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Understanding Pooling in Graph Neural Networks [article]

Daniele Grattarola, Daniele Zambon, Filippo Maria Bianchi, Cesare Alippi
2021 arXiv   pre-print
Inspired by the conventional pooling layers in convolutional neural networks, many recent works in the field of graph machine learning have introduced pooling operators to reduce the size of graphs. The great variety in the literature stems from the many possible strategies for coarsening a graph, which may depend on different assumptions on the graph structure or the specific downstream task. In this paper we propose a formal characterization of graph pooling based on three main operations,
more » ... led selection, reduction, and connection, with the goal of unifying the literature under a common framework. Following this formalization, we introduce a taxonomy of pooling operators and categorize more than thirty pooling methods proposed in recent literature. We propose criteria to evaluate the performance of a pooling operator and use them to investigate and contrast the behavior of different classes of the taxonomy on a variety of tasks.
arXiv:2110.05292v1 fatcat:dgbtrxwndzh4pcvbyrpaamqmhu

Dipotassium dialuminium cyclooctaphosphate

Abdelghani Oudahmane, Daniel Avignant, Daniel Zambon
2010 Acta Crystallographica Section E  
E66, i49-i50 [doi:10.1107/S1600536810020751] Dipotassium dialuminium cyclooctaphosphate Abdelghani Oudahmane, Daniel Avignant and Daniel Zambon S1.  ... 
doi:10.1107/s1600536810020751 pmid:21587666 pmcid:PMC3007075 fatcat:d76wmftjyrdspd45py4bnwf7xa

Lutetium(III) cyclotetraphosphate

Aïcha Mbarek, Mohieddine Fourati, Daniel Zambon, Daniel Avignant
2010 Acta Crystallographica Section E  
E66, i46 [https://doi.org/10.1107/S1600536810016363] Lutetium(III) cyclotetraphosphate Aïcha Mbarek, Mohieddine Fourati, Daniel Zambon and Daniel Avignant A III element (.3. symmetry) are in general  ... 
doi:10.1107/s1600536810016363 pmid:21579264 pmcid:PMC2979408 fatcat:ze52npeka5ewlgzdiqlsrf5xvy

KPr(PO3)4

Abdelghani Oudahmane, Mohamed Daoud, Boumediene Tanouti, Daniel Avignant, Daniel Zambon
2010 Acta Crystallographica Section E  
Key indicators: single-crystal X-ray study; T = 296 K; mean (P-O) = 0.001 Å; R factor = 0.018; wR factor = 0.043; data-to-parameter ratio = 82.0. Single crystals of the title compound, potassium praseodymium(III) polyphosphate, were obtained by solid-state reaction. The monoclinic non-centrosymmetric structure is isotypic with all other KLn(PO 3 ) 4 analogues from Ln = La to Er, inclusive. The crystal structure of these long-chain polyphosphates is built up from infinite crenelated
more » ... chains of corner-sharing PO 4 tetrahedra with a repeating unit of four tetrahedra. These chains, running along [100], are arranged in a pseudo-tetragonal rod packing and are further linked by isolated PrO 8 square antiprisms [Pr-O = 2.3787 (9)-2.5091 (8) Å ], forming a three-dimensional framework. The K + ions reside in channels parallel to [010] and exhibit a highly distorted coordination sphere by eight O atoms at distances ranging from 2.7908 (9) to 3.1924 (11) Å . inorganic compounds i60 Oudahmane et al. KPr(PO3) 4 Acta Cryst. (2010). E66, i59-i60 supporting information sup-1 Acta Cryst. (2010). E66, i59-i60 supporting information Acta Cryst. (2010). E66, i59-i60 [https://doi.
doi:10.1107/s1600536810026942 pmid:21588081 pmcid:PMC3007571 fatcat:lelpjq6hpne4nbqxfra4qybtui

