3,322 research outputs found

    Computational Analyses of Metagenomic Data

    Get PDF
    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

    Stretching demi-bits and nondeterministic-secure pseudorandomness

    Get PDF
    We develop the theory of cryptographic nondeterministic-secure pseudorandomness beyond the point reached by Rudich's original work [25], and apply it to draw new consequences in average-case complexity and proof complexity. Specifically, we show the following: Demi-bit stretch: Super-bits and demi-bits are variants of cryptographic pseudorandom generators which are secure against nondeterministic statistical tests [25]. They were introduced to rule out certain approaches to proving strong complexity lower bounds beyond the limitations set out by the Natural Proofs barrier of Razborov and Rudich [23]. Whether demi-bits are stretchable at all had been an open problem since their introduction. We answer this question affirmatively by showing that: every demi-bit b : {0, 1}n → {0, 1}n+1 can be stretched into sublinear many demi-bits b′: {0, 1}n → {0, 1}n+nc , for every constant 0 < c < 1. Average-case hardness: Using work by Santhanam [26], we apply our results to obtain new averagecase Kolmogorov complexity results: we show that Kpoly[n-O(1)] is zero-error average-case hard against NP/poly machines iff Kpoly[n-o(n)] is, where for a function s(n) : N → N, Kpoly[s(n)] denotes the languages of all strings x ∈ {0, 1}n for which there are (fixed) polytime Turing machines of description-length at most s(n) that output x. Characterising super-bits by nondeterministic unpredictability: In the deterministic setting, Yao [31] proved that super-polynomial hardness of pseudorandom generators is equivalent to ("nextbit") unpredictability. Unpredictability roughly means that given any strict prefix of a random string, it is infeasible to predict the next bit. We initiate the study of unpredictability beyond the deterministic setting (in the cryptographic regime), and characterise the nondeterministic hardness of generators from an unpredictability perspective. Specifically, we propose four stronger notions of unpredictability: NP/poly-unpredictability, coNP/poly-unpredictability, ∩-unpredictability and ∪unpredictability, and show that super-polynomial nondeterministic hardness of generators lies between ∩-unpredictability and ∪unpredictability. Characterising super-bits by nondeterministic hard-core predicates: We introduce a nondeterministic variant of hard-core predicates, called super-core predicates. We show that the existence of a super-bit is equivalent to the existence of a super-core of some non-shrinking function. This serves as an analogue of the equivalence between the existence of a strong pseudorandom generator and the existence of a hard-core of some one-way function [8, 12], and provides a first alternative characterisation of super-bits. We also prove that a certain class of functions, which may have hard-cores, cannot possess any super-core

    Algorithms and complexity for approximately counting hypergraph colourings and related problems

    Get PDF
    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

    Get PDF
    LIPIcs, Volume 251, ITCS 2023, Complete Volum

    Testing Serial Independence of Object-Valued Time Series

    Full text link
    We propose a novel method for testing serial independence of object-valued time series in metric spaces, which is more general than Euclidean or Hilbert spaces. The proposed method is fully nonparametric, free of tuning parameters, and can capture all nonlinear pairwise dependence. The key concept used in this paper is the distance covariance in metric spaces, which is extended to auto distance covariance for object-valued time series. Furthermore, we propose a generalized spectral density function to account for pairwise dependence at all lags and construct a Cramer-von Mises type test statistic. New theoretical arguments are developed to establish the asymptotic behavior of the test statistic. A wild bootstrap is also introduced to obtain the critical values of the non-pivotal limiting null distribution. Extensive numerical simulations and two real data applications are conducted to illustrate the effectiveness and versatility of our proposed method

    Bounded Relativization

    Get PDF
    Relativization is one of the most fundamental concepts in complexity theory, which explains the difficulty of resolving major open problems. In this paper, we propose a weaker notion of relativization called bounded relativization. For a complexity class ?, we say that a statement is ?-relativizing if the statement holds relative to every oracle ? ? ?. It is easy to see that every result that relativizes also ?-relativizes for every complexity class ?. On the other hand, we observe that many non-relativizing results, such as IP = PSPACE, are in fact PSPACE-relativizing. First, we use the idea of bounded relativization to obtain new lower bound results, including the following nearly maximum circuit lower bound: for every constant ? > 0, BPE^{MCSP}/2^{?n} ? SIZE[2?/n]. We prove this by PSPACE-relativizing the recent pseudodeterministic pseudorandom generator by Lu, Oliveira, and Santhanam (STOC 2021). Next, we study the limitations of PSPACE-relativizing proof techniques, and show that a seemingly minor improvement over the known results using PSPACE-relativizing techniques would imply a breakthrough separation NP ? L. For example: - Impagliazzo and Wigderson (JCSS 2001) proved that if EXP ? BPP, then BPP admits infinitely-often subexponential-time heuristic derandomization. We show that their result is PSPACE-relativizing, and that improving it to worst-case derandomization using PSPACE-relativizing techniques implies NP ? L. - Oliveira and Santhanam (STOC 2017) recently proved that every dense subset in P admits an infinitely-often subexponential-time pseudodeterministic construction, which we observe is PSPACE-relativizing. Improving this to almost-everywhere (pseudodeterministic) or (infinitely-often) deterministic constructions by PSPACE-relativizing techniques implies NP ? L. - Santhanam (SICOMP 2009) proved that pr-MA does not have fixed polynomial-size circuits. This lower bound can be shown PSPACE-relativizing, and we show that improving it to an almost-everywhere lower bound using PSPACE-relativizing techniques implies NP ? L. In fact, we show that if we can use PSPACE-relativizing techniques to obtain the above-mentioned improvements, then PSPACE ? EXPH. We obtain our barrier results by constructing suitable oracles computable in EXPH relative to which these improvements are impossible

