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Research output

Selected publications, papers, and posters

A curated list of work across knowledge graphs, neuro-symbolic AI, ontology alignment, biomedical informatics, and machine learning for biological systems.

Journal articles & preprints

Conference & workshop papers

Book chapter / proceedings

Poster collections

Publication list

Browse by output type.

Journal Articles Conference Papers Posters Book Chapters

Journal Article Scientific Reports 2026

Exploring the limits of pre-trained embeddings in machine-guided protein design: a case study on predicting AAV vector viability

A. F. Rodrigues, L. Ferraz, L. Balbi, P. G. Cotovio, and C. Pesquita

Scientific Reports, 16, Article 10974 · 2026. DOI: 10.1038/s41598-026-45458-5

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Preprint

ECKO: Explainable Clinical Knowledge for Oncology

M. Contreiras Silva, D. Faria, L. Balbi, S. Nunes, A. F. Rodrigues, A. Palkowski, M. Waleron, E. Daghir-Wojtkowiak, A. Kallor, C. Battail, F. Corazza, M. Fiorelli, A. Stellato, J. Alfaro, F. Zanzotto, C. Pesquita
arXiv preprint · 2025

Workshop paper

A Semantic Framework for Evaluating Post-hoc Explanations in Link Prediction

L. Balbi, F. Bindt, K. Breitenfelder, R. Campi, J. De Smet, C. d'Amato
XAI-KRKG Workshop @ ECAI 2025 · 2025

Book chapter / proceedings

Neuro-Symbolic AI for Conflict-Aware Learning over Knowledge Graphs

L. Balbi
In: Proceedings of the 22nd Extended Semantic Web Conference (ESWC 2025): Satellite Events · 2025

Conference paper

Results in OAEI 2024 for Matcha

D. Faria, M. C. Silva, P. Cotovio, L. Ferraz, L. Balbi, C. Pesquita
OM @ International Semantic Web Conference · 2024

Journal article

The Immunopeptidomics Ontology (ImPO)

D. Faria, P. Eugénio, M. C. Silva, L. Balbi, C. Pesquita, et al.
Database · 2024

Conference paper

Results for Matcha and Matcha-DL in OAEI 2023

D. Faria, M. C. Silva, P. Cotovio, L. Ferraz, L. Balbi, C. Pesquita
OM @ International Semantic Web Conference · 2023

Journal article

Matcha-DL: a tool for supervised ontology alignment

P. G. Cotovio, L. Ferraz, D. Faria, L. Balbi, M. C. Silva, C. Pesquita
Semantic Web Journal · 2024

Preprint

Injecting domain knowledge into graph neural networks for protein-protein interactions

L. Balbi, R. T. Sousa, P. G. Cotovio, C. Pesquita
Research Square · 2024

Posters

Scientific poster collections from PhD and MSc work.

PhD scientific posters

Browse doctoral research poster materials.

MSc scientific posters

Browse master’s research poster materials.