Sodium terbium(III) polyphosphate

Abdelghani Oudahmane, Mohamed Daoud, Boumediene Tanouti, Daniel Avignant, Daniel Zambon
2010 Acta Crystallographica Section E  
Key indicators: single-crystal X-ray study; T = 296 K; mean (P-O) = 0.001 Å; R factor = 0.022; wR factor = 0.055; data-to-parameter ratio = 42.8. Single crystals of the title compound, NaTb(PO 3 ) 4 , were obtained by solid-state reaction. This compound belongs to type II of long-chain polyphosphates with the general formula A I B III (PO 3 ) 4 . It is isotypic with the NaNd(PO 3 ) 4 and NaEr(PO 3 ) 4 homologues. The crystal structure is built up of infinite crenelated chains of corner-sharing
more » ... O 4 tetrahedra with a repeating unit of four tetrahedra. These chains, extending parallel to [100], are linked by isolated TbO 8 square antiprisms, forming a three-dimensional framework. The Na + ions are located in channels running along [010] and are surrounded by six oxygen atoms in a distorted octahedral environment within a cut-off distance <2.9 Å . inorganic compounds Acta Cryst. (2010). E66, i28-i29 Oudahmane et al. NaTb(PO 3 ) 4 i29 supporting information sup-1 Acta Cryst. (2010). E66, i28-i29 supporting information Acta Cryst. (2010). E66, i28-i29 [
doi:10.1107/s1600536810010093 pmid:21580462 pmcid:PMC2983799 fatcat:i75ksipf5vel3guf6mhxjz7f64

Autoregressive Models for Sequences of Graphs

Daniele Zambon, Daniele Grattarola, Lorenzo Livi, Cesare Alippi
2019 2019 International Joint Conference on Neural Networks (IJCNN)  
This paper proposes an autoregressive (AR) model for sequences of graphs, which generalises traditional AR models. A first novelty consists in formalising the AR model for a very general family of graphs, characterised by a variable topology, and attributes associated with nodes and edges. A graph neural network (GNN) is also proposed to learn the AR function associated with the graph-generating process (GGP), and subsequently predict the next graph in a sequence. The proposed method is
more » ... with four baselines on synthetic GGPs, denoting a significantly better performance on all considered problems.
doi:10.1109/ijcnn.2019.8852131 dblp:conf/ijcnn/ZambonGLA19 fatcat:5oxhw4cjmbdozhkx4g7yp6wyiq

AZ-whiteness test: a test for uncorrelated noise on spatio-temporal graphs [article]

Daniele Zambon, Cesare Alippi
2022 arXiv   pre-print
We present the first whiteness test for graphs, i.e., a whiteness test for multivariate time series associated with the nodes of a dynamic graph. The statistical test aims at finding serial dependencies among close-in-time observations, as well as spatial dependencies among neighboring observations given the underlying graph. The proposed test is a spatio-temporal extension of traditional tests from the system identification literature and finds applications in similar, yet more general,
more » ... tion scenarios involving graph signals. The AZ-test is versatile, allowing the underlying graph to be dynamic, changing in topology and set of nodes, and weighted, thus accounting for connections of different strength, as is the case in many application scenarios like transportation networks and sensor grids. The asymptotic distribution -- as the number of graph edges or temporal observations increases -- is known, and does not assume identically distributed data. We validate the practical value of the test on both synthetic and real-world problems, and show how the test can be employed to assess the quality of spatio-temporal forecasting models by analyzing the prediction residuals appended to the graphs stream.
arXiv:2204.11135v1 fatcat:kdem4rwjrvhjrcdnp4r2lzkmem

The type IV polymorph of KEu(PO3)4

Abdelghani Oudahmane, Mohamed Daoud, Boumediene Tanouti, Daniel Avignant, Daniel Zambon
2009 Acta Crystallographica Section E  
E65, i91-i92 [doi:10.1107/S1600536809048788] The type IV polymorph of KEu(PO 3 ) 4 Abdelghani Oudahmane, Mohamed Daoud, Boumediene Tanouti, Daniel Avignant and Daniel Zambon S1.  ... 
doi:10.1107/s1600536809048788 pmid:21578546 pmcid:PMC2972142 fatcat:eadbkwd2kbc35cygx2qpkdw7dm

Change Point Methods on a Sequence of Graphs [article]

Daniele Zambon, Cesare Alippi, Lorenzo Livi
2018 arXiv   pre-print
Daniele Zambon is with the Faculty of Informatics, Università della Svizzera italiana, Lugano, Switzerland (e-mail: daniele.zambon@usi.ch).  ...  Change Point Methods on a Sequence of Graphs Daniele Zambon, Student Member, IEEE, Cesare Alippi, Fellow, IEEE, and Lorenzo Livi, Member, IEEE Abstract-Given a finite sequence of graphs, e.g., coming from  ... 
arXiv:1805.07113v2 fatcat:ktj2ftkvvrdlphugmxqj77pvyq

