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Add BERTopic model

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README.md ADDED
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+
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+ ---
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+ tags:
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+ - bertopic
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+ library_name: bertopic
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+ pipeline_tag: text-classification
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+ ---
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+
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+ # am25_abstract_topic_model
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+
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+ This is a [BERTopic](https://github.com/MaartenGr/BERTopic) model.
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+ BERTopic is a flexible and modular topic modeling framework that allows for the generation of easily interpretable topics from large datasets.
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+
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+ ## Usage
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+
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+ To use this model, please install BERTopic:
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+
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+ ```
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+ pip install -U bertopic
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+ ```
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+
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+ You can use the model as follows:
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+
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+ ```python
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+ from bertopic import BERTopic
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+ topic_model = BERTopic.load("djordan/am25_abstract_topic_model")
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+
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+ topic_model.get_topic_info()
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+ ```
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+
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+ ## Topic overview
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+
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+ * Number of topics: 171
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+ * Number of training documents: 7863
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+
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+ <details>
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+ <summary>Click here for an overview of all topics.</summary>
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+
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+ | Topic ID | Topic Keywords | Topic Frequency | Label |
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+ |----------|----------------|-----------------|-------|
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+ | -1 | and - the - of - in - to | 5 | -1_and_the_of_in |
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+ | 0 | adc - adcs - dxd - payload - her2 | 3431 | 0_adc_adcs_dxd_payload |
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+ | 1 | kras - ras - g12c - mutant - g12d | 196 | 1_kras_ras_g12c_mutant |
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+ | 2 | ici - patients - immune - response - responders | 179 | 2_ici_patients_immune_response |
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+ | 3 | health - care - women - among - black | 165 | 3_health_care_women_among |
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+ | 4 | aml - leukemia - myeloid - venetoclax - acute | 150 | 4_aml_leukemia_myeloid_venetoclax |
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+ | 5 | gbm - glioblastoma - brain - glioma - tmz | 140 | 5_gbm_glioblastoma_brain_glioma |
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+ | 6 | pd - l1 - anti - ccr8 - antibody | 135 | 6_pd_l1_anti_ccr8 |
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+ | 7 | parpi - parp - usp1 - dna - repair | 100 | 7_parpi_parp_usp1_dna |
