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.
Simone, Lorenzo; Bacciu, Davide ECGAN: generative adversarial network for electrocardiography Conference Proceedings of Artificial Intelligence In Medicine 2023 (AIME 2023), 2023. Caro, Valerio De; Danzinger, Herbert; Gallicchio, Claudio; Könczöl, Clemens; Lomonaco, Vincenzo; Marmpena, Mina; Marpena, Mina; Politi, Sevasti; Veledar, Omar; Bacciu, Davide Prediction of Driver's Stress Affection in Simulated Autonomous Driving Scenarios Conference Proceedings of 2023 IEEE International Conference on Acoustics, Speech and Signal Processing, 2023. Bacciu, Davide; Errica, Federico; Gravina, Alessio; Madeddu, Lorenzo; Podda, Marco; Stilo, Giovanni Deep Graph Networks for Drug Repurposing with Multi-Protein Targets Journal Article In: IEEE Transactions on Emerging Topics in Computing, 2023, 2023. Ferrari, Elisa; Gargani, Luna; Barbieri, Greta; Ghiadoni, Lorenzo; Faita, Francesco; Bacciu, Davide A causal learning framework for the analysis and interpretation of COVID-19 clinical data Journal Article In: Plos One, vol. 17, no. 5, 2022. Bacciu, Davide; Morelli, Davide; Pandelea, Vlad Modeling Mood Polarity and Declaration Occurrence by Neural Temporal Point Processes Journal Article In: IEEE Transactions on Neural Networks and Learning Systems, pp. 1-8, 2022. Gravina, Alessio; Wilson, Jennifer L.; Bacciu, Davide; Grimes, Kevin J.; Priami, Corrado Controlling astrocyte-mediated synaptic pruning signals for schizophrenia drug repurposing with Deep Graph Networks Journal Article In: Plos Computational Biology, vol. 18, no. 5, 2022. Bacciu, Davide; Lisboa, Paulo J. G.; Vellido, Alfredo Deep Learning in Biology and Medicine Book World Scientific Publisher, 2022, ISBN: 978-1-80061-093-4. Resta, Michele; Monreale, Anna; Bacciu, Davide Occlusion-based Explanations in Deep Recurrent Models for Biomedical Signals Journal Article In: Entropy, vol. 23, no. 8, pp. 1064, 2021, (Special issue on Representation Learning). Ferrari, Elisa; Bacciu, Davide Addressing Fairness, Bias and Class Imbalance in Machine Learning: the FBI-loss Unpublished Online on Arxiv, 2021. Bontempi, Gianluca; Chavarriaga, Ricardo; Canck, Hans De; Girardi, Emanuela; Hoos, Holger; Kilbane-Dawe, Iarla; Ball, Tonio; Nowé, Ann; Sousa, Jose; Bacciu, Davide; Aldinucci, Marco; Domenico, Manlio De; Saffiotti, Alessandro; Maratea, Marco The CLAIRE COVID-19 initiative: approach, experiences and recommendations Journal Article In: Ethics and Information Technology, 2021. Michele Barsotti Andrea Valenti, Davide Bacciu; Ascari, Luca A Deep Classifier for Upper-Limbs Motor Anticipation Tasks in an Online BCI Setting Journal Article In: Bioengineering , 2021. Bacciu, Davide; Bertoncini, Gioele; Morelli, Davide Topographic mapping for quality inspection and intelligent filtering of smart-bracelet data Journal Article In: Neural Computing Applications, 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; Barsotti, Michele; Brondi, Raffaello; Bacciu, Davide; Ascari, Luca Proceedings of the 2020 IEEE International Conference on Systems, Man, and Cybernetics (SMC), IEEE, 2020. Podda, Marco; Micheli, Alessio; Bacciu, Davide; Milazzo, Paolo Biochemical Pathway Robustness Prediction with Graph Neural Networks Conference Proceedings of the European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning (ESANN'20), 2020. Ferrari, Elisa; Retico, Alessandra; Bacciu, Davide Measuring the effects of confounders in medical supervised classification problems: the Confounding Index (CI) Journal Article In: Artificial Intelligence in Medicine, vol. 103, 2020. Marco, Podda; Davide, Bacciu; Alessio, Micheli; Roberto, Bellu; Giulia, Placidi; Luigi, Gagliardi A machine learning approach to estimating preterm infants survival: development of the Preterm Infants Survival Assessment (PISA) predictor Journal Article In: Nature Scientific Reports, vol. 8, 2018. Davide, Bacciu; Michele, Colombo; Davide, Morelli; David, Plans Randomized neural networks for preference learning with physiological data Journal Article In: Neurocomputing, vol. 298, pp. 9-20, 2018. Davide, Bacciu; JG, Lisboa Paulo; D, Martin Jose; Ruxandra, Stoean; Alfredo, Vellido Bioinformatics and medicine in the era of deep learning Conference Proceedings of the European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning (ESANN'18), i6doc.com, Louvain-la-Neuve, Belgium, 2018, ISBN: 978-287587047-6. Filippo, Palumbo; Davide, La Rosa; Erina, Ferro; Davide, Bacciu; Claudio, Gallicchio; Alession, Micheli; Stefano, Chessa; Federico, Vozzi; Oberdan, Parodi Reliability and human factors in Ambient Assisted Living environments: The DOREMI case study Journal Article In: Journal of Reliable Intelligent Environments, vol. 3, no. 3, pp. 139–157, 2017, ISBN: 2199-4668. Davide, Bacciu; Michele, Colombo; Davide, Morelli; David, Plans ELM Preference Learning for Physiological Data Conference Proceedings of the European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning (ESANN'17), i6doc.com, Louvain-la-Neuve, Belgium, 2017, ISBN: 978-2-875870384. Davide, Bacciu; Stefano, Chessa; Claudio, Gallicchio; Alessio, Micheli; Erina, Ferro; Luigi, Fortunati; Filippo, Palumbo; Oberdan, Parodi; Federico, Vozzi; Sten, Hanke; Johannes, Kropf; Karl, Kreiner Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 9273, Springer Verlag, 2015. G, Lisboa Paulo