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djordan/
am25_abstract_topic_model

bertopic

text-classification

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am25_abstract_topic_model

This is a BERTopic model. BERTopic is a flexible and modular topic modeling framework that allows for the generation of easily interpretable topics from large datasets.

Usage

To use this model, please install BERTopic:

pip install -U bertopic

You can use the model as follows:

python

from bertopic import BERTopic
topic_model = BERTopic.load("djordan/am25_abstract_topic_model")

topic_model.get_topic_info()

Topic overview

Number of topics: 171
Number of training documents: 7863

Click here for an overview of all topics.

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

Training hyperparameters

calculate_probabilities: False
language: None
low_memory: False
min_topic_size: 10
n_gram_range: (1, 1)
nr_topics: None
seed_topic_list: None
top_n_words: 10
verbose: True
zeroshot_min_similarity: 0.7
zeroshot_topic_list: None

Framework versions

Numpy: 1.26.4
HDBSCAN: 0.8.40
UMAP: 0.5.7
Pandas: 2.2.2
Scikit-Learn: 1.6.1
Sentence-transformers: 3.4.1
Transformers: 4.48.2
Numba: 0.61.0
Plotly: 5.24.1
Python: 3.11.11