Classificação do tomate por atacadistas e produtores Curitiba

Luciana R Rodrigues, Fernanda Rita A Zambon, Daniel Muraro
2007 Horticultura Brasileira  
Classificação do tomate por atacadistas e produtores Curitiba Luciana R Rodrigues; Fernanda Rita A Zambon; Daniel Muraro UFPR, Dep to Fitotecnia e Fitossanitarismo, Rua dos Funcionários, n o. 1540, 80035  ...  Entretanto, observa-RODRIGUES LR; ZAMBON FRA; MURARO D. 2007 . Classificação do tomate por atacadistas e produtores Curitiba. Horticultura Brasileira 25: 521-526.  ... 
doi:10.1590/s0102-05362007000400006 fatcat:6zuqztgkfvcjvdtbogmrjfnaem

Hospitalized Pets as a Source of Carbapenem-Resistance

Fabio Gentilini, Maria Elena Turba, Frederique Pasquali, Domenico Mion, Noemi Romagnoli, Elisa Zambon, Daniele Terni, Gisele Peirano, Johann Dawid Daniel Pitout, Antonio Parisi, Vittorio Sambri, Renato Giulio Zanoni
2018 Frontiers in Microbiology  
The massive and irrational use of antibiotics in livestock productions has fostered the occurrence and spread of resistance to "old class antimicrobials." To cope with that phenomenon, some regulations have been already enforced in the member states of the European Union. However, a role of livestock animals in the relatively recent alerts on the rapid worldwide increase of resistance to last-choice antimicrobials as carbapenems is very unlikely. Conversely, these antimicrobials are
more » ... administered in veterinary hospitals whose role in spreading bacteria or mobile genetic elements has not adequately been addressed so far. A cross-sectional study was carried out on 105 hospitalized and 100 non-hospitalized pets with the aim of measuring the prevalence of carbapenem-resistant Gram-negative bacteria (GNB) colonizing dogs and cats, either hospitalized or not hospitalized and estimating the relative odds. Stool samples were inoculated on MacConkey agar plates containing 1 mg/L imipenem which were then incubated aerobically at 37°C ± 1 for 48 h. Isolated bacteria were identified first by Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and were confirmed by 16S rRNA sequencing. The genetic basis of resistance was investigated using PCR methods, gene or whole genome sequencing (WGS). The prevalence of pets harboring carbapenem-resistant bacteria was 11.4 and 1.0% in hospitalized and not-hospitalized animals, respectively, with an odds ratio of 12.8 (p < 0.01). One pet carried two diverse isolates. Overall, 14 gram-negative non-fermenting bacteria, specifically, one Acinetobacter radioresistens, five Acinetobacter baumannii, six Pseudomonas aeruginosa and two Stenotrophomonas maltophilia were isolated. The Acinetobacter species carried acquired carbapenemases genes encoded by bla NDM-1 and bla OXA-23. In contrast, Pseudomonas phenotypic resistance was associated with the presence of mutations in the oprD gene. Notably, inherent carbapenem-resistant isolates of S. maltophilia were also resistant to the first-line recommended chemotherapeutic trimethoprim/sulfamethoxazole. This study estimates the risk of colonization by carbapenem-resistant non-fermenting GNB in pets hospitalized in veterinary tertiary care centers and highlights their potential role in spreading resistance genes among the animal and human community. Public health authorities should consider extending surveillance systems and putting the release of critical antibiotics under more strict control in order to manage the infection/colonization of pets in veterinary settings.
doi:10.3389/fmicb.2018.02872 pmid:30574124 pmcid:PMC6291488 fatcat:efigv5ud4jbyxe6kvh5devvm4i

COSTS-BENEFITS ANALYSIS OF A SMALL-SCALE BIOGAS PLANT AND ELECTRIC ENERGY PRODUCTION

MARIANGELA SALERNO, FRANCESCO GALLUCCI, LUIGI PARI, ILARIA ZAMBON, DANIELE SARRI, ANDREA COLANTONI
2017 Zenodo  
The present work concerns the economic and fi nancial evaluation of a small biogas plant (power plant of 250 kWel), with reference to the case of a biogas plant fed with a bio-matrix classifi able as both a by-product and a product. The study was focused on the comparison of several incentive systems that have followed over time. According to the analysis carried out using some economic indicators, results revealed that the investment profi tability was descending passing from the old
more » ... ive rate to the current incentive scheme. Furthermore, it is possible to emphasize that the use of products, rather than by-products, penalizes investment by reducing the incentive rate, thus putting the investment in a high fi nancial risk. Thanks to the present study, it can be assumed that the small biogas production plants enable positive benefi ts in social, economic and environmental terms.
doi:10.5281/zenodo.4147453 fatcat:bwz4vzijdbe43egiz24wboastu

