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DEL CORSO, ILARIA, open, In my thesis I enumerate the Hopf-Galois structures on Galois extensions of order p^2q. This will be done, using the gamma functions, by enumerating the regular subgroups of the holomorph of groups G of order p^2q. The last objects are also connected to skew braces, and I also provide the number of isomorphism classes of skew braces of size p^2q., Nella mia tesi enumero le strutture Hopf-Galois su estensioni di Galois di ordine p^2q. Questo sarà fatto, mediante l'uso delle funzioni gamma, contando i sottogruppi regolari dell'olomorfo di gruppi di ordine p^2q. Questi ultimi oggetti sono anche connessi con le skew braces, e fornisco anche il numero di classi di isomorfismo di skew braces di ordine p^2q., 0, open, Campedel, E

STOPPINO, LIDIA, open, On a fibred algebraic variety, is defined a relative invariant called slope which classifies the variety itself. For these fibration a main character is played by the Hodge bundle and by the geometric invariants of the general fibers. In particular in this thesis we focus on surfaces and threefolds fibred over curves, and we give a lower bound for the slope which depends on the unitary rank of the hodge bundle and on: -the clifford index of the general curve, in case of fibred surfaces; - the geometric genus ($p_{g}$) of the general surface, in case of threefolds. Finally we use these results on fibred threefolds to make a new upper bound for the unitary rank $u_{f}$ depending on $p_{g}$ under the hypothesis that the genus of the base curve is zero or one., Su una varieta algebrica fibrata si definesce un invariante relativo detto slope che ne specifica la natura. Per queste fibrazioni un ruolo importante è svolto del fibrato di Hodge e dagli invarianti geometrici delle fibre generiche. In particulare in questa tesi ci concentreremo su superfici e threefold fibrati su curve, dando un stima dal basso della slope che dipenda del rango unitario del fibrato di hodge e da: - indice di clifford cella curva generale, nel caso di superfici; -dal genere geometrico ($p_{g}$) della superficie generale nel caso di threefold. infine sfrutteremo i risultati ottenuti sui threefold per definere un upper bound del rango unitario $u_{f}$ in funzione di $p_{g}$ sotto l'ipotesi che il genere della curva base sia zero o uno., 0, open, Riva, E

ANTOLIN, YAGO, open, This thesis consists of three main chapters, and they all evolve around Artin groups. Proving results for all Artin groups is a serious challenge, so one usually focuses on particular subclasses. Among the most well-understood subfamilies of Artin groups is the family of right-angled Artin groups (RAAGs shortly). One can define them using simplicial graphs, which determine the group up to isomorphism. They are also interesting as there are a variety of methods for studying them, coming from different viewpoints, such as geometry, algebra, and combinatorics. This has resulted in the understanding of many problems in RAAGs, like the word problem, the spherical growth, intersections of parabolic subgroups, etc. In Chapter 2 we focus on the geodesic growth of RAAGs, over link-regular graphs, and we extend a result in that direction, by providing a formula of the growth over link-regular graphs without tetrahedrons. In Chapter 3 we work with slightly different groups, the class of twisted right-angled Artin groups (tRAAGs shortly). They are defined using mixed graphs, which are simplicial graphs where edges are allowed to be directed edges. We find a normal form for presenting the elements in a tRAAG. If we forget about the directions of edges, we obtain an underlying undirected graph, which we call the naïve graph. Over the naïve graph, which is simplicial, one can define a RAAG, which corresponds naturally to our tRAAG. We will discuss some algebraic and geometric similarities and differences between tRAAGs and RAAGs. Using the normal form we are able to conclude that the spherical and geodesic growth of a tRAAG agrees with the respective growth of the underlying RAAG. Chapter 4 has a different theme, and it consists of the study of parabolic subgroups in even Artin groups. The work is motivated by the corresponding results in RAAGs, and we generalize some of these results to certain subclasses of even Artin groups. ​, Questa tesi consiste in tre capitoli principali, e tutti si evolvono intorno ai gruppi di Artin. Dimostrare risultati per tutti i gruppi di Artin è una sfida seria, quindi di solito ci si concentra su particolari sottoclassi. Tra le sottofamiglie più conosciute dei gruppi di Artin c'è la famiglia dei gruppi Artin ad angolo retto (RAAGs in breve). Si possono definire usando i grafici simpliciali, che determinano il gruppo fino all'isomorfismo. Sono anche interessanti perché ci sono una varietà di metodi per studiarli, provenienti da diversi punti di vista, come la geometria, l'algebra e la combinatoria. Questo ha portato alla comprensione di molti problemi dei RAAG, come il problema delle parole, la crescita sferica, le intersezioni di sottogruppi parabolici, ecc. Nel Capitolo 2 ci concentriamo sulla crescita geodetica dei RAAG, su grafi link-regolari, ed estendiamo un risultato in quella direzione, fornendo una formula della crescita su grafi link-regolari senza tetraedri. Nel capitolo 3 lavoriamo con gruppi leggermente diversi, la classe dei gruppi Artin contorti ad angolo retto (tRAAGs in breve). Sono definiti usando grafi misti, che sono grafi semplici in cui i bordi possono essere diretti. Troviamo una forma normale per presentare gli elementi in un tRAAG. Se dimentichiamo le direzioni dei bordi, otteniamo un grafo non diretto sottostante, che chiamiamo grafo ingenuo. Sul grafo ingenuo, che è semplice, si può definire un RAAG, che corrisponde naturalmente al nostro tRAAG. Discuteremo alcune somiglianze e differenze algebriche e geometriche tra i tRAAG e i RAAG. Usando la forma normale siamo in grado di concludere che la crescita sferica e geodetica di un tRAAG concorda con la rispettiva crescita del RAAG sottostante. Il capitolo 4 ha un tema diverso, e consiste nello studio dei sottogruppi parabolici nei gruppi pari di Artin. Il lavoro è motivato dai risultati corrispondenti nei RAAG, e generalizziamo alcuni di questi risultati a certe sottoclassi di gruppi pari, 0, open, Foniqi, I

open, The aim of the present thesis is to discuss the results obtained during my PhD studies, mainly devoted to nonlocal issues. We first deal with strong unique continuation principles and local asymptotic expansions at certain boundary points for solutions of two different classes of elliptic equations. We start the investigation by a class of fractional elliptic equations in a bounded domain under some outer homogeneous Dirichlet boundary condition. To do this, we exploit the Caffarelli-Silvestre extension procedure, which allows us to get an equivalent formulation of the nonlocal problem as a local problem in one dimension more, consisting in a mixed Dirichlet-Neumann boundary value problem. Then, we use a classical idea by Garofalo and Lin to obtain a doubling-type condition via a monotonicity formula for a suitable Almgren-type frequency function. To overcome the difficulties related to the lack of regularity at the Dirichlet-Neumann junction, we introduce a new technique based on an approximation argument, which leads us to derive a so-called Pohozaev-type identity needed to estimate the derivative of the Almgren function. Thus we gain a strong unique continuation result in the local context, which is in turn combined with blow-up arguments to deduce local asymptotics and, consequently, a strong unique continuation result in the nonlocal setting as well. We also provide a strong unique continuation result from the edge of a crack for the solutions to a specific class of second order elliptic equations in an open bounded domain with a fracture, on which a homogeneous Dirichlet boundary condition is prescribed, in the presence of potentials satisfying either a negligibility condition with respect to the inverse-square weight or some suitable integrability properties. This local problem is related to a particular case of the setting described above, by virtue of a strong connection between this type of problems and the mixed Dirichlet-Neumann boundary value problems., Lo scopo della presente tesi è quello di discutere i risultati ottenuti durante i miei studi di dottorato, principalmente rivolti a problemi non locali. Per prima cosa ci occupiamo di principi di continuazione unica forte ed espansioni asintotiche locali in determinati punti del bordo per soluzioni di due diverse classi di equazioni ellittiche. In particolare, partiamo con lo studio di una classe di equazioni ellittiche frazionarie in un dominio limitato sotto una condizione al contorno di Dirichlet omogenea esterna. Per fare ciò, sfruttiamo la procedura di estensione di Caffarelli-Silvestre, grazie alla quale il problema non locale può essere riformulato in modo equivalente come problema locale in una dimensione in più, generando un problema con condizioni miste. Dopodichè, utilizziamo un'idea classica di Garofalo e Lin per ottenere una condizione di raddoppio tramite una formula di monotonia per la funzione di Almgren. Per superare le difficoltà legate alla perdita di regolarità in corrispondenza della transizione tra le regioni di Dirichlet e di Neumann, introduciamo una nuova tecnica basata su un argomento di approssimazione, che ci permette di derivare una cosiddetta identità di tipo Pohozaev necessaria per stimare la derivata della funzione di Almgren . Otteniamo così un risultato di continuazione unica forte nel contesto locale, che viene a sua volta combinato con l’analisi di blow-up per dedurre espansioni asintotiche locali e, di conseguenza, una continuazione unica forte anche nel contesto non locale. Inoltre forniamo anche un risultato di continuazione unica forte dal bordo di una fessura per le soluzioni di una classe specifica di equazioni ellittiche del secondo ordine in un dominio limitato aperto con una frattura, su cui è assegnata una condizione al contorno di Dirichlet omogenea. Questo problema locale è correlato a un caso particolare dello studio descritto sopra, in virtù di una forte connessione tra questo tipo di problemi e i problemi al contorn, 0, open, DE LUCA, A

GRAUDENZI, ALEX, open, Heterogeneity pervades biological systems and manifests itself in the structural and functional differences observed both among different individuals of the same group (e.g., organisms or disease systems) and among the constituent elements of a single individual (e.g., cells). The study of the heterogeneity of biological systems and, in particular, of multicellular systems is fundamental for the mechanistic understanding of complex physiological and pathological phenomena (e.g., cancer), as well as for the definition of effective prognostic, diagnostic, and therapeutic strategies. This work focuses on developing and applying computational methods and mathematical models for characterising the heterogeneity of multicellular systems and, especially, cancer cell subpopulations underlying the evolution of neoplastic pathology. Similar methodologies have been developed to characterise viral evolution and heterogeneity effectively. The research is divided into two complementary portions, the first aimed at defining methods for the analysis and integration of omics data generated by sequencing experiments, the second at modelling and multiscale simulation of multicellular systems. Regarding the first strand, next-generation sequencing technologies allow us to generate vast amounts of omics data, for example, related to the genome or transcriptome of a given individual, through bulk or single-cell sequencing experiments. One of the main challenges in computer science is to define computational methods to extract useful information from such data, taking into account the high levels of data-specific errors, mainly due to technological limitations. In particular, in the context of this work, we focused on developing methods for the analysis of gene expression and genomic mutation data. In detail, an exhaustive comparison of machine-learning methods for denoising and imputation of single-cell RNA-sequencing data has been performed. Moreover, methods for mapping expression prof, L'eterogeneità pervade i sistemi biologici e si manifesta in differenze strutturali e funzionali osservate sia tra diversi individui di uno stesso gruppo (es. organismi o patologie), sia fra gli elementi costituenti di un singolo individuo (es. cellule). Lo studio dell’eterogeneità dei sistemi biologici e, in particolare, di quelli multicellulari è fondamentale per la comprensione meccanicistica di fenomeni fisiologici e patologici complessi (es. il cancro), così come per la definizione di strategie prognostiche, diagnostiche e terapeutiche efficaci. Questo lavoro è focalizzato sullo sviluppo e l’applicazione di metodi computazionali e modelli matematici per la caratterizzazione dell’eterogeneità di sistemi multicellulari e delle sottopopolazioni di cellule tumorali che sottendono l’evoluzione di una patologia neoplastica. Analoghe metodologie sono state sviluppate per caratterizzare efficacemente l’evoluzione e l’eterogeneità virale. La ricerca è suddivisa in due porzioni complementari, la prima finalizzata alla definizione di metodi per l’analisi e l’integrazione di dati omici generati da esperimenti di sequenziamento, la seconda alla modellazione e simulazione multiscala di sistemi multicellulari. Per quanto riguarda il primo filone, le tecnologie di next-generation sequencing permettono di generare enormi moli di dati omici, relativi per esempio al genoma o trascrittoma di un determinato individuo, attraverso esperimenti di bulk o single-cell sequencing. Una delle sfide principale in informatica è quella di definire metodi computazionali per estrarre informazione utile da tali dati, tenendo conto degli alti livelli di errori dato-specifico, dovuti principalmente a limiti tecnologici. In particolare, nell’ambito di questo lavoro, ci si è concentrati sullo sviluppo di metodi per l’analisi di dati di espressione genica e di mutazioni genomiche. In dettaglio, è stata effettuata una comparazione esaustiva dei metodi di machine-learning per il denoising e l’imputation, 0, open, Maspero, D

