diff --git a/services/embedder/api.yaml b/services/embedder/api.yaml index 7073770e..f387183a 100644 --- a/services/embedder/api.yaml +++ b/services/embedder/api.yaml @@ -64,7 +64,7 @@ paths: '404' description: Is returned when the model does not exist. - /models/{model_name}/details/{component}: + /models/{model_name}/{component}: get: summary: Get details on the embedding model component. Component values can be "preprocessor", "embedder", "similarity-processor" diff --git a/services/embedder/app.py b/services/embedder/app.py index 4d482177..2470db49 100644 --- a/services/embedder/app.py +++ b/services/embedder/app.py @@ -102,7 +102,7 @@ def _get_meta_data(model_name, file): for f in os.listdir(app.config["DOWNLOAD_DIR"]): try: os.remove(os.path.join(app.config["DOWNLOAD_DIR"], f)) - except: + except Exception: shutil.rmtree(os.path.join(app.config["DOWNLOAD_DIR"], f)) else: # Fetch from a local dir @@ -338,7 +338,7 @@ def handle_similar_points_request(model_name): ) -@app.route("/models//info//") +@app.route("/models///") def handle_info_request(model_name, component_name): """Handle request of details on different model components.""" if model_name in app.models: diff --git a/services/embedder/configs/forge_configs/forge-config.yml b/services/embedder/configs/forge_configs/forge-config.yml index bd7690bb..1308f22a 100644 --- a/services/embedder/configs/forge_configs/forge-config.yml +++ b/services/embedder/configs/forge_configs/forge-config.yml @@ -8,16 +8,17 @@ Model: Store: name: BlueBrainNexus - endpoint: https://staging.nexus.ocp.bbp.epfl.ch/v1 - bucket: dke/embedder_catalog + endpoint: https://bbp.epfl.ch/nexus/v1 + bucket: "dke/embedding-pipelines" searchendpoints: sparql: endpoint: "https://bluebrain.github.io/nexus/vocabulary/defaultSparqlIndex" vocabulary: - iri: "https://bluebrain.github.io/nexus/contexts/resource.json" + iri: "https://bluebrain.github.io/nexus/contexts/metadata.json" namespace: "https://bluebrain.github.io/nexus/vocabulary/" deprecated_property: "https://bluebrain.github.io/nexus/vocabulary/deprecated" project_property: "https://bluebrain.github.io/nexus/vocabulary/project" + max_connection: 50 versioned_id_template: "{x.id}?rev={x._store_metadata._rev}" file_resource_mapping: https://raw.githubusercontent.com/BlueBrain/nexus-forge/master/examples/configurations/nexus-store/file-to-resource-mapping.hjson diff --git a/services/embedder/downloads/Attri2vec_test_model.zip b/services/embedder/downloads/Attri2vec_test_model.zip index 04c3e32d..361fa593 100644 Binary files a/services/embedder/downloads/Attri2vec_test_model.zip and b/services/embedder/downloads/Attri2vec_test_model.zip differ diff --git a/services/embedder/examples/notebooks/Embedder API for node embedding.ipynb b/services/embedder/examples/notebooks/Embedder API for node embedding.ipynb index 5e1382d4..b17b5e7c 100644 --- a/services/embedder/examples/notebooks/Embedder API for node embedding.ipynb +++ b/services/embedder/examples/notebooks/Embedder API for node embedding.ipynb @@ -23,7 +23,11 @@ }, { "cell_type": "code", +<<<<<<< HEAD + "execution_count": 50, +======= "execution_count": null, +>>>>>>> 2536c2807f912d0f5fed5f9115002f9416d45cca "metadata": {}, "outputs": [], "source": [ @@ -34,7 +38,11 @@ }, { "cell_type": "code", +<<<<<<< HEAD + "execution_count": 51, +======= "execution_count": null, +>>>>>>> 2536c2807f912d0f5fed5f9115002f9416d45cca "metadata": {}, "outputs": [], "source": [ @@ -50,9 +58,50 @@ }, { "cell_type": "code", +<<<<<<< HEAD + "execution_count": 52, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n" + ] + }, + { + "data": { + "text/plain": [ + "{'models': {'Attri2vec_test_model': {'id': 'Attri2vec_test_model',\n", + " 'name': 'Attri2vec_test_model',\n", + " 'description': 'Attri2vec_test_model',\n", + " 'filename': 'downloads/Attri2vec_test_model.zip',\n", + " 'created': 'Tue Jul 6 15:16:16 2021',\n", + " 'modified': 'Tue Jul 6 15:15:48 2021'},\n", + " 'SEU_morph_attri2vec_euclidean': {'id': 'SEU_morph_attri2vec_euclidean',\n", + " 'name': 'SEU_morph_attri2vec_euclidean',\n", + " 'description': 'SEU_morph_attri2vec_euclidean',\n", + " 'filename': 'downloads/SEU_morph_attri2vec_euclidean.zip',\n", + " 'created': 'Tue Jul 6 14:42:46 2021',\n", + " 'modified': 'Mon Jul 5 12:41:44 2021'},\n", + " 'Cord-19-NCIT-linking': {'id': 'Cord-19-NCIT-linking',\n", + " 'name': 'Cord-19-NCIT-linking',\n", + " 'description': 'Cord-19-NCIT-linking',\n", + " 'filename': 'downloads/Cord-19-NCIT-linking.zip',\n", + " 'created': 'Tue Jun 1 12:36:56 2021',\n", + " 'modified': 'Tue Jun 1 12:36:56 2021'}}}" + ] + }, + "execution_count": 52, + "metadata": {}, + "output_type": "execute_result" + } + ], +======= "execution_count": null, "metadata": {}, "outputs": [], +>>>>>>> 2536c2807f912d0f5fed5f9115002f9416d45cca "source": [ "r = requests.get(\n", " f'{ENDPOINT}/models/')\n", @@ -69,7 +118,11 @@ }, { "cell_type": "code", +<<<<<<< HEAD + "execution_count": 53, +======= "execution_count": null, +>>>>>>> 2536c2807f912d0f5fed5f9115002f9416d45cca "metadata": {}, "outputs": [], "source": [ @@ -78,9 +131,38 @@ }, { "cell_type": "code", +<<<<<<< HEAD + "execution_count": 54, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n" + ] + }, + { + "data": { + "text/plain": [ + "{'id': 'Attri2vec_test_model',\n", + " 'name': 'Attri2vec_test_model',\n", + " 'description': 'Attri2vec_test_model',\n", + " 'filename': 'downloads/Attri2vec_test_model.zip',\n", + " 'created': 'Tue Jul 6 15:16:16 2021',\n", + " 'modified': 'Tue Jul 6 15:15:48 2021'}" + ] + }, + "execution_count": 54, + "metadata": {}, + "output_type": "execute_result" + } + ], +======= "execution_count": null, "metadata": {}, "outputs": [], +>>>>>>> 2536c2807f912d0f5fed5f9115002f9416d45cca "source": [ "r = requests.get(\n", " f'{ENDPOINT}/models/{MODEL_NAME}')\n", @@ -97,36 +179,141 @@ }, { "cell_type": "code", +<<<<<<< HEAD + "execution_count": 55, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n" + ] + }, + { + "data": { + "text/plain": [ + "{'heterogeneous': 'False',\n", + " 'drop_types': 'False',\n", + " 'encode_types': 'False',\n", + " 'edge_features': 'False',\n", + " 'categorical_encoding': 'multibin',\n", + " 'text_encoding': 'tfidf',\n", + " 'text_encoding_max_dimension': '512',\n", + " 'missing_numeric': 'drop',\n", + " 'imputation_strategy': 'mean',\n", + " 'standardize_numeric': 'True',\n", + " 'node_properties': \"['definition']\",\n", + " 'edge_properties': 'None',\n", + " 'reduce_node_dims': 'False',\n", + " 'reduce_edge_dims': 'False',\n", + " 'n_node_components': 'None',\n", + " 'n_edge_components': 'None',\n", + " 'interface': 'ScikitLearnPGEncoder'}" + ] + }, + "execution_count": 55, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "r = requests.get(\n", + " f'{ENDPOINT}/models/{MODEL_NAME}/preprocessor/')\n", +======= "execution_count": null, "metadata": {}, "outputs": [], "source": [ "r = requests.get(\n", " f'{ENDPOINT}/models/{MODEL_NAME}/info/preprocessor/')\n", +>>>>>>> 2536c2807f912d0f5fed5f9115002f9416d45cca "print(r)\n", "r.json()" ] }, { "cell_type": "code", +<<<<<<< HEAD + "execution_count": 56, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n" + ] + }, + { + "data": { + "text/plain": [ + "{'interface': 'StellarGraphNodeEmbedder',\n", + " 'model_type': 'inductive',\n", + " 'trained': 'True',\n", + " 'model_name': 'attri2vec',\n", + " 'model_params': \"{'length': 5, 'number_of_walks': 10, 'epochs': 5, 'embedding_dimension': 128, 'batch_size': 20, 'negative_samples': 10, 'num_samples': [10, 5], 'random_walk_p': 0.5, 'random_walk_q': 2.0, 'clusters': 2, 'clusters_q': 1}\",\n", + " 'graph_configs': \"{'directed': True, 'include_type': False, 'feature_props': None, 'feature_vector_prop': 'features', 'edge_weight': 'npmi'}\"}" + ] + }, + "execution_count": 56, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "r = requests.get(\n", + " f'{ENDPOINT}/models/{MODEL_NAME}/embedder/')\n", +======= "execution_count": null, "metadata": {}, "outputs": [], "source": [ "r = requests.get(\n", " f'{ENDPOINT}/models/{MODEL_NAME}/info/embedder/')\n", +>>>>>>> 2536c2807f912d0f5fed5f9115002f9416d45cca "print(r)\n", "r.json()" ] }, { "cell_type": "code", +<<<<<<< HEAD + "execution_count": 57, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n" + ] + }, + { + "data": { + "text/plain": [ + "{'similarity': 'cosine',\n", + " 'dimension': '128',\n", + " 'segmented': 'False',\n", + " 'interface': 'SimilarityProcessor'}" + ] + }, + "execution_count": 57, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "r = requests.get(\n", + " f'{ENDPOINT}/models/{MODEL_NAME}/similarity-processor/')\n", +======= "execution_count": null, "metadata": {}, "outputs": [], "source": [ "r = requests.get(\n", " f'{ENDPOINT}/models/{MODEL_NAME}/info/similarity-processor/')\n", +>>>>>>> 2536c2807f912d0f5fed5f9115002f9416d45cca "print(r)\n", "r.json()" ] @@ -140,11 +327,296 @@ }, { "cell_type": "code", +<<<<<<< HEAD + "execution_count": 58, + "metadata": { + "scrolled": true + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "CPU times: user 3.62 ms, sys: 1.64 ms, total: 5.27 ms\n", + "Wall time: 10.8 ms\n" + ] + }, + { + "data": { + "text/plain": [ + "{'vectors': {'dna replication': [0.09018382430076599,\n", + " 0.0818086639046669,\n", + " 0.08301800489425659,\n", + " 0.10191024094820023,\n", + " 0.09029056131839752,\n", + " 0.06174599379301071,\n", + " 0.08552592992782593,\n", + " 0.1774897277355194,\n", + " 0.08188088983297348,\n", + " 0.15809817612171173,\n", + " 0.07814916223287582,\n", + " 0.056634772568941116,\n", + " 0.07830986380577087,\n", + " 0.10154026001691818,\n", + " 0.10137305408716202,\n", + " 0.10980508476495743,\n", + " 0.07304294407367706,\n", + " 0.07692369818687439,\n", + " 0.08322767168283463,\n", + " 0.07359818369150162,\n", + " 0.06316495686769485,\n", + " 0.06976249814033508,\n", + " 0.06179897487163544,\n", + " 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0.10700694471597672,\n", + " 0.09484472870826721,\n", + " 0.12423460930585861,\n", + " 0.09736296534538269,\n", + " 0.07988183200359344,\n", + " 0.12724067270755768,\n", + " 0.08258107304573059,\n", + " 0.08201000839471817,\n", + " 0.07710529863834381,\n", + " 0.07840847223997116,\n", + " 0.10592275112867355,\n", + " 0.07519745081663132,\n", + " 0.06189802289009094,\n", + " 0.07845254987478256,\n", + " 0.10798022150993347,\n", + " 0.10273926705121994,\n", + " 0.0704103335738182,\n", + " 0.08464070409536362,\n", + " 0.08257313072681427,\n", + " 0.08360534906387329,\n", + " 0.08787655085325241,\n", + " 