J; H, Jarman Ian; A, Etchells Terence; J, Chambers Simon; Davide, Bacciu; Joe, Whittaker; M, Garibaldi Jon; Sandra, Ortega-Martorell; Alfredo, Vellido; O, Ellis Ian Discovering Hidden Pathways in Bioinformatics Conference Lecture Notes in Computer ScienceComputational Intelligence Methods for Bioinformatics and Biostatistics, vol. 7548, 2012. H, Jarman Ian; A, Etchells Terence; Davide, Bacciu; M, Garibaldi John; O, Ellis Ian; JG, Lisboa Paulo Clustering of protein expression data: a benchmark of statistical and neural approaches Journal Article In: Soft Computing-A Fusion of Foundations, Methodologies and Applications, vol. 15, no. 8, pp. 1459–1469, 2011, ISSN: 1432-7643. S, Fernandes Ana; Davide, Bacciu; H, Jarman Ian; A, Etchells Terence; M, Fonseca Jose; JG, Lisboa Paulo Different Methodologies for Patient Stratification Using Survival Data Conference Lecture Notes in Computer ScienceComputational Intelligence Methods for Bioinformatics and Biostatistics, vol. 6160, 2010. JG, Lisboa Paulo; H, Jarman Ian; A, Etchells Terence; Davide, Bacciu; M, Garibaldi John Model-based and model-free clustering: a case study of protein expression data for breast cancer Conference PROCEEDINGS OF THE 2009 UK WORKSHOP ON COMPUTATIONAL INTELLIGENCE, 2009. S, Fernandes Ana; Davide, Bacciu; H, Jarman Ian; A, Etchells Terence; M, Fonseca Jose; Lisboa, Paulo J G p-Health in Breast Oncology: A Framework for Predictive and Participatory e-Systems Conference 2009 Second International Conference on Developments in eSystems Engineering, IEEE, 2009. 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. Davide, BACCIU; Elia, BIGANZOLI; JG, LISBOA Paulo; Antonina, Starita Are Model-based Clustering and Neural Clustering Consistent? A Case Study from Bioinformatics Conference Proceedings of the 12th International Conference on Knowledge-Based and Intelligent Information & Engineering Systems (KES'08), vol. 5178, Springer, 2008. Davide, Bacciu; Antonina, Starita A Robust Bio-Inspired Clustering Algorithm for the Automatic Determination of Unknown Cluster Number Conference 2007 International Joint Conference on Neural Networks, IEEE, 2007. Davide, Bacciu; Alessio, Micheli; Antonina, Starita Feature-wise Competitive Repetition Suppression Learning for Gene Data Clustering and Feature Ranking Technical Report Università di Pisa 2007. Davide, BACCIU; Alessio, MICHELI; Antonina, STARITA Simultaneous clustering and feature ranking by competitive repetition suppression learning with application to gene data analysis Conference Proceedings of the Third International Conference on Computational Intelligence in Medicine and Healthcare (CIMED 2007), 2007. J, Cinkelj; M, Mihelj; Davide, Bacciu; M, Jurak; Eugenio, Guglielmelli; A, Toth; J, De Lafonteyne; J, Verschelde; S, Mazzoleni; J, Van Vaerenbergh; D, Ruijter S; M, Munih Assessment of stroke patients by whole-body isometric force-torque measurements II: software design of the ALLADIN Diagnostic Device Conference Proceedings of the 3rd European Medical and Biological Engineering Conference, vol. 1, IFMBE, 2005.@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{DeCaro2023,
title = {Prediction of Driver's Stress Affection in Simulated Autonomous Driving Scenarios},
author = {Valerio De Caro and Herbert Danzinger and Claudio Gallicchio and Clemens Könczöl and Vincenzo Lomonaco and Mina Marmpena and Mina Marpena and Sevasti Politi and Omar Veledar and Davide Bacciu},
year = {2023},
date = {2023-06-04},
urldate = {2023-06-04},
booktitle = {Proceedings of 2023 IEEE International Conference on Acoustics, Speech and Signal Processing},
abstract = {We investigate the task of predicting stress affection from physiological data of users experiencing simulations of autonomous driving. We approach this task on two levels of granularity, depending on whether the prediction is performed at end of the simulation, or along the simulation. In the former, denoted as coarse-grained prediction, we employed Decision Trees. In the latter, denoted as fine-grained prediction, we employed Echo State Networks, a Recurrent Neural Network
that allows efficient learning from temporal data and hence is
suitable for pervasive environments. We conduct experiments on a private dataset of physiological data from people participating in multiple driving scenarios simulating different stressful events. The results show that the proposed model is capable of detecting conditions of event-related cognitive stress proving, the existence of a correlation between stressful events and the physiological data.},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
that allows efficient learning from temporal data and hence is
suitable for pervasive environments. We conduct experiments on a private dataset of physiological data from people participating in multiple driving scenarios simulating different stressful events. The results show that the proposed model is capable of detecting conditions of event-related cognitive stress proving, the existence of a correlation between stressful events and the physiological data.@article{Bacciu2023b,
title = {Deep Graph Networks for Drug Repurposing with Multi-Protein Targets},
author = {Davide Bacciu and Federico Errica and Alessio Gravina and Lorenzo Madeddu and Marco Podda and Giovanni Stilo},
doi = {10.1109/TETC.2023.3238963},
year = {2023},
date = {2023-02-01},