GHIGI, ALESSANDRO CALLISTO, open, This thesis deals with totally geodesic subvarieties of the moduli space A_g of principally polarized abelian varieties and their relation with the Torelli locus. This is the closure in A_g of the image of the moduli space M_g of smooth, complex algebraic curves of genus g via the Torelli map j: M_g-->A_g. The moduli space A_g is a quotient of the Siegel space, which is a Riemannian symmetric space. An algebraic subvariety of A_g is totally geodesic if it is the image, under the natural projection map, of some totally geodesic submanifold of the Siegel space. Geometric considerations lead to the expectation that j(M_g) should contain very few totally geodesic subvarieties of A_g. This expectation also agrees with the Coleman-Oort conjecture. The differential geometry of symmetric spaces is described through Lie theory. In particular, totally geodesic submanifolds can be characterized via Lie algebras. This motivates the discussion carried out in this thesis, in which we use some Lie-theoretic tools to investigate geometric aspects of the inclusion of j(M_g) in A_g. The main results presented are the following. In Chapter 2, we consider the pull-back of the Lie bracket operation on the tangent space of A_g via the Torelli map, and we characterize it in terms of the geometry of the curve. We use the Bergman kernel form associated with the curve. Also, we link the Bergman kernel form to the second fundamental form of the Torelli map. In Chapter 3, we determine which symmetric space uniformizes each of the known counterexamples to the Coleman-Oort conjecture via the computation of the associated Lie algebra decomposition. These known examples were obtained studying families of Galois coverings of curves. Chapter 4 focuses on these families for their own sake, and we describe a new topological construction of families of G-coverings of the line., Oggetto di questa tesi sono le sottovarietà totalmente geodetiche dello spazio dei moduli A_g di varietà abeliane principalmente polarizzate e la loro relazione con il luogo di Torelli. Questo è definito come la chiusura in A_g dell'immagine dello spazio dei moduli M_g di curve algebriche complesse lisce di genere g tramite la mappa di Torelli j: M_g-->A_g. Lo spazio dei moduli A_g è un quoziente dello spazio di Siegel, che è uno spazio simmetrico. Una sottovarietà algebrica di A_g è totalmente geodetica se è l'immagine, tramite la naturale mappa di proiezione, di una qualche sottovarietà totalmente geodetica dello spazio di Siegel. Ci si aspetta che j(M_g) contenga poche sottovarietà totalmente geodetiche di A_g. Questo è anche in accordo con la congettura di Coleman-Oort. La geometria differenziale degli spazi simmetrici si può descrivere attraverso la teoria di gruppi e algebre di Lie. In particolare, le sottovarietà totalmente geodetiche di spazi simmetrici possono essere caratterizzate in termini di algebre di Lie. Queste considerazioni sono alla base della trattazione svolta in questa tesi, in cui utilizziamo alcuni strumenti della teoria di Lie per indagare alcuni aspetti geometrici dell'inclusione di j(M_g) in A_g. I principali risultati presentati sono i seguenti. Nel Capitolo 2, consideriamo il pull-back dell'operazione di Lie-bracket sullo spazio tangente ad A_g tramite la mappa di Torelli e lo caratterizziamo in termini della geometria della curva. Per farlo usiamo il nucleo di Bergman associato alla curva. Inoltre, colleghiamo il nucleo di Bergman alla seconda forma fondamentale della mappa Torelli. Nel Capitolo 3, determiniamo quale spazio simmetrico uniforma ciascuno dei controesempi noti alla congettura di Coleman-Oort attraverso il calcolo della decomposizione dell'algebra di Lie associata. Questi esempi noti erano stati ottenuti studiando famiglie di rivestimenti di Galois. Nel capitolo 4 ci concentriamo sullo studio di queste famiglie e descriviam, 0, open, Tamborini, C

open, The Möbius function of locally finite partially ordered sets is a classical tool in enumerative combinatorics. It is a generalization of the number-theoretic Möbius function and it has several applications in group theory, from the Euler characteristic of subgroup complexes to algebraic aspects of cellular automata. In the first part of the thesis, we recall some basic notions about the order structures which are related to the Möbius function, and we present its main properties, such as the Möbius inversion formula and Crapo's theorems. Moreover, we investigate some relevant connections with group-theoretical topics to motivate our interest in the Möbius function of finite linear groups. In the second part, we work on these groups to obtain information about their Möbius function, and our original results are useful to compute it if we know the structure of some special subspace lattices related to subgroups. We study in detail the case of distributive subspace lattices. Then we show an example of a subgroup in the general linear group, such that the subspace lattice associated to the subgroup is non-distributive. In this way, we see that our arguments can also be applied to different situations, under certain conditions. In the last part of the thesis, we connect the previously obtained results to an open question about finitely generated profinite groups and finite almost-simple groups, introducing an original approach to the problem. Although we do not completely answer to this last question, we get some useful partial results., La funzione di Möbius definita per insiemi parzialmente ordinati localmente finiti è un classico strumento di analisi combinatoria. Si tratta di una generalizzazione della funzione di Möbius nota in teoria dei numeri e ha varie applicazioni pure in teoria dei gruppi, dalla caratteristica di Eulero di complessi di sottogruppi fino allo studio di aspetti algebrici in automi cellulari. Nella prima parte della tesi richiamiamo alcune informazioni elementari per strutture d'ordine che sono legate alla funzione di Möbius, e ne presentiamo le principali proprietà, quali ad esempio la formula di inversione di Möbius e i teoremi di Crapo. Inoltre analizziamo alcuni legami importanti con argomenti di teoria dei gruppi, al fine di motivare il nostro interesse nei confronti della funzione di Möbius di gruppi lineari finiti. Nella seconda parte, lavoriamo su questi gruppi per studiarne la funzione di Möbius e otteniamo risultati originali che si rivelano utili per calcolarla, nota la struttura di alcuni particolari reticoli di sottospazi associati ai sottogruppi. Vediamo in dettaglio il caso in cui abbiamo un reticolo di sottospazi distributivo. In seguito mostriamo un esempio di sottogruppo del gruppo lineare generale, tale che il reticolo di sottospazi associato al sottogruppo non è distributivo. In questo modo osserviamo che i nostri ragionamenti hanno una validità più ampia e possono essere applicati a situazioni differenti, sotto determinate condizioni. Nell'ultima parte della tesi, colleghiamo i risultati ottenuti in precedenza ad alcune questioni aperte che riguardano gruppi profiniti finitamente generati e gruppi finiti almost-simple, presentando un approccio originale al problema. Benché poi questo problema non venga completamente risolto, otteniamo degli utili risultati parziali che possono essere sviluppati in futuro., 0, open, DI GRAVINA, L

CALABRIA, ANDREA, open, Gene Therapy (GT), the recent approach to cure rare and inherited genetic disorders by delivering therapeutic gene in targeted cells interacted with bioinformatics and data analysis-related domains. In GT applications, the molecular monitoring of the treatment is required and exploits Next generation sequencing (NGS) to assess efficacy and safety. One of the principal efforts in IS identification is mapping millions of sequenced reads to the reference genome. Today, several aligners are available for this aim. However, still improving the IS detection performance by choice of appropriate algorithm and testing various pre-/post-alignment filtering strategies is the scope of some works. Since despite the current improvements in the field, some factors like length of sequence reads, repeat regions in the reference genomes and sequence errors decrease the mapping accuracy. False Positive IS, is an IS that is reported at the end of IS identification when it is not present. Mis-alignment is one of the possible sources for False Positive IS.Here, to solve the problem of False Positive and discarding the noise in our clinical IS databases, we first focused on alignment and post-alignment filtering. For this aim, we generated a ground truth of simulated reads overall composed by 125,778,685 sequencing reads containing a total number of 4,333,904 IS and tried to test several steps of our bioinformatics pipeline. We confirmed that BWA-MEM, the widely-used aligner which is also the choice of VISPA2 has a good performance with 91% accuracy. Further analyses revealed that some of the statistic measurements such as Mapping Quality (MAPQ) and Sub optimal Alignment Score (XS) that are reported for each mapping result are not well-correlated with alignment accuracy. Therefore, filtering steps after alignment might lead to discarding many reads without improving the accuracy. Discarding reads which are aligned correctly might highly reduce sequence count. Moreover, knowing that intera, La terapia genica (GT), il recente approccio per curare malattie genetiche rare ed ereditarie fornendo geni terapeutici in cellule mirate, ha interagito con la bioinformatica e i domini correlati all'analisi dei dati. Nelle applicazioni GT, è richiesto il monitoraggio molecolare del trattamento e sfrutta il sequenziamento di nuova generazione (NGS) per valutare l'efficacia e la sicurezza. Uno degli sforzi principali nell'identificazione dell'IS è mappare milioni di letture sequenziate nel genoma di riferimento. Oggi sono disponibili diversi allineatori per questo scopo. Tuttavia, lo scopo di alcuni lavori è ancora migliorare le prestazioni di rilevamento dell'IS tramite la scelta dell'algoritmo appropriato e testare varie strategie di filtraggio pre/post-allineamento. Poiché nonostante gli attuali miglioramenti nel campo, alcuni fattori come la lunghezza delle letture della sequenza, le regioni ripetute nei genomi di riferimento e gli errori di sequenza riducono l'accuratezza della mappatura. SI falso positivo, è un SI che viene riportato alla fine dell'identificazione SI quando non è presente. Il disallineamento è una delle possibili fonti di False Positive IS.Qui, per risolvere il problema dei False Positive e scartare il rumore nei nostri database clinici di IS, ci siamo prima concentrati sull'allineamento e sul filtraggio post-allineamento. A questo scopo, abbiamo generato una verità di base di letture simulate complessivamente composta da 125.778.685 letture di sequenziamento contenenti un numero totale di 4.333.904 IS e abbiamo provato a testare diversi passaggi della nostra pipeline bioinformatica. Abbiamo confermato che BWA-MEM, l'allineatore ampiamente utilizzato che è anche la scelta di VISPA2, ha buone prestazioni con una precisione del 91%. Ulteriori analisi hanno rivelato che alcune delle misurazioni statistiche come la qualità della mappatura (MAPQ) e il punteggio di allineamento subottimale (XS) riportate per ciascun risultato della mappatura non sono, 0, open, Omrani, M

VIRGA, EPIFANIO, open, This dissertation is concerned with a peculiar class of lyotropics: chromatic liquid crystals (CLCs). Chromonics in the nematic phase enjoy the head-tail symmetry, that is, they are non-chiral materials with a tendency for their constitutive to bundle together so that a director can be defined at a mesoscopic scale which lacks polarity. The ground state of ordinary nematic liquid crystals is attained when the director is uniform in space. When CLCs are confined in capillary cylinders with degenerate boundary conditions that would be compatible with the uniform alignment of the director along the cylinder's axis, they are observed to acquire a nonuniform arrangement instead. Expecially, their ground state in cylindrical capillary, often referred to as escaped twist (ET) ground state, is two-fold; it consists of two symmetric twisted configurations (left- and right-handed), each variant occurring with the same likelihood, as was to be expected from the lack of chirality in the molecular aggregates that constitute these materials. Despite the clear indication that CLCs in three-dimensional space exhibit a different behavior from common nematic liquid crystals, the Oseen-Frank theory for nematics has been applied to rationalize the experiments with capillary tubes and so to determine the configuration of the ET ground state. This is a variational theory which posits a free energy density quadratic in the director gradient that penalizes all distortions of the director away from the unifom alignment. Four basic distortions are classically identified, which correspond to four independent elastic constants; these are the splay K_{11}, twist K_{22}, bend K_{33}, and saddle-splay K_{24} constants, which have recently been re-interpreted in a new light by Selinger. Ericksen's inequalities ensure that Frank's energy density is positive definite, and the spontaneous emergence of chirality in the nematic texture is not conceivable when they hold. Thus, Frank's elastic theory jus, Questa tesi si occupa di una classe particolare di liotropici: i cristalli liquidi cromatici (CLCs). Essi in fase nematica godono della simmetria testa-coda, cioè sono materiali non chirali con una tendenza dei loro elementi costitutivi a raggrupparsi in modo da poter definire un direttore su scala mesoscopica che non ha polarità. Lo stato fondamentale dei cristalli liquidi nematici ordinari è raggiunto quando il direttore è uniforme nello spazio. Quando i CLCs sono confinati in capillari cilindrici con condizioni al contorno degeneri, si osserva che acquisiscono una configurazione non uniforme. In particolare, il loro stato fondamentale nel capillare cilindrico, spesso indicato come 'escaped twist' (ET), consiste in due configurazioni simmetriche di opposta chiralità, ognuna che si verifica con la stessa probabilità come ci si aspetta dalla mancanza di chiralità negli aggregati molecolari che costituiscono questi materiali. Nonostante la chiara indicazione che i CLCs nello spazio tridimensionale mostrano un comportamento diverso dai comuni cristalli liquidi nematici, la teoria di Oseen-Frank per i nematici è stata applicata per razionalizzare gli esperimenti con i capillari e quindi per determinare la configurazione dello stato fondamentale ET. Si tratta di una teoria variazionale che postula una densità di energia libera quadratica nel gradiente del direttore che penalizza tutte le distorsioni dall'allineamento uniforme. Classicamente vengono identificate quattro distorsioni, che corrispondono a quattro costanti elastiche indipendenti; si tratta delle costanti splay K_{11}, twist K_{22}, bend K_{33}, e saddle-splay K_{24}. Le disuguaglianze di Ericksen assicurano che la densità di energia di Frank sia positiva definita, e l'emergere spontaneo della chiralità non è concepibile quando sono valide. Così, la teoria elastica di Frank giustifica le configurazioni osservate dei CLCs sotto confinamento cilindrico solo se la disuguaglianza di Ericksen pertinente, K_{22}>=K, 0, open, Paparini, S

