A topological transformation for hidden recursive modelsarchitecture networks. - Fabrizio Costa; Paolo Frasconi; Giovanni Soda (ESANN, 1999)

Learning incremental syntactic structures with recursive neural networks. - Fabrizio Costa; Paolo Frasconi; Vincenzo Lombardo; Giovanni Soda (KES, 2000)

Wide Coverage Incremental Parsing by Learning Attachment Preferences. - Fabrizio Costa; Vincenzo Lombardo; Paolo Frasconi; Giovanni Soda (AI*IA, 2001)

Enhancing First-Pass Attachment Prediction. - Fabrizio Costa; Paolo Frasconi; Vincenzo Lombardo; Patrick Sturt; Giovanni Soda (ECAI, 2002)

Towards Incremental Parsing of Natural Language Using Recursive Neural Networks. - Fabrizio Costa; Paolo Frasconi; Vincenzo Lombardo; Giovanni Soda (Appl. Intell., 2003)

Distributed community crawling. - Fabrizio Costa; Paolo Frasconi (WWW (Alternate Track Papers & Posters), 2004)

Weighted decomposition kernels. - Sauro Menchetti; Fabrizio Costa; Paolo Frasconi (ICML, 2005)

Wide coverage natural language processing using kernel methods and neural networks for structured data. - Sauro Menchetti; Fabrizio Costa; Paolo Frasconi; Massimiliano Pontil (Pattern Recognit. Lett., 2005)

Ambiguity resolution analysis in incremental parsing of natural language. - Fabrizio Costa; Paolo Frasconi; Vincenzo Lombardo; Patrick Sturt; Giovanni Soda (IEEE Trans. Neural Networks, 2005)

Decomposition Kernels for Natural Language Processing. - Fabrizio Costa; Sauro Menchetti; Alessio Ceroni; Andrea Passerini; Paolo Frasconi (Learning Structured Information@EACL, 2006)

Classification of small molecules by two- and three-dimensional decomposition kernels. - Alessio Ceroni; Fabrizio Costa; Paolo Frasconi (Bioinform., 2007)

Comparing Sequence Classification Algorithms for Protein Subcellular Localization. - Fabrizio Costa; Sauro Menchetti; Paolo Frasconi (Perspectives of Neural-Symbolic Integration, 2007)

On the Convergence of Protein Structure and Dynamics. Statistical Learning Studies of Pseudo Folding Pathways. - Alessandro Vullo; Andrea Passerini; Paolo Frasconi; Fabrizio Costa; Gianluca Pollastri (EvoBIO, 2008)

Towards Combining Structured Pattern Mining and Graph Kernels. - Fabrizio Costa; Björn Bringmann (ICDM Workshops, 2008)

A semiparametric generative model for efficient structured-output supervised learning. - Fabrizio Costa; Andrea Passerini; Marco Lippi 001; Paolo Frasconi (Ann. Math. Artif. Intell., 2008)

Handling missing values and censored data in PCA of pharmacological matrices. - Jan Ramon; Fabrizio Costa (KDD Workshop on Statistical and Relational Learning in Bioinformatics, 2009)

Maximum Common Subgraph Mining: A Fast and Effective Approach towards Feature Generation. - Leander Schietgat; Fabrizio Costa; Jan Ramon; Luc De Raedt (MLG/SRL@ILP, 2009)

StReBio'09: statistical relational learning and mining in bioinformatics. - Jan Ramon; Fabrizio Costa; Christophe Costa Florêncio; Joost N. Kok (SIGKDD Explor., 2009)

Fast Neighborhood Subgraph Pairwise Distance Kernel. - Fabrizio Costa; Kurt De Grave (ICML, 2010)

Molecular Graph Augmentation with Rings and Functional Groups. - Kurt De Grave; Fabrizio Costa (J. Chem. Inf. Model., 2010)

Random Forest Based Feature Induction. - Celine Vens; Fabrizio Costa (ICDM, 2011)

Preface. - Jan Ramon; Fabrizio Costa; Christophe Costa Florêncio; Joost N. Kok (Fundam. Informaticae, 2011)

Effective feature construction by maximum common subgraph sampling. - Leander Schietgat; Fabrizio Costa; Jan Ramon; Luc De Raedt (Mach. Learn., 2011)

A Relational Kernel-Based Framework for Hierarchical Image Understanding. - Laura Antanas; Paolo Frasconi; Fabrizio Costa; Tinne Tuytelaars; Luc De Raedt (SSPR/SPR, 2012)

GraphClust: alignment-free structural clustering of local RNA secondary structures. - Steffen Heyne; Fabrizio Costa; Dominic Rose; Rolf Backofen (Bioinform., 2012)

Link and Node Prediction in Metabolic Networks with Probabilistic Logic. - Angelika Kimmig; Fabrizio Costa (Bisociative Knowledge Discovery, 2012)

A graph kernel approach for alignment-free domain-peptide interaction prediction with an application to human SH3 domains. - Kousik Kundu; Fabrizio Costa; Rolf Backofen (Bioinform., 2013)

kLogNLP: Graph Kernel-based Relational Learning of Natural Language. - Mathias Verbeke; Paolo Frasconi; Kurt De Grave; Fabrizio Costa; Luc De Raedt (ACL (System Demonstrations), 2014)

Scalable structural clustering of local RNA secondary structures. - Fabrizio Costa; Steffen Heyne; Dominic Rose; Rolf Backofen (CMSR@ECCB, 2014)

