7,081 research outputs found

    Decomposition of sequential and concurrent models

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    Le macchine a stati finiti (FSM), sistemi di transizioni (TS) e le reti di Petri (PN) sono importanti modelli formali per la progettazione di sistemi. Un problema fodamentale è la conversione da un modello all'altro. Questa tesi esplora il mondo delle reti di Petri e della decomposizione di sistemi di transizioni. Per quanto riguarda la decomposizione dei sistemi di transizioni, la teoria delle regioni rappresenta la colonna portante dell'intero processo di decomposizione, mirato soprattutto a decomposizioni che utilizzano due sottoclassi delle reti di Petri: macchine a stati e reti di Petri a scelta libera. Nella tesi si dimostra che una proprietà chiamata ``chiusura rispetto all'eccitazione" (excitation-closure) è sufficiente per produrre un insieme di reti di Petri la cui sincronizzazione è bisimile al sistema di transizioni (o rete di Petri di partenza, se la decomposizione parte da una rete di Petri), dimostrando costruttivamente l'esistenza di una bisimulazione. Inoltre, è stato implementato un software che esegue la decomposizione dei sistemi di transizioni, per rafforzare i risultati teorici con dati sperimentali sistematici. Nella seconda parte della dissertazione si analizza un nuovo modello chiamato MSFSM, che rappresenta un insieme di FSM sincronizzate da due primitive specifiche (Wait State - Stato d'Attesa e Transition Barrier - Barriera di Transizione). Tale modello trova un utilizzo significativo nella sintesi di circuiti sincroni a partire da reti di Petri a scelta libera. In particolare vengono identificati degli errori nell'approccio originale, fornendo delle correzioni.Finite State Machines (FSMs), transition systems (TSs) and Petri nets (PNs) are important models of computation ubiquitous in formal methods for modeling systems. Important problems involve the transition from one model to another. This thesis explores Petri nets, transition systems and Finite State Machines decomposition and optimization. The first part addresses decomposition of transition systems and Petri nets, based on the theory of regions, representing them by means of restricted PNs, e.g., State Machines (SMs) and Free-choice Petri nets (FCPNs). We show that the property called ``excitation-closure" is sufficient to produce a set of synchronized Petri nets bisimilar to the original transition system or to the initial Petri net (if the decomposition starts from a PN), proving by construction the existence of a bisimulation. Furthermore, we implemented a software performing the decomposition of transition systems, and reported extensive experiments. The second part of the dissertation discusses Multiple Synchronized Finite State Machines (MSFSMs) specifying a set of FSMs synchronized by specific primitives: Wait State and Transition Barrier. It introduces a method for converting Petri nets into synchronous circuits using MSFSM, identifies errors in the initial approach, and provides corrections

    A Unifying Theory for Graph Transformation

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    The field of graph transformation studies the rule-based transformation of graphs. An important branch is the algebraic graph transformation tradition, in which approaches are defined and studied using the language of category theory. Most algebraic graph transformation approaches (such as DPO, SPO, SqPO, and AGREE) are opinionated about the local contexts that are allowed around matches for rules, and about how replacement in context should work exactly. The approaches also differ considerably in their underlying formal theories and their general expressiveness (e.g., not all frameworks allow duplication). This dissertation proposes an expressive algebraic graph transformation approach, called PBPO+, which is an adaptation of PBPO by Corradini et al. The central contribution is a proof that PBPO+ subsumes (under mild restrictions) DPO, SqPO, AGREE, and PBPO in the important categorical setting of quasitoposes. This result allows for a more unified study of graph transformation metatheory, methods, and tools. A concrete example of this is found in the second major contribution of this dissertation: a graph transformation termination method for PBPO+, based on decreasing interpretations, and defined for general categories. By applying the proposed encodings into PBPO+, this method can also be applied for DPO, SqPO, AGREE, and PBPO