urldate = {2023-02-01},
journal = {IEEE Transactions on Emerging Topics in Computing, 2023},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{DBLP:journals/corr/abs-2105-06998,
title = {A causal learning framework for the analysis and interpretation of COVID-19 clinical data},
author = {Elisa Ferrari and Luna Gargani and Greta Barbieri and Lorenzo Ghiadoni and Francesco Faita and Davide Bacciu},
url = {https://arxiv.org/abs/2105.06998, Arxiv},
doi = {doi.org/10.1371/journal.pone.0268327},
year = {2022},
date = {2022-05-19},
urldate = {2022-05-19},
journal = {Plos One},
volume = {17},
number = {5},
abstract = {We present a workflow for clinical data analysis that relies on Bayesian Structure Learning (BSL), an unsupervised learning approach, robust to noise and biases, that allows to incorporate prior medical knowledge into the learning process and that provides explainable results in the form of a graph showing the causal connections among the analyzed features. The workflow consists in a multi-step approach that goes from identifying the main causes of patient's outcome through BSL, to the realization of a tool suitable for clinical practice, based on a Binary Decision Tree (BDT), to recognize patients at high-risk with information available already at hospital admission time. We evaluate our approach on a feature-rich COVID-19 dataset, showing that the proposed framework provides a schematic overview of the multi-factorial processes that jointly contribute to the outcome. We discuss how these computational findings are confirmed by current understanding of the COVID-19 pathogenesis. Further, our approach yields to a highly interpretable tool correctly predicting the outcome of 85% of subjects based exclusively on 3 features: age, a previous history of chronic obstructive pulmonary disease and the PaO2/FiO2 ratio at the time of arrival to the hospital. The inclusion of additional information from 4 routine blood tests (Creatinine, Glucose, pO2 and Sodium) increases predictive accuracy to 94.5%. },
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{pandelea2022,
title = {Modeling Mood Polarity and Declaration Occurrence by Neural Temporal Point Processes},
author = {Davide Bacciu and Davide Morelli and Vlad Pandelea},
doi = {10.1109/TNNLS.2022.3172871},
year = {2022},
date = {2022-05-13},
urldate = {2022-05-13},
journal = {IEEE Transactions on Neural Networks and Learning Systems},
pages = {1-8},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Gravina2022,
title = {Controlling astrocyte-mediated synaptic pruning signals for schizophrenia drug repurposing with Deep Graph Networks},
author = {Alessio Gravina and Jennifer L. Wilson and Davide Bacciu and Kevin J. Grimes and Corrado Priami},
url = {https://www.biorxiv.org/content/10.1101/2021.10.07.463459v1, BioArxiv},
doi = {doi.org/10.1371/journal.pcbi.1009531},
year = {2022},
date = {2022-04-01},
urldate = {2022-04-01},
journal = {Plos Computational Biology},
volume = {18},
number = {5},
abstract = {Schizophrenia is a debilitating psychiatric disorder, leading to both physical and social morbidity. Worldwide 1% of the population is struggling with the disease, with 100,000 new cases annually only in the United States. Despite its importance, the goal of finding effective treatments for schizophrenia remains a challenging task, and previous work conducted expensive large-scale phenotypic screens. This work investigates the benefits of Machine Learning for graphs to optimize drug phenotypic screens and predict compounds that mitigate abnormal brain reduction induced by excessive glial phagocytic activity in schizophrenia subjects. Given a compound and its concentration as input, we propose a method that predicts a score associated with three possible compound effects, ie reduce, increase, or not influence phagocytosis. We leverage a high-throughput screening to prove experimentally that our method achieves good generalization capabilities. The screening involves 2218 compounds at five different concentrations. Then, we analyze the usability of our approach in a practical setting, ie prioritizing the selection of compounds in the SWEETLEAD library. We provide a list of 64 compounds from the library that have the most potential clinical utility for glial phagocytosis mitigation. Lastly, we propose a novel approach to computationally validate their utility as possible therapies for schizophrenia.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@book{BacciuBook2022,
title = {Deep Learning in Biology and Medicine},
author = {Davide Bacciu and Paulo J. G. Lisboa and Alfredo Vellido},
doi = {doi.org/10.1142/q0322 },
isbn = {978-1-80061-093-4},
year = {2022},
date = {2022-02-01},
urldate = {2022-02-01},
publisher = {World Scientific Publisher},
abstract = {Biology, medicine and biochemistry have become data-centric fields for which Deep Learning methods are delivering groundbreaking results. Addressing high impact challenges, Deep Learning in Biology and Medicine provides an accessible and organic collection of Deep Learning essays on bioinformatics and medicine. It caters for a wide readership, ranging from machine learning practitioners and data scientists seeking methodological knowledge to address biomedical applications, to life science specialists in search of a gentle reference for advanced data analytics.