Relational Regularization and Feature Ranking. - Fabrizio Costa; Mathias Verbeke; Luc De Raedt (SDM, 2014)

kLog: A language for logical and relational learning with kernels. - Paolo Frasconi; Fabrizio Costa; Luc De Raedt; Kurt De Grave (Artif. Intell., 2014)

CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci. - Omer S. Alkhnbashi; Fabrizio Costa; Shiraz A. Shah; Roger A. Garrett; Sita J. Saunders; Rolf Backofen (Bioinform., 2014)

MoDPepInt: an interactive web server for prediction of modular domain-peptide interactions. - Kousik Kundu; Martin Mann; Fabrizio Costa; Rolf Backofen (Bioinform., 2014)

BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles. - Pavankumar Videm; Dominic Rose; Fabrizio Costa; Rolf Backofen (Bioinform., 2014)

kLog: A Language for Logical and Relational Learning with Kernels (Extended Abstract). - Paolo Frasconi; Fabrizio Costa; Luc De Raedt; Kurt De Grave (IJCAI, 2015)

ASSIsT: an automatic SNP scoring tool for in- and outbreeding species. - Mario Di Guardo; Diego Micheletti; Luca Bianco; Herma J. J. Koehorst-van Putten; Sara Longhi; Fabrizio Costa; Maria José Aranzana; Riccardo Velasco; Pere Arús; Michela Troggio; Eric W. van de Weg (Bioinform., 2015)

RNAsynth: constraints learning for RNA inverse folding. - Fabrizio Costa; Parastou Kohvaei; Robert Kleinkauf (ESANN, 2016)

AptaTRACE: Elucidating Sequence-Structure Binding Motifs by Uncovering Selection Trends in HT-SELEX Experiments. - Phuong Dao; Jan Hoinka; Yijie Wang 004; Mayumi Takahashi; Jiehua Zhou; Fabrizio Costa; John Rossi; John Burnett; Rolf Backofen; Teresa M. Przytycka (RECOMB, 2016)

Characterizing leader sequences of CRISPR loci. - Omer S. Alkhnbashi; Shiraz A. Shah; Roger A. Garrett; Sita J. Saunders; Fabrizio Costa; Rolf Backofen (Bioinform., 2016)

RNAcommender: genome-wide recommendation of RNA-protein interactions. - Gianluca Corrado; Toma Tebaldi; Fabrizio Costa; Paolo Frasconi; Andrea Passerini (Bioinform., 2016)

SnoReport 2.0: new features and a refined Support Vector Machine to improve snoRNA identification. - João Victor de Araújo Oliveira; Fabrizio Costa; Rolf Backofen; Peter F. Stadler; Maria Emília Telles Walter; Jana Hertel (BMC Bioinform., 2016)

Fast hyperparameter selection for graph kernels via subsampling and multiple kernel learning. - Michele Donini; Nicolò Navarin; Ivano Lauriola; Fabio Aiolli; Fabrizio Costa (ESANN, 2017)

The Conjunctive Disjunctive Node Kernel. - Dinh Tran-Van; Alessandro Sperduti; Fabrizio Costa (ESANN, 2017)

Link Enrichment for Diffusion-Based Graph Node Kernels. - Dinh Tran-Van; Alessandro Sperduti; Fabrizio Costa (ICANN (2), 2017)

Joint Neighborhood Subgraphs Link Prediction. - Dinh Tran-Van; Alessandro Sperduti; Fabrizio Costa (ICONIP (1), 2017)

Learning an efficient constructive sampler for graphs. - Fabrizio Costa (Artif. Intell., 2017)

RNAscClust: clustering RNA sequences using structure conservation and graph based motifs. - Milad Miladi; Alexander Junge; Fabrizio Costa; Stefan E. Seemann; Jakob Hull Havgaard; Jan Gorodkin; Rolf Backofen (Bioinform., 2017)

An efficient graph kernel method for non-coding RNA functional prediction. - Nicolò Navarin; Fabrizio Costa (Bioinform., 2017)

The conjunctive disjunctive graph node kernel for disease gene prioritization. - Dinh Tran-Van; Alessandro Sperduti; Fabrizio Costa (Neurocomputing, 2018)

Freiburg RNA tools: a central online resource for RNA-focused research and teaching. - Martin Raden; Syed M. Ali; Omer S. Alkhnbashi; Anke Busch; Fabrizio Costa; Jason A. Davis; Florian Eggenhofer; Rick Gelhausen; Jens Georg; Steffen Heyne; Michael Hiller; Kousik Kundu; et al. (Nucleic Acids Res., 2018)

Progress Towards Graph Optimization: Efficient Learning of Vector to Graph Space Mappings. - Stefan Mautner; Rolf Backofen; Fabrizio Costa (ESANN, 2019)

ShaKer: RNA SHAPE prediction using graph kernel. - Stefan Mautner; Soheila Montaseri; Milad Miladi; Martin Raden; Fabrizio Costa; Rolf Backofen (Bioinform., 2019)

Heterogeneous networks integration for disease-gene prioritization with node kernels. - Dinh Van Tran; Alessandro Sperduti; Rolf Backofen; Fabrizio Costa (Bioinform., 2020)

Learning to generate feasible graphs using graph grammars. - Stefan Mautner; Rolf Backofen; Fabrizio Costa (CoRR, 2025)