    Computational Analyses of Metagenomic Data

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    Metagenomics studies the collective microbial genomes extracted from a particular environment without requiring the culturing or isolation of individual genomes, addressing questions revolving around the composition, functionality, and dynamics of microbial communities. The intrinsic complexity of metagenomic data and the diversity of applications call for efficient and accurate computational methods in data handling. In this thesis, I present three primary projects that collectively focus on the computational analysis of metagenomic data, each addressing a distinct topic. In the first project, I designed and implemented an algorithm named Mapbin for reference-free genomic binning of metagenomic assemblies. Binning aims to group a mixture of genomic fragments based on their genome origin. Mapbin enhances binning results by building a multilayer network that combines the initial binning, assembly graph, and read-pairing information from paired-end sequencing data. The network is further partitioned by the community-detection algorithm, Infomap, to yield a new binning result. Mapbin was tested on multiple simulated and real datasets. The results indicated an overall improvement in the common binning quality metrics. The second and third projects are both derived from ImMiGeNe, a collaborative and multidisciplinary study investigating the interplay between gut microbiota, host genetics, and immunity in stem-cell transplantation (SCT) patients. In the second project, I conducted microbiome analyses for the metagenomic data. The workflow included the removal of contaminant reads and multiple taxonomic and functional profiling. The results revealed that the SCT recipients' samples yielded significantly fewer reads with heavy contamination of the host DNA, and their microbiomes displayed evident signs of dysbiosis. Finally, I discussed several inherent challenges posed by extremely low levels of target DNA and high levels of contamination in the recipient samples, which cannot be rectified solely through bioinformatics approaches. The primary goal of the third project is to design a set of primers that can be used to cover bacterial flagellin genes present in the human gut microbiota. Considering the notable diversity of flagellins, I incorporated a method to select representative bacterial flagellin gene sequences, a heuristic approach based on established primer design methods to generate a degenerate primer set, and a selection method to filter genes unlikely to occur in the human gut microbiome. As a result, I successfully curated a reduced yet representative set of primers that would be practical for experimental implementation

    Routing schemes for hybrid communication networks

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    We consider the problem of computing routing schemes in the HYBRID model of distributed computing where nodes have access to two fundamentally different communication modes. In this problem nodes have to compute small labels and routing tables that allow for efficient routing of messages in the local network, which typically offers the majority of the throughput. Recent work has shown that using the HYBRID model admits a significant speed-up compared to what would be possible if either communication mode were used in isolation. Nonetheless, if general graphs are used as the input graph the computation of routing schemes still takes polynomial rounds in the HYBRID model. We bypass this lower bound by restricting the local graph to unit-disc-graphs and solve the problem deterministically with running time O(|H|2+log⁡n), label size O(log⁡n), and size of routing tables O(|H|2⋅log⁡n) where |H| is the number of “radio holes” in the network. Our work builds on recent work by Coy et al., who obtain this result in the much simpler setting where the input graph has no radio holes. We develop new techniques to achieve this, including a decomposition of the local graph into path-convex regions, where each region contains a shortest path for any pair of nodes in it

    Large cliques or cocliques in hypergraphs with forbidden order-size pairs

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    The well-known Erdős-Hajnal conjecture states that for any graph FF, there exists ϵ>0ϵ>0 such that every nn-vertex graph GG that contains no induced copy of FF has a homogeneous set of size at least nϵn^ϵ. We consider a variant of the Erdős-Hajnal problem for hypergraphs where we forbid a family of hypergraphs described by their orders and sizes. For graphs, we observe that if we forbid induced subgraphs on mm vertices and ff edges for any positive mm and 0f(m2)0≤f≤(m2), then we obtain large homogeneous sets. For triple systems, in the first nontrivial case m=4m=4, for every S0,1,2,3,4S⊆{0,1,2,3,4}, we give bounds on the minimum size of a homogeneous set in a triple system where the number of edges spanned by every four vertices is not in SS. In most cases the bounds are essentially tight. We also determine, for all SS, whether the growth rate is polynomial or polylogarithmic. Some open problems remain