0.07589849829673767,\n", + " 0.09011205285787582,\n", + " 0.07009659707546234,\n", + " 0.06777011603116989,\n", + " 0.11442588269710541,\n", + " 0.10116538405418396,\n", + " 0.08956089615821838,\n", + " 0.07620611041784286],\n", + " 'covid-19 infection': None,\n", + " 'lalala not in the index': None}}" + ] + }, + "execution_count": 58, + "metadata": {}, + "output_type": "execute_result" + } + ], +======= "execution_count": null, "metadata": { "scrolled": true }, "outputs": [], +>>>>>>> 2536c2807f912d0f5fed5f9115002f9416d45cca "source": [ "%%time\n", "r = requests.get(\n", @@ -165,11 +637,80 @@ }, { "cell_type": "code", +<<<<<<< HEAD + "execution_count": 59, + "metadata": { + "scrolled": true + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "CPU times: user 3.5 ms, sys: 1.74 ms, total: 5.23 ms\n", + "Wall time: 7.99 ms\n" + ] + }, + { + "data": { + "text/plain": [ + "{'neighbors': {'glucose': ['glucose',\n", + " 'compact disc-interactive',\n", + " 'food',\n", + " 'fatigue',\n", + " 'molecule',\n", + " 'hydrophobicity',\n", + " 'g-cell',\n", + " 'interferon',\n", + " 'ion',\n", + " 'dehydration',\n", + " 'congenital abnormality',\n", + " 'pruritus',\n", + " 'dizziness',\n", + " 'bicarbonate ion',\n", + " 'proximal',\n", + " 'constipation',\n", + " 'anal injury',\n", + " 'subarachnoid hemorrhage',\n", + " 'nasal',\n", + " 'dog'],\n", + " 'covid-19 infection': None,\n", + " 'dna replication': ['dna replication',\n", + " 'mutation abnormality',\n", + " 'pneumococcal pneumonia',\n", + " 'nucleotide',\n", + " 'pharmacologic substance',\n", + " 'phenol',\n", + " 'human immunodeficiency virus 1',\n", + " 'aspirin',\n", + " 'ribavirin',\n", + " 'human herpesvirus 1',\n", + " 'glycopeptide',\n", + " 'salt',\n", + " 'tacrolimus',\n", + " 'encephalitis',\n", + " 'dacarbazine',\n", + " 'acetylcysteine',\n", + " 'immunocompromised',\n", + " 'cyclosporine',\n", + " 'abscess',\n", + " 'norepinephrine, dl-'],\n", + " 'lalala not in the index': None}}" + ] + }, + "execution_count": 59, + "metadata": {}, + "output_type": "execute_result" + } + ], +======= "execution_count": null, "metadata": { "scrolled": true }, "outputs": [], +>>>>>>> 2536c2807f912d0f5fed5f9115002f9416d45cca "source": [ "%%time\n", "r = requests.get(\n", @@ -184,11 +725,80 @@ }, { "cell_type": "code", +<<<<<<< HEAD + "execution_count": 60, + "metadata": { + "scrolled": true + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "CPU times: user 3.73 ms, sys: 1.57 ms, total: 5.3 ms\n", + "Wall time: 6.15 ms\n" + ] + }, + { + "data": { + "text/plain": [ + "{'neighbors': {'glucose': {'glucose': 1.0,\n", + " 'compact disc-interactive': 0.9868028163909912,\n", + " 'food': 0.9866440892219543,\n", + " 'fatigue': 0.9863864779472351,\n", + " 'molecule': 0.9857110381126404,\n", + " 'hydrophobicity': 0.985710620880127,\n", + " 'g-cell': 0.9854280948638916,\n", + " 'interferon': 0.9850452542304993,\n", + " 'ion': 0.9848295450210571,\n", + " 'dehydration': 0.9847713708877563,\n", + " 'congenital abnormality': 0.9846807718276978,\n", + " 'pruritus': 0.9846807718276978,\n", + " 'dizziness': 0.9846807718276978,\n", + " 'bicarbonate ion': 0.9846807718276978,\n", + " 'proximal': 0.9846807718276978,\n", + " 'constipation': 0.9846807718276978,\n", + " 'anal injury': 0.9846807718276978,\n", + " 'subarachnoid hemorrhage': 0.9846807718276978,\n", + " 'nasal': 0.9846807718276978,\n", + " 'dog': 0.9846807718276978},\n", + " 'covid-19 infection': None,\n", + " 'dna replication': {'dna replication': 1.0,\n", + " 'mutation abnormality': 