Determining the Mutation Bias of Favipiravir in Influenza Using Next-generation Sequencing [article]

Daniel Goldhill, Pinky Langat, Hongyao Xie, Monica Galiano, Shahjahan Miah, Paul Kellam, Maria Zambon, Angie Lackenby, Wendy S Barclay
2018 bioRxiv   pre-print
Favipiravir is a broad spectrum antiviral drug that may be used to treat influenza. Previous research has identified that favipiravir likely acts as a mutagen but the precise mutation bias that favipiravir induces in influenza virus RNAs has not been described. Here, we use next-generation sequencing (NGS) with barcoding of individual RNA molecules to accurately and quantitatively detect favipiravir-induced mutations and to sample orders of magnitude more mutations than would be possible
more » ... Sanger sequencing. We demonstrate that favipiravir causes mutations and show that favipiravir primarily acts as a guanine analogue and secondarily as an adenine analogue resulting in the accumulation of transition mutations. We also use a standard NGS pipeline to show that the mutagenic effect of favipiravir can be measured by whole genome sequencing of virus.
doi:10.1101/375378 fatcat:6jsdxfvq55ebjmdz6ulql2zn6i

Favipiravir-resistant influenza A virus shows potential for transmission [article]

Daniel Goldhill, Ada Yan, Rebecca Frise, Jie Zhou, Jennifer Shelley, Ana Gallego-Cortés, Shahjahan Miah, Omolola Akinbami, Monica Galiano, Maria Zambon, Angie Lackenby, Wendy S. Barclay
2020 bioRxiv   pre-print
Favipiravir is a nucleoside analogue which has been licensed to treat influenza in the event of a new pandemic. We previously described a favipiravir resistant influenza A virus generated by in vitro passage in presence of drug with two mutations: K229R in PB1, which conferred resistance at a cost to polymerase activity, and P653L in PA, which compensated for the cost of polymerase activity. However, the clinical relevance of these mutations is unclear as the mutations have not been found in
more » ... ural isolates and it is unknown whether viruses harbouring these mutations would replicate or transmit in vivo. Here, we infected ferrets with a mix of wild type p(H1N1) 2009 and corresponding favipiravir-resistant virus and tested for replication and transmission in the absence of drug. Favipiravir-resistant virus successfully infected ferrets and was transmitted by both contact transmission and respiratory droplet routes. However, sequencing revealed the mutation that conferred resistance, K229R, decreased in frequency over time within ferrets. Modelling revealed that due to a fitness advantage for the PA P653L mutant, reassortment with the wild-type virus to gain wild-type PB1 segment in vivo resulted in the loss of the PB1 resistance mutation K229R. We demonstrated that this fitness advantage of PA P653L in the background of our starting virus A/England/195/2009 was due to a maladapted PA in first wave isolates from the 2009 pandemic. We show there is no fitness advantage of P653L in more recent pH1N1 influenza A viruses. Therefore, whilst favipiravir-resistant virus can transmit in vivo, the likelihood that the resistance mutation is retained in the absence of drug pressure may vary depending on the genetic background of the starting viral strain.
doi:10.1101/2020.09.01.277343 fatcat:gr4k2drg5bhuxen5ldzfdjs6vy

Graph Random Neural Features for Distance-Preserving Graph Representations [article]

Daniele Zambon, Cesare Alippi, Lorenzo Livi
2020 arXiv   pre-print
Correspondence to: Daniele Zambon <daniele.zambon@usi.ch>. Proceedings of the 37 th International Conference on Machine Learning, Vienna, Austria, PMLR 108, 2020.  ...  We generated two classes of 300, 12-node Delaunay's triangulation graphs (Zambon et al., 2017; Grattarola et al., 2019) .  ... 
arXiv:1909.03790v3 fatcat:2eink7sbbrhhdjsmnuszm3kd7e
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