Here you can find a consolidated (a.k.a. slowly updated) list of my publications. A frequently updated (and possibly noisy) list of works is available on my Google Scholar profile.
Please find below a short list of highlight publications for my recent activity.
Ninniri, Matteo; Podda, Marco; Bacciu, Davide Classifier-free graph diffusion for molecular property targeting Workshop 4th workshop on Graphs and more Complex structures for Learning and Reasoning (GCLR) at AAAI 2024, 2024. Errica, Federico; Gravina, Alessio; Bacciu, Davide; Micheli, Alessio Hidden Markov Models for Temporal Graph Representation Learning Conference Proceedings of the 31th European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning , 2023. Simone, Lorenzo; Bacciu, Davide ECGAN: generative adversarial network for electrocardiography Conference Proceedings of Artificial Intelligence In Medicine 2023 (AIME 2023), 2023. Sangermano, Matteo; Carta, Antonio; Cossu, Andrea; Lomonaco, Vincenzo; Bacciu, Davide Sample Condensation in Online Continual Learning Conference Proceedings of the 2022 IEEE World Congress on Computational Intelligence, IEEE, 2022. Valenti, Andrea; Bacciu, Davide Leveraging Relational Information for Learning Weakly Disentangled Representations Conference Proceedings of the 2022 IEEE World Congress on Computational Intelligence, IEEE, 2022. Castellana, Daniele; Errica, Federico; Bacciu, Davide; Micheli, Alessio The Infinite Contextual Graph Markov Model Conference Proceedings of the 39th International Conference on Machine Learning (ICML 2022), 2022. Serramazza, Davide Italo; Bacciu, Davide Learning image captioning as a structured transduction task Conference Proceedings of the 23rd International Conference on Engineering Applications of Neural Networks (EANN 2022), vol. 1600, Communications in Computer and Information Science Springer, 2022. Bacciu, Davide; Numeroso, Danilo Explaining Deep Graph Networks via Input Perturbation Journal Article In: IEEE Transactions on Neural Networks and Learning Systems, 2022. Valenti, Andrea; Berti, Stefano; Bacciu, Davide Calliope - A Polyphonic Music Transformer Conference Proceedings of the 29th European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning (ESANN 2021), 2021. Atzeni, Daniele; Bacciu, Davide; Errica, Federico; Micheli, Alessio Modeling Edge Features with Deep Bayesian Graph Networks Conference Proceedings of the International Joint Conference on Neural Networks (IJCNN 2021), IEEE IEEE, 2021. Bacciu, Davide; Podda, Marco GraphGen-Redux: a Fast and Lightweight Recurrent Model for Labeled Graph Generation Conference Proceedings of the International Joint Conference on Neural Networks (IJCNN 2021), IEEE 2021. Errica, Federico; Bacciu, Davide; Micheli, Alessio Graph Mixture Density Networks Conference Proceedings of the 38th International Conference on Machine Learning (ICML 2021), PMLR, 2021. Ronchetti, Matteo; Bacciu, Davide Generative Tomography Reconstruction Workshop 34th Conference on Neural Information Processing Systems (NeurIPS 2020), Workshop on Deep Learning and Inverse Problems, 2020. Valenti, Andrea; Carta, Antonio; Bacciu, Davide Learning a Latent Space of Style-Aware Music Representations by Adversarial Autoencoders Conference Proceedings of the 24th European Conference on Artificial Intelligence (ECAI 2020), 2020. Podda, Marco; Bacciu, Davide; Micheli, Alessio A Deep Generative Model for Fragment-Based Molecule Generation Conference Proceedings of the 23rd International Conference on Artificial Intelligence and Statistics (AISTATS 2020) , 2020. Bacciu, Davide; Micheli, Alessio Deep Learning for Graphs Book Chapter In: Oneto, Luca; Navarin, Nicolo; Sperduti, Alessandro; Anguita, Davide (Ed.): Recent Trends in Learning From Data: Tutorials from the INNS Big Data and Deep Learning Conference (INNSBDDL2019), vol. 896, pp. 99-127, Springer International Publishing, 2020, ISBN: 978-3-030-43883-8. Bacciu, Davide; Micheli, Alessio; Podda, Marco Edge-based sequential graph generation with recurrent neural networks Journal Article In: Neurocomputing, 2019. Bacciu, Davide; Micheli, Alessio; Podda, Marco Graph generation by sequential edge prediction Conference Proceedings of the European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning (ESANN'19), i6doc.com, Louvain-la-Neuve, Belgium, 2019. Bacciu, Davide; Lisboa, Paulo J. G.; Sperduti, Alessandro; Villmann, Thomas Probabilistic Modeling in Machine Learning Book Chapter In: Kacprzyk, Janusz; Pedrycz, Witold (Ed.): pp. 545–575, Springer Berlin Heidelberg, Berlin, Heidelberg, 2015, ISBN: 978-3-662-43505-2. Davide, Bacciu; Alessio, Micheli; Alessandro, Sperduti Integrating bi-directional contexts in a generative kernel for trees Conference Neural Networks (IJCNN), 2014 International Joint Conference on, IEEE, 2014. Davide, Bacciu; Alessio, Micheli; Alessandro, Sperduti Modeling Bi-directional Tree Contexts by Generative Transductions Conference Neural Information Processing, vol. 8834, Springer International Publishing, 2014. Davide, Bacciu; Alessio, Micheli; Alessandro, Sperduti A Generative Multiset Kernel for Structured Data Conference Artificial Neural Networks and Machine Learning - ICANN 2012 proceedings, Springer LNCS series, vol. 7552, Springer-Verlag, BERLIN