Articles in Journals
- E. Cilia, N. Landwehr, A. Passerini,
Relational Feature Mining with Hierarchical Multitask kFOIL,
Fundamenta Informaticae 113: 1-26, 2011.
- A. Passerini, M. Lippi, P. Frasconi,
Predicting Metal Binding Sites from Protein
Sequence, IEEE/ACM Transactions on
Computational Biology and Bioinformatics, 9(1):203-213, 2011.
- A. Passerini, M. Lippi, P. Frasconi,
MetalDetector v2.0: predicting the geometry of
metal binding sites from protein sequence,
Nucleic Acids Research, 39(Web Server issue):W288--W292, 2011.
- Shi W, Punta M, Bohon J, Sauder JM, D'Mello R, Sullivan M, Toomey J, Abel D,
Lippi M, Passerini A, Frasconi P, Burley SK, Rost B, Chance MR,
Characterization of metalloproteins by high-throughput X-ray absorption spectroscopy,
Genome Research, 21:898-907, 2011.
- R. Battiti, A. Passerini,
Brain-Computer Evolutionary Multi-Objective
Optimization (BC-EMO): a genetic algorithm
adapting to the decision maker, IEEE
Transactions on Evolutionary Computation, 14(5):671-687, 2010.
- M. Lippi, M. Jaeger, P. Frasconi, A. Passerini,
Relational Information Gain,
Machine Learning, 2010.
- E. Cilia and A. Passerini,
Automatic prediction of catalytic residues by modeling residue structural neighborhood,
BMC Bioinformatics 2010, 11:115.
- N. Landwehr, A. Passerini, L. De Raedt, and P. Frasconi,
Fast learning of relational kernels,
Machine Learning, 79(3):305-342, 2010.
- F. Costa, A. Passerini, M. Lippi, and P. Frasconi,
A semiparametric generative model for efficient structured-output supervised learning,
in M. Jaeger, L. Getoor, and K. Kersting, editors, Annals of Mathematics and Artificial Intelligence,
54(1-3):207-222, Special issue on Probabilistic Relational Learning, 2008.
- M. Lippi, A. Passerini, M. Punta, B. Rost, P. Frasconi,
MetalDetector: a web server for predicting metal binding sites and disulfide bridges in proteins from sequence
, Bioinformatics, 2008.
- M. Vincent, A. Passerini, M. Labbè, P. Frasconi,
A simplified approach to disulfide connectivity
prediction from protein sequences, BMC Bioinformatics, 9(20), 2008.
- A. Passerini, C. Andreini, S. Menchetti,
A. Rosato, P. Frasconi,
Predicting zinc binding at the proteome
level, BMC Bioinformatics, 8:39, 2007.
- E. Francesconi, A. Passerini,
Automatic Classification of Provisions in
Legislative Texts, Artificial Intelligence
and Law, 15(1):1--17, 2007.
- A. Passerini, M. Punta, A. Ceroni, B. Rost,
P. Frasconi,
Identifying Cysteines and Histidines in
Transition-Metal-Binding Sites Using Support
Vector Machines and Neural Networks
, PROTEINS: Structure, Functions and
Bioinformatics, 65(2):305--316, 2006.
- A. Ceroni, A. Passerini, A. Vullo and
P. Frasconi,
DISULFIND: a Disulfide Bonding State and
Cysteine Connectivity Prediction Server,
Nucleic Acids Research, 34(Web Server
issue):W177--W181, 2006.
- A. Passerini, P. Frasconi and L. De Raedt, Kernels on Prolog Proof
Trees: Statistical Learning in the ILP
Setting, Journal of Machine Learning
Research (Special Topic on Inductive
Programming), 7(Feb):307--342, 2006.
- A. Passerini and P. Frasconi,
Learning to discriminate between ligand bound
and disulfide bound cysteines, Protein
Engineering, Design and Selection, 17:367--373,
2004.
- A. Passerini, M. Pontil, and P. Frasconi, New results on error
correcting output codes of kernel machines,
IEEE Transactions on Neural Networks,
15(1):45--54, 2004.
- A. Ceroni, P. Frasconi, A. Passerini, and
A. Vullo, Predicting
the Disulfide Bonding State of Cysteines with
Combinations of Kernel Machines, Journal of
VLSI Signal Processing-Systems for Signal,
Image, and Video Technology, Ed. S.Y. Kung,
35(3):287--295, 2003.
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Book Chapters
- P. Frasconi and
A. Passerini.
Learning with kernels and logical
representations, In L. De Raedt,
P. Frasconi, K. Kersting, and S. Muggleton,
editors, Probabilistic Inductive Logic
Programming: Theory and Applications, LNAI
4911, pages 56-91, Springer, 2008.
- A. Passerini and A. Vullo Machine Learning
in Structural Genomics, in "Bioinformatica. Sfide e prospettive",
Franco Angeli Press, 2007.
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Conference Proceedings
- P. Campigotto, A. Passerini and R. Battiti,
Active Learning of Combinatorial Features for Interactive Optimization,
in Learning and Intelligent OptimizatioN - LION 5, 2011.
- S. Teso, C. Di Risio, A. Passerini, and R. Battiti,
An on/off lattice approach to protein
structure prediction from contact maps, In
Proceedings of Pattern Recognition in
Bioinformatics (PRIB2010), 2010.
