A polynomial-time interior-point method for conic optimization, with inexact barrier evaluations

We consider a primal-dual short-step interior-point method for conic convex optimization problems for which exact evaluation of the gradient and Hessian of the primal and dual barrier functions is either impossible or prohibitively expensive. As our main contribution, we show that if approximate gradients and Hessians of the primal barrier function can be computed, and the relative errors in such quantities are not too large, then the method has polynomial worst-case iteration complexity. (In particular, polynomial iteration complexity ensues when the gradient and Hessian are evaluated exactly.) In addition, the algorithm requires no evaluation---or even approximate evaluation---of quantities related to the barrier function for the dual cone, even for problems in which the underlying cone is not self-dual

Universal Duality in Conic Convex Optimization

Given a primal-dual pair of linear programs, it is known that if their optimal values are viewed as lying on the extended real line, then the duality gap is zero, unless both problems are infeasible, in which case the optimal values are +infinity and -infinity. In contrast, for optimization problems over nonpolyhedral convex cones, a nonzero duality gap can exist even in the case where the primal and dual problems are both feasible. For a pair of dual conic convex programs, we provide simple conditions on the onstraint matricesand cone under which the duality gap is zero for every choice of linear objective function and ight-hand-side We refer to this property as niversal duality Our conditions possess the following properties: (i) they are necessary and sufficient, in the sense that if (and only if) they do not hold, the duality gap is nonzero for some linear objective function and ight-hand-side (ii) they are metrically and topologically generic; and (iii) they can be verified by solving a single conic convex program. As a side result, we also show that the feasible sets of a primal conic convex program and its dual cannot both be bounded, unless they are both empty, and we relate this to universal duality

The Phylogeny of the Four Pan-American MtDNA Haplogroups: Implications for Evolutionary and Disease Studies

Only a limited number of complete mitochondrial genome sequences belonging to Native American haplogroups were available until recently, which left America as the continent with the least amount of information about sequence variation of entire mitochondrial DNAs. In this study, a comprehensive overview of all available complete mitochondrial DNA (mtDNA) genomes of the four pan-American haplogroups A2, B2, C1, and D1 is provided by revising the information scattered throughout GenBank and the literature, and adding 14 novel mtDNA sequences. The phylogenies of haplogroups A2, B2, C1, and D1 reveal a large number of sub-haplogroups but suggest that the ancestral Beringian population(s) contributed only six (successful) founder haplotypes to these haplogroups. The derived clades are overall starlike with coalescence times ranging from 18,000 to 21,000 years (with one exception) using the conventional calibration. The average of about 19,000 years somewhat contrasts with the corresponding lower age of about 13,500 years that was recently proposed by employing a different calibration and estimation approach. Our estimate indicates a human entry and spread of the pan-American haplogroups into the Americas right after the peak of the Last Glacial Maximum and comfortably agrees with the undisputed ages of the earliest Paleoindians in South America. In addition, the phylogenetic approach also indicates that the pathogenic status proposed for various mtDNA mutations, which actually define branches of Native American haplogroups, was based on insufficient grounds

TRY plant trait database – enhanced coverage and open access

Plant traits - the morphological, anatomical, physiological, biochemical and phenological characteristics of plants - determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait‐based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits - almost complete coverage for ‘plant growth form’. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait–environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Meeting the challenges facing wheat production: The strategic research agenda of the Global Wheat Initiative

Wheat occupies a special role in global food security since, in addition to providing 20% of our carbohydrates and protein, almost 25% of the global production is traded internationally. The importance of wheat for food security was recognised by the Chief Agricultural Scientists of the G20 group of countries when they endorsed the establishment of the Wheat Initiative in 2011. The Wheat Initiative was tasked with supporting the wheat research community by facilitating collaboration, information and resource sharing and helping to build the capacity to address challenges facing production in an increasingly variable environment. Many countries invest in wheat research. Innovations in wheat breeding and agronomy have delivered enormous gains over the past few decades, with the average global yield increasing from just over 1 tonne per hectare in the early 1960s to around 3.5 tonnes in the past decade. These gains are threatened by climate change, the rapidly rising financial and environmental costs of fertilizer, and pesticides, combined with declines in water availability for irrigation in many regions. The international wheat research community has worked to identify major opportunities to help ensure that global wheat production can meet demand. The outcomes of these discussions are presented in this paper

Universal Duality in Conic Convex Optimization

Given a primal-dual pair of linear programs, it is well known that if their optimal values are viewed as lying on the extended real line, then the duality gap is zero, unless both problems are infeasible, in which case the optimal values are + ∞ and −∞. In contrast, for optimization problems over nonpolyhedral convex cones, a nonzero duality gap can exist when either the primal or the dual is feasible. For a pair of dual conic convex programs, we provide simple conditions on the “constraint matrices ” and cone under which the duality gap is zero for every choice of linear objective function and constraint right-hand side. We refer to this property as “universal duality”. Our conditions possess the following properties: (i) they are necessary and sufficient, in the sense that if (and only if) they do not hold, the duality gap is nonzero for some linear objective function and constraint right-hand side; (ii) they are metrically and topologically generic; and (iii) they can be verified by solving a single conic convex program. We relate to universal duality the fact that the feasible sets of a primal convex program and its dual cannot both be bounded, unless they are both empty. Finally we illustrate our theory on a class of semidefinite programs that appear in control theory applications