Marco Antoniotti

Publication Activity (10 Years)

Years Active: 1995-2023
Publications (10 Years): 32

Top Topics

Interval Arithmetic

Probabilistic Graphical Models

Top Venues

J. Comput. Sci.

Publications

Lucrezia Patruno, Salvatore Milite, Riccardo Bergamin, Nicola Calonaci, Alberto d'Onofrio, Fabio Anselmi, Marco Antoniotti, Alex Graudenzi, Giulio Caravagna
A Bayesian method to infer copy number clones from single-cell RNA and ATAC sequencing. PLoS Comput. Biol. 19 (11) (2023)
Francesco Craighero, Fabrizio Angaroni, Fabio Stella, Chiara Damiani, Marco Antoniotti, Alex Graudenzi
Unity is strength: Improving the detection of adversarial examples with ensemble approaches. Neurocomputing 554 (2023)
Gianluca Ascolani, Fabrizio Angaroni, Davide Maspero, Francesco Craighero, Narra Lakshmi Sai Bhavesh, Rocco Piazza, Chiara Damiani, Daniele Ramazzotti, Marco Antoniotti, Alex Graudenzi
LACE 2.0: an interactive R tool for the inference and visualization of longitudinal cancer evolution. BMC Bioinform. 24 (1) (2023)
Daniele Ramazzotti, Fabrizio Angaroni, Davide Maspero, Gianluca Ascolani, Isabella Castiglioni, Rocco Piazza, Marco Antoniotti, Alex Graudenzi
LACE: Inference of cancer evolution models from longitudinal single-cell sequencing data. J. Comput. Sci. 58 (2022)
Fabrizio Angaroni, Alessandro Guidi, Gianluca Ascolani, Alberto d'Onofrio, Marco Antoniotti, Alex Graudenzi
J-SPACE: a Julia package for the simulation of spatial models of cancer evolution and of sequencing experiments. BMC Bioinform. 23 (1) (2022)
Fabrizio Angaroni, Chiara Damiani, Giulia Ramunni, Marco Antoniotti
Optimal Control of a Discrete Time Stochastic Model of an Epidemic Spreading in Arbitrary Networks. ANNSIM (2021)
Francesco Craighero, Fabrizio Angaroni, Fabio Stella, Chiara Damiani, Marco Antoniotti, Alex Graudenzi
EAD: an ensemble approach to detect adversarial examples from the hidden features of deep neural networks. CoRR (2021)
Daniele Ramazzotti, Fabrizio Angaroni, Davide Maspero, Carlo Gambacorti Passerini, Marco Antoniotti, Alex Graudenzi, Rocco Piazza
VERSO: A comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples. Patterns 2 (3) (2021)
Marco Antoniotti
Why You Cannot (Yet) Write an "Interval Arithmetic" Library in Common Lisp. CoRR (2020)
Francesco Craighero, Fabrizio Angaroni, Alex Graudenzi, Fabio Stella, Marco Antoniotti
Investigating the Compositional Structure Of Deep Neural Networks. CoRR (2020)
Francesco Craighero, Alex Graudenzi, Fabrizio Angaroni, Fabio Stella, Marco Antoniotti
Understanding Deep Learning with Activation Pattern Diagrams. XAI.it@AI*IA (2020)
Davide Maspero, Chiara Damiani, Marco Antoniotti, Alex Graudenzi, Marzia Di Filippo, Marco Vanoni, Giulio Caravagna, Riccardo Colombo, Daniele Ramazzotti, Dario Pescini
The Influence of Nutrients Diffusion on a Metabolism-driven Model of a Multi-cellular System. Fundam. Informaticae 171 (1-4) (2020)
Daniele M. Papetti, Simone Spolaor, Daniela Besozzi, Paolo Cazzaniga, Marco Antoniotti, Marco S. Nobile
On the automatic calibration of fully analogical spiking neuromorphic chips. IJCNN (2020)
Francesco Craighero, Fabrizio Angaroni, Alex Graudenzi, Fabio Stella, Marco Antoniotti
Investigating the Compositional Structure of Deep Neural Networks. LOD (1) (2020)
Marco Antoniotti
Why You Cannot (Yet) Write an "Interval Arithmetic" Library in Common Lisp ... or: Hammering Some Sense into : ieee-floating-point. ELS (2020)
