Development of a retroviral strategy that efficiently creates nested chromosomal deletions in mouse embryonic stem cells and its exploitation for functional genomics

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal.

Constructive Synthesis of Memory-Intensive Accelerators for FPGA From Nested Loop Kernels

Field-programmable gate arrays are ideal hosts to custom accelerators for signal, image, and data processing but de- mand manual register transfer level design if high performance and low cost are desired. High-level synthesis reduces this design burden but requires manual design of complex on-chip and off-chip memory architectures, a major limitation in applications such as video processing. This paper presents an approach to resolve this shortcoming. A constructive process is described that can derive such accelerators, including on- and off-chip memory storage from a C description such that a user-defined throughput constraint is met. By employing a novel statement-oriented approach, dataflow intermediate models are derived and used to support simple ap- proaches for on-/off-chip buffer partitioning, derivation of custom on-chip memory hierarchies and architecture transformation to ensure user-defined throughput constraints are met with minimum cost. When applied to accelerators for full search motion estima- tion, matrix multiplication, Sobel edge detection, and fast Fourier transform, it is shown how real-time performance up to an order of magnitude in advance of existing commercial HLS tools is enabled whilst including all requisite memory infrastructure. Further, op- timizations are presented that reduce the on-chip buffer capacity and physical resource cost by up to 96% and 75%, respectively, whilst maintaining real-time performance.

The BEH Mechanism and its Scalar Boson

SCOPUS: re.j

Scalar field dark matter and the Higgs field

We discuss the possibility that dark matter corresponds to an oscillating scalar field coupled to the Higgs boson. We argue that the initial field amplitude should generically be of the order of the Hubble parameter during inflation, as a result of its quasi-de Sitter fluctuations. This implies that such a field may account for the present dark matter abundance for masses in the range 10^-6 - 10^-4 eV, if the tensor-to-scalar ratio is within the range of planned CMB experiments. We show that such mass values can naturally be obtained through either Planck-suppressed non-renormalizable interactions with the Higgs boson or, alternatively, through renormalizable interactions within the Randall–Sundrum scenario, where the dark matter scalar resides in the bulk of the warped extra-dimension and the Higgs is confined to the infrared brane.

Exploiting Nested Parallelism on Heterogeneous Processors

Heterogeneous computing systems have become common in modern processor architectures. These systems, such as those released by AMD, Intel, and Nvidia, include both CPU and GPU cores on a single die available with reduced communication overhead compared to their discrete predecessors. Currently, discrete CPU/GPU systems are limited, requiring larger, regular, highly-parallel workloads to overcome the communication costs of the system. Without the traditional communication delay assumed between GPUs and CPUs, we believe non-traditional workloads could be targeted for GPU execution. Specifically, this thesis focuses on the execution model of nested parallel workloads on heterogeneous systems. We have designed a simulation flow which utilizes widely used CPU and GPU simulators to model heterogeneous computing architectures. We then applied this simulator to non-traditional GPU workloads using different execution models. We also have proposed a new execution model for nested parallelism allowing users to exploit these heterogeneous systems to reduce execution time.

Dynamic instabilities in scalar neural field equations with space-dependent delays

In this paper we consider a class of scalar integral equations with a form of space-dependent delay. These non-local models arise naturally when modelling neural tissue with active axons and passive dendrites. Such systems are known to support a dynamic (oscillatory) Turing instability of the homogeneous steady state. In this paper we develop a weakly nonlinear analysis of the travelling and standing waves that form beyond the point of instability. The appropriate amplitude equations are found to be the coupled mean-field Ginzburg-Landau equations describing a Turing-Hopf bifurcation with modulation group velocity of O(1). Importantly we are able to obtain the coefficients of terms in the amplitude equations in terms of integral transforms of the spatio-temporal kernels defining the neural field equation of interest. Indeed our results cover not only models with axonal or dendritic delays but those which are described by a more general distribution of delayed spatio-temporal interactions. We illustrate the predictive power of this form of analysis with comparison against direct numerical simulations, paying particular attention to the competition between standing and travelling waves and the onset of Benjamin-Feir instabilities.

