scholarly journals Aligning sequences to general graphs in O(V + mE) time

2017 ◽  
Author(s):  
Mikko Rautiainen ◽  
Tobias Marschall
Keyword(s):  
Basic Problem ◽  
Variant Calling ◽  
Theory And Practice ◽  
De Bruijn Graphs ◽  
Topological Features ◽  
String Graphs ◽  
Wide Range ◽  
Read Error Correction ◽  
Genome Assemblies ◽  
General Graphs

Graphs are commonly used to represent sets of sequences. Either edges or nodes can be labeled by sequences, so that each path in the graph spells a concatenated sequence. Examples include graphs to represent genome assemblies, such as string graphs and de Bruijn graphs, and graphs to represent a pan-genome and hence the genetic variation present in a population. Being able to align sequencing reads to such graphs is a key step for many analyses and its applications include genome assembly, read error correction, and variant calling with respect to a variation graph. Given the wide range of applications of this basic problem, it is surprising that algorithms with optimal runtime are, to the best of our knowledge, yet unknown. In particular, aligning sequences to cyclic graphs currently represents a challenge both in theory and practice. Here, we introduce an algorithm to compute the minimum edit distance of a sequence of length m to any path in a node-labeled directed graph (V, E) in O(|V |+m|E|) time and O(|V |) space. The corresponding alignment can be obtained in the same runtime using space. The time complexity depends only on the length of the sequence and the size of the graph. In particular, it does not depend on the cyclicity of the graph, or any other topological features.

scholarly journals Bit-parallel sequence-to-graph alignment

2019 ◽  
Vol 35 (19) ◽  
pp. 3599-3607 ◽  
Author(s):  
Mikko Rautiainen ◽  
Veli Mäkinen ◽  
Tobias Marschall
Keyword(s):  
Variant Calling ◽  
Supplementary Information ◽  
Global Alignment ◽  
Alignment Algorithm ◽  
Exact Matching ◽  
Worst Case ◽  
De Bruijn Graphs ◽  
Graph Alignment ◽  
Linear Sequence ◽  
String Graphs

Abstract Motivation Graphs are commonly used to represent sets of sequences. Either edges or nodes can be labeled by sequences, so that each path in the graph spells a concatenated sequence. Examples include graphs to represent genome assemblies, such as string graphs and de Bruijn graphs, and graphs to represent a pan-genome and hence the genetic variation present in a population. Being able to align sequencing reads to such graphs is a key step for many analyses and its applications include genome assembly, read error correction and variant calling with respect to a variation graph. Results We generalize two linear sequence-to-sequence algorithms to graphs: the Shift-And algorithm for exact matching and Myers’ bitvector algorithm for semi-global alignment. These linear algorithms are both based on processing w sequence characters with a constant number of operations, where w is the word size of the machine (commonly 64), and achieve a speedup of up to w over naive algorithms. For a graph with |V| nodes and |E| edges and a sequence of length m, our bitvector-based graph alignment algorithm reaches a worst case runtime of O(|V|+⌈mw⌉|E| log w) for acyclic graphs and O(|V|+m|E| log w) for arbitrary cyclic graphs. We apply it to five different types of graphs and observe a speedup between 3-fold and 20-fold compared with a previous (asymptotically optimal) alignment algorithm. Availability and implementation https://github.com/maickrau/GraphAligner Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Bit-parallel sequence-to-graph alignment

2018 ◽  
Author(s):  
Mikko Rautiainen ◽  
Veli Mäkinen ◽  
Tobias Marschall
Keyword(s):  
Variant Calling ◽  
Global Alignment ◽  
Alignment Algorithm ◽  
Exact Matching ◽  
Worst Case ◽  
De Bruijn Graphs ◽  
Graph Alignment ◽  
Linear Sequence ◽  
String Graphs ◽  
Linear Algorithms

