Deep Learning Algorithms Improve Automated Identification of Chagas Disease Vectors

This is a pre-copyedited, author-produced version of an article accepted for publication in Journal of Medical Entomology following peer review. The version of record is available online at: https;//doi.org/https://doi.org/10.1093/jme/tjz065Vector-borne Chagas disease is endemic to the Americas and imposes significant economic and social burdens on public health. In a previous contribution, we presented an automated identification system that was able to discriminate among 12 Mexican and 39 Brazilian triatomine (Hemiptera: Reduviidae) species from digital images. To explore the same data more deeply using machine-learning approaches, hoping for improvements in classification, we employed TensorFlow, an open-source software platform for a deep learning algorithm. We trained the algorithm based on 405 images for Mexican triatomine species and 1,584 images for Brazilian triatomine species. Our system achieved 83.0 and 86.7% correct identification rates across all Mexican and Brazilian species, respectively, an improvement over comparable rates from statistical classifiers (80.3 and 83.9%, respectively). Incorporating distributional information to reduce numbers of species in analyses improved identification rates to 95.8% for Mexican species and 98.9% for Brazilian species. Given the ‘taxonomic impediment’ and difficulties in providing entomological expertise necessary to control such diseases, automating the identification process offers a potential partial solution to crucial challenges

Bioinformatics process management: information flow via a computational journal

This paper presents the Bioinformatics Computational Journal (BCJ), a framework for conducting and managing computational experiments in bioinformatics and computational biology. These experiments often involve series of computations, data searches, filters, and annotations which can benefit from a structured environment. Systems to manage computational experiments exist, ranging from libraries with standard data models to elaborate schemes to chain together input and output between applications. Yet, although such frameworks are available, their use is not widespread–ad hoc scripts are often required to bind applications together. The BCJ explores another solution to this problem through a computer based environment suitable for on-site use, which builds on the traditional laboratory notebook paradigm. It provides an intuitive, extensible paradigm designed for expressive composition of applications. Extensive features facilitate sharing data, computational methods, and entire experiments. By focusing on the bioinformatics and computational biology domain, the scope of the computational framework was narrowed, permitting us to implement a capable set of features for this domain. This report discusses the features determined critical by our system and other projects, along with design issues. We illustrate the use of our implementation of the BCJ on two domain-specific examples

Automated identification of insect vectors of Chagas disease in Brazil and Mexico: the Virtual Vector Lab

Identification of arthropods important in disease transmission is a crucial, yet difficult, task that can demand considerable training and experience. An important case in point is that of the 150+ species of Triatominae, vectors of Trypanosoma cruzi, causative agent of Chagas disease across the Americas. We present a fully automated system that is able to identify triatomine bugs from Mexico and Brazil with an accuracy consistently above 80%, and with considerable potential for further improvement. The system processes digital photographs from a photo apparatus into landmarks, and uses ratios of measurements among those landmarks, as well as (in a preliminary exploration) two measurements that approximate aspects of coloration, as the basis for classification. This project has thus produced a working prototype that achieves reasonably robust correct identification rates, although many more developments can and will be added, and—more broadly—the project illustrates the value of multidisciplinary collaborations in resolving difficult and complex challenges

The HERMIT in the machine: a plugin for the interactive transformation of GHC core language programs

The importance of reasoning about and refactoring programs is a central tenet of functional programming. Yet our compilers and development toolchains only provide rudimentary support for these tasks. This paper introduces a programmatic and compiler-centric interface that facilitates refactoring and equational reasoning. To develop our ideas, we have implemented HERMIT, a toolkit enabling informal but systematic transformation of Haskell programs from inside the Glasgow Haskell Compiler’s optimization pipeline. With HERMIT, users can experiment with optimizations and equational reasoning, while the tedious heavy lifting of performing the actual transformations is done for them. HERMIT provides a transformation API that can be used to build higher-level rewrite tools. One use-case is prototyping new optimizations as clients of this API before being committed to the GHC toolchain. We describe a HERMIT application - a read-eval-print shell for performing transformations using HERMIT. We also demonstrate using this shell to prototype an optimization on a specific example, and report our initial experiences and remaining challenges

DATA SETS: Automated identification of insect vectors of Chagas disease in Brazil and Mexico: The Virtual Vector Lab

Zipped file including two ASCII files (.csv format), one for Brazil, one for Mexico.Data documenting morphometric features of Brazilian and Mexican Triatominae, to accompany a manuscript presently submitted to PeerJ for consideration for publication

Modus operandi und Perseveranz

SIGLEUuStB Koeln=38*-900106444 / FIZ - Fachinformationszzentrum Karlsruhe / TIB - Technische Informationsbibliothek3., unveraend. Aufl.DEGerman

Building compilers by combining algebras

Embedded systems present a wide variety of challenges for developers of language tools. Verification of correctness, flexibility for adding new language features, and retargeting new architectures all present significant problems when developing a compiler for embedded systems. In this paper we present a domain-specific language based on modular monadic semantics which addresses many of these challenges

Informations- und Kommunikationstechnologien im Informations- und Dokumentationswesen einfuehrende Vorbereitungstexte zum Selbststudium fuer die gleichnamige Unterrichtseinheit innerhalb des Lehrblocks Grundlagen der Informationssysteme und -methoden

UuStB Koeln(38)-940106440 / FIZ - Fachinformationszzentrum Karlsruhe / TIB - Technische InformationsbibliothekSIGLEDEGerman

Staedtische Infrastruktur und Gewalt gegen Frauen der Park Tiergarten

UuStB Koeln(38)-11A9307 / FIZ - Fachinformationszzentrum Karlsruhe / TIB - Technische InformationsbibliothekSIGLEDEGerman

Die alltaegliche Gewalt der Stadt Frauen im Aussenraum Kreuzbergs

UuStB Koeln(38)-11A9306 / FIZ - Fachinformationszzentrum Karlsruhe / TIB - Technische InformationsbibliothekSIGLEDEGerman