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+ | 8 | car - cells - cd19 - antigen - cell | 93 | 8_car_cells_cd19_antigen |
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+ | 9 | egfr - osimertinib - resistance - tkis - tki | 92 | 9_egfr_osimertinib_resistance_tkis |
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+ | 10 | tnbc - breast - triple - mda - negative | 86 | 10_tnbc_breast_triple_mda |
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+ | 11 | pdos - organoids - organoid - drug - 3d | 84 | 11_pdos_organoids_organoid_drug |
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+ | 12 | pdac - pancreatic - basal - ductal - classical | 77 | 12_pdac_pancreatic_basal_ductal |
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+ | 13 | cfdna - methylation - samples - detection - urine | 62 | 13_cfdna_methylation_samples_detection |
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+ | 14 | ar - enzalutamide - prostate - androgen - resistant | 60 | 14_ar_enzalutamide_prostate_androgen |
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+ | 15 | dose - pts - mg - safety - pk | 58 | 15_dose_pts_mg_safety |
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+ | 16 | glucose - glutamine - mitochondrial - metabolism - metabolic | 56 | 16_glucose_glutamine_mitochondrial_metabolism |
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+ | 17 | hcc - liver - sorafenib - hepatocellular - lenvatinib | 52 | 17_hcc_liver_sorafenib_hepatocellular |
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+ | 18 | variants - ffpe - sequencing - variant - samples | 49 | 18_variants_ffpe_sequencing_variant |
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+ | 19 | microbiome - microbial - bacterial - bacteria - microbiota | 49 | 19_microbiome_microbial_bacterial_bacteria |
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+ | 20 | spatial - tissue - imaging - plex - image | 48 | 20_spatial_tissue_imaging_plex |
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+ | 21 | sclc - elavl4 - hnf4a - lung - ne | 48 | 21_sclc_elavl4_hnf4a_lung |
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+ | 22 | mice - human - humanized - mouse - engraftment | 46 | 22_mice_human_humanized_mouse |
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+ | 23 | bone - os - metastasis - osteosarcoma - metastatic | 45 | 23_bone_os_metastasis_osteosarcoma |
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+ | 24 | braf - tead - raf - melanoma - mek | 44 | 24_braf_tead_raf_melanoma |
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+ | 25 | pca - prostate - psa - gleason - men | 44 | 25_pca_prostate_psa_gleason |
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+ | 26 | cldn18 - cldn6 - claudin - cldn1 - cldn3 | 41 | 26_cldn18_cldn6_claudin_cldn1 |
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+ | 27 | psma - 177lu - fap - uptake - 68ga | 41 | 27_psma_177lu_fap_uptake |
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+ | 28 | mtap - prmt5 - mta - deleted - cooperative | 40 | 28_mtap_prmt5_mta_deleted |
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+ | 29 | mm - myeloma - bone - cd38 - cst6 | 40 | 29_mm_myeloma_bone_cd38 |
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+ | 30 | ecdna - somatic - skin - genome - mutational | 37 | 30_ecdna_somatic_skin_genome |
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+ | 31 | incidence - risk - cancer - exposure - lifestyle | 37 | 31_incidence_risk_cancer_exposure |
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+ | 32 | tce - cd3 - tces - gd - engagers | 36 | 32_tce_cd3_tces_gd |
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+ | 33 | ctdna - mrd - recurrence - patients - months | 36 | 33_ctdna_mrd_recurrence_patients |
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+ | 34 | ctcs - ctc - blood - biopsy - v7 | 35 | 34_ctcs_ctc_blood_biopsy |
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+ | 35 | capsaicin - vialinin - apoptosis - apoptotic - compounds | 35 | 35_capsaicin_vialinin_apoptosis_apoptotic |
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+ | 36 | crc - apc - wnt - colonic - intestinal | 34 | 36_crc_apc_wnt_colonic |