With contributions from internationally renowned experts, the book covers foundational methodologies in a wide spectrum of life sciences applications, including electronic health record processing, diagnostic imaging, text processing, as well as omics-data processing. This survey of consolidated problems is complemented by a selection of advanced applications, including cheminformatics and biomedical interaction network analysis. A modern and mindful approach to the use of data-driven methodologies in the life sciences also requires careful consideration of the associated societal, ethical, legal and transparency challenges, which are covered in the concluding chapters of this book.},
keywords = {},
pubstate = {published},
tppubtype = {book}
}
With contributions from internationally renowned experts, the book covers foundational methodologies in a wide spectrum of life sciences applications, including electronic health record processing, diagnostic imaging, text processing, as well as omics-data processing. This survey of consolidated problems is complemented by a selection of advanced applications, including cheminformatics and biomedical interaction network analysis. A modern and mindful approach to the use of data-driven methodologies in the life sciences also requires careful consideration of the associated societal, ethical, legal and transparency challenges, which are covered in the concluding chapters of this book.@article{Resta2021,
title = { Occlusion-based Explanations in Deep Recurrent Models for Biomedical Signals },
author = {Michele Resta and Anna Monreale and Davide Bacciu},
editor = {Fabio Aiolli and Mirko Polato},
doi = {10.3390/e23081064},
year = {2021},
date = {2021-09-01},
urldate = {2021-09-01},
journal = {Entropy},
volume = {23},
number = {8},
pages = {1064},
abstract = { The biomedical field is characterized by an ever-increasing production of sequential data, which often come under the form of biosignals capturing the time-evolution of physiological processes, such as blood pressure and brain activity. This has motivated a large body of research dealing with the development of machine learning techniques for the predictive analysis of such biosignals. Unfortunately, in high-stakes decision making, such as clinical diagnosis, the opacity of machine learning models becomes a crucial aspect to be addressed in order to increase the trust and adoption of AI technology. In this paper we propose a model agnostic explanation method, based on occlusion, enabling the learning of the input influence on the model predictions. We specifically target problems involving the predictive analysis of time-series data and the models which are typically used to deal with data of such nature, i.e. recurrent neural networks. Our approach is able to provide two different kinds of explanations: one suitable for technical experts, who need to verify the quality and correctness of machine learning models, and one suited to physicians, who need to understand the rationale underlying the prediction to take aware decisions. A wide experimentation on different physiological data demonstrate the effectiveness of our approach, both in classification and regression tasks. },
note = {Special issue on Representation Learning},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@unpublished{Ferrari2021,
title = {Addressing Fairness, Bias and Class Imbalance in Machine Learning: the FBI-loss},
author = {Elisa Ferrari and Davide Bacciu},
url = {https://arxiv.org/abs/2105.06345, Arxiv},
year = {2021},
date = {2021-05-13},
urldate = {2021-05-13},
abstract = {Resilience to class imbalance and confounding biases, together with the assurance of fairness guarantees are highly desirable properties of autonomous decision-making systems with real-life impact. Many different targeted solutions have been proposed to address separately these three problems, however a unifying perspective seems to be missing. With this work, we provide a general formalization, showing that they are different expressions of unbalance. Following this intuition, we formulate a unified loss correction to address issues related to Fairness, Biases and Imbalances (FBI-loss). The correction capabilities of the proposed approach are assessed on three real-world benchmarks, each associated to one of the issues under consideration, and on a family of synthetic data in order to better investigate the effectiveness of our loss on tasks with different complexities. The empirical results highlight that the flexible formulation of the FBI-loss leads also to competitive performances with respect to literature solutions specialised for the single problems.},
howpublished = {Online on Arxiv},
keywords = {},
pubstate = {published},
tppubtype = {unpublished}
}
@article{Bontempi2021,
title = {The CLAIRE COVID-19 initiative: approach, experiences and recommendations},
author = {Gianluca Bontempi and Ricardo Chavarriaga and Hans De Canck and Emanuela Girardi and Holger Hoos and Iarla Kilbane-Dawe and Tonio Ball and Ann Nowé and Jose Sousa and Davide Bacciu and Marco Aldinucci and Manlio De Domenico and Alessandro Saffiotti and Marco Maratea},
doi = {10.1007/s10676-020-09567-7},
year = {2021},
date = {2021-02-09},
journal = {Ethics and Information Technology},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{Valenti2021,
title = {A Deep Classifier for Upper-Limbs Motor Anticipation Tasks in an Online BCI Setting},