Graphs are commonly used to represent sets of sequences. Either edges or nodes can be labeled by sequences, so that each path in the graph spells a concatenated sequence. Examples include graphs to represent genome assemblies, such as string graphs and de Bruijn graphs, and graphs to represent a pan-genome and hence the genetic variation present in a population. Being able to align sequencing reads to such graphs is a key step for many analyses and its applications include genome assembly, read error correction, and variant calling with respect to a variation graph. Here, we generalize two linear sequence-to-sequence algorithms to graphs: the Shift-And algorithm for exact matching and Myers’ bitvector algorithm for semi-global alignment. These linear algorithms are both based on processing w sequence characters with a constant number of operations, where w is the word size of the machine (commonly 64), and achieve a speedup of w over naive algorithms. Our bitvector-based graph alignment algorithm reaches a worst case runtime of for acyclic graphs and O(V + mE log w) for arbitrary cyclic graphs. We apply it to four different types of graphs and observe a speedup between 3.1-fold and 10.1-fold compared to previous algorithms.

Theory and Practice of Quality Management in Lifelong Learning at a Public University

2018 ◽  
Vol 8 (2) ◽  
pp. 49-73
Author(s):  
Petr Adamec
Keyword(s):  
Lifelong Learning ◽  
Public University ◽  
Further Education ◽  
Point Of View ◽  
Theory And Practice ◽  
University Policy ◽  
Higher Education Act ◽  
Wide Range ◽  
Learning Programs ◽  
Education Act

The core issue of this paper is a quality in the lifelong learning. The aim of the contribution is to describe the area, level and dimensions of quality in a wide range of lifelong learning programs, respectively of further education, which are realized in the sense of § 60 and 60a of the Higher Education Act. The content of the paper also focuses on the theoretical and practical starting points of the quality phenomenon, both from the historical point of view and especially from the perspective of the current focus and concept of university policy in the European and Czech region. The paper also presents the results of a survey focusing on approaches to the quality assurance systems in the concept of components at selected public university.

scholarly journals Bad World: The Negativity Bias in International Politics

2019 ◽  
Vol 43 (3) ◽  
pp. 96-140 ◽  
Author(s):  
Dominic D.P. Johnson ◽  
Dominic Tierney
Keyword(s):  
International Relations ◽  
Fundamental Principle ◽  
Human Mind ◽  
Negative Information ◽  
Theory And Practice ◽  
Negativity Bias ◽  
Positive Information ◽  
Psychological Phenomena ◽  
Wide Range ◽  
New Research

A major puzzle in international relations is why states privilege negative over positive information. States tend to inflate threats, exhibit loss aversion, and learn more from failures than from successes. Rationalist accounts fail to explain this phenomenon, because systematically overweighting bad over good may in fact undermine state interests. New research in psychology, however, offers an explanation. The “negativity bias” has emerged as a fundamental principle of the human mind, in which people's response to positive and negative information is asymmetric. Negative factors have greater effects than positive factors across a wide range of psychological phenomena, including cognition, motivation, emotion, information processing, decision-making, learning, and memory. Put simply, bad is stronger than good. Scholars have long pointed to the role of positive biases, such as overconfidence, in causing war, but negative biases are actually more pervasive and may represent a core explanation for patterns of conflict. Positive and negative dispositions apply in different contexts. People privilege negative information about the external environment and other actors, but positive information about themselves. The coexistence of biases can increase the potential for conflict. Decisionmakers simultaneously exaggerate the severity of threats and exhibit overconfidence about their capacity to deal with them. Overall, the negativity bias is a potent force in human judgment and decisionmaking, with important implications for international relations theory and practice.

scholarly journals Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Zev N. Kronenberg ◽  
Arang Rhie ◽  
Sergey Koren ◽  
Gregory T. Concepcion ◽  
Paul Peluso ◽  
...  
Keyword(s):  
Zebra Finch ◽  
Cultured Cells ◽  
De Novo ◽  
Single Cells ◽  
Variant Calling ◽  
Chromatin Interaction ◽  
Extended Haplotype ◽  
Benchmark Datasets ◽  
And Performance ◽  
Genome Assemblies