open, The electroencephalogram (EEG) provides the non-invasive recording of brain activities and functions as time-series, characterized by a temporal and spatial (sensor-dependent) resolution, and by brain condition-bounded frequency bands. Moreover, it presents some cost-effective device solutions. However, the resulting EEG signals are non-stationary, time-varying, and heterogeneous, being recorded from different subjects and being influenced by specific experimental paradigms, environmental conditions, and devices. Moreover, they are easily affected by noise and they can be recorded for a limited time, thus they provide a restricted number of brain conditions to work with. Therefore, in this thesis a flexible pipeline for signal processing and management is proposed to have a better understanding of the EEG signals and exploit them for a variety of applications. Moreover, the proposed flexible pipeline is divided in 4 modules concerning signal pre-processing, normalization, feature computation and management, and EEG data classification. The EEG signal pre-processing exploits the multivariate empirical mode decomposition (MEMD) to decompose the signal in oscillatory modes, called intrinsic mode functions (IMFs), and uses an entropy criterion to select the most relevant IMFs that should maintain the natural brain dynamics, while discarding uninformative components. The resulting relevant IMFs are then exploited for signal substitution and data augmentation. Even though MEMD is adapt to the EEG signal non-stationarity, further processing steps should be undertaken to mitigate these data heterogeneity. Therefore, a normalization step is introduced to obtain comparable data inter- and intra-subject and between different experimental conditions, allowing the extraction of general features in the time, frequency, and time-frequency domain for EEG signal characterization. Even though the use of a variety of feature types may provide new data patterns, they may also present s, L'elettroencefalogramma (EEG) fornisce registrazioni non-invasive delle attività e delle funzioni cerebrali sotto forma di serie temporali, a loro volta caratterizzate da una risoluzione temporale e spaziale (dipendente dai sensori), e da bande di frequenza specifiche per alcuni tipi di condizioni cerebrali. Tuttavia, i segnali EEG risultanti sono non-stazionari, cambiano nel tempo e sono eterogenei, essendo prodotti da differenti soggetti e venendo influenzati da specifici paradigmi sperimentali, condizioni ambientali e dispositivi. Inoltre, questi segnali sono facilmente soggetti a rumore e possono venire acquisiti per un tempo limitato, fornendo un numero ristretto di condizioni cerebrali sulle quali poter lavorare. Pertanto, in questa tesi viene proposta una pipeline flessibile per l'elaborazione e la gestione dei segnali EEG, affinchè possano essere più facilmente comprensibili e quindi più facilmente sfruttabili in diversi tipi di applicazioni. Inoltre, la pipeline flessibile proposta è divisa in quattro moduli riguardanti la pre-elaborazione del segnale, la sua normalizzazione, l'estrazione e la gestione di feature e la classificazione dei dati EEG. La pre-elaborazione del segnale EEG sfrutta la multivariate empirical mode decomposition (MEMD) per scomporre il segnale nelle sue modalità oscillatorie, chiamate intrinsic mode function (IMF), ed usa un criterio basato sull'entropia per selezionare le IMF più relevanti. Queste IMF dovrebbero mantenere le naturali dinamiche cerebrali e rimuovere componenti non-informative. Le risultati IMF rilevanti sono in seguito sfruttate per sostituire il segnale o aumentare la numerosità dei dati. Nonostante MEMD sia adatto alla non-stazionarietà del segnale EEG, ulteriori passi computazionali dovrebbero essere svolti per mitigare la caratteristica eterogeneità di questi dati. Pertanto, un passo di normalizzazione viene introdotto per ottenere dati comparabili per uno stesso soggetto o più soggetti e tra differenti condizioni, 1, open, Saibene, A

FREDIANI, PAOLA, open, In this thesis we study Shimura subvarieties in the moduli space of complex abelian varieties. These subvarieties arise from families of Galois covers compatible with a fixed group action on the base curve such that the quotient of the base curve by the group is isomorphic to the projective line. We give a criterion for the image of these families under the Prym map to be a special subvariety and, using computer algebra, we build several Shimura subvarieties contained in the Prym loci., In questa tesi si studiano le sottovarietà di Shimura negli spazi di moduli delle varietà abeliane complesse. Queste sottovarietà derivano da famiglie di rivestimenti di Galois compatibili con un'azione di gruppo fissata sulla curva base tale che il quoziente della curva base per il gruppo è isomorfo alla retta proiettiva. Si da un criterio affinché l'immagine di queste famiglie tramite la mappa di Prym sia una sottovarietà speciale e, sfruttando il computer, si costruiscono numerose sottovarietà di Shimura contenute nei luoghi di Prym., 0, open, Grosselli, G

CARBONE, RAFFAELLA, open, This thesis addresses the study of absorption dynamics in invariant domains (enclosures) for semigroups of quantum Markov maps. The work is divided in three chapters. In Chapter 1 we recall the main definitions, properties and results about the mathematical objects involved in this work: W*-algebras, normal states, semigroups of quantum Markov maps. In Chapter 2 we introduce the notion of absorption operator associated to an invariant domain, which is a generalization of absorption probabilities in the noncommutative setting; absorption operators turn out to share many remarkable features with their classical counterpart. We start showing some first properties of absorption operators, especially the interplay between their spectral resolution and the communication structure of the semigroup. We then move on to study the relationship between absorption operators and recurrence; as a relevant byproduct, we show that the null recurrent space is an enclosure and this allows to complete the result about the decomposition of semigroups of quantum Markov maps into their transient, positive recurrent and null recurrent restrictions. Absorption operators are also fixed points of the semigroup and, under the assumption that the recurrent space is absorbing, we are able to provide a description in terms of absorption operators of the fixed points set of the semigroup; this allows us to deduce some useful properties about fixed points and enclosures. Moreover, we analyze the role played by absorption operators in ergodic theory and we are able to prove a noncommutative generalization of the ergodic theorem for Markov chains. We conclude the chapter presenting and studying some concrete models showing non-trivial absorption dynamics and ranging from finite to infinite dimension, from discrete to continuous time. Chapter 3 is devoted to study the long-time behavior of the position process associated to a homogeneous open quantum random walk on a lattice with finite dimensional lo, Lo scopo del presente lavoro di tesi è lo studio delle dinamiche di assorbimento in domini invarianti (enclosures) per semigruppi markoviani quantistici. Il lavoro è diviso in tre capitoli. Nel primo capitolo ricordiamo le principali definizioni, proprietà e risultati riguardanti gli oggetti matematici con cui si avrà a che fare: W*-algebre, stati normali e semigruppi markoviani quantistici. Nel secondo capitolo introduciamo la nozione di operatore di assorbimento associato ad un determinato dominio invariante, che è la generalizzazione non commutativa delle probabilità di assorbimento; gli operatori di assorbimento condividono numerose proprietà con la loro controparte classica. Inizialmente mostriamo le prime proprietà degli operatori di assorbimento, specialmente l'interazione tra la loro risoluzione spettrale e la struttura di comunicazione del semigruppo. Successivamente spostiamo l'attenzione sullo studio della relazione tra operatori di assorbimento e ricorrenza; un risultato collaterale rilevante è che lo spazio ricorrente nullo è un dominio invariante e questo completa il risultato sulla decomposizione dei semigruppi markoviani quantistici nelle loro restrizioni transiente, ricorrente positiva e ricorrente nulla. Gli operatori di assorbimento sono anche punti fissi del semigruppo e, a condizione che lo spazio ricorrente sia assorbente, siamo in grado di fornire una descrizione dei punti fissi in termini degli operatori di assorbimento; questo permette di dedurre alcune utili proprietà dei punti fissi e dei domini invarianti. Inoltre, analizziamo il ruolo rivestito dagli operatori di assorbimento nel quadro della teoria ergodica e mostriamo la generalizzazione non commutativa del teorema ergodico per le catene di Markov. Concludiamo il capitolo presentando e studiando alcuni modelli concreti che possiedono delle dinamiche di assorbimento non banali e che variano tra dimensione finita o infinita e tempo discreto o continuo., 0, open, Girotti, F

open, A software architecture is eroded (or degraded) if it shows a progressive loss of structural integrity due to design principle violations which leads to the deviation of the implemented architecture from the intended architecture. Eroded systems suffer from Architectural Technical Debt (ATD), the additional effort required by developers to manage the shortcomings caused by the erosion. A symptom of the accumulation of ATD is the presence of Architectural Smells (AS), design decisions that impact negatively on the internal system quality. Systems affected by AS suffer from higher maintenance costs and are harder to evolve. This thesis investigates six different types of AS violating different design principles in Open-Source and industrial monolithic Java projects. We identify AS with our tool, Arcan, and introduce its new extension for the representation of software concerns. We then discuss AS from the point of view of practitioners, trying to summarise how AS are perceived and validating Arcan results. We also report the results of our empirical studies concerning AS and ATD evolution and correlation. Finally, we present our first results concerning the migration and maintenance of microservices architectures, with a focus on the detection of microservices smells., Un'architettura software è erosa (o degradata) se mostra una progressiva perdita di integrità strutturale a causa di violazioni dei principi di progettazione. I sistemi erosi soffrono di Architectural Technical Debt (ATD), lo sforzo aggiuntivo richiesto agli sviluppatori per gestire i difetti causati dall'erosione. Un sintomo dell'accumulo di ATD è la presenza di Architectural Smells (AS), decisioni di software design che hanno un impatto negativo sulla qualità interna del sistema software. I sistemi affetti da AS soffrono di maggiori costi di manutenzione e sono più difficili da evolvere. Questa tesi indaga sei diversi tipi di AS che violano diversi principi di design in progetti Java monolitici Open-Source e industriali. Identifichiamo gli AS con il nostro strumento, Arcan, e introduciamo la sua nuova estensione per la rappresentazione dei software concerns. Discutiamo poi gli AS dal punto di vista dei professionisti, cercando di riassumere come gli AS sono percepiti e validando i risultati di Arcan. Riportiamo anche i risultati dei nostri studi empirici riguardanti l'evoluzione e la correlazione di AS e ATD. Infine, presentiamo i nostri primi risultati riguardanti la migrazione e la manutenzione di architetture a microservizi, con particolare attenzione al rilevamento degli odori dei microservizi., 0, open, Pigazzini, I

ROZZA, ALESSANDRO, open, Almost everyone carries a high-quality camera in their smartphone and uses it to communicate with other individuals and for the last two decades, people are increasingly making use of images and videos in their transportable communication. As the prices of the storage are decreasing, the number of photos stored is increasing, leading to collections of images whose sizes begin to be a barrier for relieving the captured moments and exploring them. We are submerged by images. In order to ease the problem of oversized image collections, methods that aim to select a subset of photos that best represents them have been designed and proposed in the literature. Those methods typically rely upon the prediction of perceptual features such as, for example, the image quality, aesthetics, and memorability, to select the best images. This thesis starts from the fundamental image properties that guide the image selection, respectively the image quality and image aesthetics. First, the perceived image quality assessment is investigated in an anomaly detection manner, contrary to the most common regression task. This is because rather than predict a score that best correlates to the average human opinion, being able to distinguish good quality images from bad ones, is more suitable for the image collection management problem, furthermore, it requires fewer images to tune the model. Then the problem of automatic assessment of image aesthetics is introduced. In the beginning, presenting a method that learns the aesthetics of a picture on the basis of the prediction of aesthetics-related attributes. Then, a new solution that takes into account the semantic content, the artistic style, and the composition of the image is presented. One of the reasons people take photos is to capture important situations to recall them later on, usually with the intention of afterwards sharing their photos with other people like friends or family members. Photos can be seen as a concrete link between our, Al giorno d’oggi ormai quasi chiunque possiede uno smartphone dotato di una telecamera ad alta risoluzione. Negli ultimi decenni, i contenuti multimediali (immagini e video) stanno sempre più spesso diventando il principale mezzo di comunicazione. Dato il continuo calo dei prezzi dei dispositivi di archiviazione, il numero totale di immagini salvate sta aumentando notevolmente, andando così a creare collezioni di immagini sempre più grandi, a tal punto da essere una problema per chi vuole le vuole esplorare. Data una libreria di immagini, il processo di selezione di un gruppo di foto che rappresenti al meglio le informazioni contenute in essa è condizionato dalle proprietà percettive delle immagini. Al fine di gestire in modo automatico questa selezione, in letteratura sono stati proposti diversi metodi che sfruttano le proprietà percettive delle immagini. Questi metodi hanno come scopo quello di associare alle immagini un valore numerico che ne rappresenta la presenza o meno di queste proprietà, come ad esempio la qualità, l'estetica o la memorabilità, per poi sfruttarle per selezionare le immagini migliori. La presente tesi comincia trattando quelle che sono le proprietà delle immagini fondamentali al processo di selezione delle immagini, rispettivamente la qualità e l’estetica delle immagini. Per prima cosa viene studiata la qualità delle immagini mediante un processo di rilevamento delle anomalie. Questo perché dal punto di vista di un sistema automatico di selezione delle immagini, è più indicato un metodo che sia in grado di distinguere le immagini belle da quelle brutte, piuttosto che un metodo che predica un valore ben correlato con la qualità delle immagini. Successivamente l’attenzione viene spostata sul problema della valutazione automatica dell’estetica delle immagini. In particolare viene prima proposto un metodo in grado di stimare il grado di bellezza di un'immagine a partire dalla predizione di attributi correlati all’estetica. Successivamente introd, 0, open, Leonardi, M

