2,140 research outputs found

    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

    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

    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

    The success probability in Levine's hat problem, and independent sets in graphs

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    Lionel Levine's hat challenge has tt players, each with a (very large, or infinite) stack of hats on their head, each hat independently colored at random black or white. The players are allowed to coordinate before the random colors are chosen, but not after. Each player sees all hats except for those on her own head. They then proceed to simultaneously try and each pick a black hat from their respective stacks. They are proclaimed successful only if they are all correct. Levine's conjecture is that the success probability tends to zero when the number of players grows. We prove that this success probability is strictly decreasing in the number of players, and present some connections to problems in graph theory: relating the size of the largest independent set in a graph and in a random induced subgraph of it, and bounding the size of a set of vertices intersecting every maximum-size independent set in a graph.Comment: arXiv admin note: substantial text overlap with arXiv:2103.01541, arXiv:2103.0599

    A precise condition for independent transversals in bipartite covers

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    Given a bipartite graph H=(V=VAVB,E)H=(V=V_A\cup V_B,E) in which any vertex in VAV_A (resp. VBV_B) has degree at most DAD_A (resp. DBD_B), suppose there is a partition of VV that is a refinement of the bipartition VAVBV_A\cup V_B such that the parts in VAV_A (resp. VBV_B) have size at least kAk_A (resp. kBk_B). We prove that the condition DA/kA+DB/kB1D_A/k_A+D_B/k_B\le 1 is sufficient for the existence of an independent set of vertices of HH that is simultaneously transversal to the partition, and show moreover that this condition is sharp. This result is a bipartite refinement of two well-known results on independent transversals, one due to the second author the other due to Szab\'o and Tardos.Comment: 10 pages, 2 figure

    Borel versions of the Local Lemma and LOCAL algorithms for graphs of finite asymptotic separation index

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    Asymptotic separation index is a parameter that measures how easily a Borel graph can be approximated by its subgraphs with finite components. In contrast to the more classical notion of hyperfiniteness, asymptotic separation index is well-suited for combinatorial applications in the Borel setting. The main result of this paper is a Borel version of the Lov\'asz Local Lemma -- a powerful general-purpose tool in probabilistic combinatorics -- under a finite asymptotic separation index assumption. As a consequence, we show that locally checkable labeling problems that are solvable by efficient randomized distributed algorithms admit Borel solutions on bounded degree Borel graphs with finite asymptotic separation index. From this we derive a number of corollaries, for example a Borel version of Brooks's theorem for graphs with finite asymptotic separation index

    Nonlocal games and their device-independent quantum applications

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    Device-independence is a property of certain protocols that allows one to ensure their proper execution given only classical interaction with devices and assuming the correctness of the laws of physics. This scenario describes the most general form of cryptographic security, in which no trust is placed in the hardware involved; indeed, one may even take it to have been prepared by an adversary. Many quantum tasks have been shown to admit device-independent protocols by augmentation with "nonlocal games". These are games in which noncommunicating parties jointly attempt to fulfil some conditions imposed by a referee. We introduce examples of such games and examine the optimal strategies of players who are allowed access to different possible shared resources, such as entangled quantum states. We then study their role in self-testing, private random number generation, and secure delegated quantum computation. Hardware imperfections are naturally incorporated in the device-independent scenario as adversarial, and we thus also perform noise robustness analysis where feasible. We first study a generalization of the Mermin–Peres magic square game to arbitrary rectangular dimensions. After exhibiting some general properties, these "magic rectangle" games are fully characterized in terms of their optimal win probabilities for quantum strategies. We find that for m×n magic rectangle games with dimensions m,n≥3, there are quantum strategies that win with certainty, while for dimensions 1×n quantum strategies do not outperform classical strategies. The final case of dimensions 2×n is richer, and we give upper and lower bounds that both outperform the classical strategies. As an initial usage scenario, we apply our findings to quantum certified randomness expansion to find noise tolerances and rates for all magic rectangle games. To do this, we use our previous results to obtain the winning probabilities of games with a distinguished input for which the devices give a deterministic outcome and follow the analysis of C. A. Miller and Y. Shi [SIAM J. Comput. 46, 1304 (2017)]. Self-testing is a method to verify that one has a particular quantum state from purely classical statistics. For practical applications, such as device-independent delegated verifiable quantum computation, it is crucial that one self-tests multiple Bell states in parallel while keeping the quantum capabilities required of one side to a minimum. We use our 3×n magic rectangle games to obtain a self-test for n Bell states where one side needs only to measure single-qubit Pauli observables. The protocol requires small input sizes [constant for Alice and O(log n) bits for Bob] and is robust with robustness O(n⁵/²√ε), where ε is the closeness of the ideal (perfect) correlations to those observed. To achieve the desired self-test, we introduce a one-side-local quantum strategy for the magic square game that wins with certainty, we generalize this strategy to the family of 3×n magic rectangle games, and we supplement these nonlocal games with extra check rounds (of single and pairs of observables). Finally, we introduce a device-independent two-prover scheme in which a classical verifier can use a simple untrusted quantum measurement device (the client device) to securely delegate a quantum computation to an untrusted quantum server. To do this, we construct a parallel self-testing protocol to perform device-independent remote state preparation of n qubits and compose this with the unconditionally secure universal verifiable blind quantum computation (VBQC) scheme of J. F. Fitzsimons and E. Kashefi [Phys. Rev. A 96, 012303 (2017)]. Our self-test achieves a multitude of desirable properties for the application we consider, giving rise to practical and fully device-independent VBQC. It certifies parallel measurements of all cardinal and intercardinal directions in the XY-plane as well as the computational basis, uses few input questions (of size logarithmic in n for the client and a constant number communicated to the server), and requires only single-qubit measurements to be performed by the client device

