Improved ontology-based similarity calculations using a study-wise annotation model

A typical use case of ontologies is the calculation of similarity scores between items that are annotated with classes of the ontology. For example, in differential diagnostics and disease gene prioritization, the human phenotype ontology (HPO) is often used to compare a query phenotype profile against gold-standard phenotype profiles of diseases or genes. The latter have long been constructed as flat lists of ontology classes, which, as we show in this work, can be improved by exploiting existing structure and information in annotation datasets or full text disease descriptions. We derive a study-wise annotation model of diseases and genes and show that this can improve the performance of semantic similarity measures. Inferred weights of individual annotations are one reason for this improvement, but more importantly using the study-wise structure further boosts the results of the algorithms according to precision-recall analyses. We test the study-wise annotation model for diseases annotated with classes from the HPO and for genes annotated with gene ontology (GO) classes. We incorporate this annotation model into similarity algorithms and show how this leads to improved performance. This work adds weight to the need for enhancing simple list-based representations of disease or gene annotations. We show how study-wise annotations can be automatically derived from full text summaries of disease descriptions and from the annotation data provided by the GO Consortium and how semantic similarity measure can utilize this extended annotation model

Learning an Approximate Model Predictive Controller with Guarantees

A supervised learning framework is proposed to approximate a model predictive controller (MPC) with reduced computational complexity and guarantees on stability and constraint satisfaction. The framework can be used for a wide class of nonlinear systems. Any standard supervised learning technique (e.g. neural networks) can be employed to approximate the MPC from samples. In order to obtain closed-loop guarantees for the learned MPC, a robust MPC design is combined with statistical learning bounds. The MPC design ensures robustness to inaccurate inputs within given bounds, and Hoeffding's Inequality is used to validate that the learned MPC satisfies these bounds with high confidence. The result is a closed-loop statistical guarantee on stability and constraint satisfaction for the learned MPC. The proposed learning-based MPC framework is illustrated on a nonlinear benchmark problem, for which we learn a neural network controller with guarantees.Comment: 6 pages, 3 figures, to appear in IEEE Control Systems Letter

Cryptic Diversity in the Neotropical Gecko Genus \u3cem\u3ePhyllopezus\u3c/em\u3e Peters, 1878 (Reptilia: Squamata: Phyllodactylidae): A New Species from Paraguay

The gecko genus Phyllopezus is distributed mainly along South America’s “Dry Diagonal” (Caatinga, Cerrado, and Chaco). The genus has been the subject of recent taxonomic analyses and includes four described species and seven candidate species referred to here as Phyllopezus pollicaris sensu lato. In Paraguay, Phyllopezus is known from the Chaco and Cerrado where it is abundant, and also from a small isolated population from a rocky hill formation named “Cordillera de Los Altos” (Los Altos mountain range). Here we analyzed genetic samples from across its range, including new samples from Paraguay, using DNA barcoding analysis of the mitochondrial 16S gene and phylogenetic analyses using both Bayesian and Maximum Likelihood methods. We found genetic and morphological differences among geckos from the Los Altos mountain range and the remaining Phyllopezus populations. Using both molecular and morphological evidence we describe a new Phyllopezus species, sister toP. przewalskii. Genetic differentiation among described and putative Phyllopezus species is greater than their morphological differences, which likely accounts for these cryptic taxa remaining undescribed for so long

A new golden frog species of the genus Diasporus (Amphibia, Eleutherodactylidae) from the Cordillera Central, western Panama