AbstractHaplotype-resolved genome assemblies are important for understanding how combinations of variants impact phenotypes. To date, these assemblies have been best created with complex protocols, such as cultured cells that contain a single-haplotype (haploid) genome, single cells where haplotypes are separated, or co-sequencing of parental genomes in a trio-based approach. These approaches are impractical in most situations. To address this issue, we present FALCON-Phase, a phasing tool that uses ultra-long-range Hi-C chromatin interaction data to extend phase blocks of partially-phased diploid assembles to chromosome or scaffold scale. FALCON-Phase uses the inherent phasing information in Hi-C reads, skipping variant calling, and reduces the computational complexity of phasing. Our method is validated on three benchmark datasets generated as part of the Vertebrate Genomes Project (VGP), including human, cow, and zebra finch, for which high-quality, fully haplotype-resolved assemblies are available using the trio-based approach. FALCON-Phase is accurate without having parental data and performance is better in samples with higher heterozygosity. For cow and zebra finch the accuracy is 97% compared to 80–91% for human. FALCON-Phase is applicable to any draft assembly that contains long primary contigs and phased associate contigs.

The Oxford Handbook of Quintilian

2021 ◽  
Keyword(s):  
Literary Criticism ◽  
Middle Ages ◽  
Performing Arts ◽  
Late Antiquity ◽  
The United States ◽  
Educational Programme ◽  
Theory And Practice ◽  
Visual And Performing Arts ◽  
Wide Range ◽  
History Of

M. Fabius Quintilianus was a prominent orator, declaimer, and teacher of eloquence in the first century ce. After his retirement he wrote the Institutio oratoria, a unique treatise in Antiquity because it is a handbook of rhetoric and an educational treatise in one. Quintilian’s fame and influence are not only based on the Institutio, but also on the two collections of Declamations which were attributed to him in late Antiquity. The Oxford Handbook of Quintilian aims to present Quintilian’s Institutio as a key treatise in the history of Graeco-Roman rhetoric and its influence on the theory and practice of rhetoric and education, from late Antiquity until the present day. It contains chapters on Quintilian’s educational programme, his concepts and classifications of rhetoric, his discussion of the five canons of rhetoric, his style, his views on literary criticism, declamation, and the relationship between rhetoric and law, and the importance of the visual and performing arts in his work. His huge legacy is presented in successive chapters devoted to Quintilian in late Antiquity, the Middle Ages, the Italian Renaissance, Northern Europe during the Renaissance, Europe from the Eighteenth to the Twentieth Century, and the United States of America. There are also chapters devoted to the biographical tradition, the history of printed editions, and modern assessments of Quintilian. The twenty-one authors of the chapters represent a wide range of expertise and scholarly traditions and thus offer a unique mixture of current approaches to Quintilian from a multidisciplinary perspective.

scholarly journals Omitted Variable Bias in GLMs of Neural Spiking Activity

2018 ◽  
Vol 30 (12) ◽  
pp. 3227-3258 ◽  
Author(s):  
Ian H. Stevenson
Keyword(s):  
Neural Activity ◽  
Single Neuron ◽  
Linear Models ◽  
Theory And Practice ◽  
Parameter Estimates ◽  
Omitted Variables ◽  
History Effects ◽  
Omitted Variable Bias ◽  
Wide Range ◽  
Variable Bias

Generalized linear models (GLMs) have a wide range of applications in systems neuroscience describing the encoding of stimulus and behavioral variables, as well as the dynamics of single neurons. However, in any given experiment, many variables that have an impact on neural activity are not observed or not modeled. Here we demonstrate, in both theory and practice, how these omitted variables can result in biased parameter estimates for the effects that are included. In three case studies, we estimate tuning functions for common experiments in motor cortex, hippocampus, and visual cortex. We find that including traditionally omitted variables changes estimates of the original parameters and that modulation originally attributed to one variable is reduced after new variables are included. In GLMs describing single-neuron dynamics, we then demonstrate how postspike history effects can also be biased by omitted variables. Here we find that omitted variable bias can lead to mistaken conclusions about the stability of single-neuron firing. Omitted variable bias can appear in any model with confounders—where omitted variables modulate neural activity and the effects of the omitted variables covary with the included effects. Understanding how and to what extent omitted variable bias affects parameter estimates is likely to be important for interpreting the parameters and predictions of many neural encoding models.

