |
| "cation channel complex", | |
| "cilium", | |
| "actin filament", | |
| "vesicle lumen", | |
| "synaptic membrane", | |
| "thylakoid membrane", | |
| "nuclear periphery", | |
| "histone methyltransferase complex", | |
| "mitochondrial membrane", | |
| "perikaryon", | |
| "endomembrane system", | |
| "MCM complex", | |
| "chromatin", | |
| "endocytic vesicle", | |
| "condensed nuclear chromosome kinetochore", | |
| "DNA polymerase complex", | |
| "clathrin-coated vesicle membrane", | |
| "catalytic step 2 spliceosome", | |
| "cell surface", | |
| "mitochondrial intermembrane space", | |
| "plastid thylakoid membrane", | |
| "exoribonuclease complex", | |
| "INO80-type complex", | |
| "neuron projection", | |
| "intrinsic component of mitochondrial membrane", | |
| "cell envelope", | |
| "origin recognition complex", | |
| "nuclear matrix", | |
| "host intracellular membrane-bounded organelle", | |
| "organelle lumen", | |
| "large ribosomal subunit", | |
| "neuron projection terminus", | |
| "Golgi stack", | |
| "cytoplasmic side of membrane", | |
| "plasma membrane bounded cell projection", | |
| "transcription repressor complex", | |
| "pre-replicative complex", | |
| "protein kinase complex", | |
| "neuronal cell body", | |
| "chloroplast thylakoid", | |
| "carboxy-terminal domain protein kinase complex", | |
| "RNA polymerase II, core complex", | |
| "distal axon", | |
| "cell outer membrane", | |
| "mitochondrion", | |
| "PcG protein complex", | |
| "mitochondrial nucleoid", | |
| "chloroplast thylakoid membrane", | |
| "cell cortex", | |
| "H4/H2A histone acetyltransferase complex", | |
| "AP-type membrane coat adaptor complex", | |
| "DNA packaging complex", | |
| "anchored component of membrane", | |
| "supramolecular polymer", | |
| "bicellular tight junction", | |
| "translation preinitiation complex", | |
| "tight junction", | |
| "endosome lumen", | |
| "viral membrane", | |
| "supramolecular fiber", | |
| "cytoskeleton", | |
| "caveola", | |
| "chromosome, centromeric region", | |
| "host cell membrane", | |
| "mitotic spindle", | |
| "nuclear pre-replicative complex", | |
| "integral component of plasma membrane", | |
| "cell body", | |
| "extracellular vesicle", | |
| "membrane microdomain", | |
| "axon", | |
| "methyltransferase complex", | |
| "transcription regulator complex", | |
| "integral component of endoplasmic reticulum membrane", | |
| "host intracellular part", | |
| "haptoglobin-hemoglobin complex", | |
| "U4 snRNP", | |
| "somatodendritic compartment", | |
| "exocytic vesicle membrane", | |
| "kinetoplast", | |
| "eukaryotic 43S preinitiation complex", | |
| "endoplasmic reticulum lumen", | |
| "Z disc", | |
| "organellar large ribosomal subunit", | |
| "coated membrane", | |
| "early endosome membrane", | |
| "cytosolic ribosome", | |
| "growth cone", | |
| "extracellular organelle", | |
| "Golgi-associated vesicle", | |
| "photosystem I reaction center", | |
| "lipid droplet", | |
| "synaptic vesicle membrane", | |
| "autophagosome", | |
| "RSC-type complex", | |
| "COPII-coated ER to Golgi transport vesicle", | |
| "sperm flagellum", | |
| "cortical actin cytoskeleton", | |
| "nuclear membrane", | |
| "carboxysome", | |
| "extracellular matrix", | |
| "transmembrane transporter complex", | |
| "H4 histone acetyltransferase complex", | |
| "microtubule", | |
| "virus tail", | |
| "dynein complex", | |
| "ribosomal subunit", | |
| "U12-type spliceosomal complex", | |
| "focal adhesion", | |
| "ER to Golgi transport vesicle membrane", | |
| "organelle membrane contact site", | |
| "proteasome core complex, alpha-subunit complex", | |
| "ribonuclease P complex", | |
| "pilus", | |
| "transporter complex", | |
| "cytosolic small ribosomal subunit", | |
| "photoreceptor inner segment", | |
| "ESCRT complex", | |
| "chloroplast stroma", | |
| "intracellular vesicle", | |
| "transcription elongation factor complex", | |
| "intrinsic component of cell outer membrane", | |
| "collagen-containing extracellular matrix", | |
| "U2-type prespliceosome", | |
| "brush border", | |
| "site of double-strand break", | |
| "viral capsid", | |
| "postsynaptic density", | |
| "T=3 icosahedral viral capsid", | |
| "COPI-coated vesicle", | |
| "NuA4 histone acetyltransferase complex", | |
| "replication fork", | |
| "SAGA complex", | |
| "DNA polymerase III complex", | |
| "vacuole", | |
| "hemoglobin complex", | |
| "U2-type spliceosomal complex", | |
| "U2 snRNP", | |
| "cytoplasmic vesicle", | |
| "DNA replication preinitiation complex", | |
| "nucleus", | |