MESSINA, VINCENZINA, open, Textual knowledge is one of the main pillars of our society. Indeed, human knowledge is often passed along using words. Since the invention of writing, humans have narrated and described their existence with words over pieces of papers. This amount of knowledge builds up to what the entire civilization has collected over more than 5'000 years. Historians and social and political scientists look for ways to understand better this vast amount of collective knowledge that cannot be manually explored. To this end, researchers from machine learning, statistics and computational linguistic have developed topic models, a suite of algorithms that aim to annotate large archives of documents with thematic information. The popularity of these models is due to the fact that they are unsupervised and that they are interpretable. Topic models analyze and summarize the main themes, or topics, of large collections of documents, presenting the information in a compact and understandable form. Most topic models focus only on the words encoded in the documents. However, additional information can be introduced into topic models to improve their performance. In fact, in many real-world cases, we seldom have only the mere texts to analyze. Instead, we have additional information or metadata related to the documents, e.g., the document's author, the date, hyperlinks to other documents, a set of hashtags, mentions or labels. We can use this prior information to help a topic model discover better topics. For example, knowing that a document cites another document increases our confidence that the documents talk about the same topics. Also, topic models often ignore word order and contextual information, making it difficult to infer high-quality topics. Another problem in the field is related to the hyperparameters used to train the topics models. The hyperparameters are often fixed in experimental settings and few researchers have tried to study their impact on the results. In this thesis, La conoscenza testuale è uno dei pilastri principali della nostra società. Infatti, la conoscenza umana è spesso trasmessa attraverso le parole. Dall'invenzione della scrittura, gli uomini hanno raccontato e descritto la loro esistenza con parole su pezzi di carta. Questa quantità di conoscenza si accumula fino a ciò che l'intera civiltà ha raccolto in più di 5000 anni. Gli storici e gli scienziati sociali e politici cercano modi per capire meglio questa vasta quantità di conoscenza collettiva che non può essere esplorata manualmente. A questo scopo, i ricercatori di machine learning, statistica e linguistica computazionale hanno sviluppato i topic model, una suite di algoritmi che mirano ad annotare grandi archivi di documenti con informazioni tematiche. La popolarità di questi modelli è dovuta al fatto che sono non supervisionati e che sono interpretabili. I topic model analizzano e riassumono i temi principali, anche detti topic, di grandi collezioni di documenti, presentando le informazioni in una forma compatta e comprensibile. La maggior parte dei topic model si concentrano solo sulle parole codificate nei documenti. Tuttavia, informazioni aggiuntive possono essere introdotte nei topic model per migliorare le loro prestazioni. Infatti, in molti casi del mondo reale, raramente abbiamo solo i semplici testi da analizzare. Invece, abbiamo informazioni aggiuntive o metadati relativi ai documenti, ad esempio, l'autore del documento, la data, collegamenti ipertestuali ad altri documenti, un insieme di hashtag, menzioni o etichette. Possiamo usare queste informazioni precedenti per aiutare un topic model a scoprire topic di qualità. Per esempio, sapere che un documento cita un altro documento aumenta la nostra fiducia che i documenti parlano degli stessi argomenti.Inoltre, i topic model spesso ignorano l'ordine delle parole e le informazioni contestuali, rendendo difficile dedurre gli topic coerenti e significativi. Un altro problema nel campo è legato agli iperparam, 0, open, Terragni, S

PIROLA, YURI, open, In this manuscript we described the main computational challenges of the cancer phylogenetic field and we proposed different solutions for the three main problems of (i) the progression reconstruction of a tumor sample, (ii) the clustering of SCS data to allow for a cleaner and faster inference and (iii) the evaluation of different phylogenies. Furthermore we combined them into a usable pipeline to allow for a faster analysis., In questo manoscritto vengono discussi le principali sfide computazionali nel campo della inferenza di filogenesi tumorale a vengono proposte diverse soluzione per i tre principali problemi di (i) ricostruzione dell'evoluzioni di un campione tumorale, (ii) clustering di dati SCS per una piu' pulita e veloce inferenza e (iii) il confronto di diverse filogenesi. Inoltre viene discusso come combinare le diverse soluzioni in una singola pipeline per una piu' rapida analisi., 0, open, Ciccolella, S

open, Debugging and bug fixing are extremely important activities that are regularly performed to eliminate defects from software. They are however time consuming, and thus improving their degree of automation is increasingly important in a competitive world. A possible solution is offered by Automatic Program Repair (APR) techniques, through which it is possible to automatically generate patches that can be either presented to developers as candidate patches or directly integrated into the target programs. Although many different APR techniques have been developed in the last few years, there are still open challenges related to their introduction as stable and working solutions in development pipelines. Indeed, most of the APR techniques rely on test cases to evaluate the correctness of patches, which is a weak validation method that can lead to the generation of incorrect patches. In particular, recent empirical studies show that APR techniques often result in the generation of code-removal patches, that are patches that drop functionalities to address the faults that afflict programs. Yet another aspect that strongly influences the success of APR is fault localization. Indeed, if the correct location to generate the patch is not found, it is hard or even impossible to generate a patch. Experimental evidence shows that current strategies used for the fault localization are often unable to identify the correct statements to be modified, making the generation of patches extremely hard. In this context, this Ph.D. thesis provides two key contributions: 1) an empirical study about the factors that influence the generation of code-removal patches and an analysis of the useful information that can be extracted from them; and 2) a new fault localization technique that exploits the semantic of exceptions to accurately guide the fault localization process., Le attività di debugging e risoluzione dei bug sono estremamente importanti e sono eseguite regolarmente per eliminare i difetti presenti nei programmi. Tuttavia, la loro esecuzione richiede molto tempo, e dunque migliorare il loro grado di automazione è sempre più importante in un mondo altamente competitivo. Una possibile soluzione è offerta dalle tecniche di riparazione automatica del programma (Automatic Program Repair, APR), attraverso le quali è possibile generare in modo automatico le patch che possono essere fornite agli sviluppatori come possibili soluzioni oppure possono essere integrate direttamente nel programma contenente il difetto. Nonostante negli ultimi anni siano state sviluppate numerose tecniche di APR, ci sono ancora numerose sfide aperte legate alla loro introduzione come soluzione stabile e funzionante da integrare nelle pipeline di sviluppo. Infatti, la maggior parte delle tecniche di APR si appoggiano ai casi di test per valutare la correttezza delle patch, i quali però costituiscono un metodo di valutazione fragile che può portare alla generazione di patch non corrette. In particolare, recenti studi empirici mostrano che le tecniche di APR spesso generano patch di rimozione del codice (code-removal patches), che sono patch che rimuovono le funzionalità per risolvere i difetti che affliggono i programmi. Un altro aspetto che influenza fortemente il successo delle tecniche di APR è la localizzazione dei difetti. Infatti, se la posizione corretta per generare la patch non viene trovata, è difficile o persino impossibile generare una patch. Prove sperimentali mostrano che le strategie attuali utilizzate per la localizzazione dei difetti spesso non sono in grado di identificare i punti del codice corretti da modificare, rendendo la generazione delle patch estremamente difficile. In questo contesto, questa tesi di dottorato fornisce due contributi chiave: 1) uno studio empirico riguardo ai fattori che influenzano la generazione delle patch di rim, 0, open, Ginelli, D

open, In Next generation sequencing technologies, hundreds or thousands of DNA samples can be sequenced simultaneously (multiplexing) and the obtained sequencing reads can be distinguished by the presence of sample-specific nucleotide sequences (indexes) embedded in the primers used for the DNA amplification. Custom bioinformatics pipelines, by reading the indexes present in the sequencing reads assign them to a specific sample (demultiplexing). Multiplexing however is plagued by index switching, a phenomenon occurring when free index primers are randomly fused to DNA sequences belonging to other unrelated samples of the library pool and resulting in the incorrect assignment of sequences to one or multiple wrong samples. In the field of gene therapy (GT) (see Appendix A), vector integration site (IS) studies heavily depend on sequencing of DNA fragments (containing proviral-cellular genome junctions) from several samples and are affected by index switching. This issue is particularly relevant in clonal tracking studies, where the level of shared IS between different cell lineages or different time points of the same GT patient are required to define the levels of multilineage reconstitution and estimate the number of stem cells and other calculations. Therefore, the spreading of IS between datasets caused by index switching could result in inflated sharing IS levels which could lead to misinterpretation of the results. To evaluate the extent of index switching in IS analyses, we analysed 123,431,269 sequencing reads originating from a pool composed by 54 samples amplified in triplicate, each tagged by two indexes fused to the ends of the PCR products containing the LTR and Linker Cassette (LC) sequences resulting in 162 index combinations (combining a total of 48 LTR and 32 LC indexes). From this analysis we found that >95% of sequencing reads belonged to the correct 162 index combinations while a the remaining 5% of reads belonging to 1374 false index combinations result, Nelle tecnologie di sequenziamento di nuova generazione, centinaia o migliaia di campioni di DNA possono essere sequenziati simultaneamente (multiplexing) e le letture di sequenziamento ottenute possono essere distinte dalla presenza di sequenze nucleotidiche specifiche del campione (indici) incorporate nei primer utilizzati per l'amplificazione del DNA. Pipeline bioinformatiche personalizzate, leggendo gli indici presenti nelle letture di sequenziamento li assegnano ad uno specifico campione (demultiplexing). Il multiplexing, tuttavia, è afflitto dal cambio di indice, un fenomeno che si verifica quando i primer di indice libero vengono fusi in modo casuale a sequenze di DNA appartenenti ad altri campioni non correlati del pool di librerie e determinano l'assegnazione errata delle sequenze a uno o più campioni errati. Nel campo della terapia genica (GT), gli studi sui siti di integrazione dei vettori (IS) dipendono fortemente dal sequenziamento di frammenti di DNA (contenenti giunzioni genomiche provirali-cellulari) da diversi campioni e sono influenzati dallo scambio dell'indice. Questo problema è particolarmente rilevante negli studi di tracciamento clonale, dove il livello di IS condiviso tra diverse linee cellulari o diversi punti temporali dello stesso paziente con GT è richiesto per definire i livelli di ricostituzione multilineare e stimare il numero di cellule staminali e altri calcoli. Pertanto, la diffusione dell'IS tra i set di dati causata dalla scambio dell'indice potrebbe comportare livelli di condivisione IS non veritieri che potrebbero portare a un'interpretazione errata dei risultati. Per valutare l'entità della scambio dell'indice nelle analisi IS, abbiamo analizzato 123.431.269 letture di sequenziamento provenienti da un pool composto da 54 campioni amplificati in triplice copia, ciascuno contrassegnato da due indici fusi alle estremità dei prodotti PCR contenenti LTR e Linker Sequenze di cassette (LC) risultanti in 162 combinazioni di indici (che, 0, open, DE MARINO, A

open, In an increasingly technological and interconnected world, the amount of data is continuously growing, and as a consequence, decision-making algorithms are also continually evolving to adapt to it. One of the major sources of this vast amount of data is the Internet of Things, in which billions of sensors exchange information over the network to perform various types of activities such as industrial and medical monitoring. In recent years, technological development has made it possible to define new high-performance hardware architectures for sensors, called Microcontrollers, which enabled the creation of a new kind of decentralized computing named Edge Computing. This new computing paradigm allowed sensors to run decision-making algorithm at the edge in order to take immediate and local decisions instead of transferring the data on central server processing. To support Edge Computing, the research community started developing new advanced techniques to efficiently manage the limited resources on these devices for applying the most advanced Machine Learning models, especially the Deep Neural Networks. Automated Machine Learning is a branch of the Machine Learning field aimed at disclosing the power of Machine Learning to non-experts as well as efficiently supporting data scientists in designing their own data analysis pipelines. The adoption of Automated Machine Learning has made it possible to develop increasingly high-performance models almost automatically. However, with the advent of Edge Computing, a specialization of Machine Learning, defined as Tiny Machine Learning (Tiny ML), has been arising, that is, the application of Machine Learning algorithms on devices having limited hardware resources. This thesis mainly addresses the applicability of Automated Machine Learning to generate accurate models which must be also deployable on tiny devices, specifically Microcontroller Units. More specifically, the proposed approach is aimed at maximizing the performances, In un mondo sempre più tecnologico e interconnesso, la quantità di dati è in continua crescita e, di conseguenza, anche gli algoritmi di decision-making sono in continua evoluzione per adattarsi ad essi. Una delle principali fonti di questa grande quantità di dati è l'Internet of Things, in cui miliardi di sensori si scambiano informazioni attraverso la rete per svolgere vari tipi di attività come il monitoraggio industriale e medico. Negli ultimi anni lo sviluppo tecnologico ha permesso di definire nuove architetture hardware ad alte prestazioni per i sensori, detti microcontrollori, che hanno permesso la creazione di un nuovo tipo di calcolo decentralizzato denominato Edge Computing. Questo nuovo paradigma di calcolo ha permesso ai sensori di eseguire algoritmi di decision-making per prendere decisioni immediate e locali invece di trasferire i dati su un server centrale di elaborazione. Per supportare l'Edge Computing, la comunità di ricerca ha iniziato a sviluppare nuove tecniche avanzate per gestire in modo efficiente le limitate risorse su questi dispositivi per l'applicazione dei più avanzati modelli di Machine Learning, in particolare le Deep Neural Network. Automated Machine Learning è una branca del campo del Machine Learning che mira a divulgare la potenza del Machine Learning ai non esperti, oltre a supportare in modo efficiente i data scientists nella progettazione delle proprie pipeline di analisi dei dati. L'adozione del Automated Machine Learning ha reso possibile lo sviluppo quasi automatico di modelli sempre più performanti. Tuttavia, con l'avvento dell'Edge Computing, è nata una specializzazione del Machine Learning, definita come Tiny Machine Learning (Tiny ML), ovvero l'applicazione di algoritmi di Machine Learning su dispositivi con risorse hardware limitate. Questa tesi si occupa principalmente dell'applicabilità del Automated Machine Learning per generare modelli accurati che devono essere anche implementabili su dispositivi minuscoli, in part, 0, open, Perego, R