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+ | 37 | ebv - npc - hpv - nasopharyngeal - hnscc | 34 | 37_ebv_npc_hpv_nasopharyngeal |
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+ | 38 | pdac - pancreatic - nets - tme - immunosuppressive | 34 | 38_pdac_pancreatic_nets_tme |
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+ | 39 | spatial - resolution - transcriptomics - tissue - xenium | 34 | 39_spatial_resolution_transcriptomics_tissue |
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+ | 40 | cafs - caf - fibroblasts - axl - gc | 33 | 40_cafs_caf_fibroblasts_axl |
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+ | 41 | test - abstract - text - you - your | 33 | 41_test_abstract_text_you |
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+ | 42 | p53 - y220c - ddr - dna - repair | 33 | 42_p53_y220c_ddr_dna |
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+ | 43 | data - ai - 500 - datasets - research | 33 | 43_data_ai_500_datasets |
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+ | 44 | luad - lung - xage1 - znf687 - lusc | 32 | 44_luad_lung_xage1_znf687 |
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+ | 45 | variants - brca1 - chek2 - bc - germline | 29 | 45_variants_brca1_chek2_bc |
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+ | 46 | sting - agonist - cgas - interferon - activation | 29 | 46_sting_agonist_cgas_interferon |
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+ | 47 | pdt - light - elp - nanoparticles - ph | 28 | 47_pdt_light_elp_nanoparticles |
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+ | 48 | il - 12 - obp - 702 - tumor | 28 | 48_il_12_obp_702 |
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+ | 49 | ccrcc - rcc - renal - vhl - carcinoma | 28 | 49_ccrcc_rcc_renal_vhl |
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+ | 50 | vaccines - vaccine - neoantigen - mrna - peptides | 26 | 50_vaccines_vaccine_neoantigen_mrna |
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+ | 51 | notch4 - dormancy - evs - e7011 - exosomes | 26 | 51_notch4_dormancy_evs_e7011 |
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+ | 52 | slides - images - model - wsi - slide | 26 | 52_slides_images_model_wsi |
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+ | 53 | smarca4 - smarca2 - smarca1 - 3236 - smd | 26 | 53_smarca4_smarca2_smarca1_3236 |
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+ | 54 | cytof - spectral - cytometry - flow - xt | 24 | 54_cytof_spectral_cytometry_flow |
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+ | 55 | mb - medulloblastoma - shh - nesc - tert | 23 | 55_mb_medulloblastoma_shh_nesc |
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+ | 56 | cca - cholangiocarcinoma - bile - postn - duct | 22 | 56_cca_cholangiocarcinoma_bile_postn |
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+ | 57 | ezh2 - ezh1 - fads2 - prc2 - h3k27me3 | 22 | 57_ezh2_ezh1_fads2_prc2 |
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+ | 58 | wrn - msi - helicase - gsk4418959 - hro761 | 22 | 58_wrn_msi_helicase_gsk4418959 |
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+ | 59 | ews - fli1 - ewing - ewsr1 - sarcoma | 22 | 59_ews_fli1_ewing_ewsr1 |
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+ | 60 | cdk4 - 6i - resistant - resistance - er | 21 | 60_cdk4_6i_resistant_resistance |
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+ | 61 | pdac - gemcitabine - pikfyve - pancreatic - metabolic | 21 | 61_pdac_gemcitabine_pikfyve_pancreatic |
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+ | 62 | nb - mycn - neuroblastoma - 17q - gd2 | 21 | 62_nb_mycn_neuroblastoma_17q |
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+ | 63 | macrophages - m1 - m2 - macrophage - tams | 20 | 63_macrophages_m1_m2_macrophage |
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+ | 64 | egfr - bispecific - her3 - cmet - adc | 20 | 64_egfr_bispecific_her3_cmet |
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+ | 65 | discovery - drug - library - covalent - hit | 20 | 65_discovery_drug_library_covalent |
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+ | 66 | ferroptosis - gpx4 - peroxidation - ferroptotic - lipid | 20 | 66_ferroptosis_gpx4_peroxidation_ferroptotic |
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+ | 67 | hnscc - hpv - fst - oscc - cyh33 | 19 | 67_hnscc_hpv_fst_oscc |