HEIDELBERG, 2012. Davide, Bacciu; Alessio, Micheli; Alessandro, Sperduti Input-Output Hidden Markov Models for Trees Conference ESANN 2012 - The 20th European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning - Proceedings, Ciaco scrl - i6doc.com, 2012. Davide, Bacciu; Alessio, Micheli; Alessandro, Sperduti Adaptive Tree Kernel by Multinomial Generative Topographic Mapping Conference Proceedings of the International Joint Conference on Neural Networks, IEEE, Piscataway (NJ), 2011. Davide, Bacciu; Alessio, Micheli; Alessandro, Sperduti A Bottom-up Hidden Tree Markov Model Technical Report Università di Pisa no. TR-10-08, 2010. Davide, Bacciu; Alessio, Micheli; Alessandro, Sperduti Bottom-Up Generative Modeling of Tree-Structured Data Conference LNCS 6443: Neural Information Processing. Theory and Algorithms. Part I, vol. 6443, Springer-Verlag, BERLIN HEIDELBERG, 2010. Davide, Bacciu; H, Jarman Ian; A, Etchells Terence; G, Lisboa Paulo J Patient stratification with competing risks by multivariate Fisher distance Conference 2009 International Joint Conference on Neural Networks, IEEE, 2009. Davide, Bacciu A Perceptual Learning Model to Discover the Hierarchical Latent Structure of Image Collections PhD Thesis 2008.
@workshop{Ninniri2024,
title = {Classifier-free graph diffusion for molecular property targeting},
author = {Matteo Ninniri and Marco Podda and Davide Bacciu},
url = {https://arxiv.org/abs/2312.17397, Arxiv},
year = {2024},
date = {2024-02-27},
booktitle = {4th workshop on Graphs and more Complex structures for Learning and Reasoning (GCLR) at AAAI 2024},
abstract = {This work focuses on the task of property targeting: that is, generating molecules conditioned on target chemical properties to expedite candidate screening for novel drug and materials development. DiGress is a recent diffusion model for molecular graphs whose distinctive feature is allowing property targeting through classifier-based (CB) guidance. While CB guidance may work to generate molecular-like graphs, we hint at the fact that its assumptions apply poorly to the chemical domain. Based on this insight we propose a classifier-free DiGress (FreeGress), which works by directly injecting the conditioning information into the training process. CF guidance is convenient given its less stringent assumptions and since it does not require to train an auxiliary property regressor, thus halving the number of trainable parameters in the model. We empirically show that our model yields up to 79% improvement in Mean Absolute Error with respect to DiGress on property targeting tasks on QM9 and ZINC-250k benchmarks. As an additional contribution, we propose a simple yet powerful approach to improve chemical validity of generated samples, based on the observation that certain chemical properties such as molecular weight correlate with the number of atoms in molecules. },
keywords = {},
pubstate = {published},
tppubtype = {workshop}
}
@conference{Errica2023,
title = {Hidden Markov Models for Temporal Graph Representation Learning},
author = {Federico Errica and Alessio Gravina and Davide Bacciu and Alessio Micheli},
editor = {Michel Verleysen},
year = {2023},
date = {2023-10-04},
urldate = {2023-10-04},
booktitle = {Proceedings of the 31th European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning },
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
@conference{nokey,
title = {ECGAN: generative adversarial network for electrocardiography},
author = {Lorenzo Simone and Davide Bacciu },
year = {2023},
date = {2023-06-12},
urldate = {2023-06-12},
booktitle = {Proceedings of Artificial Intelligence In Medicine 2023 (AIME 2023)},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
@conference{Sangermano2022,
title = {Sample Condensation in Online Continual Learning},
author = {Matteo Sangermano and Antonio Carta and Andrea Cossu and Vincenzo Lomonaco and Davide Bacciu
},
url = {https://arxiv.org/abs/2206.11849, Arxiv},
year = {2022},
date = {2022-07-18},
urldate = {2022-07-18},
booktitle = {Proceedings of the 2022 IEEE World Congress on Computational Intelligence},
publisher = {IEEE},
abstract = {Online Continual learning is a challenging learning scenario where the model observes a non-stationary stream of data and learns online. The main challenge is to incrementally learn while avoiding catastrophic forgetting, namely the problem of forgetting previously acquired knowledge while learning from new data. A popular solution in these scenario is to use a small memory to retain old data and rehearse them over time. Unfortunately, due to the limited memory size, the quality of the memory will deteriorate over time. In this paper we propose OLCGM, a novel replay-based continual learning strategy that uses knowledge condensation techniques to continuously compress the memory and achieve a better use of its limited size. The sample condensation step compresses old samples, instead of removing them like other replay strategies. As a result, the experiments show that, whenever the memory budget is limited compared to the complexity of the data, OLCGM improves the final accuracy compared to state-of-the-art replay strategies.},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
@conference{Valenti2022,