open, The main goal of this thesis is to develop new algorithmic frameworks to deal with (i) a convenient representation of a set of similar genomes and (ii) phylogenetic data, with particular attention to the increasingly accurate tumor phylogenies. A “pan-genome” is, in general, any collection of genomic sequences to be analyzed jointly or to be used as a reference for a population. A phylogeny, in turn, is meant to describe the evolutionary relationships among a group of items, be they species of living beings, genes, natural languages, ancient manuscripts or cancer cells. With the exception of one of the results included in this thesis, related to the analysis of tumor phylogenies, the focus of the whole work is mainly theoretical, the intent being to lay firm algorithmic foundations for the problems by investigating their combinatorial aspects, rather than to provide practical tools for attacking them. Deep theoretical insights on the problems allow a rigorous analysis of existing methods, identifying their strong and weak points, providing details on how they perform and helping to decide which problems need to be further addressed. In addition, it is often the case where new theoretical results (algorithms, data structures and reductions to other well-studied problems) can either be directly applied or adapted to fit the model of a practical problem, or at least they serve as inspiration for developing new practical tools. The first part of this thesis is devoted to methods for handling an elastic-degenerate text, a computational object that compactly encodes a collection of similar texts, like a pan-genome. Specifically, we attack the problem of matching a sequence in an elastic-degenerate text, both exactly and allowing a certain amount of errors, and the problem of comparing two degenerate texts. In the second part we consider both tumor phylogenies, describing the evolution of a tumor, and “classical” phylogenies, representing, for instance, the evolutionary hi, Lo scopo di questa tesi è di elaborare e analizzare metodi rigorosi dal punto di vista matematico per l’analisi di due tipi di dati biologici: dati relativi a pan-genomi e filogenesi. Con il termine “pan-genoma” si indica, in generale, un insieme di sequenze genomiche strettamente correlate (tipicamente appartenenti a individui della stessa specie) che si vogliano utilizzare congiuntamente come sequenze di riferimento per un’intera popolazione. Una filogenesi, invece, rappresenta le relazioni evolutive in un gruppo di entità, che siano esseri viventi, geni, lingue naturali, manoscritti antichi o cellule tumorali. Con l’eccezione di uno dei risultati presentati in questa tesi, relativo all’analisi di filogenesi tumorali, il taglio della dissertazione è prevalentemente teorico: lo scopo è studiare gli aspetti combinatori dei problemi affrontati, più che fornire soluzioni efficaci in pratica. Una conoscenza approfondita degli aspetti teorici di un problema, del resto, permette un'analisi matematicamente rigorosa delle soluzioni già esistenti, individuandone i punti deboli e quelli di forza, fornendo preziosi dettagli sul loro funzionamento e aiutando a decidere quali problemi vadano ulteriormente investigati. Oltretutto, è spesso il caso che nuovi risultati teorici (algoritmi, strutture dati o riduzioni ad altri problemi più noti) si possano direttamente applicare o adattare come soluzione ad un problema pratico, o come minimo servano ad ispirare lo sviluppo di nuovi metodi efficaci in pratica. La prima parte della tesi è dedicata a nuovi metodi per eseguire delle operazioni fondamentali su un testo elastico-degenerato, un oggetto computazionale che codifica in maniera compatta un insieme di testi simili tra loro, come, ad esempio, un pan-genoma. Nello specifico, si affrontano il problema di cercare una sequenza di lettere in un testo elastico-degenerato, sia in maniera esatta che tollerando un numero prefissato di errori, e quello di confrontare due testi degenerati., 1, open, Bernardini, G

NAPOLETANO, PAOLO, open, Recognizing human activities and monitoring population behavior are fun- damental needs of our society. Population security, crowd surveillance, healthcare support and living assistance, lifestyle and behavior tracking are some of the main applications which require the recognition of activities. Activity recognition involves many phases, i.e. the collection, the elaboration and the analysis of information about human activities and behavior. These tasks can be fulfilled manually or automatically, even though a human-based recognition system is not long-term sustainable and scalable. Nevertheless, transforming a human-based recognition system to computer- based automatic system is not a simple task because it requires dedicated hardware and a sophisticated engineering computational and statistical techniques for data preprocessing and analysis. Recently, considerable changes in tech- nologies are largely facilitating this transformation. Indeed, new hardwares and softwares have drastically modified the activity recognition systems. For example, Micro-Electro-Mechanical Systems (MEMS) progress has enabled a reduction in the size of the hardware. Consequently, costs have decreased. Size and cost reduction allows to embed sophisticated sensors into simple devices, such as phones, watches, and even into shoes and clothes, also called wearable devices. Furthermore, low costs, lightness, and small size have made wearable devices’ highly pervasive and accelerated their spread among the population. Today, a very small part of the world population doesn’t own a smartphone. According to Digital 2020: Global Digital Overview, more than 5.19 billion people now use mobile phones. Among the western countries, smartphones and smartwatches are gadgets of people everyday life. The pervasiveness is an undoubted advantage in terms of data generation. Huge amount of data, that is big data, are produced every day. Furthermore, wearable devices together with new advanced software technol, Recognizing human activities and monitoring population behavior are fun- damental needs of our society. Population security, crowd surveillance, healthcare support and living assistance, lifestyle and behavior tracking are some of the main applications which require the recognition of activities. Activity recognition involves many phases, i.e. the collection, the elaboration and the analysis of information about human activities and behavior. These tasks can be fulfilled manually or automatically, even though a human-based recognition system is not long-term sustainable and scalable. Nevertheless, transforming a human-based recognition system to computer- based automatic system is not a simple task because it requires dedicated hardware and a sophisticated engineering computational and statistical techniques for data preprocessing and analysis. Recently, considerable changes in tech- nologies are largely facilitating this transformation. Indeed, new hardwares and softwares have drastically modified the activity recognition systems. For example, Micro-Electro-Mechanical Systems (MEMS) progress has enabled a reduction in the size of the hardware. Consequently, costs have decreased. Size and cost reduction allows to embed sophisticated sensors into simple devices, such as phones, watches, and even into shoes and clothes, also called wearable devices. Furthermore, low costs, lightness, and small size have made wearable devices’ highly pervasive and accelerated their spread among the population. Today, a very small part of the world population doesn’t own a smartphone. According to Digital 2020: Global Digital Overview, more than 5.19 billion people now use mobile phones. Among the western countries, smartphones and smartwatches are gadgets of people everyday life. The pervasiveness is an undoubted advantage in terms of data generation. Huge amount of data, that is big data, are produced every day. Furthermore, wearable devices together with new advanced software technol, 0, open, Ferrari, A

RIZZI, RAFFAELLA, open, DNA contains the genetic information that is essential for the correct development of any organism. Being able to investigate DNA is of utmost importance for analyzing the reasons behind diseases and for improving the quality of life. Development of DNA sequencing technologies has revolutionized the way this kind of investigation is performed. Due to the huge amount of sequencing data available, nowadays computer science plays a key role in their analysis. Luckily, in many applications, the biological information contained in a DNA molecule can be represented as a string in which each character represents a nucleotide. Strings are a well-known and well-studied notion in computer science and therefore it is possible to exploit the huge literature related to storing and processing strings for improving the analysis of DNA. Within this context, this thesis focuses on two specific problems arising from the analysis of sequencing data: the study of transcript variability due to alternative splicing and the investigation of genetic variability among different individuals due to small variations such as Single Nucleotide Polymorphisms and indels. Regarding both these problems, we investigate two novel computational approaches by devising original strategies and we prove their efficacy by comparing them with the most used state-of-the-art approaches. In both these areas, our focus is on the development of bioinformatics tools that combine accurate algorithms with efficient data structures. The first problem we tackle is the detection of alternative splicing events from RNA-Seq data. Alternative splicing plays an important role in many different life aspects, from the correct evolution of an individual to the development of diseases. Differently from current techniques that rely on the reconstruction of transcripts or on the spliced alignment of RNA-Seq reads against a reference genome, we investigate an alternative algorithmic approach that exploits the novel notion of alig, Il DNA contiene l'informazione genetica che è essenziale per il corretto sviluppo di qualsiasi organismo. Essere in grado di analizzare il DNA risulta indispensabile per comprendere le cause di malattie e tumori e per migliorare la qualità delle nostre vite. Lo sviluppo delle tecniche di sequenziamento del DNA ha rivoluzionato il modo in cui queste analisi sono eseguite. A causa dell'immensa quantità di dati biologici disponibili, oggigiorno l'informatica gioca un ruolo fondamentale nella loro analisi. Fortunatamente in molte applicazioni l'informazione biologica contenuta in una molecola di DNA può essere rappresentata come una stringa nella quale ogni carattere rappresenta un nucleotide. Il concetto di stringa è molto studiato in informatica ed è possibile sfruttare l'estesa letteratura relativa alla memorizzazione e all'analisi di stringhe per migliorare lo studio del DNA. In questo contesto, questa tesi si focalizza su due problemi che emergono dall'analisi di dati di sequenziamento: lo studio della variabilità trascrittomica dovuta allo splicing alternativo e l'analisi della variabilità genetica dovuta a variazioni genetiche quali Single Nucleotide Polymorphisms e indels. Riguardo entrambi i problemi, investighiamo due originali approcci computazionali e ne dimostriamo l'efficacia confrontandoli con i tools più utilizzati nel relativo stato dell'arte. Il nostro obiettivo è lo sviluppo di tool bioinformatici che combinano algoritmi accurati con strutture dati efficienti. Il primo problema che affrontiamo è l'identificazione di eventi di splicing alternativo a partire da dati RNA-Seq. Lo splicing alternativo gioca un ruolo fondamentale in molti aspetti della vita, dal corretto sviluppo di un individuo al sorgere di malattie. Diversamente dagli approcci proposti in letteratura che si basano sulla quantificazione di trascritti o sull'allineamento spliced contro un genoma di riferimento, proponiamo un approccio algoritmico alternativo che sfrutta l'originale concett, No, open, Denti, L

open, Monitoring techniques can extract accurate data about the behavior of software systems. When used in the field, they can reveal how applications behave in real-world contexts and how programs are actually exercised by their users. However, the collection, processing, and distribution of field data must be done seamlessly and unobtrusively while users interact with their applications. To limit the intrusiveness of field monitoring a common approach is to reduce the amount of collected data (e.g., to rare events and to crash dumps), which, however, may severely affect the effectiveness of the techniques that exploit field data. This Ph.D. thesis investigates the trade-off between field monitoring and the degradation of the user experience in interactive applications, that is, applications that require user inputs to continue its operations. In particular, we identified two big challenges: to understand how the user perceives monitoring overhead and, to study how to collect data in a non-intrusive way without losing too much information. In brief, we provide three main contributions. In the first place, we present an empirical study aimed at quantifying if and to what extent the monitoring overhead introduced in an interactive application is perceived by users. The reported results can be exploited to carefully design analysis procedures running in the field. In particular, we realized that users do not perceive significant differences for an overhead of 80\% and seldom perceived an overhead of 140\%. Secondly, we introduce a monitoring framework for deriving comprehensive runtime data without affecting the quality of the user experience. The technique produces a finite state automaton that shows possible usages of the application from the events observed in the field. From the model, it is also possible to extract accurate and comprehensive traces that could be used to support various tasks, such as debugging, field failures reproduction and profiling. Finally, we pre, Le tecniche di monitoraggio possono estrarre dati accurati sul comportamento dei sistemi software. Se utilizzati nel campo, possono rivelare come le applicazioni si comportano in contesti del mondo reale e come i programmi sono effettivamente esercitati dai loro utenti. Tuttavia, la raccolta, l'elaborazione e la distribuzione dei dati sul campo devono essere eseguiti senza interruzioni e in modo non invasivo mentre gli utenti interagiscono con le loro applicazioni. Per limitare l'intrusività del monitoraggio sul campo, un approccio comune consiste nel ridurre la quantità di dati raccolti (ad esempio, in pochi eventi e in crash dump), che tuttavia possono influire gravemente sull'efficacia delle tecniche che sfruttano i dati sul campo. Questa tesi di dottorato indaga il trade-off tra il monitoraggio sul campo e il degrado dell'esperienza utente nelle applicazioni interattive, cioè le applicazioni che richiedono input dell'utente per continuare le sue operazioni. In particolare, abbiamo identificato due grandi sfide: capire come l'utente percepisce il sovraccarico del monitoraggio e studiare come raccogliere dati in modo non intrusivo senza perdere troppe informazioni. In breve, forniamo tre contributi principali. In primo luogo, presentiamo uno studio empirico volto a quantificare se e in che misura il sovraccarico di monitoraggio introdotto in un'applicazione interattiva è percepito dagli utenti. I risultati riportati possono essere sfruttati per progettare attentamente le procedure di analisi in esecuzione sul campo. In particolare, abbiamo scoperto che gli utenti non percepivano differenze significative per un overhead dell'80% e raramente percepivano un overhead del 140%. In secondo luogo, introduciamo un framework di monitoraggio per ricavare dati a runtime completi senza influire sulla qualità dell'esperienza utente. La tecnica produce un automa a stati finiti che mostra i possibili usi dell'applicazione dagli eventi osservati sul campo. Dal modello, è anche po, No, open, CORNEJO OLIVARES, O

