Pearson (r) and Spearman (<i>ρ</i>) correlation values, harmonic score (<i>h</i>), and harmonic average (AVG) score obtained by the LiBlock method in combination with each NER tool using the best pre-processing configuration detailed in Table 7.

In addition, the last column (p-val) shows the p-values for the comparison of the LiBlock method with cTAKES and the remaining NER combinations.</p

Pearson (r), Spearman (<i>ρ</i>), harmonic (<i>h</i>), and harmonic average (AVG) scores obtained by each sentence similarity method evaluated herein in the three biomedical sentence similarity benchmarks arranged by families.

All reported values were obtained using the best pre-processing configurations detailed in Table 7. The results in bold show the best scores whilst results in show the best average harmonic score for each family.</p

Raw and pre-processed sentence pairs obtaining the lowest and highest similarity error <i>E</i>_<i>sim</i> together with their corresponding Normalized human similarity score (Human) and normalized similarity value (Method) estimated by the BioWordVec_<i>int</i> (M26) method for the raw and pre-processed sentence pairs with the lowest (L) and highest (H) similarity error <i>E</i>_<i>sim</i>.

Raw and pre-processed sentence pairs obtaining the lowest and highest similarity error Esim together with their corresponding Normalized human similarity score (Human) and normalized similarity value (Method) estimated by the BioWordVecint (M26) method for the raw and pre-processed sentence pairs with the lowest (L) and highest (H) similarity error Esim.</p

Detailed setup for the sentence similarity methods based on pre-trained language models evaluated in this work.

Detailed setup for the sentence similarity methods based on pre-trained language models evaluated in this work.</p

Raw and pre-processed sentence pairs obtaining the lowest and highest similarity error <i>E</i>_<i>sim</i> together with their corresponding Normalized human similarity score (Human) and normalized similarity value (Method) estimated by the OuBioBert (M47) method for the raw and pre-processed sentence pairs with the lowest (L) and highest (H) similarity error <i>E</i>_<i>sim</i>.

Raw and pre-processed sentence pairs obtaining the lowest and highest similarity error Esim together with their corresponding Normalized human similarity score (Human) and normalized similarity value (Method) estimated by the OuBioBert (M47) method for the raw and pre-processed sentence pairs with the lowest (L) and highest (H) similarity error Esim.</p

Detailed workflow implemented by our experiments for pre-processing the input sentences, calculating the raw similarity scores, and post-processing the results obtained in the evaluation of the biomedical datasets.

This workflow generates a collection of raw and processed data files.</p

Raw and pre-processed sentence pairs obtaining the lowest and highest similarity error <i>E</i>_<i>sim</i> together with their corresponding Normalized human similarity score (Human) and normalized similarity value (Method) estimated by the LiBlock (M4) method for the raw and pre-processed sentence pairs with the lowest (L) and highest (H) similarity error <i>E</i>_<i>sim</i>.

Raw and pre-processed sentence pairs obtaining the lowest and highest similarity error Esim together with their corresponding Normalized human similarity score (Human) and normalized similarity value (Method) estimated by the LiBlock (M4) method for the raw and pre-processed sentence pairs with the lowest (L) and highest (H) similarity error Esim.</p

The statistical significance results.

We provide a series of tables reporting the p-values for each pair of methods evaluated in this work as supplementary material. (PDF)</p

Detailed setup for the ontology-based sentence similarity measures evaluated in this work.

The evaluation of the methods using Rada [69], coswJ&C [46], and Cai [68] word similarity measures use a reformulation of the original path-based measures based on the new Ancestors-based Shortest-Path Length (AncSPL) algorithm [42].</p

Pearson (r), Spearman (<i>ρ</i>) and harmonic (<i>h</i>) values obtained in our experiments from the evaluation of ontology similarity methods detailed below in the MedSTS_<i>full</i> [52] dataset for each NER tool.

Pearson (r), Spearman (ρ) and harmonic (h) values obtained in our experiments from the evaluation of ontology similarity methods detailed below in the MedSTSfull [52] dataset for each NER tool.</p