    Self-supervised learning for transferable representations

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    Machine learning has undeniably achieved remarkable advances thanks to large labelled datasets and supervised learning. However, this progress is constrained by the labour-intensive annotation process. It is not feasible to generate extensive labelled datasets for every problem we aim to address. Consequently, there has been a notable shift in recent times toward approaches that solely leverage raw data. Among these, self-supervised learning has emerged as a particularly powerful approach, offering scalability to massive datasets and showcasing considerable potential for effective knowledge transfer. This thesis investigates self-supervised representation learning with a strong focus on computer vision applications. We provide a comprehensive survey of self-supervised methods across various modalities, introducing a taxonomy that categorises them into four distinct families while also highlighting practical considerations for real-world implementation. Our focus thenceforth is on the computer vision modality, where we perform a comprehensive benchmark evaluation of state-of-the-art self supervised models against many diverse downstream transfer tasks. Our findings reveal that self-supervised models often outperform supervised learning across a spectrum of tasks, albeit with correlations weakening as tasks transition beyond classification, particularly for datasets with distribution shifts. Digging deeper, we investigate the influence of data augmentation on the transferability of contrastive learners, uncovering a trade-off between spatial and appearance-based invariances that generalise to real-world transformations. This begins to explain the differing empirical performances achieved by self-supervised learners on different downstream tasks, and it showcases the advantages of specialised representations produced with tailored augmentation. Finally, we introduce a novel self-supervised pre-training algorithm for object detection, aligning pre-training with downstream architecture and objectives, leading to reduced localisation errors and improved label efficiency. In conclusion, this thesis contributes a comprehensive understanding of self-supervised representation learning and its role in enabling effective transfer across computer vision tasks

    Algorithms and complexity for approximately counting hypergraph colourings and related problems

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    The past decade has witnessed advancements in designing efficient algorithms for approximating the number of solutions to constraint satisfaction problems (CSPs), especially in the local lemma regime. However, the phase transition for the computational tractability is not known. This thesis is dedicated to the prototypical problem of this kind of CSPs, the hypergraph colouring. Parameterised by the number of colours q, the arity of each hyperedge k, and the vertex maximum degree Δ, this problem falls into the regime of Lovász local lemma when Δ ≲ qᵏ. In prior, however, fast approximate counting algorithms exist when Δ ≲ qᵏ/³, and there is no known inapproximability result. In pursuit of this, our contribution is two-folded, stated as follows. • When q, k ≥ 4 are evens and Δ ≥ 5·qᵏ/², approximating the number of hypergraph colourings is NP-hard. • When the input hypergraph is linear and Δ ≲ qᵏ/², a fast approximate counting algorithm does exist

    LIPIcs, Volume 251, ITCS 2023, Complete Volume

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    LIPIcs, Volume 251, ITCS 2023, Complete Volum

    On the Power of Threshold-Based Algorithms for Detecting Cycles in the CONGEST Model

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    It is known that, for every k2k\geq 2, C2kC_{2k}-freeness can be decided by a generic Monte-Carlo algorithm running in n11/Θ(k2)n^{1-1/\Theta(k^2)} rounds in the CONGEST model. For 2k52\leq k\leq 5, faster Monte-Carlo algorithms do exist, running in O(n11/k)O(n^{1-1/k}) rounds, based on upper bounding the number of messages to be forwarded, and aborting search sub-routines for which this number exceeds certain thresholds. We investigate the possible extension of these threshold-based algorithms, for the detection of larger cycles. We first show that, for every k6k\geq 6, there exists an infinite family of graphs containing a 2k2k-cycle for which any threshold-based algorithm fails to detect that cycle. Hence, in particular, neither C12C_{12}-freeness nor C14C_{14}-freeness can be decided by threshold-based algorithms. Nevertheless, we show that {C12,C14}\{C_{12},C_{14}\}-freeness can still be decided by a threshold-based algorithm, running in O(n11/7)=O(n0.857)O(n^{1-1/7})= O(n^{0.857\dots}) rounds, which is faster than using the generic algorithm, which would run in O(n11/22)O(n0.954)O(n^{1-1/22})\simeq O(n^{0.954\dots}) rounds. Moreover, we exhibit an infinite collection of families of cycles such that threshold-based algorithms can decide F\mathcal{F}-freeness for every F\mathcal{F} in this collection.Comment: to be published in SIROCCO 202
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