COLOMBO, RINALDO, 4402, open, Scalar hyperbolic balance laws in several space dimensions play a central role in this thesis. First, we deal with a new class of mixed parabolic-hyperbolic systems on all R^n: we obtain the basic well-posedness theorems, devise an ad hoc numerical algorithm, prove its convergence and investigate the qualitative properties of the solutions. The extension of these results to bounded domains requires a deep understanding of the initial boundary value problem (IBVP) for hyperbolic balance laws. The last part of the thesis provides rigorous estimates on the solution to this IBVP, under precise regularity assumptions. In Chapter 1 we introduce a predator-prey model. A non local and non linear balance law is coupled with a parabolic equation: the former describes the evolution of the predator density, the latter that of prey. The two equations are coupled both through the convective part of the balance law and the source terms. The drift term is a non local function of the prey density. This allows the movement of predators to be directed towards the regions where the concentration of prey is higher. We prove the well-posedness of the system, hence the existence and uniqueness of solution, the continuous dependence from the initial data and various stability estimates. In Chapter 2 we devise an algorithm to compute approximate solutions to the mixed system introduced above. The balance law is solved numerically by a Lax-Friedrichs type method via dimensional splitting, while the parabolic equation is approximated through explicit finite-differences. Both source terms are integrated by means of a second order Runge-Kutta scheme. The key result in Chapter 2 is the convergence of this algorithm. The proof relies on a careful tuning between the parabolic and the hyperbolic methods and exploits the non local nature of the convective part in the balance law. This algorithm has been implemented in a series of Python scripts. Using them, we obtain information about the possible o, No, open, Rossi, E, Rossi, E

4402, open, In this thesis we consider a connected locally finite graph G that possesses the Cheeger isoperimetric property. We define a decreasing one parameter family of Hardy-type spaces associated with the standard nearest neighbour Laplacian on G. We show that the space with parameter ½ is the space of all integrable functions whose Riesz transform is integrable. We show that if G has bounded geometry and the parameter is an integer, the corresponding Hardy-type space admits an atomic decomposition. We also show that if G is a homogeneous tree and the parameter is not an integer, the corresponding Hardy-type space does not admit an atomic decomposition. Furthermore, we consider the Hardy-type spaces defined in terms of the heat and Poisson maximal operators, and we analyse their relationships with the family of spaces defined previously. We also show that the space associated with the heat maximal operator is properly contained in the one associated with the heat maximal operator, a phenomenon which has no counterpart in the euclidean setting. Applications to the purely imaginary powers of the Laplacian are also given. Finally, we characterise, for every p, the class of spherical multipliers on the p-integrable functions on homogeneous trees in terms of Fourier multipliers on the torus. Furthermore we give a sharp sufficient condition on spherical multipliers on the product of homogeneous trees., No, open, Celotto, D, Celotto, D

open, The thesis provides a formal framework for liveness and security of distributed systems. It proposes new approaches for defining secure and serviceable systems, and discusses associated model-checking methods. In modeling distributed systems, we assume that components are classified as either 'service provider' or 'user'. The actions performed in the system are either observable by the users or hidden internal actions. A service provider is responsible for providing a reliable service to the users and protection of sensitive information. Regarding the serviceability, the thesis examines distributed systems in which an attacker can try to break down the system and provides a novel notion of liveness called 'observable liveness' which guarantees that the service provider will continue to give the requested services to the users. In the observable liveness setting, we give the control of some observable actions to the user. Intuitively, a distributed system is observably live if, whatever state is reached, a user can force the system to get the requested service by using the controllable actions. This notion is formalized with '1-safe' Petri nets, its properties are studied and it is compared with the classical liveness notion. The thesis also discusses a possible application of infinite games on finite graphs for checking observable liveness. On the security side, the thesis considers information flow and non-interference. It provides several new notions of non-interference for Petri nets, and compares them with notions already proposed in the literature. In the considered setting, the transitions of a Petri net are partitioned into two disjoint sets: the 'low' (observable) and the 'high' (unobservable/hidden) transitions. The attacker knows the structure of the system and tries to deduce information about the high transitions by observing the low transitions. A Petri net is considered 'secure', or 'free from interference', if, from the observation of the occurrence o, La tesi propone una cornice formale per la vivezza e la sicurezza di sistemi distribuiti, e nuovi approcci per definire sistemi sicuri e 'serviceable'. Discute inoltre i relativi metodi di model-checking. Nel modellare sistemi distribuiti, classifichiamo i componenti di un sistema come 'service provider' o 'utenti'. Le azioni che occorrono sono osservabili dagli utenti o interne e nascoste. Un service provider deve garantire agli utenti un servizio affidabile e la protezione delle informazioni riservate. Per quanto riguarda la serviceability, la tesi esamina sistemi distribuiti nei quali un attaccante cerca di interrompere il funzionamento del sistema, e propone una nuova nozione di vivezza, detta 'vivezza osservabile', che garantisce che il server continui a erogare il servizio richiesto agli utenti. In tale contesto supponiamo che l'utente controlli alcune azioni osservabili. Intuitivamente, un sistema distribuito è osservabilmente vivo se da qualunque stato un utente può guidare il sistema, per mezzo delle azioni controllabili, fino a ricevere il servizio richiesto. Questa nozione è formalizzata per mezzo delle reti di Petri '1-safe'; se ne studiano le proprietà, e la si confronta con la nozione tradizionale di vivezza. La tesi discute l'applicazione di giochi infiniti su grafi finiti per verificare la vivezza osservabile. Per quanto riguarda a sicurezza, la tesi considera il flusso di informazione e la non-interferenza. Si danno diverse nuove nozioni di non-interferenza per le reti di Petri, e le si confrontano con quelle presenti nella letteratura. In questo approccio, le transizioni di una rete di Petri sono ripartite in due insiemi: transizioni 'basse' (osservabili) e transizioni 'alte' (nascoste). L'attaccante conosce la struttura del sistema e cerca di dedurre informazioni sulle transizioni alte dall'osservazione delle transizioni basse. Una rete di Petri è 'sicura', o 'libera da interferenza' se non è possibile inferire informazioni sull'occorrenza di una, No, open, Kilinc, G, Kilinc, G

4402, open, This thesis deals with the problem of localization for the Riesz means for eigenfunction expansions of the Laplace-Beltrami operator. The classical Riemann localization principle states that if an integrable function of one variable vanishes in an open set, then its trigonometric Fourier expansion converges to zero in this set. This localization principle fails in R^d with d>=2. In order to recover localization one has to use suitable summability methods, such as the Bochner-Riesz means. In the first chapter of the thesis we focus on the compact rank one symmetric spaces case. While in the second chapter we show how some of the results obtained in the first chapter can be generalize to smooth compact and connected Riemannian manifolds. Consider a d-dimensional compact rank one symmetric space. To every square integrable function, and more generally tempered distribution, one can associate a Fourier series, i.e. an eigenfunction expansion of the Laplace-Beltrami operator. These Fourier series converge in the metric of L^2 and in the topology of distributions, but in general one cannot ensure the pointwise convergence. For this reason we introduce the summability method of Bochner-Riesz means: S_R^\alpha f(x). When \alpha=0 one obtains the spherical partial sums, which are a natural analogue of the partial sums of one-dimensional Fourier series in the Euclidean space. There are examples of the failure of localization in Holder, Lebesgue and Sobolev spaces. Despite the negative results, it has been proved by A.I. Basatis and C. Meaney that there is an almost everywhere localization principle for square integrable functions on compact rank one symmetric spaces; that is, if a square integrable function vanishes almost everywhere in an open set, then its Fourier series is equal to zero for almost every point in this open set. On the other hand, it is known that for square integrable functions localization holds everywhere above the so-called critical index \alpha=(d-1)/2, No, open, Tenconi, M, Tenconi, M

4413, open, The present thesis has, as one of its main goals, the objective to introduce the phenomenon of Ageing Society, particularly focusing on the theme of elderly population mobility in urban environment. The originality of this thesis comes from the study of elderly dyads walking dynamics in urban settings and senior citizens' perception about the neighbourhood they live in, in terms of safety and walkable conditions. The final purpose is to demonstrate, through the analysis of institutional and scientific literature, with the help of qualitative and quantitative data collection tools, how the quality of life in older years is related to the maintenance of physical and social activities outdoor, and to infrastructure and services supporting walking mobility. After the introduction to the theme Ageing Society (Chapter 1), the first part of the thesis (Chapters 2-3-4) discusses the importance of the concept of Independent Living as a new lifestyle for senior persons, and investigates the meaning of Walkability, the measure of walking condition, and of living conditions in general, in a definite area. These concepts can be associated to the word Age-Friendly City, which not only refers to a city attentive to citizen's needs but to every age, a city that is inclusive and aware of the wellbeing of its inhabitants. Moreover, we cannot ignore the important role that technology plays in elderly assistance and to the improvement of the quality of life. In particular, nowadays technology can make domestic living more comfortable, avoiding institutionalisation. Data collected through the administration of a long questionnaire "The perception of longevity", aiming at investigating the perception of the population regarding themes such as seniority and assistive technology, are presented in this section. Data indicates that older persons are perceived as autonomous in their daily activities and full of resources, confirming the necessity to promote an active and independent lifestyle, No, open, Avento, N, Avento, N

open, Recently, there has been a resurgence of interest in rigorous and scalable algorithms for efficient inference of cancer progression using genomic patient data. The motivations are manifold: (i) rapidly growing NGS and single cell data from cancer patients, (ii) long-felt need for novel Data Science and Machine Learning algorithms well-suited for inferring models of cancer progression, and finally, (iii) a desire to understand the temporal and heterogeneous structure of tumor so as to tame its natural progression through most efficacious therapeutic intervention. This thesis presents a multi-disciplinary effort to algorithmically and efficiently model tumor progression involving successive accumulation of genetic alterations, each resulting populations manifesting themselves with a novel cancer phenotype. The framework presented in this work along with efficient algorithms derived from it, represents a novel and versatile approach for inferring cancer progression, whose accuracy and convergence rates surpass other existing techniques. The approach derives its power from many insights from, and contributes to, several fields including algorithms in machine learning, theory of causality, and cancer biology. Furthermore, an optimal, versatile and modular pipeline to extract ensemble-level progression models from cross-sectional sequenced cancer genomes is also proposed. The pipeline combines state-of-the-art techniques for sample stratification, driver selection, identification of fitness-equivalent exclusive alterations and progression model inference. Finally, the results are rigorously validated using synthetic data created with realistic generative models, and empirically interpreted in the context of real cancer datasets; in the later case, biologically significant conclusions revealed by the reconstructed progressions are also highlighted. Specifically, the pipeline's ability to reproduce much of the current knowledge on colorectal cancer progression, as well as t, No, open, Ramazzotti, D, Ramazzotti, D

open, Due to their intrinsic nature, biological entities are universally considered as complex systems. Over years, many different computational methods pertaining to the Systems Biology field, have been devised to unravel this complexity. However, when taken alone, most of times these methods are not able to provide a deep comprehension of structural, spatial and dynamical aspects of the systems under evaluation. For this reason, approaches exploiting different levels of analysis are today a hot research topic in different areas, such as the theoretical formalization of the method, and the development of computational tools for the integration of different modeling perspectives. In the present dissertation I developed a computational pipeline able to perform analyses exploiting, one after the other, the three main modeling frameworks for biological systems, gaining, from every level, a different type of information: i.e. identification of flux distributions and metabolic sub-phenotypes from the ensemble evolutionary FBA (a novel method inspired by Flux Balance Analysis); information on network structural properties and topological metrics from graph theory approaches; estimation of kinetic constants for mechanism-based modeling through the definition of an efficient version of the Particle Swarm Optimizer based on Fuzzy Logic. Moreover, I also redefined a network visualization strategy able to overlay flux values and topological metrics to network structure. In order to validate the proposed pipeline I also developed a “core model” of yeast metabolism from which I identified two ensembles of flux distributions (possible solutions) in agreement with the “Crabtree-positive” and “Crabtree-negative” metabolic phenotypes. Moreover, by means of a cluster analysis, devised methods were able to define groups inside each ensemble that I identified as putative “sub-phenotypes”. Lastly, I contributed to reconstruct four reduced metabolic “core models”, deriving from the Human Metab, A causa della loro natura intrinseca, le entità biologiche sono universalmente considerate sistemi complessi. Per dirimere tale complessità, nel corso degli anni, sono stati sviluppati innumerevoli metodi computazionali appartenenti all’ambito della Systems Biology. Tuttavia, quando utilizzati da soli, questi metodi non sono solitamente sufficienti per fornire un’approfondita comprensione degli aspetti strutturali, spaziali e dinamici dei sistemi studiati. Per questa ragione, approcci che coinvolgono diversi livelli di analisi sono oggi un promettente ambito di ricerca sotto diversi aspetti quali la formalizzazione del metodo e lo sviluppo di strumenti computazionali per l’integrazione delle diverse prospettive di modellazione. Nel mio lavoro di tesi, ho sviluppato una pipeline computazionale in grado di svolgere analisi che sfruttano, l’uno dopo l’altro, i tre principali framework di modellazione dei sistemi biologici, ottenendo da ogni livello un diverso tipo di informazione. In particolare sono state identificate distribuzioni di flusso e sotto-fenotipi metabolici attraverso la “Ensemble Evolutionary FBA” (un metodo innovativo inspirato dalla Flux Balance Analysis); informazioni su metriche topologiche e proprietà strutturali della rete da approcci di graph theory; stima di costanti cinetiche per la modellazione meccanicistica attraverso una versione efficiente del Particle Swarm Optimizer basato sulla Logica Fuzzy. Inoltre, ho anche ridefinito una strategia di visualizzazione della rete metabolica in grado di sovraimporre il valore dei flussi e le metriche topologiche alla struttura del network. Al fine di validare la pipeline ho sviluppato un “core model” del metabolismo di lievito, grazie al quale ho identificato due “ensemble” di distribuzioni di flusso (possibili soluzioni) in accordo con i fenotipi metabolici “Crabtree-positive" e “Crabtree-negative". Inoltre, attraverso i metodi sviluppati, è stato possibile isolare dei sottogruppi all’interno di ogni ense, No, open, Colombo, Colombo, R

