A Tighter Bound for the Determinization of Visibly Pushdown Automata

Visibly pushdown automata (VPA), introduced by Alur and Madhusuan in 2004, is a subclass of pushdown automata whose stack behavior is completely determined by the input symbol according to a fixed partition of the input alphabet. Since its introduce, VPAs have been shown to be useful in various context, e.g., as specification formalism for verification and as automaton model for processing XML streams. Due to high complexity, however, implementation of formal verification based on VPA framework is a challenge. In this paper we consider the problem of implementing VPA-based model checking algorithms. For doing so, we first present an improvement on upper bound for determinization of VPA. Next, we propose simple on-the-fly algorithms to check universality and inclusion problems of this automata class. Then, we implement the proposed algorithms in a prototype tool. Finally, we conduct experiments on randomly generated VPAs. The experimental results show that the proposed algorithms are considerably faster than the standard ones

Bowdoin College Course Guide (2017-2018)

https://digitalcommons.bowdoin.edu/course-catalogues/1301/thumbnail.jp

Cell Nuclear Morphology Analysis Using 3D Shape Modeling, Machine Learning and Visual Analytics

Quantitative analysis of morphological changes in a cell nucleus is important for the understanding of nuclear architecture and its relationship with cell differentiation, development, proliferation, and disease. Changes in the nuclear form are associated with reorganization of chromatin architecture related to altered functional properties such as gene regulation and expression. Understanding these processes through quantitative analysis of morphological changes is important not only for investigating nuclear organization, but also has clinical implications, for example, in detection and treatment of pathological conditions such as cancer. While efforts have been made to characterize nuclear shapes in two or pseudo-three dimensions, several studies have demonstrated that three dimensional (3D) representations provide better nuclear shape description, in part due to the high variability of nuclear morphologies. 3D shape descriptors that permit robust morphological analysis and facilitate human interpretation are still under active investigation. A few methods have been proposed to classify nuclear morphologies in 3D, however, there is a lack of publicly available 3D data for the evaluation and comparison of such algorithms. There is a compelling need for robust 3D nuclear morphometric techniques to carry out population-wide analyses. In this work, we address a number of these existing limitations. First, we present a largest publicly available, to-date, 3D microscopy imaging dataset for cell nuclear morphology analysis and classification. We provide a detailed description of the image analysis protocol, from segmentation to baseline evaluation of a number of popular classification algorithms using 2D and 3D voxel-based morphometric measures. We proposed a specific cross-validation scheme that accounts for possible batch effects in data. Second, we propose a new technique that combines mathematical modeling, machine learning, and interpretation of morphometric characteristics of cell nuclei and nucleoli in 3D. Employing robust and smooth surface reconstruction methods to accurately approximate 3D object boundary enables the establishment of homologies between different biological shapes. Then, we compute geometric morphological measures characterizing the form of cell nuclei and nucleoli. We combine these methods into a highly parallel computational pipeline workflow for automated morphological analysis of thousands of nuclei and nucleoli in 3D. We also describe the use of visual analytics and deep learning techniques for the analysis of nuclear morphology data. Third, we evaluate proposed methods for 3D surface morphometric analysis of our data. We improved the performance of morphological classification between epithelial vs mesenchymal human prostate cancer cells compared to the previously reported results due to the more accurate shape representation and the use of combined nuclear and nucleolar morphometry. We confirmed previously reported relevant morphological characteristics, and also reported new features that can provide insight in the underlying biological mechanisms of pathology of prostate cancer. We also assessed nuclear morphology changes associated with chromatin remodeling in drug-induced cellular reprogramming. We computed temporal trajectories reflecting morphological differences in astroglial cell sub-populations administered with 2 different treatments vs controls. We described specific changes in nuclear morphology that are characteristic of chromatin re-organization under each treatment, which previously has been only tentatively hypothesized in literature. Our approach demonstrated high classification performance on each of 3 different cell lines and reported the most salient morphometric characteristics. We conclude with the discussion of the potential impact of method development in nuclear morphology analysis on clinical decision-making and fundamental investigation of 3D nuclear architecture. We consider some open problems and future trends in this field.PHDBioinformaticsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/147598/1/akalinin_1.pd