- F. Mascia, E. Cilia, M. Brunato and A. Passerini,
Predicting structural and functional sites
in proteins by searching for maximum-weight cliques,
In Proceedings of the Twenty-Fourth AAAI Conference on Artificial Intelligence (AAAI-10), 2010.
- Lippi, M., Jaeger, M., Frasconi, P., and Passerini, A.,
Relational Information Gain, 19th International Conference on
Inductive Logic Programming (ILP'09), 2009.
- P. Frasconi and A. Passerini, Predicting
the Geometry of Metal Binding Sites from
Protein Sequence, in Twenty-Second
Annual Conference on Neural Information
Processing Systems (NIPS'08), 2008.
- P. Frasconi, M. Jaeger and A.
Passerini, Feature
Discovery with Type Extension Trees, in
18th International Conference on Inductive
Logic Programming (ILP'08), 2008.
- A. Vullo, A. Passerini, P. Frasconi, F. Costa, and G. Pollastri,
On the Convergence of Protein Structure and Dynamics.
Statistical Learning Studies of Pseudo Folding Pathways,
in 6th European Conference on Evolutionary Computation,
Machine Learning and Data Mining in Bioinformatics (EVOBIO'08), 2008.
- N. Landwehr, A. Passerini, L. De Raedt and
P. Frasconi, kFOIL:
Learning Simple Relational Kernels, in
Proceedings of AAAI'06, Boston, Massachusetts,
USA, July 16--20 2006.
- S. Menchetti, A. Passerini, P. Frasconi,
C. Andreini and A. Rosato, Improving Prediction
of Zinc Binding Sites by Modeling the Linkage
between Residues Close in Sequence, in
Proceedings of RECOMB'06, 309--320, Venice,
Italy, April 2-5 2006.
- A. Passerini and P. Frasconi, Kernels on Prolog
Ground Terms, in Int. Joint Conf. on
Artificial Intelligence (IJCAI'05), Edinburgh,
Scotland, 30 July - 5 August, 2005.
- C. Biagioli, E. Francesconi, A. Passerini,
S. Montemagni and C. Soria, Automatic semantics
extraction in law documents, in Proceedings
of ICAIL'05, 133--140, Bologna, Italy, June
6-11, 2005.
- A. Ceroni, P. Frasconi, A. Passerini, and
A. Vullo, A combination
of support vector machines and bidirectional
recurrent neural networks for protein secondary
structure prediction, in A. Cappelli and
F. Turini, editors, AI*IA 2003: Advances in
Artificial Intelligence, pages 142--153, 2003.
- P. Frasconi, A. Passerini, and A. Vullo, A two-stage SVM
architecture for predicting the disulfide
bonding state of cysteines, in Proc. of the
IEEE Workshop on Neural Networks for Signal
Processing, 2002.
- A. Passerini, M. Pontil, P. Frasconi, From Margins to
Probabilities in Multiclass Learning
Problems, in F. van Harmelen (ed.),
Proceedings of the 15th European Conference on
Artificial Intelligence, 2002.
- A. Passerini, P. Frasconi, G. Soda, Evaluation Methods for
Focused Crawling, Proceedings of the 7th
Congress of the Italian Association for
Artificial Intelligence, Bari, Italy, September
25-28, 2001.
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Workshops
- E. Cilia and A. Passerini, Frankenstein Junior: a relational
learning approach toward protein engineering, in ECCB 2010
Workshop on Annotation, Interpretation, and Management of Mutations
(AIMM 2010), Ghent (Belgium), September 2010.
- P. Campigotto, A. Passerini and R. Battiti,
Handling concept drift in preference learning for
interactive decision making, in ECML/PKDD 2010 Workshop
on Handling Concept Drift in Adaptive Information Systems
(HaCDAIS 2010), Barcelona (Spain), September 2010.
- C. Nicolini, B. Lepri, S. Teso and A. Passerini,
From on-going to complete activity recognition
exploiting related activities, in ICPR 2010 Workshop
on Human Behaviour Understanding (HBU 2010), Istanbul (Turkey), August 2010.
- E. Cilia, N. Landwehr and A. Passerini,
Mining Drug Resistance Relational Features with Hierarchical Multitask kFOIL
In Bio-Logical@AI*IA2009 Workshop (BIO-LOGICAL 2009), Reggio Emilia (Italy), December 12, 2009.
- P. Frasconi, M. Jaeger and A.
Passerini, Learning
Type Extension Trees for Metal Bonding State
Prediction, in ECML'08 Workshop on
Statistical and Relational Learning in
Bioinformatics, 2008.
- A. Passerini and P. Frasconi,
Proof tree kernels: a candidate ingredient for
intelligent optimization, in Learning and Intelligent
OptimizatioN - LION 2007 II, 2007.
- F. Costa, A. Passerini, and P. Frasconi,
Learning structured outputs via kernel dependency
estimation and stochastic grammars, in ECML'06 Workshop on
Mining and Learning with Graphs (MLG 2006), 2006.
- F. Costa, S. Menchetti, A. Ceroni, A. Passerini
and P. Frasconi,
Decomposition Kernels for Natural Language
Processing, In EACL'06 Workshop on Learning
Structured Information in Natural Language
Applications.
- A. Passerini, P. Frasconi and L. De Raedt, Kernels on Prolog
Proof Trees: Statistical Learning in the ILP
Setting, In ICML '05 Workshop on Approaches
and Applications of Inductive Programming.
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