author = {Andrea Valenti, Michele Barsotti, Davide Bacciu and Luca Ascari
},
url = {https://www.mdpi.com/2306-5354/8/2/21, Open Access },
doi = {10.3390/bioengineering8020021},
year = {2021},
date = {2021-02-05},
urldate = {2021-02-05},
journal = {Bioengineering },
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{BacciuNCA2020,
title = {Topographic mapping for quality inspection and intelligent filtering of smart-bracelet data},
author = {Davide Bacciu and Gioele Bertoncini and Davide Morelli},
doi = {10.1007/s00521-020-05600-4},
year = {2021},
date = {2021-01-04},
urldate = {2021-01-04},
journal = {Neural Computing Applications},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@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{smc2020,
title = {ROS-Neuro Integration of Deep Convolutional Autoencoders for EEG Signal Compression in Real-time BCIs},
author = {Andrea Valenti and Michele Barsotti and Raffaello Brondi and Davide Bacciu and Luca Ascari},
url = {https://arxiv.org/abs/2008.13485, Arxiv},
year = {2020},
date = {2020-10-11},
urldate = {2020-10-11},
booktitle = {Proceedings of the 2020 IEEE International Conference on Systems, Man, and Cybernetics (SMC)},
publisher = {IEEE},
abstract = { Typical EEG-based BCI applications require the computation of complex functions over the noisy EEG channels to be carried out in an efficient way. Deep learning algorithms are capable of learning flexible nonlinear functions directly from data, and their constant processing latency is perfect for their deployment into online BCI systems. However, it is crucial for the jitter of the processing system to be as low as possible, in order to avoid unpredictable behaviour that can ruin the system's overall usability. In this paper, we present a novel encoding method, based on on deep convolutional autoencoders, that is able to perform efficient compression of the raw EEG inputs. We deploy our model in a ROS-Neuro node, thus making it suitable for the integration in ROS-based BCI and robotic systems in real world scenarios. The experimental results show that our system is capable to generate meaningful compressed encoding preserving to original information contained in the raw input. They also show that the ROS-Neuro node is able to produce such encodings at a steady rate, with minimal jitter. We believe that our system can represent an important step towards the development of an effective BCI processing pipeline fully standardized in ROS-Neuro framework. },
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
@conference{esann20Podda,
title = { Biochemical Pathway Robustness Prediction with Graph Neural Networks },
author = {Marco Podda and Alessio Micheli and Davide Bacciu and Paolo Milazzo},
editor = {Michel Verleysen},
year = {2020},
date = {2020-04-21},
booktitle = {Proceedings of the European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning (ESANN'20)},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
@article{aime20Confound,
title = {Measuring the effects of confounders in medical supervised classification problems: the Confounding Index (CI)},
author = {Elisa Ferrari and Alessandra Retico and Davide Bacciu},
url = {https://arxiv.org/abs/1905.08871},
doi = {10.1016/j.artmed.2020.101804},
year = {2020},
date = {2020-03-01},
journal = {Artificial Intelligence in Medicine},
volume = {103},
abstract = {Over the years, there has been growing interest in using Machine Learning techniques for biomedical data processing. When tackling these tasks, one needs to bear in mind that biomedical data depends on a variety of characteristics, such as demographic aspects (age, gender, etc) or the acquisition technology, which might be unrelated with the target of the analysis. In supervised tasks, failing to match the ground truth targets with respect to such characteristics, called confounders, may lead to very misleading estimates of the predictive performance. Many strategies have been proposed to handle confounders, ranging from data selection, to normalization techniques, up to the use of training algorithm for learning with imbalanced data. However, all these solutions require the confounders to be known a priori. To this aim, we introduce a novel index that is able to measure the confounding effect of a data attribute in a bias-agnostic way. This index can be used to quantitatively compare the confounding effects of different variables and to inform correction methods such as normalization procedures or ad-hoc-prepared learning algorithms. The effectiveness of this index is validated on both simulated data and real-world neuroimaging data. },
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{naturescirep2018,
title = {A machine learning approach to estimating preterm infants survival: development of the Preterm Infants Survival Assessment (PISA) predictor},
author = {Podda Marco and Bacciu Davide and Micheli Alessio and Bellu Roberto and Placidi Giulia and Gagliardi Luigi },
url = {https://doi.org/10.1038/s41598-018-31920-6},
doi = {10.1038/s41598-018-31920-6},
year = {2018},
date = {2018-09-13},
urldate = {2018-09-13},
journal = {Nature Scientific Reports},
volume = {8},