0.9898869395256042,\n", + " 'pneumococcal pneumonia': 0.9853894710540771,\n", + " 'nucleotide': 0.984702467918396,\n", + " 'pharmacologic substance': 0.9844593405723572,\n", + " 'phenol': 0.9843074083328247,\n", + " 'human immunodeficiency virus 1': 0.9836665987968445,\n", + " 'aspirin': 0.9831295609474182,\n", + " 'ribavirin': 0.9829986095428467,\n", + " 'human herpesvirus 1': 0.9829602837562561,\n", + " 'glycopeptide': 0.9828788042068481,\n", + " 'salt': 0.9827151298522949,\n", + " 'tacrolimus': 0.9827004671096802,\n", + " 'encephalitis': 0.9822028875350952,\n", + " 'dacarbazine': 0.9820472002029419,\n", + " 'acetylcysteine': 0.9819145202636719,\n", + " 'immunocompromised': 0.9818955659866333,\n", + " 'cyclosporine': 0.9815682172775269,\n", + " 'abscess': 0.9814446568489075,\n", + " 'norepinephrine, dl-': 0.9807848930358887},\n", + " 'lalala not in the index': None}}" + ] + }, + "execution_count": 60, + "metadata": {}, + "output_type": "execute_result" + } + ], +======= "execution_count": null, "metadata": { "scrolled": true }, "outputs": [], +>>>>>>> 2536c2807f912d0f5fed5f9115002f9416d45cca "source": [ "%%time\n", "r = requests.get(\n", @@ -211,7 +821,11 @@ }, { "cell_type": "code", +<<<<<<< HEAD + "execution_count": 61, +======= "execution_count": null, +>>>>>>> 2536c2807f912d0f5fed5f9115002f9416d45cca "metadata": {}, "outputs": [], "source": [ @@ -221,9 +835,25 @@ }, { "cell_type": "code", +<<<<<<< HEAD + "execution_count": 62, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "CPU times: user 42.5 ms, sys: 6.32 ms, total: 48.8 ms\n", + "Wall time: 443 ms\n" + ] + } + ], +======= "execution_count": null, "metadata": {}, "outputs": [], +>>>>>>> 2536c2807f912d0f5fed5f9115002f9416d45cca "source": [ "%%time\n", "r = requests.post(\n", @@ -267,7 +897,11 @@ }, { "cell_type": "code", +<<<<<<< HEAD + "execution_count": 43, +======= "execution_count": null, +>>>>>>> 2536c2807f912d0f5fed5f9115002f9416d45cca "metadata": {}, "outputs": [], "source": [ @@ -276,7 +910,11 @@ }, { "cell_type": "code", +<<<<<<< HEAD + "execution_count": 44, +======= "execution_count": null, +>>>>>>> 2536c2807f912d0f5fed5f9115002f9416d45cca "metadata": {}, "outputs": [], "source": [ @@ -288,27 +926,10073 @@ }, { "cell_type": "code", +<<<<<<< HEAD + "execution_count": 46, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "········\n" + ] + } + ], +======= "execution_count": null, "metadata": {}, "outputs": [], +>>>>>>> 2536c2807f912d0f5fed5f9115002f9416d45cca "source": [ "TOKEN = getpass.getpass()" ] }, { "cell_type": "code", +<<<<<<< HEAD + "execution_count": 47, + "metadata": {}, + "outputs": [ + { + "data": { 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'levofloxacin': 0.9786515235900879,\n", + " 'daptomycin': 0.9784270524978638}]}" + ] + }, + "execution_count": 47, + "metadata": {}, + "output_type": "execute_result" + } + ], +======= "execution_count": null, "metadata": {}, "outputs": [], +>>>>>>> 2536c2807f912d0f5fed5f9115002f9416d45cca "source": [ "r.json()" ] }, { "cell_type": "code", +<<<<<<< HEAD + "execution_count": 48, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "CPU times: user 21.1 ms, sys: 2.65 ms, total: 23.7 ms\n", + "Wall time: 5.65 s\n" + ] + } + ], +======= "execution_count": null, "metadata": {}, "outputs": [], +>>>>>>> 2536c2807f912d0f5fed5f9115002f9416d45cca "source": [ "%%time\n", "r = requests.post(\n", @@ -328,9 +11012,10034 @@ }, { "cell_type": "code", +<<<<<<< HEAD + "execution_count": 49, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "CPU