title = { Leveraging Relational Information for Learning Weakly Disentangled Representations },
author = {Andrea Valenti and Davide Bacciu
},
url = {https://arxiv.org/abs/2205.10056, Arxiv},
year = {2022},
date = {2022-07-18},
urldate = {2022-07-18},
booktitle = {Proceedings of the 2022 IEEE World Congress on Computational Intelligence},
publisher = {IEEE},
abstract = {Disentanglement is a difficult property to enforce in neural representations. This might be due, in part, to a formalization of the disentanglement problem that focuses too heavily on separating relevant factors of variation of the data in single isolated dimensions of the neural representation. We argue that such a definition might be too restrictive and not necessarily beneficial in terms of downstream tasks. In this work, we present an alternative view over learning (weakly) disentangled representations, which leverages concepts from relational learning. We identify the regions of the latent space that correspond to specific instances of generative factors, and we learn the relationships among these regions in order to perform controlled changes to the latent codes. We also introduce a compound generative model that implements such a weak disentanglement approach. Our experiments shows that the learned representations can separate the relevant factors of variation in the data, while preserving the information needed for effectively generating high quality data samples.},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
@conference{nokey,
title = {The Infinite Contextual Graph Markov Model},
author = {Daniele Castellana and Federico Errica and Davide Bacciu and Alessio Micheli
},
year = {2022},
date = {2022-07-18},
urldate = {2022-07-18},
booktitle = {Proceedings of the 39th International Conference on Machine Learning (ICML 2022)},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
@conference{Serramazza2022,
title = {Learning image captioning as a structured transduction task},
author = {Davide Italo Serramazza and Davide Bacciu},
doi = {doi.org/10.1007/978-3-031-08223-8_20},
year = {2022},
date = {2022-06-20},
urldate = {2022-06-20},
booktitle = {Proceedings of the 23rd International Conference on Engineering Applications of Neural Networks (EANN 2022)},
volume = {1600},
pages = {235–246},
publisher = {Springer},
series = {Communications in Computer and Information Science },
abstract = {Image captioning is a task typically approached by deep encoder-decoder architectures, where the encoder component works on a flat representation of the image while the decoder considers a sequential representation of natural language sentences. As such, these encoder-decoder architectures implement a simple and very specific form of structured transduction, that is a generalization of a predictive problem where the input data and output predictions might have substantially different structures and topologies. In this paper, we explore a generalization of such an approach by addressing the problem as a general structured transduction problem. In particular, we provide a framework that allows considering input and output information with a tree-structured representation. This allows taking into account the hierarchical nature underlying both images and sentences. To this end, we introduce an approach to generate tree-structured representations from images along with an autoencoder working with this kind of data. We empirically assess our approach on both synthetic and realistic tasks.},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
@article{Bacciu2022,
title = {Explaining Deep Graph Networks via Input Perturbation},
author = {Davide Bacciu and Danilo Numeroso
},
doi = {10.1109/TNNLS.2022.3165618},
year = {2022},
date = {2022-04-21},
urldate = {2022-04-21},
journal = {IEEE Transactions on Neural Networks and Learning Systems},
abstract = {Deep Graph Networks are a family of machine learning models for structured data which are finding heavy application in life-sciences (drug repurposing, molecular property predictions) and on social network data (recommendation systems). The privacy and safety-critical nature of such domains motivates the need for developing effective explainability methods for this family of models. So far, progress in this field has been challenged by the combinatorial nature and complexity of graph structures. In this respect, we present a novel local explanation framework specifically tailored to graph data and deep graph networks. Our approach leverages reinforcement learning to generate meaningful local perturbations of the input graph, whose prediction we seek an interpretation for. These perturbed data points are obtained by optimising a multi-objective score taking into account similarities both at a structural level as well as at the level of the deep model outputs. By this means, we are able to populate a set of informative neighbouring samples for the query graph, which is then used to fit an interpretable model for the predictive behaviour of the deep network locally to the query graph prediction. We show the effectiveness of the proposed explainer by a qualitative analysis on two chemistry datasets, TOS and ESOL and by quantitative results on a benchmark dataset for explanations, CYCLIQ.
