abc_model               Apply the ABC model for literature-based
                        discovery with improved filtering
abc_model_opt           Optimize ABC model calculations for large
                        matrices
abc_model_sig           Apply the ABC model with statistical
                        significance testing
abc_timeslice           Apply time-sliced ABC model for validation
anc_model               ANC model for literature-based discovery with
                        biomedical term filtering
bitola_model            Apply BITOLA-style discovery model
calc_bibliometrics      Calculate basic bibliometric statistics
calc_doc_sim            Calculate document similarity using TF-IDF and
                        cosine similarity
clear_pubmed_cache      Clear PubMed cache
cluster_docs            Cluster documents using K-means
compare_terms           Compare term frequencies between two corpora
create_citation_net     Create a citation network from article data
create_comat            Create co-occurrence matrix without explicit
                        entity type constraints
create_report           Generate a comprehensive discovery report
create_sparse_comat     Create a sparse co-occurrence matrix
create_tdm              Create a term-document matrix from preprocessed
                        text
create_term_document_matrix
                        Create a term-document matrix from preprocessed
                        text
detect_lang             Detect language of text
diversify_abc           Enforce diversity in ABC model results
enhance_abc_kb          Enhance ABC results with external knowledge
eval_evidence           Evaluate literature support for discovery
                        results
export_chord            Export interactive HTML chord diagram for ABC
                        connections
export_chord_diagram    Export interactive HTML chord diagram for ABC
                        connections
export_network          Export ABC results to simple HTML network
extract_entities        Extract and classify entities from text with
                        multi-domain types
extract_entities_workflow
                        Extract entities from text with improved
                        efficiency using only base R
extract_ner             Perform named entity recognition on text
extract_ngrams          Extract n-grams from text
extract_terms           Extract common terms from a corpus
extract_topics          Apply topic modeling to a corpus
filter_by_type          Filter a co-occurrence matrix by entity type
find_abc_all            Find all potential ABC connections
find_similar_docs       Find similar documents for a given document
find_term               Find primary term in co-occurrence matrix
gen_report              Generate comprehensive discovery report
get_dict_cache          Get dictionary cache environment
get_pmc_fulltext        Retrieve full text from PubMed Central
get_term_vars           Extract term variations from text corpus
get_type_dist           Get entity type distribution from co-occurrence
                        matrix
is_valid_biomedical_entity
                        Determine if a term is likely a specific
                        biomedical entity with improved accuracy
load_dictionary         Load biomedical dictionaries with improved
                        error handling
load_results            Load saved results from a file
lsi_model               LSI model with enhanced biomedical term
                        filtering and NLP verification
map_ontology            Map terms to biomedical ontologies
merge_entities          Combine and deduplicate entity datasets
merge_results           Merge multiple search results
min_results             Ensure minimum results for visualization
ncbi_search             Search NCBI databases for articles or data
parallel_analysis       Apply parallel processing for document analysis
perm_test_abc           Perform randomization test for ABC model
plot_heatmap            Create heatmap visualization from results
plot_network            Create network visualization from results
prep_articles           Prepare articles for report generation
preprocess_text         Preprocess article text
pubmed_search           Search PubMed for articles with optimized
                        performance
query_external_api      Query external biomedical APIs to validate
                        entity types
query_mesh              Query for MeSH terms using E-utilities
query_umls              Query UMLS for term information
run_lbd                 Perform comprehensive literature-based
                        discovery without type constraints
safe_diversify          Diversify ABC results with error handling
sanitize_dictionary     Enhanced sanitize dictionary function
save_results            Save search results to a file
segment_sentences       Perform sentence segmentation on text
valid_entities          Filter entities to include only valid
                        biomedical terms
validate_abc            Apply statistical validation to ABC model
                        results with support for large matrices
validate_biomedical_entity
                        Validate biomedical entities using BioBERT or
                        other ML models
validate_entity_comprehensive
                        Comprehensive entity validation using multiple
                        techniques
validate_entity_with_nlp
                        Validate entity types using NLP-based entity
                        recognition with improved accuracy
validate_umls_key       Validate a UMLS API key
vec_preprocess          Vectorized preprocessing of text
vis_abc_heatmap         Create a heatmap of ABC connections
vis_heatmap             Create an enhanced heatmap of ABC connections
vis_network             Create an enhanced network visualization of ABC
                        connections
visualize_abc_network   Visualize ABC model results as a network