open, In silico analysis of biological systems represents a valuable alternative and complementary approach to experimental research. Computational methodologies, indeed, allow to mimic some conditions of cellular processes that might be difficult to dissect by exploiting traditional laboratory techniques, therefore potentially achieving a thorough comprehension of the molecular mechanisms that rule the functioning of cells and organisms. In spite of the benefits that it can bring about in biology, the computational approach still has two main limitations: first, there is often a lack of adequate knowledge on the biological system of interest, which prevents the creation of a proper mathematical model able to produce faithful and quantitative predictions; second, the analysis of the model can require a massive number of simulations and calculations, which are computationally burdensome. The goal of the present thesis is to develop novel computational methodologies to efficiently tackle these two issues, at multiple scales of biological complexity (from single molecular structures to networks of biochemical reactions). The inference of the missing data — related to the three-dimensional structures of proteins, the number and type of chemical species and their mutual interactions, the kinetic parameters — is performed by means of novel methods based on Evolutionary Computation and Swarm Intelligence techniques. General purpose GPU computing has been adopted to reduce the computational time, achieving a relevant speedup with respect to the sequential execution of the same algorithms. The results presented in this thesis show that these novel evolutionary-based and GPU-accelerated methodologies are indeed feasible and advantageous from both the points of view of inference quality and computational performances., No, open, Nobile, Nobile, M

LORENZI, LUCA, 4402, open, The aim of this thesis is to improve some results on parabolic Cauchy problems with unbounded coefficients and their connection with stochastic optimal games. In the first part we summarize the recent results on parabolic operators with unbounded coefficients and on stochastic optimal control problem. In particular, in the matter of analyitic results, we recall the main exstence and uniqueness theorems for parabolic Cauchy problems with unbounded coefficients, the gradient estimates for the associated evolution operator, and its continuity and compactness properties. About the stochastic part, we briefly show the strong and weak formulation, which are the settings where the stochastic control problems are located, and we introduce the backward stochastic differential equations, which allow to connect a semilinear Cauchy problem with a class of stochastic control problem. In the second part we prove the existence and uniqueness of a mild solution to a semilinear parabolic Cauchy problem of Hamilton-Jacobi-Bellman (HJB) type. Moreover, we show that the solution to a Forward Backward Stochastic Differential Equation (FBSDE) can be expressed in terms of the solution to the HJB equation. Combining HJB equation and FBSDE, we show that, for a class of stochastic control problemin weak formulation, there exists an optimal control, and by means of the regularity of the solution to the HJB equation, we can identify the feedback law. The third part of the thesis is devoted to the study of a class of system of nonautonomous linear parabolic equations with unbounded coefficients, coupled both at first and zero order. We provide sufficient conditions which guarantee the existence and uniqueness of a classical solution to the Cauchy problem, and throughout this classical solution we define an evolution operator on the space of bounded and continuous functions. Further, we prove continuity properties of the evolution operator and that, under additional hypotheses, it is compact on, No, open, Addona, Addona, D

open, The main problem this thesis deals with is the characterization of profinite groups which are realizable as absolute Galois groups of fields: this is currently one of the major problems in Galois theory. Usually one reduces the problem to the pro-p case, i.e., one would like to know which pro-p groups occur as maximal pro-p Galois groups, i.e., maximal pro-p quotients of absolute Galois groups. Indeed, pro-p groups are easier to deal with than general profinite groups, yet they carry a lot of information on the whole absolute Galois group. We define a new class of pro-p groups, called Bloch-Kato pro-p group, whose Galois cohomology satisfies the consequences of the Bloch-Kato conjecture. Also we introduce the notion of cyclotomic orientation for a pro-p group. With this approach, we are able to recover new substantial information about the structure of maximal pro-p Galois groups, and in particular on theta-abelian pro-p groups, which represent the "upper bound" of such groups. Also, we study the restricted Lie algebra and the universal envelope induced by the Zassenhaus filtration of a maximal pro-p Galois group, and their relations with Galois cohomology via Koszul duality. Altogether, this thesis provides a rather new approach to maximal pro-p Galois groups, besides new substantial results., No, open, Quadrelli, Quadrelli, C

Complex Systems and Artificial Intelligence (CSAI), 4413, open, The thesis work is organized in two main parts. The first includes a review of the social science framework about crowd dynamics and proxemics, and the methodological approach. The second part consists of several empirical studies. A summary of the contents is provided as follows. Starting from the pioneering study of Gustave Le Bon (1897), the social science contributions about crowds are reviewed in Chapter 2 (Contagion-Transformation Theory, Elaborated Social Identity Model, Emergent Norm Theory, Affiliative Approach). Chapter 3 presents the proxemic theory, with reference to the notion of personal space and the group proxemic behavior in static and motion situations. Chapter 4 presents the methodological approach, as composed of: in vivo observation, in vitro experiments and in silico simulations. Chapter 5 proposed the results achieved by means of two observations performed at the Campus of the University of Milano-Bicocca (Italy) and the Vittorio Emanuele II gallery (Milan, Italy). Chapter 6 presents two experiments focused on the combined impact of turning path and grouping on pedestrian crowd dynamics and the size of pedestrian personal space. Chapter 7 presents a simulation campaign performed by using the platform MAKKSim. The results achieved have been compared with the collected empirical data for sake of model validation. The thesis ends with final remarks about the achieved results and future works towards the improvement of the computational model of MAKKSim., No, open, Gorrini, Gorrini, A

The projec developed in collaboration with Professor D.Mari, Ospedale Maggiore Policlinico of Milan, the expert advice on anticoagulation in elderly, open, A machine learning investigation on Oral Anticoagulation Therapy (OAT) in elderly patients to improve the dynamic network modelization of the bioclinical process of coagulation cascade. We compared and tested techniques of supervised Machine Learning for classification and regression analysis, in order to develop an innovative model, compared to those currently available in the literature. The results of this investigation can provide adequate support for dual purpose: give an advantage in managing the therapy in patients with an increased risk of adverse drug events (ADRs), as elderly patients are; define pharmacodynamics characteristics of the drug employed in the oral anticoagulant therapy to finely configure a mechanistic model of involved pathway, providing further insights in therapy management. Therefore, simultaneously, we investigated and tested techniques of modeling and simulation in order to analyze the system in terms of both structure and dynamics to specify the qualitative and quantitative properties of the system. Such an approach would make it possible to profile a manageable model of the coagulation cascade which is able to adapt to the need for integration of recent pharmacological and genetic data, distinctive of modern pharmacogenomic characterization of anticoagulant therapy. Among the different mathematical modeling frameworks that have evaluated, the Temporal Extension of Petri Nets (Timed Petri Net), in particular the Stochastic Petri Net (SPN), seem to offer the most suitable characteristics. They permit an approach to modelization, combining an intuitive graphical representation to a valid solid mathematical, which give rise to a model numerically solving, able to represent the relational components and the quantitative time-dependent behaviors, including randomness, of a complex biological system such as coagulation cascade. The employment of such a framework, compared to the most popular models to differential equations provides a tool t, No, open, Castaldi, Castaldi, D

open, Since its standardization by the World Wide Web Consortium (W3C) in 1998, the XML (acronym for eXtensible Markup Language) has been acknowledged as the de-facto standard format for data, besides being a data format employed by a wide and increasing number of application domains. XML allows data and textual contents to be structured; the structural elements are specified in plain text using strings of characters that can be easily read by computer programs, while maintaining human-readability. XPath and XQuery represent the two main standard languages that have been defined to inquire XML data; the two languages allow to select a subset of elements from an XML document, and to further manipulate its contents and to restructure the document tree form. Both XPath and XQuery are based on a Database perspective of XML documents, where the evaluation of the query clauses is performed like in the database query language SQL, from which both the XML languages took inspiration. The data-centric perspective adopted by the XQuery and XPath languages has been recently extended by an Information Retrieval oriented approach, where a new set of content-based constraints have been defined that allow a full-text search in an IR-style, with an element relevance scoring computation. This extension is called XQuery/XPath Full-Text and has been standardized by the W3C. In the Information Retrieval community other approaches have appeared that take into account the document structure and propose a set of approximate structural matching techniques, where the standard XQuery and XPath structural constraints are evaluated by path relaxation algorithms. Such approaches, however, do not offer the user the possibility to express vague structural constraints the approximate evaluation of which produces a set of weighted fragments, where the weight express the relevance of the fragment with respect to the structural constraints. This thesis describes the definition and the implementation of a fo, No, open, Panzeri, Panzeri, E

Dipartimento di Informatica, Sistemistica e Comunicazione; Imaging and Vision Laboratory, open, This thesis focuses on No Reference (NR) methods for Image Quality Assessment (IQA). A review of the IQA field is presented in Chapter 2; where the different IQA methods are described and classified. In particular, the application of IQA methods within a workflow chain is discussed. In Chapter 3 we focus on NR metrics for JPEG-blockiness and noise artifacts. It is in general assumed that subjective methods produce an actual estimate of the perceived quality while objective methods produce values that should be correlated with human perceptions as best as possible. From the analysis of the regression curves that correlate objective and subjective data we have found that in some cases the metric's predictions are not in correspondence with the subjective scores. After reviewing the available databases, we realize that the distortion ranges considered are not in general representative of real case applications. Therefore, in Chapter 4 the Imaging and Vision Lab (IVL) database is introduced. It was generated with the aim of assessing the quality of images corrupted by JPEG and noise. In Chapter 5 we approach the NR-IQA field by focusing on a classification problem. A framework based on machine learning classification is proposed that let us evaluate how images can be classified within different groups or classes, according to their quality. NR metrics are considered as features and the assigned classes are obtained from the psychovisual data. For the JPEG distortion case, the feature space of the classifiers is built using each NR metric as single feature and also a pool of eleven NR metrics. Classification within five and three classes was addressed. In the former case, the five classes are in correspondence to the five categories recommended by the ITU (excellent, good, fair, poor, and bad) when designing image quality experiments. In the latter case we were interested in classifying images as high, medium or low quality ones. The classifiers are trained and tested on, No, open, Corchs, Corchs, S

Tutor: Chiarissimo Prof. Giorgio De Michelis, 4401, open, Documents are a fundamental player in professional practices. Since the introduction of computer-based systems, an ever increasing number of organizations considered the full transition to digital documents in order to manage the exponential amount of information that they generate with their activities. However, this "imposed" transition has not been painless: usually the employees work together to reach a common goal, and during time they develop and constantly maintain some unwritten conventions with the aim to support them in performing their collaborative activities. Several field studies demonstrated that in these work settings documents are a fundamental part of these conventions, highlighting at the same time the problems that arose after the transition to a document-based system. Actually, the flexibility of paper-based documents is lost with the transitions to digital documents, since employees can not autonomously adapt both the informative content and the arrangement of their digital documents. Consequently, the limits of document-based systems hinder their acceptance among employees, with the risk of nullifying the advantages that the organization management expected with the transition to digital documents. In order to avoid this kind of problems, collaborative systems should be conceived to not force users to change their work habits, and in particular these systems should provide users with (i) a flexible support for their work practices, taking into account the existence of local and informal conventions and proactively promoting "collaboration awareness" among users, and (ii) a customizable environment that they can autonomously adapt to their actual and constantly evolving needs. These two requirements are at the basis of the work that is presented in this thesis, which focuses on document-based collaborative systems. In order to meet such requirements in the design of this kind of applications, this work puts its roots in both the Computer-Suppor, open, Gesso, Gesso, I