We describe the frog species Diasporus citrinobapheussp. n. from the Cordillera Central of western Panama. The new species differs from all other species in its genus in coloration, disk cover and disk pad shape, skin texture, advertisement call, and size. It is most similar to Diasporus tigrillo, from which it differs in dorsal skin texture, relative tibia length, number of vomerine teeth, ventral coloration, dorsal markings, and relative tympanum size, and to Diasporus gularis, from which it can be distinguished by the lack of membranes between the toes, adult size, posterior thigh coloration, and position of the choanae. We provide data on morpho- logy, vocalization, and distribution of the new species, as well as brief information on its natural history.Describimos la especie de rana Diasporus citrinobapheus sp. n. de la Cordillera Central, occidente de Panamá. La nueva especie se distingue de otras especies del género por su coloración, su forma de la cubierta y la almohadilla de los discos, textura de la piel, canto de anúncio, y tamaño corporal. Se asemeja mas a D. tigrillo, del cual se distingue por la textura de la piel dorsal, longitud relativa de la tibia, número de dientes vomerianos, coloración ventral, patrón dorsal, y tamaño relativo del tímpano, y a D. gularis, del cual se diferencia por la ausencia de membranas entre los dedos de pie, tamaño corporal, coloración de la parte trasera del muslo, y posición de las coanas. Presentamos datos de la morfología, vocalización, y distribución de la nueva especie, así como notas concisas de su historia natural

Field notes on findings of threatened amphibian species in the central mountain range of western Panama

During field work along a transect in the Cordillera Central of western Panama between 2008 and 2010, we detected several populations of amphibian species which are considered as “Endangered” or “Critically Endangered” by the IUCN. Some of these species had suffered from serious population declines, probably due to chytridiomycosis, but all are generally threatened by habitat loss. We detected 53% of the Endangered and 56% of the Critically Endangered amphibian species that have previously been reported from within the investigated area. We report on findings of species that have not been found in Panama for many years, and provide locality data of newly discovered populations. There is a need to create a new protected area in the Cerro Colorado area of the Serranía de Tabasará, where we found 15% of the Endangered and Critically Endangered amphibian species known to Panama.Durante trabajo de campo en un transecto a lo largo de la Cordillera Central en el oeste de Panamá entre 2008 y 2010, encontramos varias poblaciones de anfibios que son considerados “En Peligro” o “En Peligro Crítico” por la UICN. Algunas de estas especies habían sufrido serias disminuciones de sus poblaciones, probablemente causadas por la quitridiomicosis, pero todas se encuentran amenazadas por pérdida de hábitat. Detectamos el 53% de las especies En Peligro y el 56% de las especies En Peligro Crítico que se habían reportado previamente en el área de estudio. Reportamos hallazgos de especies que no se habían avistado en Panamá por muchos años, así como localidades de poblaciones descubiertas por primera vez. Se requiere crear una nueva área de protección en los alrededores del Cerro Colorado en la Serranía de Tabasará, donde se han encontrado 15% de los anfibios En Peligro y En Peligro Crítico de todo Panamá

Good Authors = Good Articles? - How Wikis Work

Wikis are websites to develop content collaboratively. The question arises to what extent the reputation of participants influences the quality of wiki sites. We analyze the impact of author reputation using the example of Wikipedia. We extend previous research by considering a set of different reputation metrics and a new model for aggregating reputation values. Since anonymous authors tend to have a lower reputation, we also quantify the level of participation of anonymous authors as an indicator for the reputation of the crowd. Our analysis finds out that reputation matters, but strongly depends on the used reputation metric and therefore on the corresponding author characteristics. The study shows that the experience of authors in the development of high-quality articles is highly relevant whereas the number of edits and the quality of contributions are of lower importance. Finally, our investigation proves the open editing model and the self-healing mechanism of wikis

Managed Wikis - A New Approach for Web 2.0

Wiki projects can be edited by everyday web users directly within the web browser. Consequently, undesirable contributions like vandalism and spam cannot be ruled out. In this paper, Managed Wikis are introduced as a new approach to avoid such undesirable contributions. Editing rights are assigned according to author reputation, the quality of articles and the occurrence of patterns of suspicious edits. In the paper, the concept of Managed Wikis is evaluated by means of a simulation on the basis of Wikipedia data. The analysis proves that undesirable contributions are blocked effectively. In contrast, desirable contributions are rarely affected by the editing rights restriction. The concept of Managed Wikis addresses open as well as corporate wiki projects where undesirable edits cause significant harm. Furthermore, it can be applied to make traditional websites accessible for the web community