Nested Rollout Policy Adaptation for optimizing vehicle selection in complex VRPs

The goal of Vehicle Routing Problems (VRP) and their variations is to transport a set of orders with the minimum number of vehicles at least cost. Most approaches are designed to solve specific problem variations independently, whereas in real world applications, different constraints are handled concurrently. This research extends solutions obtained for the traveling salesman problem with time windows to a much wider class of route planning problems in logistics. The work describes a novel approach that: ï‚· supports a heterogeneous fleet of vehicles ï‚· dynamically reduces the number of vehicles ï‚· respects individual capacity restrictions ï‚· satisfies pickup and delivery constraints ï‚· takes Hamiltonian paths (rather than cycles) The proposed approach uses Monte-Carlo Tree Search and in particular Nested Rollout Policy Adaptation. For the evaluation of the work, real data from the industry was obtained and tested and the results are reported.

All one-loop scalar vertices in the effective potential approach

Using the one-loop Coleman-Weinberg effective potential, we derive a general analytic expression for all the derivatives of the effective potential with respect to any number of classical scalar fields. The result is valid for a renormalisable theory in four dimensions with any number of scalars, fermions or gauge bosons. This result corresponds to the zero-external momentum contribution to a general one-loop diagram with N scalar external legs. We illustrate the use of the general result in two simple scalar singlet extensions of the Standard Model, to obtain the dominant contributions to the triple couplings of light scalar particles under the zero external momentum approximation.

Performance and Robustness Analysis of Co-Prime and Nested Sampling

Coprime and nested sampling are well known deterministic sampling techniques that operate at rates significantly lower than the Nyquist rate, and yet allow perfect reconstruction of the spectra of wide sense stationary signals. However, theoretical guarantees for these samplers assume ideal conditions such as synchronous sampling, and ability to perfectly compute statistical expectations. This thesis studies the performance of coprime and nested samplers in spatial and temporal domains, when these assumptions are violated. In spatial domain, the robustness of these samplers is studied by considering arrays with perturbed sensor locations (with unknown perturbations). Simplified expressions for the Fisher Information matrix for perturbed coprime and nested arrays are derived, which explicitly highlight the role of co-array. It is shown that even in presence of perturbations, it is possible to resolve $O(M^2)$ under appropriate conditions on the size of the grid. The assumption of small perturbations leads to a novel ``bi-affine" model in terms of source powers and perturbations. The redundancies in the co-array are then exploited to eliminate the nuisance perturbation variable, and reduce the bi-affine problem to a linear underdetermined (sparse) problem in source powers. This thesis also studies the robustness of coprime sampling to finite number of samples and sampling jitter, by analyzing their effects on the quality of the estimated autocorrelation sequence. A variety of bounds on the error introduced by such non ideal sampling schemes are computed by considering a statistical model for the perturbation. They indicate that coprime sampling leads to stable estimation of the autocorrelation sequence, in presence of small perturbations. Under appropriate assumptions on the distribution of WSS signals, sharp bounds on the estimation error are established which indicate that the error decays exponentially with the number of samples. The theoretical claims are supported by extensive numerical experiments.

Nested Sampling and its Applications in Stable Compressive Covariance Estimation and Phase Retrieval with Near-Minimal Measurements

Compressed covariance sensing using quadratic samplers is gaining increasing interest in recent literature. Covariance matrix often plays the role of a sufficient statistic in many signal and information processing tasks. However, owing to the large dimension of the data, it may become necessary to obtain a compressed sketch of the high dimensional covariance matrix to reduce the associated storage and communication costs. Nested sampling has been proposed in the past as an efficient sub-Nyquist sampling strategy that enables perfect reconstruction of the autocorrelation sequence of Wide-Sense Stationary (WSS) signals, as though it was sampled at the Nyquist rate. The key idea behind nested sampling is to exploit properties of the difference set that naturally arises in quadratic measurement model associated with covariance compression. In this thesis, we will focus on developing novel versions of nested sampling for low rank Toeplitz covariance estimation, and phase retrieval, where the latter problem finds many applications in high resolution optical imaging, X-ray crystallography and molecular imaging. The problem of low rank compressive Toeplitz covariance estimation is first shown to be fundamentally related to that of line spectrum recovery. In absence if noise, this connection can be exploited to develop a particular kind of sampler called the Generalized Nested Sampler (GNS), that can achieve optimal compression rates. In presence of bounded noise, we develop a regularization-free algorithm that provably leads to stable recovery of the high dimensional Toeplitz matrix from its order-wise minimal sketch acquired using a GNS. Contrary to existing TV-norm and nuclear norm based reconstruction algorithms, our technique does not use any tuning parameters, which can be of great practical value. The idea of nested sampling idea also finds a surprising use in the problem of phase retrieval, which has been of great interest in recent times for its convex formulation via PhaseLift, By using another modified version of nested sampling, namely the Partial Nested Fourier Sampler (PNFS), we show that with probability one, it is possible to achieve a certain conjectured lower bound on the necessary measurement size. Moreover, for sparse data, an l1 minimization based algorithm is proposed that can lead to stable phase retrieval using order-wise minimal number of measurements.