Fabrizio Angaroni, Mattia Pennati, Lucrezia Patruno, Davide Maspero, Marco Antoniotti, Alex Graudenzi
A closed-loop optimization framework for personalized cancer therapy design. CIBCB (2020)
Daniele Ramazzotti, Marco S. Nobile, Marco Antoniotti, Alex Graudenzi
Efficient computational strategies to learn the structure of probabilistic graphical models of cumulative phenomena. J. Comput. Sci. 30 (2019)
Daniele Ramazzotti, Alex Graudenzi, Luca De Sano, Marco Antoniotti, Giulio Caravagna
Learning mutational graphs of individual tumour evolution from single-cell and multi-region sequencing data. BMC Bioinform. 20 (1) (2019)
Lucrezia Patruno, Edoardo Galimberti, Daniele Ramazzotti, Giulio Caravagna, Luca De Sano, Marco Antoniotti, Alex Graudenzi
cyTRON and cyTRON/JS: Two Cytoscape-Based Applications for the Inference of Cancer Evolution Models. CIBB (2019)
Davide Maspero, Alex Graudenzi, Satwinder Singh, Dario Pescini, Giancarlo Mauri, Marco Antoniotti, Chiara Damiani
Synchronization Effects in a Metabolism-Driven Model of Multi-cellular System. WIVACE (2018)
Daniele Ramazzotti, Marco S. Nobile, Marco Antoniotti, Alex Graudenzi
Structural Learning of Probabilistic Graphical Models of Cumulative Phenomena. ICCS (1) (2018)
Alex Graudenzi, Davide Maspero, Marzia Di Filippo, Marco Gnugnoli, Claudio Isella, Giancarlo Mauri, Enzo Medico, Marco Antoniotti, Chiara Damiani
Integration of transcriptomic data and metabolic networks in cancer samples reveals highly significant prognostic power. J. Biomed. Informatics 87 (2018)
Lucrezia Patruno, Edoardo Galimberti, Daniele Ramazzotti, Giulio Caravagna, Luca De Sano, Marco Antoniotti, Alex Graudenzi
cyTRON and cyTRON/JS: two Cytoscape-based applications for the inference of cancer evolution models. CoRR (2017)
Daniele Ramazzotti, Marco S. Nobile, Marco Antoniotti, Alex Graudenzi
Learning the Probabilistic Structure of Cumulative Phenomena with Suppes-Bayes Causal Networks. CoRR (2017)
Daniele Ramazzotti, Alex Graudenzi, Luca De Sano, Marco Antoniotti, Giulio Caravagna
Learning mutational graphs of individual tumor evolution from multi-sample sequencing data. CoRR (2017)
Daniele Ramazzotti, Marco S. Nobile, Paolo Cazzaniga, Giancarlo Mauri, Marco Antoniotti
Parallel Implementation of Efficient Search Schemes for the Inference of Cancer Progression Models. CoRR (2017)
Daniele Ramazzotti, Alex Graudenzi, Marco Antoniotti
Modeling cumulative biological phenomena with Suppes-Bayes causal networks. CoRR (2016)
Alex Graudenzi, Giulio Caravagna, Iuliana M. Bocicor, Claudia Cava, Marco Antoniotti, Giancarlo Mauri
Ordering cancer mutational profiles of cross-sectional copy number alterations. Int. J. Data Min. Bioinform. 15 (1) (2016)
Luca De Sano, Giulio Caravagna, Daniele Ramazzotti, Alex Graudenzi, Giancarlo Mauri, Bud Mishra, Marco Antoniotti
TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data. Bioinform. 32 (12) (2016)
Marco Antoniotti, Giulio Caravagna, Luca De Sano, Alex Graudenzi, Giancarlo Mauri, Bud Mishra, Daniele Ramazzotti
Design of the TRONCO BioConductor Package for TRanslational ONCOlogy. R J. 8 (2) (2016)
Daniele Ramazzotti, Marco S. Nobile, Paolo Cazzaniga, Giancarlo Mauri, Marco Antoniotti
Parallel implementation of efficient search schemes for the inference of cancer progression models. CIBCB (2016)
Andrea Paroni, Alex Graudenzi, Giulio Caravagna, Chiara Damiani, Giancarlo Mauri, Marco Antoniotti
