Distributions associated with general runs and patterns in hidden Markov models

This paper gives a method for computing distributions associated with patterns in the state sequence of a hidden Markov model, conditional on observing all or part of the observation sequence. Probabilities are computed for very general classes of patterns (competing patterns and generalized later patterns), and thus, the theory includes as special cases results for a large class of problems that have wide application. The unobserved state sequence is assumed to be Markovian with a general order of dependence. An auxiliary Markov chain is associated with the state sequence and is used to simplify the computations. Two examples are given to illustrate the use of the methodology. Whereas the first application is more to illustrate the basic steps in applying the theory, the second is a more detailed application to DNA sequences, and shows that the methods can be adapted to include restrictions related to biological knowledge.Comment: Published in at http://dx.doi.org/10.1214/07-AOAS125 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

A Coverage Criterion for Spaced Seeds and its Applications to Support Vector Machine String Kernels and k-Mer Distances

Spaced seeds have been recently shown to not only detect more alignments, but also to give a more accurate measure of phylogenetic distances (Boden et al., 2013, Horwege et al., 2014, Leimeister et al., 2014), and to provide a lower misclassification rate when used with Support Vector Machines (SVMs) (On-odera and Shibuya, 2013), We confirm by independent experiments these two results, and propose in this article to use a coverage criterion (Benson and Mak, 2008, Martin, 2013, Martin and No{\'e}, 2014), to measure the seed efficiency in both cases in order to design better seed patterns. We show first how this coverage criterion can be directly measured by a full automaton-based approach. We then illustrate how this criterion performs when compared with two other criteria frequently used, namely the single-hit and multiple-hit criteria, through correlation coefficients with the correct classification/the true distance. At the end, for alignment-free distances, we propose an extension by adopting the coverage criterion, show how it performs, and indicate how it can be efficiently computed.Comment: http://online.liebertpub.com/doi/abs/10.1089/cmb.2014.017

High resolution structural characterisation of laser-induced defect clusters inside diamond

Laser writing with ultrashort pulses provides a potential route for the manufacture of three-dimensional wires, waveguides and defects within diamond. We present a transmission electron microscopy (TEM) study of the intrinsic structure of the laser modifications and reveal a complex distribution of defects. Electron energy loss spectroscopy (EELS) indicates that the majority of the irradiated region remains as $sp^3$ bonded diamond. Electrically-conductive paths are attributed to the formation of multiple nano-scale, $sp^2$-bonded graphitic wires and a network of strain-relieving micro-cracks

Evaluation of Agricultural Statistics for ADAP

The Agricultural Development in the American Pacific (ADAP) Directors requested that the USDA, National Agricultural Statistics Service (NASS) extend its statistical program to the ADAP region: American Samoa, the Federated States of Micronesia (FSM), Palau, the Republic of the Marshall Islands (RMI), Guam, and the Commonwealth of the Northern Marianas (CNMI).This is the final report on the feasibility of, and our recommendations on establishing agricultural statistics in the region. The current section presents material that is generally applicable over the region, with separate sections containing relevant notes for each jurisdictionFunded through the US Department of Agriculture Cooperative Extension Service Grant Number 92-EXCA-1-0187

Biosynthesis of the modified tetrapyrroles: the pigments of life

Modified tetrapyrroles are large macrocyclic compounds, consisting of diverse conjugation and metal chelation systems and imparting an array of colors to the biological structures that contain them. Tetrapyrroles represent some of the most complex small molecules synthesized by cells and are involved in many essential processes that are fundamental to life on Earth, including photosynthesis, respiration, and catalysis. These molecules are all derived from a common template through a series of enzyme-mediated transformations that alter the oxidation state of the macrocycle, and also modify its size, side chain composition, and the nature of the centrally chelated metal ion. The different modified tetrapyrroles include chlorophylls, hemes, siroheme, corrins (including vitamin B12), coenzyme F430, heme d1 and bilins. After nearly a century of study, almost all of the more than 90 different enzymes that synthesize this family of compounds are now known, and expression of reconstructed operons in heterologous hosts has confirmed that most pathways are complete. Aside from the highly diverse nature of the chemical reactions catalyzed, an interesting aspect of comparative biochemistry is to see how different enzymes and even entire pathways have evolved to perform alternative chemical reactions to produce the same end products in the presence and absence of oxygen. Although there is still much to learn, our current understanding of tetrapyrrole biogenesis represents a remarkable biochemical milestone that is summarized in this review