    Jake pozicione igre

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    In this thesis, we study 2-player combinatorial games on graphs. We devote a lot of attention to strong positional games, where both players have the same goal. First, we consider the so-called fixed graph strong Avoider-Avoider game in which two players called Red and Blue alternately claim edges of the complete graph Kn, and the player who first completes a copy of a fixed graph F loses the game. If neither of the players claimed a copy of F in his graph and all the elements of the board are claimed, the game is declared a draw. Even though these games have been studied for decades, there are very few known results. We make a step forward by proving that Blue has a winning strategy it two different games of this kind. Furthermore, we introduce strong CAvoiderCAvoider F games where the claimed edges of each player must form a connected graph throughout the game. This is a natural extension of the strong Avoider-Avoider games, with a connectedness constraint. We prove that Blue can win in three standard CAvoider-CAvoider F games. Next, we study strong Maker-Maker F games, where now, the player who first occupies a copy of F is the winner. It is well-known that the outcome of these games when both players play optimally can be either the first player's win or a draw. We are interested in finding the achievement number a(F) of a strong Maker-Maker F game, that is, the smallest n for which Red has a winning strategy. We can find the exact value a(F) for several graphs F, including paths, cycles, perfect matchings, and a subclass of trees on n vertices. We also give the upper and lower bounds for the achievement number of stars and trees. Finally, we introduce generalized saturation games as a natural extension of two different types of combinatorial games, saturation games and Constructor-Blocker games. In the generalized saturation game, two graphs H and F are given in advance. Two players called Max and Mini alternately claim unclaimed edges of the complete graph Kn and together gradually building the game graph G, the graph that consists of all edges claimed by both players. The graph G must never contain a copy of F, and the game ends when there are no more moves, i.e. when G is a saturated F-free graph. We are interested in the score of this game, that is, the number of copies of the graph H in G at the end of the game. Max wants to maximize this score, whereas Mini tries to minimize it. The game is played under the assumption that both players play optimally. We study several generalized saturation games for natural choices of F and H, in an effort to locate the score of the game as precisely as possible.У овој тези проучавамо комбинаторне игре на графовима које играју 2 играча. Посебну пажњу посвећујемо јаким позиционим играма, у којима оба играча имају исти циљ. Прво, посматрамо такозвану јаку Авојдер-Авојдер игру са задатим фиксним графом у којој два играча, Црвени и Плави наизменично селектују гране комплетног графа Kn, а играч који први селектује копију фиксног графа F губи игру. Ако ниједан од играча не садржи копију од F у свом графу и сви елементи табле су селектовани, игра се проглашава нерешеном. Иако су ове игре проучаване деценијама, врло је мало познатих резултата. Ми смо направили корак напред доказавши да Плави има победничку стратегију у две различите игре ове врсте. Такође, уводимо јаке ЦАвојдер-ЦАвојдер F игре у којима граф сваког играча мора остати повезан током игре. Ово је природно проширење јаких Авојдер-Авојдер игара, са ограничењем повезаности. Доказујемо да Плави може да победи у три стандардне ЦАвојдер-ЦАвојдер F игре. Затим проучавамо јаке Мејкер-Мејкер F игре, у којима је играч који први селектује копију од F победник. Познато је да исход ових игара уколико оба играча играју оптимално може бити или победа првог играча или нерешено. Циљ нам је да пронађемо ачивмент број а(F) јаке Мејкер-Мејкер F игре, односно најмање n за које Црвени има победничку стратегију. Дајемо тачну вредност a(F) за неколико графова F, укључујући путеве, циклусе, савршене мечинге и поткласу стабала са n чворова. Такође, дајемо горње и доње ограничење ачивмент броја за звезде и стабла. Коначно, уводимо уопштене игре сатурације као природно проширење две различите врсте комбинаторних игара, игара сатурације и Конструктор-Блокер игара. У уопштеној игри сатурације унапред су дата два графа H и F. Два играча по имену Макс и Мини наизменично селектују слободне гране комплетног графа Kn и заједно постепено граде граф игре G, који се састоји од свих грана које су селектовала оба играча. Граф G не сме да садржи копију од F, а игра се завршава када више нема потеза, односно када је G сатуриран граф који не садржи F. Занима нас резултат ове игре, односно, број копија графа H у G на крају игре. Макс жели да максимизира овај резултат, док Мини покушава да га минимизира. Игра се под претпоставком да оба играча играју оптимално. Проучавамо неколико уопштених игара сатурације за природне изборе F и H, у настојању да што прецизније одредимо резултат игре.U ovoj tezi proučavamo kombinatorne igre na grafovima koje igraju 2 igrača. Posebnu pažnju posvećujemo jakim pozicionim igrama, u kojima oba igrača imaju isti cilj. Prvo, posmatramo takozvanu jaku Avojder-Avojder igru sa zadatim fiksnim grafom u kojoj dva igrača, Crveni i Plavi naizmenično selektuju grane kompletnog grafa Kn, a igrač koji prvi selektuje kopiju fiksnog grafa F gubi igru. Ako nijedan od igrača ne sadrži kopiju od F u svom grafu i svi elementi table su selektovani, igra se proglašava nerešenom. Iako su ove igre proučavane decenijama, vrlo je malo poznatih rezultata. Mi smo napravili korak napred dokazavši da Plavi ima pobedničku strategiju u dve različite igre ove vrste. Takođe, uvodimo jake CAvojder-CAvojder F igre u kojima graf svakog igrača mora ostati povezan tokom igre. Ovo je prirodno proširenje jakih Avojder-Avojder igara, sa ograničenjem povezanosti. Dokazujemo da Plavi može da pobedi u tri standardne CAvojder-CAvojder F igre. Zatim proučavamo jake Mejker-Mejker F igre, u kojima je igrač koji prvi selektuje kopiju od F pobednik. Poznato je da ishod ovih igara ukoliko oba igrača igraju optimalno može biti ili pobeda prvog igrača ili nerešeno. Cilj nam je da pronađemo ačivment broj a(F) jake Mejker-Mejker F igre, odnosno najmanje n za koje Crveni ima pobedničku strategiju. Dajemo tačnu vrednost a(F) za nekoliko grafova F, uključujući puteve, cikluse, savršene mečinge i potklasu stabala sa n čvorova. Takođe, dajemo gornje i donje ograničenje ačivment broja za zvezde i stabla. Konačno, uvodimo uopštene igre saturacije kao prirodno proširenje dve različite vrste kombinatornih igara, igara saturacije i Konstruktor-Bloker igara. U uopštenoj igri saturacije unapred su data dva grafa H i F. Dva igrača po imenu Maks i Mini naizmenično selektuju slobodne grane kompletnog grafa Kn i zajedno postepeno grade graf igre G, koji se sastoji od svih grana koje su selektovala oba igrača. Graf G ne sme da sadrži kopiju od F, a igra se završava kada više nema poteza, odnosno kada je G saturiran graf koji ne sadrži F. Zanima nas rezultat ove igre, odnosno, broj kopija grafa H u G na kraju igre. Maks želi da maksimizira ovaj rezultat, dok Mini pokušava da ga minimizira. Igra se pod pretpostavkom da oba igrača igraju optimalno. Proučavamo nekoliko uopštenih igara saturacije za prirodne izbore F i H, u nastojanju da što preciznije odredimo rezultat igre