CABeRNET: a Cytoscape app for augmented Boolean models of gene regulatory NETworks. BMC Bioinform. 17 (2016)
Giulio Caravagna, Luca De Sano, Marco Antoniotti
Automatising the analysis of stochastic biochemical time-series. BMC Bioinform. 16 (S-9) (2015)
Daniele Ramazzotti, Giulio Caravagna, Loes Olde Loohuis, Alex Graudenzi, Ilya Korsunsky, Giancarlo Mauri, Marco Antoniotti, Bud Mishra
CAPRI: efficient inference of cancer progression models from cross-sectional data. Bioinform. 31 (18) (2015)
Marco Antoniotti
CLAZY: Lazy Calling for Common Lisp. CoRR (2014)
Alex Graudenzi, Chiara Damiani, Andrea Paroni, Alessandro Filisetti, Marco Villani, Roberto Serra, Marco Antoniotti
Investigating the Role of Network Topology and Dynamical Regimes on the Dynamics of a Cell Differentiation Model. WIVACE (2014)
Claudia Cava, Italo Zoppis, Manuela Gariboldi, Isabella Castiglioni, Giancarlo Mauri, Marco Antoniotti
Combined analysis of chromosomal instabilities and gene expression for colon cancer progression inference. J. Clin. Bioinform. 4 (2014)
Giulio Caravagna, Alberto d'Onofrio, Marco Antoniotti, Giancarlo Mauri
Stochastic Hybrid Automata with delayed transitions to model biochemical systems with delays. Inf. Comput. 236 (2014)
Daniele Ramazzotti, Carlo Maj, Marco Antoniotti
A Model of Colonic Crypts using SBML Spatial. WIVACE (2013)
Giulio Caravagna, Alex Graudenzi, Marco Antoniotti, Giovanni De Matteis
Analysis of the spatial and dynamical properties of a multiscale model of intestinal crypts. WIVACE (2013)
Artiom Alhazov, Marco Antoniotti, Alberto Leporati
Characterizing the computational power of energy-based P systems. Int. J. Comput. Math. 90 (4) (2013)
Marco Antoniotti, Gary D. Bader, Giulio Caravagna, Silvia Crippa, Alex Graudenzi, Giancarlo Mauri
GeStoDifferent: a Cytoscape plugin for the generation and the identification of gene regulatory networks describing a stochastic cell differentiation process. Bioinform. 29 (4) (2013)
Claudia Cava, Italo Zoppis, Manuela Gariboldi, Isabella Castiglioni, Giancarlo Mauri, Marco Antoniotti
Copy-Number Alterations for Tumor Progression Inference. AIME (2013)
Marco Antoniotti, Rudolf Freund, Alberto Leporati, Giancarlo Mauri
Self-Stabilization in Membrane Systems. Comput. Sci. J. Moldova 20 (2) (2012)
Italo Zoppis, Massimiliano Borsani, Erica Gianazza, Clizia Chinello, Francesco Rocco, Giancarlo Albo, André M. Deelder, Yuri E. M. van der Burgt, Fulvio Magni, Marco Antoniotti, Giancarlo Mauri
Analysis of Correlation Structures in Renal Cell Carcinoma Patient Data. BIOINFORMATICS (2012)
Italo Zoppis, Massimiliano Borsani, Erica Gianazza, Clizia Chinello, Giancarlo Albo, Francesco Rocco, André M. Deelder, Yuri E. M. van der Burgt, Marco Antoniotti, Fulvio Magni, Giancarlo Mauri
Poster: Characterization of distinguishing regions for Renal Cell Carcinoma discrimination. ICCABS (2012)
Italo Zoppis, Erica Gianazza, Massimiliano Borsani, Clizia Chinello, Veronica Mainini, Carmen Galbusera, Carlo Ferrarese, Gloria Galimberti, Alessandro Sorbi, Barbara Borroni, Fulvio Magni, Marco Antoniotti, Giancarlo Mauri
Mutual Information Optimization for Mass Spectra Data Alignment. IEEE ACM Trans. Comput. Biol. Bioinform. 9 (3) (2012)
Giulio Caravagna, Alex Graudenzi, Marco Antoniotti, Giancarlo Mauri, Alberto d'Onofrio
Effects of delayed immune-response in tumor immune-system interplay HSB (2012)
Leonardo Vanneschi, Antonella Farinaccio, Giancarlo Mauri, Marco Antoniotti, Paolo Provero, Mario Giacobini