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+ | 68 | drug - predictive - drugs - framework - enlight | 19 | 68_drug_predictive_drugs_framework |
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+ | 69 | bcma - car - gprc5d - mm - cel | 19 | 69_bcma_car_gprc5d_mm |
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+ | 70 | ackr1 - extravasation - metastatic - niche - endothelial | 18 | 70_ackr1_extravasation_metastatic_niche |
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+ | 71 | gut - microbiome - microbiota - fmt - ici | 18 | 71_gut_microbiome_microbiota_fmt |
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+ | 72 | cachexia - muscle - senescent - fisetin - gdf15 | 17 | 72_cachexia_muscle_senescent_fisetin |
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+ | 73 | egfr - nsclc - egfrm - tki - mutations | 17 | 73_egfr_nsclc_egfrm_tki |
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+ | 74 | icg - imaging - sln - nir - fluorescence | 17 | 74_icg_imaging_sln_nir |
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+ | 75 | e3 - degradation - ligase - protacs - protac | 17 | 75_e3_degradation_ligase_protacs |
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+ | 76 | pik3ca - pi3ka - alpelisib - pi3k - mutant | 17 | 76_pik3ca_pi3ka_alpelisib_pi3k |
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+ | 77 | oncokb - variants - variant - oncotagger - somatic | 17 | 77_oncokb_variants_variant_oncotagger |
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+ | 78 | ffpe - rna - samples - seq - fixed | 17 | 78_ffpe_rna_samples_seq |
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+ | 79 | copd - risk - proteins - igfbp7 - mortality | 17 | 79_copd_risk_proteins_igfbp7 |
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+ | 80 | hpv - opscc - pwh - infection - hiv | 16 | 80_hpv_opscc_pwh_infection |
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+ | 81 | dietary - intake - food - risk - plant | 16 | 81_dietary_intake_food_risk |
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+ | 82 | er - mcf - endocrine - estrogen - e2 | 16 | 82_er_mcf_endocrine_estrogen |
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+ | 83 | pkmyt1 - wee1 - ccne1 - lunresertib - cdk1 | 16 | 83_pkmyt1_wee1_ccne1_lunresertib |
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+ | 84 | lcs - screening - lung - sdm - risk | 15 | 84_lcs_screening_lung_sdm |
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+ | 85 | cdh17 - cadherin - 054 - lbl - gi | 15 | 85_cdh17_cadherin_054_lbl |
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+ | 86 | rms - fp - foxo1 - p3f - pax3 | 14 | 86_rms_fp_foxo1_p3f |
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+ | 87 | myc - mycg4 - g4 - nucleolin - ddx5 | 14 | 87_myc_mycg4_g4_nucleolin |
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+ | 88 | eac - ec - esophageal - pro - rkp | 14 | 88_eac_ec_esophageal_pro |
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+ | 89 | hdac3 - hdac - gem144 - hdac8 - hdaci | 14 | 89_hdac3_hdac_gem144_hdac8 |
132
+ | 90 | culture - organoids - immune - co - tios | 14 | 90_culture_organoids_immune_co |
133
+ | 91 | ttfields - fields - dox - concomitant - electric | 13 | 91_ttfields_fields_dox_concomitant |
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+ | 92 | cdk2 - ccne1 - cdk4 - cyclin - amplified | 13 | 92_cdk2_ccne1_cdk4_cyclin |
135
+ | 93 | cd73 - adenosine - a2ar - cd68 - immune | 13 | 93_cd73_adenosine_a2ar_cd68 |
136
+ | 94 | ilc - cdh1 - tfap2b - breast - lobular | 13 | 94_ilc_cdh1_tfap2b_breast |
137
+ | 95 | btk - nx - 5948 - lymphoma - c481s | 13 | 95_btk_nx_5948_lymphoma |
138
+ | 96 | hrd - hrr - biallelic - recombination - homologous | 13 | 96_hrd_hrr_biallelic_recombination |
139
+ | 97 | runx3 - paint - pkp3 - snord67 - 3q | 13 | 97_runx3_paint_pkp3_snord67 |
140
+ | 98 | kat6a - kat6 - er - kat6b - breast | 12 | 98_kat6a_kat6_er_kat6b |
141
+ | 99 | lncrnas - coding - ner - uterine - lncrna | 12 | 99_lncrnas_coding_ner_uterine |
142
+ | 100 | bca - numb - bladder - rock - muscle | 12 | 100_bca_numb_bladder_rock |
143
+ | 101 | vaccination - hpv - vaccine - hesitancy - covid | 12 | 101_vaccination_hpv_vaccine_hesitancy |
144
+ | 102 | blca - bladder - fgfr3 - mibc - nmibc | 12 | 102_blca_bladder_fgfr3_mibc |