abstract = {Estimation of mortality risk of very preterm neonates is carried out in clinical and research settings. We aimed at elaborating a prediction tool using machine learning methods. We developed models on a cohort of 23747 neonates <30 weeks gestational age, or <1501 g birth weight, enrolled in the Italian Neonatal Network in 2008–2014 (development set), using 12 easily collected perinatal variables. We used a cohort from 2015–2016 (N = 5810) as a test set. Among several machine learning methods we chose artificial Neural Networks (NN). The resulting predictor was compared with logistic regression models. In the test cohort, NN had a slightly better discrimination than logistic regression (P < 0.002). The differences were greater in subgroups of neonates (at various gestational age or birth weight intervals, singletons). Using a cutoff of death probability of 0.5, logistic regression misclassified 67/5810 neonates (1.2 percent) more than NN. In conclusion our study – the largest published so far – shows that even in this very simplified scenario, using only limited information available up to 5 minutes after birth, a NN approach had a small but significant advantage over current approaches. The software implementing the predictor is made freely available to the community.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@article{neurocomp2017,
title = {Randomized neural networks for preference learning with physiological data},
author = {Bacciu Davide and Colombo Michele and Morelli Davide and Plans David},
editor = {Fabio Aiolli and Luca Oneto and Michael Biehl },
url = {https://authors.elsevier.com/a/1Wxbz_L2Otpsb3},
doi = {10.1016/j.neucom.2017.11.070},
year = {2018},
date = {2018-07-12},
journal = {Neurocomputing},
volume = {298},
pages = {9-20},
abstract = {The paper discusses the use of randomized neural networks to learn a complete ordering between samples of heart-rate variability data by relying solely on partial and subject-dependent information concerning pairwise relations between samples. We confront two approaches, i.e. Extreme Learning Machines and Echo State Networks, assessing the effectiveness in exploiting hand-engineered heart-rate variability features versus using raw beat-to-beat sequential data. Additionally, we introduce a weight sharing architecture and a preference learning error function whose performance is compared with a standard architecture realizing pairwise ranking as a binary-classification task. The models are evaluated on real-world data from a mobile application realizing a guided breathing exercise, using a dataset of over 54K exercising sessions. Results show how a randomized neural model processing information in its raw sequential form can outperform its vectorial counterpart, increasing accuracy in predicting the correct sample ordering by about 20%. Further, the experiments highlight the importance of using weight sharing architectures to learn smooth and generalizable complete orders induced by the preference relation.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@conference{esann2018Tut,
title = {Bioinformatics and medicine in the era of deep learning},
author = {Bacciu Davide and Lisboa Paulo JG and Martin Jose D and Stoean Ruxandra and Vellido Alfredo},
editor = {Michel Verleysen},
url = {http://arxiv.org/abs/1802.09791},
isbn = {978-287587047-6},
year = {2018},
date = {2018-04-26},
urldate = {2018-04-26},
booktitle = {Proceedings of the European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning (ESANN'18)},
pages = {345-354},
publisher = {i6doc.com},
address = {Louvain-la-Neuve, Belgium},
abstract = {Many of the current scientific advances in the life sciences have their origin in the intensive use of data for knowledge discovery. In no area this is so clear as in bioinformatics, led by technological breakthroughs in data acquisition technologies. It has been argued that bioinformatics could quickly become the field of research generating the largest data repositories, beating other data-intensive areas such as high-energy physics or astroinformatics. Over the last decade, deep learning has become a disruptive advance in machine learning, giving new live to the long-standing connectionist paradigm in artificial intelligence. Deep learning methods are ideally suited to large-scale data and, therefore, they should be ideally suited to knowledge discovery in bioinformatics and biomedicine at large. In this brief paper, we review key aspects of the application of deep learning in bioinformatics and medicine, drawing from the themes covered by the contributions to an ESANN 2018 special session devoted to this topic.},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
@article{jrie2017,
title = {Reliability and human factors in Ambient Assisted Living environments: The DOREMI case study},
author = {Palumbo Filippo and La Rosa Davide and Ferro Erina and Bacciu Davide and Gallicchio Claudio and Micheli Alession and Chessa Stefano and Vozzi Federico and Parodi Oberdan},
doi = {10.1007/s40860-017-0042-1},
isbn = {2199-4668},
year = {2017},
date = {2017-06-17},
journal = {Journal of Reliable Intelligent Environments},
volume = {3},
number = {3},
pages = {139–157},
publisher = {Springer},