times: user 47.3 ms, sys: 4.35 ms, total: 51.7 ms\n", + "Wall time: 109 ms\n" + ] + }, + { + "data": { + "text/plain": [ + "{'neighbors': [{'water': 1.0,\n", + " 'depression': 1.0,\n", + " 'intracranial hemorrhage': 1.0,\n", + " 'dizziness': 1.0,\n", + " 'bicarbonate ion': 1.0,\n", + " 'cerebral hemorrhage': 1.0,\n", + " 'congenital abnormality': 1.0,\n", + " 'caddo language': 1.0,\n", + " 'constipation': 1.0,\n", + " 'nasal': 1.0,\n", + " 'subarachnoid hemorrhage': 1.0,\n", + " 'proximal': 1.0,\n", + " 'anxiety': 1.0,\n", + " 'dog': 1.0,\n", + " 'cat': 1.0,\n", + " 'pruritus': 1.0,\n", + " 'deny': 1.0,\n", + " 'brother': 1.0,\n", + " 'endotracheal': 1.0,\n", + " 'anal injury': 1.0},\n", + " {'urinary system': 0.9965946674346924,\n", + " 'rodentia': 0.9921068549156189,\n", + " 'muscle': 0.9916718006134033,\n", + " 'proximal': 0.9907795190811157,\n", + " 'dog': 0.9907795190811157,\n", + " 'water': 0.9907795190811157,\n", + " 'congenital abnormality': 0.9907795190811157,\n", + " 'cerebral hemorrhage': 0.9907795190811157,\n", + " 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'water': 0.9876339435577393,\n", + " 'pruritus': 0.9876339435577393,\n", + " 'cerebral hemorrhage': 0.9876339435577393,\n", + " 'endotracheal': 0.9876339435577393,\n", + " 'constipation': 0.9876339435577393},\n", + " {'tumor necrosis factor': 0.9923617839813232,\n", + " 'serine/threonine-protein kinase mtor': 0.9919082522392273,\n", + " 'tissue factor': 0.9917693138122559,\n", + " 'cd44 antigen': 0.9913846254348755,\n", + " 'adiponectin': 0.991315484046936,\n", + " 'caax prenyl protease 2': 0.991302490234375,\n", + " 'plasminogen activator inhibitor 1': 0.9910920262336731,\n", + " 'alanine aminotransferase': 0.9909096956253052,\n", + " 'caspase-5': 0.9908235669136047,\n", + " 'corticoliberin': 0.9906193017959595,\n", + " 'myeloperoxidase': 0.9904072284698486,\n", + " 'caspase-3': 0.9904011487960815,\n", + " 'dipeptidyl peptidase 4': 0.9903478622436523,\n", + " 'vascular endothelial growth factor a': 0.990086555480957,\n", + " 'interleukin-4': 0.9897820353507996,\n", + " '72kda type iv collagenase': 0.9896783828735352,\n", + " 'intercellular adhesion molecule 1': 0.9895258545875549,\n", + " 'granulocyte-macrophage colony-stimulating factor': 0.9892817735671997,\n", + " 'caspase-1': 0.9891095161437988,\n", + " 'interleukin-2': 0.9891087412834167},\n", + " {'cefepime': 0.9999997615814209,\n", + " 'cephalosporin antibiotic': 0.9990013241767883,\n", + " 'penicillin g sodium': 0.9989047050476074,\n", + " 'amoxicillin': 0.9973400235176086,\n", + " 'ampicillin': 0.9962109923362732,\n", + " 'piperacillin-tazobactam': 0.9960567355155945,\n", + " 'oxacillin': 0.9955019950866699,\n", + " 'cefotaxime': 0.9950597882270813,\n", + " 'amikacin': 0.9929844737052917,\n", + " 'methicillin': 0.992709219455719,\n", + " 'meropenem': 0.9913114309310913,\n", + " 'erythromycin': 0.9910375475883484,\n", + " 'ceftazidime': 0.9903815984725952,\n", + " 'ceftriaxone': 0.9903815984725952,\n", + " 'ciprofloxacin': 0.9886021018028259,\n", + " 'tigecycline': 0.9864334464073181,\n", + " 'imipenem': 0.9854371547698975,\n", + " 'gentamicin': 0.9830957055091858,\n", + " 'levofloxacin': 0.9786515235900879,\n", + " 'daptomycin': 0.9784270524978638}]}" + ] + }, + "execution_count": 49, + "metadata": {}, + "output_type": "execute_result" + } + ], +======= "execution_count": null, "metadata": {}, "outputs": [], +>>>>>>> 2536c2807f912d0f5fed5f9115002f9416d45cca "source": [ "%%time\n", "r = requests.post(\n",