George Washington: a revolutionary approach to leadership

2018 ◽  
Vol 39 (8) ◽  
pp. 995-1009
Author(s):  
Todd C. Harris
Keyword(s):  
Leadership Competencies ◽  
Theory And Practice ◽  
Academic Disciplines ◽  
Leadership Traits ◽  
Journal Articles ◽  
George Washington ◽  
Leadership Theories ◽  
Content Type ◽  
Wide Range ◽  
Tools And Techniques

PurposeThe purpose of this paper is twofold: first, to examine George Washington’s approach to leadership through the lens of contemporary leadership theory and practice; and second, to help modern managers further reflect upon and develop their own leadership capabilities through a historiographic examination of Washington’s leadership traits and skills.Design/methodology/approachCombining three different academic disciplines, management, psychology and history, the author utilized a historiographic and interdisciplinary research methodology, conducting a detailed exploration of the life of George Washington through an examination of a wide range of original archival materials, books, journal articles and other sources.FindingsThe present analysis reveals that Washington demonstrated a variety of well-validated leadership competencies (e.g. emotional intelligence, resilience, integrity, etc.) that are largely consistent with leader-centered theoretical conceptions of leadership.Originality/valueThis is the first historiographic study of George Washington’s approach to leadership within the management literature. Additionally, through the development of a competency model, the study demonstrates how Washington employed tools and techniques from a host of modern leadership theories to achieve critically important results.

An Organisational Evaluation Capability Hierarchy Model for Self-diagnosis1

2005 ◽  
Vol 4 (1-2) ◽  
pp. 27-32 ◽  
Author(s):  
Colin A Sharp
Keyword(s):  
Project Management ◽  
Financial Management ◽  
Theory And Practice ◽  
Evaluation Theory ◽  
Information Systems Management ◽  
Capability Maturity ◽  
Wide Range ◽  
Hierarchy Model ◽  
Management Project

The use of Capability Maturity Models in financial management, project management, people management and information systems management in a wide variety of organisations indicates the potential for an Organisational Evaluation Capability Hierarchy to guide the self-diagnosis of organisations in building their evaluation maturity. This paper is about the theory behind this growing trend in organisational governance and organisational diagnosis, and explores its relevance to evaluation theory and practice. This theoretical analysis may have long-term practical benefits for evaluation practitioners, as is being developed in the fields of project management, financial management, and people management in a wide range of organisations.

scholarly journals Transposing Aristophanes: The Theory and Practice of Translating Aristophanic Lyric

2012 ◽  
Vol 59 (2) ◽  
pp. 214-244 ◽  
Author(s):  
JAMES ROBSON
Keyword(s):  
Theory And Practice ◽  
Academic Interest ◽  
Text Type ◽  
Wide Range ◽  
End Products ◽  
History Of ◽  
English Speaking ◽  
Modern Greece ◽  
English Speaking World ◽  
Insight Into

The reception of Aristophanes has gained extraordinary momentum as a topic of academic interest in the last few years. Contributions range from Gonda Van Steen's ground-breaking Venom in Verse. Aristophanes in Modern Greece to Hall and Wrigley's Aristophanes in Performance 421 BC–AD 2007, which contains contributions from a wide range of scholars and writers, a number of whom have had experience of staging Aristophanes' plays as live theatre. In Found in Translation, J. Michael Walton has also made strides towards marrying the theory of translation to the practice of translating Aristophanes (something I have myself also sought to do in print). And with the history of Aristophanic translation, adaptation, and staging being rapidly pieced together (in the English-speaking world at least, where Hall, Steggle, Halliwell, Sowerby, Walsh, and Walton, for example, have all made their own contributions), much of the groundwork has been laid for a study such as is attempted in this article. Here I aim to take a broad look across a range of translations in order to see how one particular text type within Aristophanic drama has been approached by translators, namely Aristophanes' lyric passages. The aim of this study will be to give both an insight into the numerous considerations that translators take into account when translating Aristophanic lyric and an impression of the range of end products that have emerged over the last two hundred years.

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