},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@conference{Valenti2021b,
title = {Calliope - A Polyphonic Music Transformer},
author = {Andrea Valenti and Stefano Berti and Davide Bacciu},
editor = {Michel Verleysen},
url = { The polyphonic nature of music makes the application of deep learning to music modelling a challenging task. On the other hand, the Transformer architecture seems to be a good fit for this kind of data. In this work, we present Calliope, a novel autoencoder model based on Transformers for the efficient modelling of multi-track sequences of polyphonic music. The experiments show that our model is able to improve the state of the art on musical sequence reconstruction and generation, with remarkably good results especially on long sequences. },
doi = {10.14428/esann/2021.ES2021-63},
year = {2021},
date = {2021-10-06},
urldate = {2021-10-06},
booktitle = {Proceedings of the 29th European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning (ESANN 2021)},
pages = {405-410},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
@conference{Atzeni2021,
title = { Modeling Edge Features with Deep Bayesian Graph Networks},
author = {Daniele Atzeni and Davide Bacciu and Federico Errica and Alessio Micheli},
doi = {10.1109/IJCNN52387.2021.9533430},
year = {2021},
date = {2021-07-18},
urldate = {2021-07-18},
booktitle = {Proceedings of the International Joint Conference on Neural Networks (IJCNN 2021)},
publisher = {IEEE},
organization = {IEEE},
abstract = {We propose an extension of the Contextual Graph Markov Model, a deep and probabilistic machine learning model for graphs, to model the distribution of edge features. Our approach is architectural, as we introduce an additional Bayesian network mapping edge features into discrete states to be used by the original model. In doing so, we are also able to build richer graph representations even in the absence of edge features, which is confirmed by the performance improvements on standard graph classification benchmarks. Moreover, we successfully test our proposal in a graph regression scenario where edge features are of fundamental importance, and we show that the learned edge representation provides substantial performance improvements against the original model on three link prediction tasks. By keeping the computational complexity linear in the number of edges, the proposed model is amenable to large-scale graph processing.},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
@conference{BacciuPoddaIJCNN2021,
title = {GraphGen-Redux: a Fast and Lightweight Recurrent Model for Labeled Graph Generation},
author = {Davide Bacciu and Marco Podda},
doi = {10.1109/IJCNN52387.2021.9533743},
year = {2021},
date = {2021-07-18},
urldate = {2021-07-18},
booktitle = {Proceedings of the International Joint Conference on Neural Networks (IJCNN 2021)},
organization = {IEEE},
abstract = {The problem of labeled graph generation is gaining attention in the Deep Learning community. The task is challenging due to the sparse and discrete nature of graph spaces. Several approaches have been proposed in the literature, most of which require to transform the graphs into sequences that encode their structure and labels and to learn the distribution of such sequences through an auto-regressive generative model. Among this family of approaches, we focus on the Graphgen model. The preprocessing phase of Graphgen transforms graphs into unique edge sequences called Depth-First Search (DFS) codes, such that two isomorphic graphs are assigned the same DFS code. Each element of a DFS code is associated with a graph edge: specifically, it is a quintuple comprising one node identifier for each of the two endpoints, their node labels, and the edge label. Graphgen learns to generate such sequences auto-regressively and models the probability of each component of the quintuple independently. While effective, the independence assumption made by the model is too loose to capture the complex label dependencies of real-world graphs precisely. By introducing a novel graph preprocessing approach, we are able to process the labeling information of both nodes and edges jointly. The corresponding model, which we term Graphgen-redux, improves upon the generative performances of Graphgen in a wide range of datasets of chemical and social graphs. In addition, it uses approximately 78% fewer parameters than the vanilla variant and requires 50% fewer epochs of training on average.},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
@conference{Errica2021,
title = {Graph Mixture Density Networks},
author = {Federico Errica and Davide Bacciu and Alessio Micheli},
url = {https://proceedings.mlr.press/v139/errica21a.html, PDF},
year = {2021},
date = {2021-07-18},
urldate = {2021-07-18},
booktitle = {Proceedings of the 38th International Conference on Machine Learning (ICML 2021)},
pages = {3025-3035},
