Comparison of mean interconcept distance for embedding with WordNet synonym replacement (WN) and without (PM). The initial number of unique concepts in the total corpus was 3,018,918. The Table summarizes results for different thresholds () and categories of concept/gene sets (M,B,K,G,P). Columns: : Replacement threshold; replaced: Unique Replaced Concepts; Category: M = MeSH, B = Biocarta, K = KEGG, G = GP(bp), P = PID; # sets: Number of concept/gene sets in the categories; #Concepts: number of concept vectors in the category; WN better: The count and percentage of concept/gene sets for which the mean interconcept distance was smaller for WN than for PM. “Winners” are shown in bold.; PM better: Analogous to “WN better” but for PM.

Comparison of mean interconcept distance for embedding with WordNet synonym replacement (WN) and without (PM). The initial number of unique concepts in the total corpus was 3,018,918. The Table summarizes results for different thresholds () and categories of concept/gene sets (M,B,K,G,P). C...

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Bibliographic Details
Main Author:	Enock Niyonkuru (21246879) (author)
Other Authors:	Mauricio Soto Gomez (21246882) (author), Elena Casarighi (13205074) (author), Stephan Antogiovanni (21246885) (author), Hannah Blau (6206984) (author), Justin T. Reese (12547269) (author), Giorgio Valentini (45586) (author), Peter N. Robinson (7814636) (author)
Published:	2025
Subjects:	Cancer Science Policy Space Science Environmental Sciences not elsewhere classified Biological Sciences not elsewhere classified Mathematical Sciences not elsewhere classified Information Systems not elsewhere classified semantically meaningful representations received less attention python code implementing ensuring consistent representation combined approach aimed cell lung carcinoma additionally leveraged wordnet 8 %, suggesting reduce embedding noise improving embedding quality higher embedding quality biomedical synonym replacement biomedical concept representations xlink "> embeddings word2vec algorithm applied span multiple words mean pairwise distance single concept identifier biomedical concept synonyms embedding techniques biomedical terms biomedical synonyms mean intra cluster distance vector space unique token results demonstrate replace sets replace concepts potential impact medical concepts medical categories greater intra generated using future work downstream tasks commonly used common representatives cluster coherence
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