145
+ | 103 | lnp - lnps - formulation - dsrna - lipid | 12 | 103_lnp_lnps_formulation_dsrna |
146
+ | 104 | germline - variants - pathogenic - ddx41 - read | 11 | 104_germline_variants_pathogenic_ddx41 |
147
+ | 105 | age - aged - aging - young - mice | 11 | 105_age_aged_aging_young |
148
+ | 106 | pdx - hci - models - hbcu - drug | 11 | 106_pdx_hci_models_hbcu |
149
+ | 107 | obesity - butyrate - diet - fto - obese | 11 | 107_obesity_butyrate_diet_fto |
150
+ | 108 | hpk1 - hdm2006 - 306 - s109 - ubx | 10 | 108_hpk1_hdm2006_306_s109 |
151
+ | 109 | ldrt - metabolic - cd8 - lactylation - tcredcd39koher2 | 10 | 109_ldrt_metabolic_cd8_lactylation |
152
+ | 110 | hypoxia - hypoxic - hif1a - mhc1pp - ifn | 10 | 110_hypoxia_hypoxic_hif1a_mhc1pp |
153
+ | 111 | cd47 - sirpa - smagp - avfc - imc | 10 | 111_cd47_sirpa_smagp_avfc |
154
+ | 112 | nepc - prostate - pik3r1 - ceacam5 - ar | 10 | 112_nepc_prostate_pik3r1_ceacam5 |
155
+ | 113 | eif4e - translation - cap - eif4f - ovarian | 9 | 113_eif4e_translation_cap_eif4f |
156
+ | 114 | ev - evs - mgm - plasma - biomarkers | 9 | 114_ev_evs_mgm_plasma |
157
+ | 115 | ipro - prediction - performance - rpslearner - ct | 9 | 115_ipro_prediction_performance_rpslearner |
158
+ | 116 | tf - xb371 - adce - uparap - coagulation | 9 | 116_tf_xb371_adce_uparap |
159
+ | 117 | icis - ali - cish - anti - lag | 9 | 117_icis_ali_cish_anti |
160
+ | 118 | nicotine - cigarette - memantine - bw813u - smoking | 9 | 118_nicotine_cigarette_memantine_bw813u |
161
+ | 119 | nnmt - dnmt1 - stm9005 - mettl1 - rrm1 | 9 | 119_nnmt_dnmt1_stm9005_mettl1 |
162
+ | 120 | eps - states - state - single - sub | 9 | 120_eps_states_state_single |
163
+ | 121 | gastric - gc - tsrna - eo - cops5 | 9 | 121_gastric_gc_tsrna_eo |
164
+ | 122 | risk - women - bbd - breast - missing | 9 | 122_risk_women_bbd_breast |
165
+ | 123 | h7 - bispecific - b7 - npx372 - tim | 9 | 123_h7_bispecific_b7_npx372 |
166
+ | 124 | nat - rectal - course - neoadjuvant - ild | 9 | 124_nat_rectal_course_neoadjuvant |
167
+ | 125 | xpo1 - hsp90 - xpr1 - selinexor - slc34a2 | 9 | 125_xpo1_hsp90_xpr1_selinexor |
168
+ | 126 | p2x4 - pca - sqle - crisp3 - cxcr7 | 9 | 126_p2x4_pca_sqle_crisp3 |
169
+ | 127 | ripk1 - lig1 - ctps2 - cisplatin - lig1het | 8 | 127_ripk1_lig1_ctps2_cisplatin |
170
+ | 128 | age - dnam - risk - cpg - mage | 8 | 128_age_dnam_risk_cpg |
171
+ | 129 | women - breast - lrig1 - duffy - bpe | 8 | 129_women_breast_lrig1_duffy |
172
+ | 130 | nectin - ev - uc - glr1059 - iph4502 | 8 | 130_nectin_ev_uc_glr1059 |
173
+ | 131 | ros1 - egfr - tkd - nsclc - zongertinib | 8 | 131_ros1_egfr_tkd_nsclc |
174
+ | 132 | abd147 - clickable - binder - 225ac - capac | 8 | 132_abd147_clickable_binder_225ac |
175
+ | 133 | 34a - mir - endosomal - fm - nigericin | 8 | 133_34a_mir_endosomal_fm |
176
+ | 134 | tcr - tcrs - prame - hla - supercharged | 8 | 134_tcr_tcrs_prame_hla |
177
+ | 135 | spatial - l2 - immune - geomx - microenvironment | 8 | 135_spatial_l2_immune_geomx |
178
+ | 136 | sedentary - physical - 93 - able - spent | 8 | 136_sedentary_physical_93_able |
179
+ | 137 | fulvestrant - pts - bireociclib - endocrine - cdk4 | 8 | 137_fulvestrant_pts_bireociclib_endocrine |
180
+ | 138 | mal - trials - dose - oncology - cost | 8 | 138_mal_trials_dose_oncology |
181
+ | 139 | adar1 - editing - p150 - rna - ribi | 8 | 139_adar1_editing_p150_rna |
182
+ | 140 | adulthood - bmi - bri - alcohol - selenium | 8 | 140_adulthood_bmi_bri_alcohol |
183
+ | 141 | ctdna - ddpcr - mutations - plasma - monitoring | 8 | 141_ctdna_ddpcr_mutations_plasma |
184
+ | 142 | cadonilimab - bnt116 - safety - resectable - penpulimab | 7 | 142_cadonilimab_bnt116_safety_resectable |
185
+ | 143 | irf4 - tbxt - persistence - resistant - drug | 7 | 143_irf4_tbxt_persistence_resistant |
186
+ | 144 | btz - pi - proteasome - mm - ceritinib | 7 | 144_btz_pi_proteasome_mm |
187
+ | 145 | nps - til - tgfb - brg399 - helios | 7 | 145_nps_til_tgfb_brg399 |
188
+ | 146 | lymphotoxin - hnscc - cd24 - il - ctla2a | 7 | 146_lymphotoxin_hnscc_cd24_il |
189
+ | 147 | kif18a - cin - mitotic - yf550 - hw221043 | 7 | 147_kif18a_cin_mitotic_yf550 |
190
+ | 148 | nad - nampt - nmn - ot - 82 | 7 | 148_nad_nampt_nmn_ot |
191
+ | 149 | arid1a - arid1b - swi - snf - eo3001 | 7 | 149_arid1a_arid1b_swi_snf |
192