| "plasma membrane", | |
| "proteasome core complex", | |
| "exosome (RNase complex)", | |
| "neuron spine", | |
| "intracellular non-membrane-bounded organelle", | |
| "fungal-type vacuole", | |
| "centriole", | |
| "COP9 signalosome", | |
| "polyhedral organelle", | |
| "autophagosome membrane", | |
| "cluster of actin-based cell projections", | |
| "fungal-type vacuole membrane", | |
| "exocytic vesicle", | |
| "microbody lumen", | |
| "cell wall", | |
| "respirasome", | |
| "ribonucleoprotein complex", | |
| "vacuolar membrane", | |
| "lamellipodium", | |
| "intrinsic component of plasma membrane", | |
| "host cell part", | |
| "azurophil granule", | |
| "nuclear replisome", | |
| "proteasome regulatory particle, lid subcomplex", | |
| "host cell plasma membrane", | |
| "ciliary membrane", | |
| "eukaryotic 48S preinitiation complex", | |
| "MHC class II protein complex", | |
| "asymmetric synapse", | |
| "ruffle", | |
| "preribosome, large subunit precursor", | |
| "vacuolar proton-transporting V-type ATPase complex", | |
| "specific granule", | |
| "plasma membrane protein complex", | |
| "specific granule lumen", | |
| "filopodium", | |
| "9+2 motile cilium", | |
| "oxidoreductase complex", | |
| "presynapse", | |
| "voltage-gated potassium channel complex", | |
| "cell projection", | |
| "cortical cytoskeleton", | |
| "photosystem II", | |
| "tricarboxylic acid cycle enzyme complex", | |
| "lytic vacuole membrane", | |
| "bacterial-type flagellum basal body", | |
| "proton-transporting ATP synthase complex", | |
| "motile cilium", | |
| "tertiary granule lumen", | |
| "plastid stroma", | |
| "small-subunit processome", | |
| "endoplasmic reticulum-Golgi intermediate compartment", | |
| "pigment granule", | |
| "vesicle coat", | |
| "late endosome membrane", | |
| "transferase complex", | |
| "Golgi apparatus subcompartment", | |
| "integral component of organelle membrane", | |
| "extracellular exosome", | |
| "MHC class I peptide loading complex", | |
| "phagocytic vesicle", | |
| "endoplasmic reticulum", | |
| "photoreceptor outer segment", | |
| "plasmodesma", | |
| "90S preribosome", | |
| "cell-substrate junction", | |
| "RNA polymerase II transcription regulator complex", | |
| "host cell cytoplasm part", | |
| "endocytic vesicle membrane", | |
| "periplasmic space", | |
| "ribosome", | |
| "site of polarized growth", | |
| "nuclear speck", | |
| "nuclear replication fork", | |
| "nuclear chromosome", | |
| "proteasome core complex, beta-subunit complex", | |
| "rough endoplasmic reticulum", | |
| "nucleoplasm", | |
| "organellar ribosome", | |
| "cytoplasmic exosome (RNase complex)", | |
| "cytoplasmic vesicle membrane", | |
| "membrane protein complex", | |
| "non-membrane-bounded organelle", | |
| "cytoplasmic microtubule", | |
| "mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1)", | |
| "cytoplasmic ribonucleoprotein granule", | |
| "U2-type precatalytic spliceosome", | |
| "U1 snRNP", | |
| "microtubule organizing center", | |
| "core mediator complex", | |
| "nucleoid", | |
| "Golgi apparatus", | |
| "respiratory chain complex IV", | |
| "condensed chromosome, centromeric region", | |
| "cell periphery", | |
| "mitochondrial envelope", | |
| "cytochrome complex", | |
| "transport vesicle", | |
| "lysosomal lumen", | |
| "U4/U6 x U5 tri-snRNP complex", | |
| "RNA polymerase II, holoenzyme", | |
| "vacuolar lumen", | |
| "DNA-directed RNA polymerase complex", | |
| "helical viral capsid", | |
| "extrinsic component of plasma membrane", | |
| "proton-transporting two-sector ATPase complex, proton-transporting domain", | |
| "dendrite", | |
| "extracellular space", | |
| "organelle outer membrane", | |
| "U2-type catalytic step 1 spliceosome", | |
| "nuclear outer membrane-endoplasmic reticulum membrane network", | |
| "ubiquitin ligase complex", | |
| "clathrin-coated vesicle", | |
| "endoplasmic reticulum subcompartment", | |
| "cell junction", | |
| "CCR4-NOT complex", | |
| "transcription factor TFIIH core complex", | |
| "condensed chromosome", | |
| "apical junction complex", | |
| "microtubule associated complex", | |
| "proteasome complex", | |
| "trans-Golgi network", | |
| "vesicle tethering complex", | |
| "stereocilium bundle", | |
| "extrinsic component of membrane", | |
| "bacterial-type flagellum", | |
| "lysosomal membrane", | |
| "plastid", | |
| "proteasome storage granule", | |
| "T cell receptor complex", | |
| "neuron to neuron synapse", | |
| "axon terminus", | |
| "nuclear inner membrane", | |
| "nuclear exosome (RNase complex)" | |
| ] | |
| } |