publisher = {PMLR},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
@workshop{tomographyNeurips2020,
title = {Generative Tomography Reconstruction},
author = {Matteo Ronchetti and Davide Bacciu},
url = {https://arxiv.org/pdf/2010.14933.pdf, PDF},
year = {2020},
date = {2020-12-11},
urldate = {2020-12-11},
booktitle = {34th Conference on Neural Information Processing Systems (NeurIPS 2020), Workshop on Deep Learning and Inverse Problems},
abstract = {We propose an end-to-end differentiable architecture for tomography reconstruc-1tion that directly maps a noisy sinogram into a denoised reconstruction. Compared2to existing approaches our end-to-end architecture produces more accurate recon-3structions while using less parameters and time. We also propose a generative4model that, given a noisy sinogram, can sample realistic reconstructions. This5generative model can be used as prior inside an iterative process that, by tak-6ing into consideration the physical model, can reduce artifacts and errors in the7reconstructions.},
keywords = {},
pubstate = {published},
tppubtype = {workshop}
}
@conference{ecai2020,
title = { Learning a Latent Space of Style-Aware Music Representations by Adversarial Autoencoders},
author = {Andrea Valenti and Antonio Carta and Davide Bacciu},
url = {https://arxiv.org/abs/2001.05494},
year = {2020},
date = {2020-06-08},
booktitle = {Proceedings of the 24th European Conference on Artificial Intelligence (ECAI 2020)},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
@conference{aistats2020,
title = {A Deep Generative Model for Fragment-Based Molecule Generation},
author = {Marco Podda and Davide Bacciu and Alessio Micheli},
url = {https://arxiv.org/abs/2002.12826},
year = {2020},
date = {2020-06-03},
urldate = {2020-06-03},
booktitle = {Proceedings of the 23rd International Conference on Artificial Intelligence and Statistics (AISTATS 2020) },
abstract = {Molecule generation is a challenging open problem in cheminformatics. Currently, deep generative approaches addressing the challenge belong to two broad categories, differing in how molecules are represented. One approach encodes molecular graphs as strings of text, and learn their corresponding character-based language model. Another, more expressive, approach operates directly on the molecular graph. In this work, we address two limitations of the former: generation of invalid or duplicate molecules. To improve validity rates, we develop a language model for small molecular substructures called fragments, loosely inspired by the well-known paradigm of Fragment-Based Drug Design. In other words, we generate molecules fragment by fragment, instead of atom by atom. To improve uniqueness rates, we present a frequency-based clustering strategy that helps to generate molecules with infrequent fragments. We show experimentally that our model largely outperforms other language model-based competitors, reaching state-of-the-art performances typical of graph-based approaches. Moreover, generated molecules display molecular properties similar to those in the training sample, even in absence of explicit task-specific supervision.},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
@inbook{graphsBDDL2020,
title = {Deep Learning for Graphs},
author = {Davide Bacciu and Alessio Micheli},
editor = {Luca Oneto and Nicolo Navarin and Alessandro Sperduti and Davide Anguita
},
url = {https://link.springer.com/chapter/10.1007/978-3-030-43883-8_5},
doi = {10.1007/978-3-030-43883-8_5},
isbn = {978-3-030-43883-8},
year = {2020},
date = {2020-04-04},
booktitle = {Recent Trends in Learning From Data: Tutorials from the INNS Big Data and Deep Learning Conference (INNSBDDL2019)},
volume = {896},
pages = {99-127},
publisher = {Springer International Publishing},
series = {Studies in Computational Intelligence Series},
abstract = {We introduce an overview of methods for learning in structured domains covering foundational works developed within the last twenty years to deal with a whole range of complex data representations, including hierarchical structures, graphs and networks, and giving special attention to recent deep learning models for graphs. While we provide a general introduction to the field, we explicitly focus on the neural network paradigm showing how, across the years, these models have been extended to the adaptive processing of incrementally more complex classes of structured data. The ultimate aim is to show how to cope with the fundamental issue of learning adaptive representations for samples with varying size and topology.},
keywords = {},
pubstate = {published},
tppubtype = {inbook}
}
@article{neucompEsann19,
title = {Edge-based sequential graph generation with recurrent neural networks},
author = {Davide Bacciu and Alessio Micheli and Marco Podda},
url = {https://arxiv.org/abs/2002.00102v1},
year = {2019},
date = {2019-12-31},
journal = {Neurocomputing},