Bowdoin College Course Guide (2015-2016)

https://digitalcommons.bowdoin.edu/course-catalogues/1297/thumbnail.jp

Transportation Implications of Coal

This report describes the direct economic relationship between the coal and railroad industries in Appalachia. It finds that between 2015 and 2016, changing electric generation strategies—including accelerated coal-powered plant retirements—combined with a downturn in coal demand contributed to losses of nearly 2,000 full-time jobs and $150 million in income across Appalachia’s railroad sector

Bowdoin College Catalogue (2013-2014)

https://digitalcommons.bowdoin.edu/course-catalogues/1294/thumbnail.jp

Bowdoin College Catalogue (2011-2012)

https://digitalcommons.bowdoin.edu/course-catalogues/1292/thumbnail.jp

Symmetry breaking/symmetry preserving circuits and symmetry restoration on quantum computers: A quantum many-body perspective

We discuss here some aspects related to symmetries of a quantum many-body problem when trying to treat it on a quantum computer. Several features related to symmetry conservation, symmetry breaking and possible symmetry restoration are reviewed. After a brief discussion of some of the standard symmetries relevant for many-particle systems, we discuss the advantage to encode directly some symmetries in quantum ansatze, especially with the aim to reduce the quantum register size. It is however well-known that the use of symmetry breaking states can also be a unique way to incorporate specific internal correlations when a spontaneous symmetry breaking occurs. These aspects are discussed in the quantum computing context. Precise description of quantum systems can however be achieved only when the symmetries that are initially broken are properly restored. Several methods are introduced to perform symmetry restoration on a quantum computer, for instance, purification of the state by means of the Grover algorithm, use of the combination of Hadamard test and oracle concepts, symmetry filtering by quantum phase estimation and by an iterative independent set of Hadamard tests.Comment: submitted to Eur. Phys. J. A in the topical issue on "Quantum computing in low-energy nuclear theory

The Brazilian Amazon Timber Industry and the International Mechanisms of Timber Trade Control – Combating Illegal Logging and Associated Trade

Illegal logging and its associated trade are one of the main causes of degradation of the Amazonian Rainforest in Brazil. They spring from several deficiencies in the regulatory and monitoring systems. The purpose of this work is to recommend mechanisms to overcome these deficiencies to eliminate illegal logging and its associated trade in the long-term and to enhance the appreciation of the standing forests and the sustainable use of their natural resources. Chapter 1 provides an overview of the Brazilian tropical timber market’s trends, and briefly describes the main stages of timber supply chain to build familiarity with the activities surrounding it. Chapter 2 presents the aspects of the Brazilian federal environmental regulatory system of timber supply chain that are essential for further analysis of illegal undertakings. Chapter 3 provides information on the factual aspects of illegal logging and associated trade in the Amazon. It analyzes the sector’s features and deficiencies and examines how effective the enforcement of the Brazilian environmental law has been to date. Chapter 4 describes the international mechanisms of timber trade control in use worldwide. It focuses on those systems that are the most effective and have beneficial impact – or potential beneficial impact if better promoted – on the Brazilian timber industry. Finally, chapter 5 recommends a multi-faceted approach to be implemented by the Brazilian Government with the cooperation of the international community, non-profit organizations, and the private sector. It suggests strategies to promote effective international timber trade control mechanisms within the Brazilian Amazon timber industry, and to adapt effective tools provided by those mechanisms to the Brazilian environmental regulatory system. These strategies include instruments from the United States Lacey Act and the European Union Forest Law Enforcement, Governance, and Trade Action Plan, forest certification schemes, and the International Forest Regime. This work also provides recommendations to improve the efficiency of control mechanisms that are currently but poorly implemented in Brazil