Advancing Community Engaged Approaches to Identifying Structural Drivers of Racial Bias in Health Diagnostic Algorithms

Much attention and concern has been raised recently about bias and the use of machine learning algorithms in healthcare, especially as it relates to perpetuating racial discrimination and health disparities. Following an initial system dynamics workshop at the Data for Black Lives II conference hosted at MIT in January of 2019, a group of conference participants interested in building capabilities to use system dynamics to understand complex societal issues convened monthly to explore issues related to racial bias in AI and implications for health disparities through qualitative and simulation modeling. In this paper we present results and insights from the modeling process and highlight the importance of centering the discussion of data and healthcare on people and their experiences with healthcare and science, and recognizing the societal context where the algorithm is operating. Collective memory of community trauma, through deaths attributed to poor healthcare, and negative experiences with healthcare are endogenous drivers of seeking treatment and experiencing effective care, which impact the availability and quality of data for algorithms. These drivers have drastically disparate initial conditions for different racial groups and point to limited impact of focusing solely on improving diagnostic algorithms for achieving better health outcomes for some groups.Comment: 2020 International System Dynamics Conference, Honorable Mention Award, 28 pages, 8 figure

Application of Advanced Nondestructive Evaluation Techniques for Cylindrical Composite Test Samples

Two nondestructive methods were applied to composite cylinder samples pressurized to failure in order to determine manufacturing quality and monitor damage progression under load. A unique computed tomography (CT) image processing methodology developed at NASA Glenn Research was used to assess the condition of the as-received samples while acoustic emission (AE) monitoring was used to identify both the extent and location of damage within the samples up to failure. Results show the effectiveness of both of these methods in identifying potentially critical fabrication issues and their resulting impact on performance

Application and Analysis of Bounded-Impulse Trajectory Models with Analytic Gradients

In the companion paper, analytic methods were presented for computing the Jacobian entries for two-sided direct shooting trajectory models that utilize the bounded-impulse approximation. In this paper we discuss practical implementation considerations. Efficient computation of the mathematical components required to compute the partials is discussed and a guiding numerical example is provided for validation purposes. A solar electric power model suitable for preliminary mission design is presented, including a method for handling thruster cut-off events that result in non-smooth derivatives. The challenges associated with incorporating the SPICE ephemeris system into an optimization framework are discussed and an alternative is presented that results in smooth time partials. Application problems illustrate the benefits of employing analytic Jacobian calculations vs. using the method of finite differences. The importance of accurately modeling hardware and operational constraints at the preliminary design stage, and the benefits of using an analytic Jacobian in a solver that combines the monotonic basin hopping heuristic method with a local gradient search are also explored

Analytic Gradient Computation for Bounded-Impulse Trajectory Models Using Two-Sided Shooting

Many optimization methods require accurate partial derivative information in order to ensure efficient, robust, and accurate convergence. This work outlines analytic methods for computing the problem Jacobian for two different bounded-impulse spacecraft trajectory models solved using two-sided shooting. The specific two-body Keplerian propagation method used by both of these models is described. Methods for incorporating realistic operational constraints and hardware models at the preliminary stage of a trajectory design effort are also demonstrated and the analytic methods derived are tested for accuracy using automatic differentiation. A companion paper will solve several relevant problems that show the utility of employing analytic derivatives, i.e. compared to using derivatives found using finite differences