DELLA VEDOVA, GIANLUCA, 4401, open, Two of the main bioinformatics fields that have been influenced by the introduction of the Next-Generation Sequencing (NGS) techniques are transcriptomics and metagenomics. The adoption of these new methods to sequence DNA/RNA molecules has drastically changed the kind and also the amount of produced data. The effect is that all the developed algorithms and tools working on traditional data cannot be applied on NGS data. For this reason, in this thesis we face two central problems in two fields: transcriptmics and metagenomics. The first one regards the characterization of the Alternative Splicing (AS) events starting from NGS sequences coming from transcripts (called RNA-Seq reads). To this aim we have modeled the structure of a gene, with respect to the AS variations occurring in it, by using a graph representation (called splicing graph). More specifically, we have identified the conditions for the correct reconstruction of the splicing graph, starting from RNA-Seq data, and we have realized an algorithm for its construction. Moreover, our method is able to correct reconstruct the splicing graph even when the input RNA-Seq reads do not respect the identified conditions. Finally, we have performed an experimental analysis of our procedure in order to validated the obtained results. The second problem we face in this thesis is the assignment of NGS read, coming from a metagenomic sample, to a reference taxonomic tree, in order to assess the composition of the sample and classify the unknown micro-organisms in it. This is done by aligning the reads to the taxonomic tree and then choosing (when there are more valid matches) the node that best represents the read. This choice is based on the calculation of a Penalty Score (PS) function for all the nodes descending from the lowest common ancestor of the valid matches in the tree. We have realized an optimal algorithm for the computation of the PS function, based on the so called skeleton tree, which improve the perform, open, Beretta, Beretta, S

TOMMASSINI, ADRIANO, MEDORI, COSTANTINO, 4402, open, We study some properties of Double Manifold, or D-Manifolds. In particular, we study of deformations of D-structures and of CR D-structures, and we found a condition which is equivalent to the classical Maurer-Cartan equation describing the integrability of the deformations. We also focus on the cohomological properties of D-Manifold, showing that a del-delbar-Lemma can not hold for any compact D-Manifold. We also state some properties of special subgroups of de-Rham cohomology, studing also their behaviour under small deformations. Finally, a result by Harvey and Lawson about the minimal Lagrangian Submanifold of a D-Kahler Ricci-flat manifold is generalized to the case of a special almost D-complex symplectic manifold., In questa tesi studiamo alcune proprietà delle "Varietà Doppie" o D-Varietà. In particolare studiamo la teoria delle deformazioni di D-Strutture e di D-Strutture CR, e troviamo una condizione che è equivalente alla classica condizione di Maurer-Cartan che descrive l'integrabilità di deformazioni di D-Strutture. Successivamente prestiamo attenzione alla coomologia delle D-Varietà, provando che una versione D-complessa del del-delbar-Lemma non può essere vera per D-varietà compatte. Inoltre sono stabilite alcune proprietà di sottogruppi speciali della coomologia di de-Rham, ottenute studiando il loro comportamento sotto l'azione di deformazioni. Infine, un risultato riguardante le sottovarietà Lagrangiane minimali dovuto ad Harvey e Lawson riguardante le varietà D-Kahler Ricci-Piatte è generalizzato a una classe di varietà simplettiche quasi D-complesse., open, Rossi, Rossi, F

4401, open, Since its birth, Computer Science has been inspired by natural phenomena. Two main approaches where developed through the years. The first one is concerned with the study of the properties nature-inspired models that can also be used to model nature. Examples in this fields are Cellular Automata and Reaction Systems. The second one uses nature-inspired model to perform optimization tasks where exact algorithms are not applicable. Evolutionary algorithms, like Genetic Algorithms and Genetic Programming are some of the most prominent examples. The main aim of this thesis is the study of the dynamics of four different nature-inspired models with the goal of providing both an improvement in the single areas and a cross-pollination of methods and techniques. The four chosen models are: Genetic Algorithms. A traditional optimization techniques that is inspired by the Darwinian theory of evolution. Genetic Programming. A more recent technique, similar to classical Genetic Algorithms, that uses programs instead of fixed length binary strings as a representation method. Reaction Systems. A recently developed formalism inspired by chemical reactions. Cellular Automata. A extensively studied model made of a lattice of identical automata that can exchange information only locally. As for Genetic Algorithm, one of their main operators, the crossover, was studied. In particular, the minimum number of iteration of the crossover operator needed to produce certain individuals was investigated. As for Genetic Programming, two new measures to quantify the quality of the solution learned were developed. To better understand the dynamics of Genetic Programming a new benchmark, inspired by a similar benchmark in Genetic Algorithms, was introduced. Finally, a method to reduce the worst case space requirements of Semantic Genetic Programming from exponential to polynomial was devised. Some combinatorial properties of Reaction Systems were studied. Furthermore, an evolutionary version of Re, open, Manzoni, Manzoni, L

1712, open, The main objective of design pattern detection is to gain better comprehension of a software system, and of the kind of problems addressed during the development of the system itself. Design patterns have informal specifications, leading to many implementation variants caused by the subjective interpretation of the pattern by developers. This thesis applies a supervised classification approach to make the detection more subjective, bringing to developers the patterns they want to find, ranked by a confidence value., open, Zanoni, Zanoni, M

Images are playing a more and more important role in sharing, expressing, mining and exchanging information in our daily lives. Now we can all easily capture and share images anywhere and anytime. Since digital images are subject to a wide variety of distortions during acquisition, processing, compression, storage, transmission and reproduction; it becomes necessary to assess the Image Quality. In this thesis, starting from an organized overview of available Image Quality Assessment methods, some original contributions in the framework of No-reference image quality metrics are described., 1712, open, open, Marini, Marini, F

Membrane systems (also called P systems) are unconventional, parallel computing devices inspired by the internal working of biological cells. Some variants of membrane systems (in particular, P systems with elementary active membranes) have been known to be able to solve NP-complete problems in polynomial time by trading space for time, exploring in parallel the whole exponential-size space of candidate solutions. Here we provide a formal notion of space complexity for P systems, in order to be able to prove results about the computing power and limitations of P systems with active membranes working in bounded space. As a result, we show that P systems working in polynomial space solve exactly the same problem as Turing machines working in polynomial space. Furthermore, we show that P systems with elementary active membranes running in exponential space not only solve NP-complete problems in polynomial time, but also counting problems and the whole polynomial hierarchy., 1712, open, open, Porreca, Porreca, A

Symmetry properties of solutions to some nonlinear Schroedinger equations are investigated. In particular, here the Laplace operator is perturbed by singular potentials which do not belong to the Kato class. A result of symmetry breaking of solutions is obtained provided a preliminary theorem about biradial solutions is stated. Further, a problem involving the biharmonic operator and exponential nonlinearity in dimension 4 is studied, connecting degree counting formulas with direct methods of calculus of variations via Morse theory and deformation lemmas., 1718, open, open, Abatangelo, Abatangelo, L

In movement science with inertial sensor many different methodologies resolving specific aspects of movement recognition have been proposed. They are very interesting, and useful, but none of them are generally explicative of what is going on in the semantic sense. When we go down to the movement recognition/classification area (for example in Ambient Intelligence) we do not have a feasible model that can be considered generally predictive or usable for activity recognition. Also, in the field of movement recognition with inertial sensors many technological issues arise: technological diversity, calibration matters, sensor model problems, orientation and position of sensors, and a lot of numerous specificities that, with all the above aspects, and the lack of public dataset of movements sufficiently generic and semantically rich, contribute to create a strong barrier to any approach to a classification matters with wearable sensors. We have also to notice that a movement is a phenomenon explicitly or implicitly (voluntary or involuntary) controlled by brain. The individual free-will introduce a further matter when we want to temporary predict the movements looking at the close past. Pattern can change at any time when ambient, psychological context, age of the subject change. Also, pathological issues, and physiological differences and the will of the subject, introduce important differences. For all these reasons I considered that a semantical /lexical approach to movement recognition with sensors, driven by machine learning techniques could be a promising way to solve some of these challenge and problems. In this Ph.D. Thesis wearable inertial sensors has been used to classify movements, the choice of inertial sensors has been driven by technological and practical advantages, they are cheap, lightweight, and - differently from video cameras - are not prone to the hidden face, or luminance problems. The main idea is to use inertial sensor to understand what a perso, Nomadis, NomadisLab, Università di Milano Bicocca., 1712, open, open, Pinardi, Pinardi, S

Clustering is one of the most common machines learning technique, which has been widely applied in genomics, proteomics and more generally in Life Sciences. In particular, clustering is an unsupervised technique that, based on geometric concepts like distance or similarity, partitions objects into groups, such that objects with similar characteristics are clustered together and dissimilar objects are in different clusters. In many domains where clustering is applied, some background knowledge is available in different forms: labelled data (specifying the category to which an instance belongs); complementary information about "true" similarity between pairs of objects or about the relationships structure present in the input data; user preferences (for example specifying whether two instances should be in same or different clusters). In particular, in many real-world applications like biological data processing, social network analysis and text mining, data do not exist in isolation, but a rich structure of relationships subsists between them. A simple example can be viewed in biological domain, where there are al lot of relationships between genes and proteins based on many experimental conditions. Another example, maybe common, is the Web search domain where there are relations between documents and words in a text or web pages, search queries and web users. Our research is focalized on how this background knowledge can be incorporated into traditional clustering algorithms to optimize the process of pattern discovery (clustering) between instances. In this thesis, we first provide an overview of traditional clustering methods with some important distance measures and then we analyze three particular challenges that we try to overcome with different proposed methods: "feature selection" to reduce high dimensional input space and remove noise from data; "mixed data types" to handle in clustering procedure both numeric and categorical values, typically of life scienc, Il lavoro di tesi è stato svolto all'interno del laboratorio MIND (Models In Decision Making and Data Analysis), ARCHETTI, FRANCESCO, 1712, open, open, Giordani, Giordani, I

After the first draft of the human genome has been published, the study of genetic variations has attracted increasing attention as a medium to map observable characteristics (phenotypic traits) of individuals to their underlying genes and biological processes. Unfortunately, observing and obtaining directly the genetic data of interest is a long and expensive operation, especially for large populations. Less informative sources of data are instead available at a fraction of cost. Computational methods are then called to recover the original data of interest from their less informative observations. The design of efficient combinatorial algorithms to infer relevant data for genetic variation studies starting from less informative observations is the main aim of the work of this thesis. In particular, we focused on two different kinds of data of crucial importance for genetic variation studies: haplotypes and transcripts. In the first part of the thesis, we studied the Haplotype Inference (HI) problem that requires to infer, for each individual of a population, the genetic sequences inherited from each parent (haplotypes) starting from their conflation (genotype). We formulated and analyzed two different computational problems of haplotype inference: the pure parsimony xor-haplotyping problem (PPXH) and the minimum event haplotype configuration problem (MinEHC). In the first problem, the haplotype inference process is guided by the pure parsimony criterion and it starts from a recently proposed representation of genotypes, called xor-genotypes. For this problem, we presented exact and approximate solutions by providing (i) polynomial time exact algorithms for some restricted cases, (ii) a fixed-parameter algorithm for the general case, and (iii) a polynomial time k-approximation algorithm, where k is the maximum number of heterozygous individuals at a given marker locus. These results are based on some interesting combinatorial properties of a graph representation of, 1712, open, open, Pirola, Pirola, Y

This PhD thesis is concerned with applications of nonlinear systems of conservation laws to gas dynamics and traffic flow modeling. The first part is devoted to the analytical description of a fluid flowing in a tube with varying cross section. We study the 2x2 model of the p-system and than, we extend the properties to the full 3x3 Euler system. We also consider a general nxn strictly hyperbolic system of balance laws; we study the Cauchy problem for this system and we apply this result to the fluid flow in a pipe wiyh varying section. Concerning traffic flow, we introduce a new macroscopic model, based on a non-smooth 2x2 system of conservation laws. We study the Riemann problem for this system and the qualitative properties of its solutions that are relevant from the point of view of traffic., COLOMBO, RINALDO M., 1718, open, open, Marcellini, Marcellini, F

The image recorded by a digital camera mainly depends on three factors: the physical content of the scene, the illumination incident on the scene, and the characteristics of the camera. This leads to a problem for many applications where the main interest is in the color rendition accuracy of the scene acquired. It is known that the color reproduction accuracy of a digital imaging acquisition device is a key factor to the overall perceived image quality, and that there are mainly two modules responsible for it: the former is the illuminant estimation and correction module, the latter is the color matrix transformation. These two modules together form what may be called the color correction pipeline. This thesis has the objective to design and test new and more robust modules for the color correction pipeline, studying and exploiting the existing crosstalks in order to obtain a higher color reproduction accuracy. The first module considered is the illuminant estimation and correction one; many illuminant estimation solutions have been proposed in the last few years, although it is known that the problem addressed is actually ill-posed as its solution lack uniqueness or stability. To cope with this problem, different solutions usually exploit some assumptions about the statistical properties of the expected illuminants and/or of the object reflectances in the scene. In the last few years two research areas that are important in the context of improving the performance of color constancy algorithms have been highlighted: making additional measurements at the time of image capture (i.e. using more color pixel information), and algorithm combining (i.e. using two or more estimations of the illuminants). In this thesis a third hypothesis is investigated: the use of low level visual information to improve illuminant estimation. The second module considered is the transformation of the camera-dependent RGB image data into a standard RGB color space. This transformation, usu, 1712, open, open, Bianco, Bianco, S