A comparison of machine learning techniques for survival prediction in breast cancer. BioData Min. 4 (2011)
Marco Antoniotti, Marco Carreras, Antonella Farinaccio, Giancarlo Mauri, Daniele Merico, Italo Zoppis
An application of kernel methods to gene cluster temporal meta-analysis. Comput. Oper. Res. 37 (8) (2010)
Leonardo Vanneschi, Antonella Farinaccio, Mario Giacobini, Giancarlo Mauri, Marco Antoniotti, Paolo Provero
Identification of Individualized Feature Combinations for Survival Prediction in Breast Cancer: A Comparison of Machine Learning Techniques. EvoBIO (2010)
Gianluca Colombo, Daniele Merico, Giorgio Boncoraglio, Flavio De Paoli, John Ellul, Giuseppe Frisoni, Zoltán Nagy, Aad van der Lugt, István Vassányi, Marco Antoniotti
An ontological modeling approach to cerebrovascular disease studies: The NEUROWEB case. J. Biomed. Informatics 43 (4) (2010)
Gianluca Colombo, Daniele Merico, Zoltán Nagy, Flavio De Paoli, Marco Antoniotti, Giancarlo Mauri
Ontological modeling at a domain interface: bridging clinical and biomolecular knowledge. Knowl. Eng. Rev. 24 (3) (2009)
Marco Antoniotti
CLAZY: Lazy Calling for Common Lisp. ELS (2008)
Daniele Merico, Italo Zoppis, Marco Antoniotti, Giancarlo Mauri
Evaluating Graph Kernel Methods for Relation Discovery in GO-Annotated Clusters. KES (3) (2007)
Jomol P. Mathew, Barry S. Taylor, Gary D. Bader, Saiju Pyarajan, Marco Antoniotti, Arul M. Chinnaiyan, Chris Sander, Steven J. Burakoff, Bud Mishra
From Bytes to Bedside: Data Integration and Computational Biology for Translational Cancer Research. PLoS Comput. Biol. 3 (2) (2007)
Gianluca Colombo, Daniele Merico, Marco Antoniotti, Flavio De Paoli, Giancarlo Mauri
Ontological Modelling for Neurovascular Disease Study: Issues in the Adoption of Description Logic. Description Logics (2007)
Italo Zoppis, Daniele Merico, Marco Antoniotti, Bud Mishra, Giancarlo Mauri
Discovering Relations Among GO-Annotated Clusters by Graph Kernel Methods. ISBRA (2007)
Carla Piazza, Marco Antoniotti, Venkatesh Mysore, Alberto Policriti, Franz Winkler, Bud Mishra
Algorithmic Algebraic Model Checking I: Challenges from Systems Biology. CAV (2005)
Marco Antoniotti, Carla Piazza, Alberto Policriti, Marta Simeoni, Bud Mishra
Taming the complexity of biochemical models through bisimulation and collapsing: theory and practice. Theor. Comput. Sci. 325 (1) (2004)
Marco Antoniotti, F. Park, Alberto Policriti, Nadia Ugel, Bud Mishra
Foundations of a Query and Simulation System for the Modeling of Biochemical and Biological Processes. Pacific Symposium on Biocomputing (2003)
Marco Antoniotti, Bhubaneswar Mishra, Carla Piazza, Alberto Policriti, Marta Simeoni
Modeling Cellular Behavior with Hybrid Automata: Bisimulation and Collapsing. CMSB (2003)
Marco Antoniotti, Alberto Policriti, Nadia Ugel, Bud Mishra
XS-systems: eXtended S-Systems and Algebraic Differential Automata for Modeling Cellular Behavior. HiPC (2002)
Marco Antoniotti, Alberto Ferrari, Luciano Lavagno, Alberto L. Sangiovanni-Vincentelli, Ellen Sentovich
Embedded system design specification: merging reactive control and data computation. CDC (2001)
Marco Antoniotti, Aleks Göllü
SHIFT and SMART-AHS: A Language for Hybrid System Engineering Modeling and Simulation. DSL (1997)
Marco Antoniotti, Bud Mishra
Descrete Events Models + Temporal Logic = Supervisory Controller: Automatic Synthesis of Locomotion Controllers. ICRA (1995)