Enock Niyonkuru, Mauricio Soto Gomez, Elena Casarighi, Stephan Antogiovanni, Hannah Blau, Justin T. Reese, Giorgio Valentini, & Peter N. Robinson. (2025). Comparison of mean interconcept distance for embedding with Word Net 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 = Me SH, 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. https://doi.org/10.1371/journal.pone.0322498.t001

ENOCK NIYONKURU, MAURICIO SOTO GOMEZ, ELENA CASARIGHI, STEPHAN ANTOGIOVANNI, HANNAH BLAU, JUSTIN T. REESE, GIORGIO VALENTINI and PETER N. ROBINSON, 2025. Comparison of mean interconcept distance for embedding with Word Net 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 = Me SH, 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.

Enock Niyonkuru, Mauricio Soto Gomez, Elena Casarighi, Stephan Antogiovanni, Hannah Blau, Justin T. Reese, Giorgio Valentini, and Peter N. Robinson. Comparison of mean interconcept distance for embedding with Word Net 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 = Me SH, 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. 2025, https://doi.org/10.1371/journal.pone.0322498.t001.

Enock Niyonkuru/Mauricio Soto Gomez/Elena Casarighi/Stephan Antogiovanni/Hannah Blau/Justin T. Reese et al.: Comparison of mean interconcept distance for embedding with Word Net 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 = Me SH, 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., 2025.

Enock Niyonkuru, Mauricio Soto Gomez, Elena Casarighi, Stephan Antogiovanni, Hannah Blau, Justin T. Reese, Giorgio Valentini and Peter N. Robinson. (2025), Comparison of mean interconcept distance for embedding with Word Net 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 = Me SH, 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., Vol. , available at:https://doi.org/10.1371/journal.pone.0322498.t001.