A study of online and blockwise updating of the EM algorithm for Gaussian mixtures.

A variant of the EM algorithm for the estimation of multivariate Gaussian mixtures, which allows for online as well as blockwise updating of sequentially obtained parameter estimates, is investigated. Several dierent update schemes are considered and compared, and the benets of articially performing EM in batches, even though all data are available, are discussed

Bivariate estimation of distribution algorithms for protein structure prediction.

A real-valued bivariate ‘Estimation of Distribution Algorithm’ specific for the ab initio and full-atom Protein Structure Prediction problem is proposed. It is known that this is a multidimensional and multimodal problem. In order to deal with the multimodality and the correlation of dihedral angles φ and ψ, we developed approaches based on Kernel Density Estimation and Finite Gaussian Mixtures. Simulation results have shown that both techniques are promising when applied to that problem

A study of online and blockwise updating of the EM algorithm for Gaussian mixtures

A variant of the EM algorithm for the estimation of multivariate Gaussian mixtures, which allows for online as well as blockwise updating of sequentially obtained parameter estimates, is investigated. Several dierent update schemes are considered and compared, and the benets of articially performing EM in batches, even though all data are available, are discussed

Bivariate Estimation of Distribution Algorithms for Protein Structure Prediction

A real-valued bivariate ‘Estimation of Distribution Algorithm’ specific for the ab initio and full-atom Protein Structure Prediction problem is proposed. It is known that this is a multidimensional and multimodal problem. In order to deal with the multimodality and the correlation of dihedral angles φ and ψ, we developed approaches based on Kernel Density Estimation and Finite Gaussian Mixtures. Simulation results have shown that both techniques are promising when applied to that problem

Turning points in multilateral trade negotiations on intellectual property

Detailed chronologies of events that transpired during the discussion of intellectual property issues (TRIPS) in the GATT Uruguay Round and prior to and during the WTO Doha Ministerial are used to trace the unfolding negotiation processes through time. Of particular interest are departures from earlier trends in the chronologies. A departure is defined as a clear and self evident change from earlier events or patterns in the form of an impactful decision taken by one or more parties. By coding the causes (precipitants) and effects (consequences) of the departures, we perform a turning points analysis. These three-part sequences reveal the triggers and impacts of departures during the extended TRIPS negotiation process. The analyses will allow a comparison of the patterns that unfolded during the two phases of TRIPS negotiations. This comparison will highlight the breakthroughs that occurred during the Uruguay Round and the crises that emerged later, prior to and during the Doha Ministerial. It will also have implications more generally for the way that comparative analyses of international negotiation are performed

Early Pastoral Economies and Herding Transitions in Eastern Eurasia

While classic models for the emergence of pastoral groups in Inner Asia describe mounted, horse-borne herders sweeping across the Eurasian Steppes during the Early or Middle Bronze Age (ca. 3000–1500 BCE), the actual economic basis of many early pastoral societies in the region is poorly characterized. In this paper, we use collagen mass fingerprinting and ancient DNA analysis of some of the first stratified and directly dated archaeofaunal assemblages from Mongolia’s early pastoral cultures to undertake species identifications of this rare and highly fragmented material. Our results provide evidence for livestock-based, herding subsistence in Mongolia during the late 3rd and early 2nd millennia BCE. We observe no evidence for dietary exploitation of horses prior to the late Bronze Age, ca. 1200 BCE – at which point horses come to dominate ritual assemblages, play a key role in pastoral diets, and greatly influence pastoral mobility. In combination with the broader archaeofaunal record of Inner Asia, our analysis supports models for widespread changes in herding ecology linked to the innovation of horseback riding in Central Asia in the final 2nd millennium BCE. Such a framework can explain key broad-scale patterns in the movement of people, ideas, and material culture in Eurasian prehistory

Early Pastoral Economies and Herding Transitions in Eastern Eurasia

While classic models for the emergence of pastoral groups in Inner Asia describe mounted, horse-borne herders sweeping across the Eurasian Steppes during the Early or Middle Bronze Age (ca. 3000-1500 BCE), the actual economic basis of many early pastoral societies in the region is poorly characterized. In this paper, we use collagen mass fingerprinting and ancient DNA analysis of some of the first stratified and directly dated archaeofaunal assemblages from Mongolia's early pastoral cultures to undertake species identifications of this rare and highly fragmented material. Our results provide evidence for livestock-based, herding subsistence in Mongolia during the late 3rd and early 2nd millennia BCE. We observe no evidence for dietary exploitation of horses prior to the late Bronze Age, ca. 1200 BCE - at which point horses come to dominate ritual assemblages, play a key role in pastoral diets, and greatly influence pastoral mobility. In combination with the broader archaeofaunal record of Inner Asia, our analysis supports models for widespread changes in herding ecology linked to the innovation of horseback riding in Central Asia in the final 2nd millennium BCE. Such a framework can explain key broad-scale patterns in the movement of people, ideas, and material culture in Eurasian prehistory

Author Correction: Early Pastoral Economies and Herding Transitions in Eastern Eurasia (Scientific Reports, (2020), 10, 1, (1001), 10.1038/s41598-020-57735-y)

This Article contains a typographical error in the Introduction section under subheading ‘Understanding Early Horse Domestication and Transport’ where, “Historical records refer to horse-mounted warriors in western Asia by the 8th century BCE, while archaeological finds from localities like Arzhan 2 in southern Tuva show specialized horse equipment (bronze snaffle bits) and equine vertebral pathologies linked with mounted riding in Central Asia by the late 9th century BCE31.” should read: “Historical records refer to horse-mounted warriors in western Asia by the 8th century BCE, while archaeological finds from localities like Arzhan in southern Tuva show specialized horse equipment (bronze snaffle bits) and equine vertebral pathologies linked with mounted riding in Central Asia by the late 9th century BCE31.”

The CHEMDNER corpus of chemicals and drugs and its annotation principles

The automatic extraction of chemical information from text requires the recognition of chemical entity mentions as one of its key steps. When developing supervised named entity recognition (NER) systems, the availability of a large, manually annotated text corpus is desirable. Furthermore, large corpora permit the robust evaluation and comparison of different approaches that detect chemicals in documents. We present the CHEMDNER corpus, a collection of 10,000 PubMed abstracts that contain a total of 84,355 chemical entity mentions labeled manually by expert chemistry literature curators, following annotation guidelines specifically defined for this task. The abstracts of the CHEMDNER corpus were selected to be representative for all major chemical disciplines. Each of the chemical entity mentions was manually labeled according to its structure-associated chemical entity mention (SACEM) class: abbreviation, family, formula, identifier, multiple, systematic and trivial. The difficulty and consistency of tagging chemicals in text was measured using an agreement study between annotators, obtaining a percentage agreement of 91. For a subset of the CHEMDNER corpus (the test set of 3,000 abstracts) we provide not only the Gold Standard manual annotations, but also mentions automatically detected by the 26 teams that participated in the BioCreative IV CHEMDNER chemical mention recognition task. In addition, we release the CHEMDNER silver standard corpus of automatically extracted mentions from 17,000 randomly selected PubMed abstracts. A version of the CHEMDNER corpus in the BioC format has been generated as well. We propose a standard for required minimum information about entity annotations for the construction of domain specific corpora on chemical and drug entities. The CHEMDNER corpus and annotation guidelines are available at: http://www.biocreative.org/resources/biocreative-iv/chemdner-corpus