abstract = { Graph generation with Machine Learning is an open problem with applications in various research fields. In this work, we propose to cast the generative process of a graph into a sequential one, relying on a node ordering procedure. We use this sequential process to design a novel generative model composed of two recurrent neural networks that learn to predict the edges of graphs: the first network generates one endpoint of each edge, while the second network generates the other endpoint conditioned on the state of the first. We test our approach extensively on five different datasets, comparing with two well-known baselines coming from graph literature, and two recurrent approaches, one of which holds state of the art performances. Evaluation is conducted considering quantitative and qualitative characteristics of the generated samples. Results show that our approach is able to yield novel, and unique graphs originating from very different distributions, while retaining structural properties very similar to those in the training sample. Under the proposed evaluation framework, our approach is able to reach performances comparable to the current state of the art on the graph generation task. },
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@conference{esann19GraphGen,
title = {Graph generation by sequential edge prediction},
author = {Davide Bacciu and Alessio Micheli and Marco Podda},
editor = {Michel Verleysen},
url = {https://www.elen.ucl.ac.be/Proceedings/esann/esannpdf/es2019-107.pdf},
year = {2019},
date = {2019-04-24},
booktitle = {Proceedings of the European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning (ESANN'19)},
publisher = {i6doc.com},
address = {Louvain-la-Neuve, Belgium},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
@inbook{Bacciu2015,
title = {Probabilistic Modeling in Machine Learning},
author = {Davide Bacciu and Paulo J.G. Lisboa and Alessandro Sperduti and Thomas Villmann},
editor = {Janusz Kacprzyk and Witold Pedrycz},
url = {http://dx.doi.org/10.1007/978-3-662-43505-2_31},
doi = {10.1007/978-3-662-43505-2_31},
isbn = {978-3-662-43505-2},
year = {2015},
date = {2015-01-01},
urldate = {2015-01-01},
pages = {545--575},
publisher = {Springer Berlin Heidelberg},
address = {Berlin, Heidelberg},
keywords = {},
pubstate = {published},
tppubtype = {inbook}
}
@conference{11568_586070,
title = {Integrating bi-directional contexts in a generative kernel for trees},
author = {Bacciu Davide and Micheli Alessio and Sperduti Alessandro},
doi = {10.1109/IJCNN.2014.6889768},
year = {2014},
date = {2014-01-01},
urldate = {2014-01-01},
booktitle = {Neural Networks (IJCNN), 2014 International Joint Conference on},
pages = {4145--4151},
publisher = {IEEE},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
@conference{11568_665864,
title = {Modeling Bi-directional Tree Contexts by Generative Transductions},
author = {Bacciu Davide and Micheli Alessio and Sperduti Alessandro},
url = {http://dx.doi.org/10.1007/978-3-319-12637-1_68},
doi = {10.1007/978-3-319-12637-1_68},
year = {2014},
date = {2014-01-01},
booktitle = {Neural Information Processing},
journal = {LECTURE NOTES IN COMPUTER SCIENCE},
volume = {8834},
pages = {543--550},
publisher = {Springer International Publishing},
abstract = {We introduce an approach to integrate bi-directional contexts in a generative tree model by means of structured transductions. We show how this can be efficiently realized as the composition of a top-down and a bottom-up generative model for trees, that are trained independently within a circular encoding-decoding scheme. The resulting input-driven generative model is shown to capture information concerning bi-directional contexts within its state-space. An experimental evaluation using the Jaccard generative kernel for trees is presented, indicating that the approach can achieve state of the art performance on tree classification benchmarks.},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
@conference{11568_156516,
title = {A Generative Multiset Kernel for Structured Data},
author = {Bacciu Davide and Micheli Alessio and Sperduti Alessandro},
doi = {10.1007/978-3-642-33269-2_8},
year = {2012},
date = {2012-01-01},
urldate = {2012-01-01},
booktitle = {Artificial Neural Networks and Machine Learning - ICANN 2012 proceedings, Springer LNCS series},
journal = {LECTURE NOTES IN COMPUTER SCIENCE},
volume = {7552},
pages = {57--64},
publisher = {Springer-Verlag},
address = {BERLIN HEIDELBERG},
abstract = {The paper introduces a novel approach for defining efficient generative kernels for structured-data based on the concept of multisets and Jaccard similarity. The multiset feature-space allows to enhance the adaptive kernel with syntactic information on structure matching. The proposed approach is validated using an input-driven hidden Markov model for trees as generative model, but it is enough general to be straightforwardly applicable to any probabilistic latent variable model. The experimental evaluation shows that the proposed Jaccard kernel has a superior classification performance with respect to the Fisher Kernel, while consistently reducing the computational requirements.},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