Preeclampsia prevention: a case-control study nested in a cohort

Introduction: Preeclampsia is the main complication of pregnancy in developing countries. Calcium starting at 14 weeks of pregnancy is indicated to prevent the disease. Recent advances in prevention of preeclampsia endorse the addition of conjugated linoleic acid. Objective: To estimate the protective effect from calcium alone, compared to calcium plus conjugated linoleic acid in nulliparous women at risk of preeclampsia. Methods: A case-control design nested in the cohort of nulliparous women attending antenatal care from 2010 to 2014. The clinical histories of 387 cases of preeclampsia were compared with 1,054 normotensive controls. The exposure was prescriptions for calcium alone, the first period, or calcium plus conjugated linoleic acid, the second period, from 12 to 16 weeks of gestational age to labor. Confounding variables were controlled, allowing only nulliparous women into the study and stratifying by age, education and ethnic group. Results: The average age was 26.4 yrs old (range= 13-45), 85% from mixed ethnic backgrounds and with high school education. There were no differences between women who received calcium carbonate and those who did not (OR= 0.96; 95% CI= 0.73–1.27). The group of adolescents (13 to 18 yrs old) in the calcium plus conjugated linoleic acid was protected for preeclampsia (OR= 0.00; 95% CI= 0.00–0.44) independent of the confounder variables. Conclusions: 1. Calcium supplementation during pregnancy did not have preventive effects on preeclampsia. 2. Calcium plus Conjugated Linoleic acid provided to adolescents was observed to have preventive effect on Preeclampsia.

Preeclampsia prevention: a case-control study nested in the cohort

Introduction: Preeclampsia is the main complication of pregnancy in developing countries. Calcium starting at 14 weeks of pregnancy is indicated to prevent the disease. Recent advances in prevention of preeclampsia endorse the addition of conjugated linoleic acid. Objective: To estimate the protective effect from calcium alone, compared to calcium plus conjugated linoleic acid in nulliparous women at risk of preeclampsia. Methods: A case-control design nested in the cohort of nulliparous women attending antenatal care from 2010 to 2014. The clinical histories of 387 cases of preeclampsia were compared with 1,054 normotensive controls. The exposure was prescriptions for calcium alone, the first period, or calcium plus conjugated linoleic acid, the second period, from 12 to 16 weeks of gestational age to labor. Confounding variables were controlled, allowing only nulliparous women into the study and stratifying by age, education and ethnic group. Results: The average age was 26.4 yrs old (range= 13-45), 85% from mixed ethnic backgrounds and with high school education. There were no differences between women who received calcium carbonate and those who did not (OR= 0.96; 95% IC= 0.73–1.27). The group of adolescents (13 to 18 yrs old) in the calcium plus conjugated linoleic acid was protected for preeclampsia (OR= 0.00; 95% CI= 0.00–0.44) independent of the confounder variables. Conclusions: 1. Calcium supplementation during pregnancy did not have preventive effects on preeclampsia. 2. Calcium plus Conjugated Linoleic acid provided to adolescents was observed to have preventive effect on Preeclampsia.

On the universality class of monopole percolation in scalar QED

We study the critical properties of the monopole-percolation transition in U(1) lattice gauge theory coupled to scalars at infinite (β = 0) gauge coupling. We find strong scaling corrections in the critical exponents that must be considered by means of an infinite-volume extrapolation. After the extrapolation, our results are as precise as the obtained for the four dimensional site-percolation and, contrary to previously stated, fully compatible with them.