    Economic preferences in the health setting. Three case studies concerning the needs of breast cancer patients, pain management in oncology and extreme end-of-life decisions

    Get PDF
    The thesis describes three studies concerning the role of the Economic Preference set investigated in the Global Preference Survey (GPS) in the following cases: 1) the needs of women with breast cancer; 2) pain undertreament in oncology; 3) legal status of euthanasia and assisted suicide. The analyses, based on regression techniques, were always conducted on the basis of aggregate data and revealed in all cases a possible role of the Economic Preferences studied, also resisting the concomitant effect of the other covariates that were considered from time to time. Regarding individual studies, the related conclusion are: 1) Economic Preferences appear to play a role in influencing the needs of women with breast cancer, albeit of non-trivial interpretation, statistically "resisting" the concomitant effect of the other independent variables considered. However, these results should be considered preliminary and need further confirmation, possibly with prospective studies conducted at the level of the individual; 2) the results show a good degree of internal consistency with regard to pro-social GPS scores, since they are all found to be non-statistically significant and united, albeit only weakly in trend, by a negative correlation with the % of pain undertreated patients. Sharper, at least statistically, is the role of Patience and Willingness to Take Risk, although of more complex empirical interpretation. 3) the results seem to indicate an obvious role of Economic Preferences, however difficult to interpret empirically. Less evidence, at least on the inferential level, emerged, however, regarding variables that, based on common sense, should play an even more obvious role than Economic Preferences in orienting attitudes toward euthanasia and assisted suicide, namely Healthcare System, Legal Origin, and Kinship Tightness; striking, in particular, is the inability to prove a role for the dominant religious orientation even with a simple bivariate analysis

    Locality and Exceptional Points in Pseudo-Hermitian Physics

    Get PDF
    Pseudo-Hermitian operators generalize the concept of Hermiticity. Included in this class of operators are the quasi-Hermitian operators, which define a generalization of quantum theory with real-valued measurement outcomes and unitary time evolution. This thesis is devoted to the study of locality in quasi-Hermitian theory, the symmetries and conserved quantities associated with non-Hermitian operators, and the perturbative features of pseudo-Hermitian matrices. An implicit assumption of the tensor product model of locality is that the inner product factorizes with the tensor product. Quasi-Hermitian quantum theory generalizes the tensor product model by modifying the Born rule via a metric operator with nontrivial Schmidt rank. Local observable algebras and expectation values are examined in chapter 5. Observable algebras of two one-dimensional fermionic quasi-Hermitian chains are explicitly constructed. Notably, there can be spatial subsystems with no nontrivial observables. Despite devising a new framework for local quantum theory, I show that expectation values of local quasi-Hermitian observables can be equivalently computed as expectation values of Hermitian observables. Thus, quasi-Hermitian theories do not increase the values of nonlocal games set by Hermitian theories. Furthermore, Bell's inequality violations in quasi-Hermitian theories never exceed the Tsirelson bound of Hermitian quantum theory. A perturbative feature present in pseudo-Hermitian curves which has no Hermitian counterpart is the exceptional point, a branch point in the set of eigenvalues. An original finding presented in section 2.6.3 is a correspondence between cusp singularities of algebraic curves and higher-order exceptional points. Eigensystems of one-dimensional lattice models admit closed-form expressions that can be used to explore the new features of non-Hermitian physics. One-dimensional lattice models with a pair of non Hermitian defect potentials with balanced gain and loss, Δ±iγ, are investigated in chapter 3. Conserved quantities and positive-definite metric operators are examined. When the defects are nearest neighbour, the entire spectrum simultaneously becomes complex when γ increases beyond a second-order exceptional point. When the defects are at the edges of the chain and the hopping amplitudes are 2-periodic, as in the Su-Schrieffer-Heeger chain, the PT-phase transition is dictated by the topological phase of the system. In the thermodynamic limit, PT-symmetry spontaneously breaks in the topologically non-trivial phase due to the presence of edge states. Chiral symmetry and representation theory are utilized in chapter 4 to derive large classes of pseudo-Hermitian operators with closed-form intertwining operators. These intertwining operators include positive-definite metric operators in the quasi-Hermitian case. The PT-phase transition is explicitly determined in a special case

    Optical ground receivers for satellite based quantum communications

    Get PDF
    Cryptography has always been a key technology in security, privacy and defence. From ancient Roman times, where messages were sent cyphered with simple encoding techniques, to modern times and the complex security protocols of the Internet. During the last decades, security of information has been assumed, since classical computers do not have the power to break the passwords used every day (if they are generated properly). However, in 1984, a new threat emerged when Peter Shor presented the Shor’s algorithm, an algorithm that could be used in quantum computers to break many of the secure communication protocols nowadays. Current quantum computers are still in their early stages, with not enough qubits to perform this algorithm in reasonable times. However, the threat is present, not future, since the messages that are being sent by important institutions can be stored, and decoded in the future once quantum computers are available. Quantum key distribution (QKD) is one of the solutions proposed for this threat, and the only one mathematically proven to be secure with no assumptions on the eavesdropper power. This optical technology has recently gained interest to be performed with satellite communications, the main reason being the relative ease to deploy a global network in this way. In satellite QKD, the parameter space and available technology to optimise are very big, so there is still a lot of work to be done to understand which is the optimal way to exploit this technology. This dissertation investigates one of these parameters, the encoding scheme. Most satellite QKD systems use polarisation schemes nowadays. This thesis presents for the first time an experimental work of a time-bin encoding scheme for free-space receivers within a full QKD system in the second chapter. The third and fourth chapter explore the advantages of having multi-protocol free-space receivers that can boost the interoperability between systems, polarisation filtering techniques to reduce background. Finally, the last chapter presents a new technology that can help increase communications rates
    corecore