+ | 150 | ptpn1 - all - bcp - nhd13 - splicing | 7 | 150_ptpn1_all_bcp_nhd13 |
193
+ | 151 | allo - asct - mm - hct - pem | 7 | 151_allo_asct_mm_hct |
194
+ | 152 | flc - dnaj - pkac - fibrolamellar - surgery | 7 | 152_flc_dnaj_pkac_fibrolamellar |
195
+ | 153 | telomerase - clpxp - telomere - g4 - clpx | 7 | 153_telomerase_clpxp_telomere_g4 |
196
+ | 154 | pc53k - tie2 - ku - yb - ovarian | 6 | 154_pc53k_tie2_ku_yb |
197
+ | 155 | hydrogel - ecm - decm - matrix - kyse30 | 6 | 155_hydrogel_ecm_decm_matrix |
198
+ | 156 | msln - rc88 - zw171 - binding - 08052666 | 6 | 156_msln_rc88_zw171_binding |
199
+ | 157 | cachexia - muscle - edema - sma - adiposity | 6 | 157_cachexia_muscle_edema_sma |
200
+ | 158 | emb - wx390 - dcr - mcrc - orr | 6 | 158_emb_wx390_dcr_mcrc |
201
+ | 159 | neoantigens - frameshift - antigens - hla - as10 | 6 | 159_neoantigens_frameshift_antigens_hla |
202
+ | 160 | smip34 - rlip - atovaquone - eoc - cddp | 6 | 160_smip34_rlip_atovaquone_eoc |
203
+ | 161 | rd3 - sided - colorectal - polyps - left | 5 | 161_rd3_sided_colorectal_polyps |
204
+ | 162 | onc212 - onc206 - onc201 - atg101 - imipridones | 5 | 162_onc212_onc206_onc201_atg101 |
205
+ | 163 | hcc - gzmk - 37 - ph102 - foxp3high | 5 | 163_hcc_gzmk_37_ph102 |
206
+ | 164 | vitae - nec - nunc - id - sed | 5 | 164_vitae_nec_nunc_id |
207
+ | 165 | emphysematous - ct - group - ca - recurrence | 5 | 165_emphysematous_ct_group_ca |
208
+ | 166 | til - stim - reactive - feeder - obx | 5 | 166_til_stim_reactive_feeder |
209
+ | 167 | fao - atp - kn510713 - cac - acaa1 | 5 | 167_fao_atp_kn510713_cac |
210
+ | 168 | 3d - 2d - pathology - specimen - sections | 5 | 168_3d_2d_pathology_specimen |
211
+ | 169 | radiation - flash - ray - fr - kvp | 5 | 169_radiation_flash_ray_fr |
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+
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+ </details>
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+
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+ ## Training hyperparameters
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+
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+ * calculate_probabilities: False
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+ * language: None
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+ * low_memory: False
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+ * min_topic_size: 10
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+ * n_gram_range: (1, 1)
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+ * nr_topics: None
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+ * seed_topic_list: None
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+ * top_n_words: 10
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+ * verbose: True
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+ * zeroshot_min_similarity: 0.7
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+ * zeroshot_topic_list: None
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+
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+ ## Framework versions
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+
231
+ * Numpy: 1.26.4
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+ * HDBSCAN: 0.8.40
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+ * UMAP: 0.5.7
234
+ * Pandas: 2.2.2
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+ * Scikit-Learn: 1.6.1
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+ * Sentence-transformers: 3.4.1
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+ * Transformers: 4.48.2
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+ * Numba: 0.61.0
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+ * Plotly: 5.24.1
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+ * Python: 3.11.11
config.json ADDED
@@ -0,0 +1,16 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "calculate_probabilities": false,
3
+ "language": null,
4
+ "low_memory": false,
5
+ "min_topic_size": 10,
6
+ "n_gram_range": [
7
+ 1,
8
+ 1
9
+ ],
10
+ "nr_topics": null,
11
+ "seed_topic_list": null,
12
+ "top_n_words": 10,
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+ "verbose": true,
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+ "zeroshot_min_similarity": 0.7,
15
+ "zeroshot_topic_list": null
16
+ }
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