    On the use of senders for minimal Ramsey theory

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    This thesis investigates problems related to extremal and probabilistic graph theory. Our focus lies on the highly dynamic field of Ramsey theory. The foundational result of this field was proved in 1930 by Franck P. Ramsey. It implies that for every integer t and every sufficiently large complete graph Kn, every colouring of the edges of Kn with colours red and blue contains a red copy or a blue copy of Kt. Let q ⩾ 2 represent a number of colours, and let H1,..., Hq be graphs. A graph G is said to be q-Ramsey for the tuple (H1,...,Hq) if, for every colouring of the edges of G with colours {1, . . . , q}, there exists a colour i and a monochromatic copy of Hi in colour i. As we often want to understand the structural properties of the collection of graphs that are q-Ramsey for (H1,..., Hq), we restrict our attention to the graphs that are minimal for this property, with respect to subgraph inclusion. Such graphs are said to be q-Ramsey-minimal for (H1,..., Hq). In 1976, Burr, Erdős, and Lovász determined, for every s, t ⩾ 3, the smallest minimum degree of a graph G that is 2-Ramsey-minimal for (Ks, Kt). Significant efforts have been dedicated to generalising this result to a higher number of colours, q⩾3, starting with the ‘symmetric’ q-tuple (Kt,..., Kt). In this thesis, we improve on the best known bounds for this parameter, providing state-of-the-art bounds in different (q, t)-regimes. These improvements rely on constructions based on finite geometry, which are then used to prove the existence of extremal graphs with certain key properties. Another crucial ingredient in these proofs is the existence of gadget graphs, called signal senders, that were initially developed by Burr, Erdős, and Lovász in 1976 for pairs of complete graphs. Until now, these senders have been shown to exist only in the two-colour setting, when q = 2, or in the symmetric multicolour setting, when H1,..., Hq are pairwise isomorphic. In this thesis, we then construct similar gadgets for all tuples of complete graphs, providing the first known constructions of these tools in the multicolour asymmetric setting. We use these new senders to prove far-reaching generalisations of several classical results in the area
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