@conference{11568_152836,
title = {Input-Output Hidden Markov Models for Trees},
author = {Bacciu Davide and Micheli Alessio and Sperduti Alessandro},
year = {2012},
date = {2012-01-01},
urldate = {2012-01-01},
booktitle = {ESANN 2012 - The 20th European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning - Proceedings},
pages = {25--30},
publisher = {Ciaco scrl - i6doc.com},
abstract = {The paper introduces an input-driven generative model for tree-structured data that extends the bottom-up hidden tree Markov model with non-homogenous transition and emission probabilities. The advantage of introducing an input-driven dynamics in structured-data pro- cessing is experimentally investigated. The results of this preliminary analysis suggest that input-driven models can capture more discrimina- tive structural information than non-input-driven approaches.},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
@conference{11568_145907,
title = {Adaptive Tree Kernel by Multinomial Generative Topographic Mapping},
author = {Bacciu Davide and Micheli Alessio and Sperduti Alessandro},
url = {http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=6033423&contentType=Conference+Publications&refinements%3D4294413850%26sortType%3Dasc_p_Sequence%26filter%3DAND%28p_IS_Number%3A6033131%29},
doi = {10.1109/IJCNN.2011.6033423},
year = {2011},
date = {2011-01-01},
urldate = {2011-01-01},
booktitle = {Proceedings of the International Joint Conference on Neural Networks},
pages = {1651--1658},
publisher = {IEEE},
address = {Piscataway (NJ)},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
@techreport{11568_254437,
title = {A Bottom-up Hidden Tree Markov Model},
author = {Bacciu Davide and Micheli Alessio and Sperduti Alessandro},
url = {http://compass2.di.unipi.it/TR/Files/TR-10-08.pdf.gz},
year = {2010},
date = {2010-04-01},
urldate = {2010-04-01},
volume = {TR-10-08},
number = {TR-10-08},
pages = {1--22},
institution = {Università di Pisa},
keywords = {},
pubstate = {published},
tppubtype = {techreport}
}
@conference{11568_142187,
title = {Bottom-Up Generative Modeling of Tree-Structured Data},
author = {Bacciu Davide and Micheli Alessio and Sperduti Alessandro},
doi = {10.1007/978-3-642-17537-4_80},
year = {2010},
date = {2010-01-01},
booktitle = {LNCS 6443: Neural Information Processing. Theory and Algorithms. Part I},
journal = {LECTURE NOTES IN COMPUTER SCIENCE},
volume = {6443},
pages = {660--668},
publisher = {Springer-Verlag},
address = {BERLIN HEIDELBERG},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
@conference{11568_465484,
title = {Patient stratification with competing risks by multivariate Fisher distance},
author = {Bacciu Davide and Jarman Ian H and Etchells Terence A and Lisboa Paulo J G},
doi = {10.1109/IJCNN.2009.5179077},
year = {2009},
date = {2009-01-01},
urldate = {2009-01-01},
booktitle = {2009 International Joint Conference on Neural Networks},
pages = {3453--3460},
publisher = {IEEE},
abstract = {Early characterization of patients with respect to their predicted response to treatment is a fundamental step towards the delivery of effective, personalized care. Starting from the results of a time-to-event model with competing risks using the framework of partial logistic artificial neural networks with automatic relevance determination (PLANNCR-ARD), we discuss an effective semi-supervised approach to patient stratification with application to Acute Myeloid Leukaemia (AML) data (n = 509) acquired prospectively by the GIMEMA consortium. Multiple prognostic indices provided by the survival model are exploited to build a metric based on the Fisher information matrix. Cluster number estimation is then performed in the Fisher-induced affine space, yielding to the discovery of a stratification of the patients into groups characterized by significantly different mortality risks following induction therapy in AML. The proposed model is shown to be able to cluster the input data, while promoting specificity of both target outcomes, namely Complete Remission (CR) and Induction Death (ID). This generic clustering methodology generates an affine transformation of the data space that is coherent with the prognostic information predicted by the PLANNCR-ARD model.},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
@phdthesis{11568_466874,
title = {A Perceptual Learning Model to Discover the Hierarchical Latent Structure of Image Collections},
author = { Bacciu Davide},
url = {http://e-theses.imtlucca.it/id/eprint/7},
doi = {10.6092/imtlucca/e-theses/7},
year = {2008},
date = {2008-01-01},
