LBDiscover0.1.0 package

Optimize ABC model calculations for large matrices

Apply the ABC model with statistical significance testing

Apply the ABC model for literature-based discovery with improved filte...

Apply time-sliced ABC model for validation

Add statistical significance testing based on hypergeometric tests

Alternative validation for large matrices

ANC model for literature-based discovery with biomedical term filterin...

Apply a flexible BITOLA-style discovery model without strict type cons...

Apply correction to p-values

Authenticate with UMLS

Apply BITOLA-style discovery model

Calculate basic bibliometric statistics

Calculate document similarity using TF-IDF and cosine similarity

Calculate ABC score based on specified method

Clear PubMed cache

Cluster documents using K-means

Compare term frequencies between two corpora

Create a citation network from article data

Create co-occurrence matrix without explicit entity type constraints

Helper function to create dummy dictionaries

Generate a comprehensive discovery report

Create a sparse co-occurrence matrix

Create a term-document matrix from preprocessed text

Create a term-document matrix from preprocessed text

Detect language of text

Enforce diversity in ABC model results

Enforce diversity by selecting top connections from each B term

Enforce diversity for C term paths

Environment to store dictionary cache data

Environment to store PubMed cache data

Enhance ABC results with external knowledge

Evaluate literature support for discovery results

Export interactive HTML chord diagram for ABC connections

Export interactive HTML chord diagram for ABC connections

Export ABC results to simple HTML network

Extract entities from text with improved efficiency using only base R

Extract and classify entities from text with multi-domain types

Extract MeSH terms from text format instead of XML

Perform named entity recognition on text

Extract n-grams from text

Extract common terms from a corpus

Apply topic modeling to a corpus

Fetch and parse Gene data

Fetch and parse PMC data

Fetch and parse Protein data

Fetch and parse PubMed data

Filter a co-occurrence matrix by entity type

Find all potential ABC connections

Find similar documents for a given document

Find primary term in co-occurrence matrix

Generate comprehensive discovery report

Get dictionary cache environment

Retrieve full text from PubMed Central

Get the pubmed cache environment

Get a service ticket from a TGT URL

Extract term variations from text corpus

Get entity type distribution from co-occurrence matrix

Get UMLS semantic types for a given dictionary type

Determine if a term is likely a specific biomedical entity with improv...

Convert a list of articles to a data frame

Load biomedical dictionaries with improved error handling

Load terms from MeSH using rentrez with improved error handling

Load terms from UMLS API

Load terms from MeSH using PubMed search

Load saved results from a file

LSI model with enhanced biomedical term filtering and NLP verification

Map terms to biomedical ontologies

Combine and deduplicate entity datasets

Merge multiple search results

Ensure minimum results for visualization

Search NCBI databases for articles or data

Null coalescing operator

Apply parallel processing for document analysis

Parse PubMed XML data with optimized memory usage

Perform randomization test for ABC model

Create heatmap visualization from results

Create network visualization from results

Prepare articles for report generation

Preprocess article text

Process MeSH data in chunks to avoid memory issues

Process MeSH XML data with improved error handling

Search PubMed for articles with optimized performance

Query external biomedical APIs to validate entity types

Query for MeSH terms using E-utilities

Query UMLS for term information

Remove A and C terms that appear as B terms

Retry an API call with exponential backoff

Perform comprehensive literature-based discovery without type constrai...

Diversify ABC results with error handling

Enhanced sanitize dictionary function

Save search results to a file

Perform sentence segmentation on text

Helper function to draw text with a shadow/background

Standard validation method using hypergeometric tests

Filter entities to include only valid biomedical terms

Apply statistical validation to ABC model results with support for lar...

Validate biomedical entities using BioBERT or other ML models

Comprehensive entity validation using multiple techniques

Validate entity types using NLP-based entity recognition with improved...

Validate a UMLS API key

Vectorized preprocessing of text

Create a heatmap of ABC connections

Create an enhanced heatmap of ABC connections

Create an enhanced network visualization of ABC connections

Visualize ABC model results as a network