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.gitignore
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*-checkpoint.ipynb
data/Omics_data/L1000__gene_attribute_edges.txt
./.git/objects/pack/pack-9dcba3ba661c581e92ed9dc4cf320767273e4538.pack
./data/Omics_data/L1000__gene_attribute_edges.txt
./data/Viral_Infections_gene_attribute_matrix_standardized.txt
./data/omics_LLM_Enrichr_DF.tsv
./data/omics_LLM_Enrichr_DF copy.tsv
errfile
outfile
3A.\[Omics_revamped\]_AnayseAnnotation_original.ipynb
data/0628_*
data/Omics_data/L1000_gene_attribute_edges.txt
data/new_GO_BP/
data/GO_term_analysis/100_GO_terms_gprofiler_res.tsv
data/CH_omics_revamped_LLM_Enrichr_simVals_failure_refs_newThresh_DF.json
data/GO_term_analysis/*.json
data/GO_term_analysis/*.log
data/GO_term_analysis/add_on*
data/GO_term_analysis/test*
data/GO_term_analysis/*promp*
data/GO_term_analysis/model_compare/*
data/GO_term_analysis/model_compare/void*
!data/GO_term_analysis/model_compare/*100set*
data/GO_term_analysis/model_compare/*review_sample*
data/GO_term_analysis/CC_MF_branch/*
!data/GO_term_analysis/CC_MF_branch/*1000_go*
!data/GO_term_analysis/CC_MF_branch/*.csv
data/GO_term_analysis/LLM_processed_gpt_4*
data/GO_term_analysis/sets_no_gpt4name.tsv
data/GO_term_analysis/best_25_worst_25_similarity_among1000GO.tsv
data/GO_term_analysis/100_GO_terms_hypergeom_res.tsv
data/GO_term_analysis/900_selected_go_contaminated.csv
data/omics_revamped_LLM_Enrichr_simVals_failure_refs_newThresh_DF_with_potential_novel.tsv
#too big
data/GO_term_analysis/all_go_sim_scores_gpt4.txt
data/omics_revamped_LLM_gprofiler_new_gene_name_*
#obsolete
data/GO_term_analysis/name_only
data/GO_term_analysis/simrank_pval_LLM_processed_selected_1000_go_terms_return_huge_matches.tsv
archived/*
logs/*
data/omics_LLM_Enrichr_DF.tsv
data/GO_term_analysis/all_go_sim_scores.txt
find . -size +100M
Set_seed_in_GPT_query.ipynb
logs/test*.log
localcopy*
jsonFiles/*test.json
pipeline_for_new_model.ipynb
check_manual_eval_stats.ipynb
data/\[LLM_eval\]Omics_revamped.xlsx
OLD*
Extract_keywords_reference_finder.ipynb
#ignore archived files
data/archived
figures/archived
#ignore cache
utils/__pycache__/*
utils/__pycache__
__pycache__/*
#ignore unused files
figures/model_compare/*raincloud*
figures/model_compare/*.pdf
figures/model_compare/*semantic_similarity_confidence*
check_result_ref_finder.ipynb
figures/LLM_name_GO_term_percentile_CDF_w_random_byGO_revertX_100to1.svg
figures/LLM_name_GO_term_percentile_CDF_w_random_byGO_revertX_100to1.svg
figures/LLM_name_GO_term_sim_against_random_cdf_response to X-ray.svg
figures/LLM_name_GO_term_sim_against_random_pdf_response to X-ray.svg
figures/LLM_GO_gene_mention_percentage.svg
figures/GO_0010897_with_bestmatch_vennDiagram.svg
figures/omics_LLM_JI_vs_gprofiler_JI_sep_by_similarity.svg