abstract = {Malnutrition, sedentariness, and cognitive decline in elderly people represent the target areas addressed by the DOREMI project. It aimed at developing a systemic solution for elderly, able to prolong their functional and cognitive capacity by empowering, stimulating, and unobtrusively monitoring the daily activities according to well-defined “Active Ageing” life-style protocols. Besides the key features of DOREMI in terms of technological and medical protocol solutions, this work is focused on the analysis of the impact of such a solution on the daily life of users and how the users’ behaviour modifies the expected results of the system in a long-term perspective. To this end, we analyse the reliability of the whole system in terms of human factors and their effects on the reliability requirements identified before starting the experimentation in the pilot sites. After giving an overview of the technological solutions we adopted in the project, this paper concentrates on the activities conducted during the two pilot site studies (32 test sites across UK and Italy), the users’ experience of the entire system, and how human factors influenced its overall reliability.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@conference{esann2017,
title = {ELM Preference Learning for Physiological Data},
author = {Bacciu Davide and Colombo Michele and Morelli Davide and Plans David},
editor = {Michel Verleysen},
isbn = {978-2-875870384},
year = {2017},
date = {2017-04-28},
urldate = {2017-04-28},
booktitle = {Proceedings of the European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning (ESANN'17)},
pages = {99-104},
publisher = {i6doc.com},
address = {Louvain-la-Neuve, Belgium},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
@conference{11568_775269,
title = {Smart environments and context-awareness for lifestyle management in a healthy active ageing framework},
author = {Bacciu Davide and Chessa Stefano and Gallicchio Claudio and Micheli Alessio and Ferro Erina and Fortunati Luigi and Palumbo Filippo and Parodi Oberdan and Vozzi Federico and Hanke Sten and Kropf Johannes and Kreiner Karl},
url = {http://springerlink.com/content/0302-9743/copyright/2005/},
doi = {10.1007/978-3-319-23485-4_6},
year = {2015},
date = {2015-01-01},
booktitle = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
volume = {9273},
pages = {54--66},
publisher = {Springer Verlag},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
@conference{11568_465481,
title = {Discovering Hidden Pathways in Bioinformatics},
author = {Lisboa Paulo J G and Jarman Ian H and Etchells Terence A and Chambers Simon J and Bacciu Davide and Whittaker Joe and Garibaldi Jon M and Ortega-Martorell Sandra and Vellido Alfredo and Ellis Ian O},
doi = {10.1007/978-3-642-35686-5_5},
year = {2012},
date = {2012-01-01},
booktitle = {Lecture Notes in Computer ScienceComputational Intelligence Methods for Bioinformatics and Biostatistics},
journal = {LECTURE NOTES IN COMPUTER SCIENCE},
volume = {7548},
pages = {49--60},
abstract = {The elucidation of biological networks regulating the metabolic basis of disease is critical for understanding disease progression and in identifying therapeutic targets. In molecular biology, this process often starts by clustering expression profiles which are candidates for disease phenotypes. However, each cluster may comprise several overlapping processes that are active in the cluster. This paper outlines empirical results using methods for blind source separation to map the pathways of biomarkers driving independent, hidden processes that underpin the clusters. The method is applied to a protein expression data set measured in tissue from breast cancer patients (n=1,076)},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
@article{soco2011,
title = {Clustering of protein expression data: a benchmark of statistical and neural approaches},
author = {Jarman Ian H and Etchells Terence A and Bacciu Davide and Garibaldi John M and Ellis Ian O and Lisboa Paulo JG},
url = {http://dx.doi.org/10.1007/s00500-010-0596-9},
doi = {10.1007/s00500-010-0596-9},
issn = {1432-7643},
year = {2011},
date = {2011-01-01},
journal = {Soft Computing-A Fusion of Foundations, Methodologies and Applications},
volume = {15},
number = {8},
pages = {1459--1469},
publisher = {Springer},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
@conference{11568_465483,
title = {Different Methodologies for Patient Stratification Using Survival Data},
author = {Fernandes Ana S and Bacciu Davide and Jarman Ian H and Etchells Terence A and Fonseca Jose M and Lisboa Paulo JG},
doi = {10.1007/978-3-642-14571-1_21},
year = {2010},
date = {2010-01-01},
booktitle = {Lecture Notes in Computer ScienceComputational Intelligence Methods for Bioinformatics and Biostatistics},
journal = {LECTURE NOTES IN COMPUTER SCIENCE},
volume = {6160},
pages = {276--290},
abstract = {Clinical characterization of breast cancer patients related to their risk and profiles is an important part for making their correct prognostic assessments. This paper first proposes a prognostic index obtained when it is applied a flexible non-linear time-to-event model and compares it to a widely used linear survival estimator. This index underpins different stratification methodologies including informed clustering utilising the principle of learning metrics, regression trees and recursive application of the log-rank test. Missing data issue was overcome using multiple imputation, which was applied to a neural network model of survival fitted to a data set for breast cancer (n=743). It was found the three methodologies broadly agree, having however important differences.},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
@conference{11568_466869,
title = {Model-based and model-free clustering: a case study of protein expression data for breast cancer},
author = {Lisboa Paulo JG and Jarman Ian H and Etchells Terence A and Bacciu Davide and Garibaldi John M},