urldate = {2008-01-01},
publisher = {IMT Lucca},
abstract = {Biology has been an unparalleled source of inspiration for the work of researchers in several scientific and engineering fields including computer vision. The starting point of this thesis is the neurophysiological properties of the human early visual system, in particular, the cortical mechanism that mediates learning by exploiting information about stimuli repetition. Repetition has long been considered a fundamental correlate of skill acquisition andmemory formation in biological aswell as computational learning models. However, recent studies have shown that biological neural networks have differentways of exploiting repetition in forming memory maps. The thesis focuses on a perceptual learning mechanism called repetition suppression, which exploits the temporal distribution of neural activations to drive an efficient neural allocation for a set of stimuli. This explores the neurophysiological hypothesis that repetition suppression serves as an unsupervised perceptual learning mechanism that can drive efficient memory formation by reducing the overall size of stimuli representation while strengthening the responses of the most selective neurons. This interpretation of repetition is different from its traditional role in computational learning models mainly to induce convergence and reach training stability, without using this information to provide focus for the neural representations of the data. The first part of the thesis introduces a novel computational model with repetition suppression, which forms an unsupervised competitive systemtermed CoRe, for Competitive Repetition-suppression learning. The model is applied to generalproblems in the fields of computational intelligence and machine learning. Particular emphasis is placed on validating the model as an effective tool for the unsupervised exploration of bio-medical data. In particular, it is shown that the repetition suppression mechanism efficiently addresses the issues of automatically estimating the number of clusters within the data, as well as filtering noise and irrelevant input components in highly dimensional data, e.g. gene expression levels from DNA Microarrays. The CoRe model produces relevance estimates for the each covariate which is useful, for instance, to discover the best discriminating bio-markers. The description of the model includes a theoretical analysis using Huber’s robust statistics to show that the model is robust to outliers and noise in the data. The convergence properties of themodel also studied. It is shown that, besides its biological underpinning, the CoRe model has useful properties in terms of asymptotic behavior. By exploiting a kernel-based formulation for the CoRe learning error, a theoretically sound motivation is provided for the model’s ability to avoid local minima of its loss function. To do this a necessary and sufficient condition for global error minimization in vector quantization is generalized by extending it to distance metrics in generic Hilbert spaces. This leads to the derivation of a family of kernel-based algorithms that address the local minima issue of unsupervised vector quantization in a principled way. The experimental results show that the algorithm can achieve a consistent performance gain compared with state-of-the-art learning vector quantizers, while retaining a lower computational complexity (linear with respect to the dataset size). Bridging the gap between the low level representation of the visual content and the underlying high-level semantics is a major research issue of current interest. The second part of the thesis focuses on this problem by introducing a hierarchical and multi-resolution approach to visual content understanding. On a spatial level, CoRe learning is used to pool together the local visual patches by organizing them into perceptually meaningful intermediate structures. On the semantical level, it provides an extension of the probabilistic Latent Semantic Analysis (pLSA) model that allows discovery and organization of the visual topics into a hierarchy of aspects. The proposed hierarchical pLSA model is shown to effectively address the unsupervised discovery of relevant visual classes from pictorial collections, at the same time learning to segment the image regions containing the discovered classes. Furthermore, by drawing on a recent pLSA-based image annotation system, the hierarchical pLSA model is extended to process and representmulti-modal collections comprising textual and visual data. The results of the experimental evaluation show that the proposed model learns to attach textual labels (available only at the level of the whole image) to the discovered image regions, while increasing the precision/ recall performance with respect to flat, pLSA annotation model.},
keywords = {},
pubstate = {published},
tppubtype = {phdthesis}
}