CASIRAGHI, ELENA
CASIRAGHI, ELENA
Dipartimento di Informatica Giovanni Degli Antoni
Modular Deep Neural Networks with Residual Connections for Predicting the Pathogenicity of Genetic Variants in Non Coding Genomic Regions
2026 F. Stacchietti, M. Nicolini, L. Chimirri, P.N. Robinson, E. Casiraghi, G. Valentini
Replacing non-biomedical concepts improves embedding of biomedical concepts
2025 E. Niyonkuru, M.S. Gomez, E. Casarighi, S. Antogiovanni, H. Blau, J.T. Reese, G. Valentini, P.N. Robinson
A Transformer-Based Model to Predict Micro RNA Interactions
2025 M. Nicolini, F. Stacchietti, C. Cano, E. Casiraghi, G. Valentini
CSGL: Chemical Synthesis Graph Learning for Molecule Representation
2025 A. Li, E. Casiraghi, J. Rousu
Intrinsic-dimension analysis for guiding dimensionality reduction and data fusion in multi-omics data processing
2025 J. Gliozzo, M. Soto-Gomez, V. Guarino, A. Bonometti, A. Cabri, E. Cavalleri, J. Reese, P.N. Robinson, M. Mesiti, G. Valentini, E. Casiraghi
RNA knowledge-graph analysis through homogeneous embedding methods
2025 F. Torgano, M. Soto Gomez, M. Zignani, J. Gliozzo, E. Cavalleri, M. Mesiti, E. Casiraghi, G. Valentini
miss-SNF: a multimodal patient similarity network integration approach to handle completely missing data sources
2025 J. Gliozzo, M.A. Soto Gomez, A. Bonometti, A. Patak, E. Casiraghi, G. Valentini
Biasing second-order random walk sampling for heterogeneous graph embedding
2025 M. Soto-Gomez, C. Cano, J. Reese, P.N. Robinson, G. Valentini, E. Casiraghi
Leveraging generative AI to assist biocuration of medical actions for rare disease
2025 E. Niyonkuru, J.H. Caufield, L.C. Carmody, M.A. Gargano, S. Toro, P.L. Whetzel, H. Blau, M. Soto Gomez, E. Casiraghi, L. Chimirri, J.T. Reese, G. Valentini, M.A. Haendel, C.J. Mungall, P.N. Robinson
Fine-tuning of conditional Transformers improves in silico enzyme prediction and generation
2025 M. Nicolini, E. Saitto, R.E. Jimenez Franco, E. Cavalleri, A.J. Galeano Alfonso, D. Malchiodi, A. Paccanaro, P.N. Robinson, E. Casiraghi, G. Valentini
Initial achievements in relation extraction from RNA-focused scientific papers
2024 E. Cavalleri, M. Soto-Gomez, A. Pashaeibarough, D. Malchiodi, H. Caufield, J. Reese, C.J. Mungall, P.N. Robinson, E. Casiraghi, G. Valentini, M. Mesiti
Fine-tuning of Conditional Transformers Improves the Generalization of Functionally Characterized Proteins
2024 M. Nicolini, D. Malchiodi, A. Cabri, E. Cavalleri, M. Mesiti, A. Paccanaro, N. Robinson Peter, J. Reese, E. Casiraghi, G. Valentini
Chemical Reaction Enhanced Graph Learning for Molecule Representation
2024 A. Li, E. Casiraghi, J. Rousu
Unbiased clustering and molecular characterisation of novel metabolic phenotypes in a heart failure cohort
2024 E. Esenkova, T. Koeck, G. Valentini, P. Wild, E. Casiraghi, E. Araldi
An ontology-based knowledge graph for representing interactions involving RNA molecules
2024 E. Cavalleri, A. Cabri, M. Soto-Gomez, S. Bonfitto, P. Perlasca, J. Gliozzo, T.J. Callahan, J. Reese, P.N. Robinson, E. Casiraghi, G. Valentini, M. Mesiti
Node-degree aware edge sampling mitigates inflated classification performance in biomedical random walk-based graph representation learning
2024 L. Cappelletti, L. Rekerle, T. Fontana, P. Hansen, E. Casiraghi, V. Ravanmehr, C.J. Mungall, J. Yang, L. Spranger, G. Karlebach, J.H. Caufield, L. Carmody, B. Coleman, T. Oprea, J. Reese, G. Valentini, P.N. Robinson
The Use of Artificial Intelligence in Head and Neck Cancers: A Multidisciplinary Survey
2024 C. Giannitto, G. Carnicelli, S. Lusi, A. Ammirabile, E. Casiraghi, A. De Virgilio, A. Esposito, D. Farina, F. Ferreli, C. Franzese, G.M. Frigerio, A. Lo Casto, L. Malvezzi, L. Lorini, A. Othman, L. Preda, M. Scorsetti, P. Bossi, G. Mercante, G. Spriano, L. Balzarini, M. Francone
SPIREX: Improving LLM-based relation extraction from RNA-focused scientific literature using graph machine learning
2024 E. Cavalleri, M. Soto Gomez, A. Pashaeibarough, D. Malchiodi, J.H. Caufield, J.T. Reese, C. Mungall, P.N. Robinson, E. Casiraghi, G. Valentini, M. Mesiti
Predicting nutrition and environmental factors associated with female reproductive disorders using a knowledge graph and random forests
2024 L.E. Chan, E. Casiraghi, J. Reese, Q.E. Harmon, K. Schaper, H. Hegde, G. Valentini, C. Schmitt, A. Motsinger-Reif, J.E. Hall, C.J. Mungall, P.N. Robinson, M.A. Haendel
Fine-Tuning of Conditional Transformers Improves the Generation of Functionally Characterized Proteins
2024 M. Nicolini, D. Malchiodi, A. Cabri, E. Cavalleri, M. Mesiti, A. Paccanaro, P.N. Robinson, J. Reese, E. Casiraghi, G. Valentini