Progressive Wasserstein Barycenters of Persistence Diagrams

This paper presents an efficient algorithm for the progressive approximation of Wasserstein barycenters of persistence diagrams, with applications to the visual analysis of ensemble data. Given a set of scalar fields, our approach enables the computation of a persistence diagram which is representative of the set, and which visually conveys the number, data ranges and saliences of the main features of interest found in the set. Such representative diagrams are obtained by computing explicitly the discrete Wasserstein barycenter of the set of persistence diagrams, a notoriously computationally intensive task. In particular, we revisit efficient algorithms for Wasserstein distance approximation [12,51] to extend previous work on barycenter estimation [94]. We present a new fast algorithm, which progressively approximates the barycenter by iteratively increasing the computation accuracy as well as the number of persistent features in the output diagram. Such a progressivity drastically improves convergence in practice and allows to design an interruptible algorithm, capable of respecting computation time constraints. This enables the approximation of Wasserstein barycenters within interactive times. We present an application to ensemble clustering where we revisit the k-means algorithm to exploit our barycenters and compute, within execution time constraints, meaningful clusters of ensemble data along with their barycenter diagram. Extensive experiments on synthetic and real-life data sets report that our algorithm converges to barycenters that are qualitatively meaningful with regard to the applications, and quantitatively comparable to previous techniques, while offering an order of magnitude speedup when run until convergence (without time constraint). Our algorithm can be trivially parallelized to provide additional speedups in practice on standard workstations. [...

The European Language Resources and Technologies Forum: Shaping the Future of the Multilingual Digital Europe

Proceedings of the 1st FLaReNet Forum on the European Language Resources and Technologies, held in Vienna, at the Austrian Academy of Science, on 12-13 February 2009

ECP-2007-LANG-617001 FLaReNet: Action Plan

Action plan of the FLaReNet project

The strategic impact of META-NET on the regional, national and international level

This article provides an overview of the dissemination work carried out in META-NET from 2010 until 2015; we describe its impact on the regional, national and international level, mainly with regard to politics and the funding situation for LT topics. The article documents the initiative's work throughout Europe in order to boost progress and innovation in our field.Peer reviewe

Lethal Mutants and Truncated Selection Together Solve a Paradox of the Origin of Life

BACKGROUND: Many attempts have been made to describe the origin of life, one of which is Eigen's cycle of autocatalytic reactions [Eigen M (1971) Naturwissenschaften 58, 465-523], in which primordial life molecules are replicated with limited accuracy through autocatalytic reactions. For successful evolution, the information carrier (either RNA or DNA or their precursor) must be transmitted to the next generation with a minimal number of misprints. In Eigen's theory, the maximum chain length that could be maintained is restricted to 100-1000 nucleotides, while for the most primitive genome the length is around 7000-20,000. This is the famous error catastrophe paradox. How to solve this puzzle is an interesting and important problem in the theory of the origin of life. METHODOLOGY/PRINCIPAL FINDINGS: We use methods of statistical physics to solve this paradox by carefully analyzing the implications of neutral and lethal mutants, and truncated selection (i.e., when fitness is zero after a certain Hamming distance from the master sequence) for the critical chain length. While neutral mutants play an important role in evolution, they do not provide a solution to the paradox. We have found that lethal mutants and truncated selection together can solve the error catastrophe paradox. There is a principal difference between prebiotic molecule self-replication and proto-cell self-replication stages in the origin of life. CONCLUSIONS/SIGNIFICANCE: We have applied methods of statistical physics to make an important breakthrough in the molecular theory of the origin of life. Our results will inspire further studies on the molecular theory of the origin of life and biological evolution

Discovery of a Non-Peptidic Inhibitor of West Nile Virus NS3 Protease by High-Throughput Docking

An estimated 2.5 billion people are at risk of diseases caused by dengue and West Nile virus. As of today, there are neither vaccines to prevent nor drugs to cure the severe infections caused by these viruses. The NS3 protease is one of the most promising targets for drug development against West Nile virus because it is an essential enzyme for viral replication and because success has been demonstrated with the closely related hepatitis C virus protease. We have discovered a small molecule that inhibits the NS3 protease of West Nile virus by computer-aided high-throughput docking, and validated it using three experimental techniques. The inhibitor has potential to be developed to a drug candidate to combat West Nile virus infections

The Strategic Impact of META-NET on the Regional, National and International Level

This article provides an overview of the dissemination work carried out in META-NET from 2010 until early 2014; we describe its impact on the regional, national and international level, mainly with regard to politics and the situation of funding for LT topics. This paper documents the initiative’s work throughout Europe in order to boost progress and innovation in our field.Peer reviewe

ECP-2007-LANG-617001 FLaReNet: Progress Report No. 4

Fourth semestrial report on the progress of the FLaReNet project

Global survey of dioxin- and thyroid hormone-like activities in consumer products and toys

Background: Children and consumers are exposed to increasingly complex mixtures of known and as-yet-unknown toxic chemicals from toys and products. However traditional chemical analysis methods only evaluate a small number of chemicals at a time thereby restricting consumer awareness of the full range of potentially harmful chemicals in products. Methods: We used high-throughput effect-based non-animal methods to investigate exposures to complex chemical mixtures of several kinds of brominated flame retardants (BFRs) for their dioxin- and thyroid hormone-like activities in various kinds of consumer products and toys from 26 different countries, on four continents (Africa, America, Asia and Europe) in combination with chemical analysis of various polybrominated flame retardants (BFRs) and their impurities (such as polyhalogenated PCDD/Fs and PBDD/Fs). Results: We found high levels of polybrominated dibenzo-p-dioxins and dibenzofurans (PBDD/Fs) in toys and now, for the first time, also in consumer products that are manufactured from black plastics containing certain brominated flame retardants (BFRs). The presence of PBDD/PBDFs as well as other BFRs in various black plastic materials from additional countries as well as additional kinds of consumer products as confirmed by effect-based in vitro reporter gene DR CALUX and TTR-TRβ CALUX assays as well as congener-specific chemical analysis. We compared total Toxicity Equivalent (TEQ) levels of PBDD/F-TEQs analysed by chemical analysis to by CALUX bioassay measured Biological equivalence (BEQ) concentrations (for further info see at ISO 23196, ISO, 2022). In the case of TBBPA, both chemical and TTR-TRβ CALUX analysis measure direct the amount of TBBPA. Finally, the daily ingestion of 2,3,7,8-TCDD equivalents from PBDD/Fs-contaminated plastic toys by child mouthing habits have been related to our earlier study (Budin et al., 2020). Conclusions: Interaction of children with such contaminated plastics may significantly contribute to the daily uptake of dioxin- and thyroid hormone transport disrupting-like compounds. Effect-based bioassays for dioxin- and thyroid hormone-like activities are relevant to pick-out such complex mixtures of known and yet unknown (and therefore not regulated) substances for safer and more sustainable plastics. Low POPs Content Levels and other mechanisms set under the Basel and Stockholm Conventions are set far too high to prevent a significant flow of BFRs and PBDD/Fs into consumer products