year = {2009},
date = {2009-01-01},
booktitle = {PROCEEDINGS OF THE 2009 UK WORKSHOP ON COMPUTATIONAL INTELLIGENCE},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
@conference{11568_465485,
title = {p-Health in Breast Oncology: A Framework for Predictive and Participatory e-Systems},
author = { Fernandes Ana S and Bacciu Davide and Jarman Ian H and Etchells Terence A and Fonseca Jose M and Paulo J G Lisboa},
doi = {10.1109/DeSE.2009.68},
year = {2009},
date = {2009-01-01},
booktitle = {2009 Second International Conference on Developments in eSystems Engineering},
pages = {123--129},
publisher = {IEEE},
abstract = {Maintaining the financial sustainability of healthcare provision makes developments in e-Systems of the utmost priority in healthcare. In particular, it leads to a radical review of healthcare delivery for the future as personalised, preventive, predictive and participatory, or p-Health. It is a vision that places e-Systems at the core of healthcare delivery, in contrast to current practice. This view of the demands of the 21st century sets an agenda that builds upon advances in engineering devices and computing infrastructure, but also computational intelligence and new models for communication between healthcare providers and the public. This paper gives an overview of p-Health with reference to decision support in breast cancer.},
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}
}
@conference{11568_465487,
title = {Are Model-based Clustering and Neural Clustering Consistent? A Case Study from Bioinformatics},
author = {BACCIU Davide and BIGANZOLI Elia and LISBOA Paulo JG and Starita Antonina},
doi = {10.1007/978-3-540-85565-1-23},
year = {2008},
date = {2008-01-01},
booktitle = {Proceedings of the 12th International Conference on Knowledge-Based and Intelligent Information & Engineering Systems (KES'08)},
journal = {LECTURE NOTES IN COMPUTER SCIENCE},
volume = {5178},
pages = {181--188},
publisher = {Springer},
abstract = {A novel neural network clustering algorithm, CoRe, is benchmarked against previously published results on a breast cancer data set and applying the method of Partition Around Medoids (PAM). The data serve to compare the samples partitions obtained with the neural network, PAM and model-based algorithms, namely Gaussian Mixture Model (GMM), Variational Bayesian Gaussian Mixture (VBG) and Variational Bayesian Mixtures with Splitting (VBS). It is found that CoRe, on the one hand, agrees with the previously published partitions; on the other hand, it supports the existence of a supplementary cluster that we hypothesize to be an additional tumor subgroup with respect to those previously identified by PAM},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
@conference{11568_466670,
title = {A Robust Bio-Inspired Clustering Algorithm for the Automatic Determination of Unknown Cluster Number},
author = {Bacciu Davide and Starita Antonina },
doi = {10.1109/IJCNN.2007.4371148},
year = {2007},
date = {2007-01-01},
urldate = {2007-01-01},
booktitle = {2007 International Joint Conference on Neural Networks},
pages = {1314--1319},
publisher = {IEEE},
abstract = {The paper introduces a robust clustering algorithm that can automatically determine the unknown cluster number from noisy data without any a-priori information. We show how our clustering algorithm can be derived from a general learning theory, named CoRe learning, that models a cortical memory mechanism called repetition suppression. Moreover, we describe CoRe clustering relationships with Rival Penalized Competitive Learning (RPCL), showing how CoRe extends this model by strengthening the rival penalization estimation by means of robust loss functions. Finally, we present the results of simulations concerning the unsupervised segmentation of noisy images.},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
@techreport{11568_255939,
title = {Feature-wise Competitive Repetition Suppression Learning for Gene Data Clustering and Feature Ranking},
author = {Bacciu Davide and Micheli Alessio and Starita Antonina},
url = {http://compass2.di.unipi.it/TR/Files/TR-07-04.pdf.gz},
year = {2007},
date = {2007-01-01},
urldate = {2007-01-01},
volume = {TR-07-04},
pages = {1--14},
institution = {Università di Pisa},
keywords = {},
pubstate = {published},
tppubtype = {techreport}
}
@conference{11568_116977,
title = {Simultaneous clustering and feature ranking by competitive repetition suppression learning with application to gene data analysis},
author = {BACCIU Davide and MICHELI Alessio and STARITA Antonina},
year = {2007},
date = {2007-01-01},
booktitle = {Proceedings of the Third International Conference on Computational Intelligence in Medicine and Healthcare (CIMED 2007)},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
@conference{11568_466877,
title = {Assessment of stroke patients by whole-body isometric force-torque measurements II: software design of the ALLADIN Diagnostic Device},
author = {Cinkelj J and Mihelj M and Bacciu Davide and Jurak M and Guglielmelli Eugenio and Toth A and De Lafonteyne J and Verschelde J and Mazzoleni S and Van Vaerenbergh J and Ruijter S D and Munih M },
year = {2005},
date = {2005-01-01},
booktitle = {Proceedings of the 3rd European Medical and Biological Engineering Conference},
journal = {IFMBE PROCEEDINGS (CD)},
volume = {1},
publisher = {IFMBE},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}