Cause of death estimation from verbal autopsies: is the open response redundant or synergistic?

Civil registration and vital statistics systems capture birth and death events to compile vital statistics and to provide legal rights to citizens. Vital statistics are a key factor in promoting public health policies and the health of the population. Medical certification of cause of death is the preferred source of cause of death information. However, two thirds of all deaths worldwide are not captured in routine mortality information systems and their cause of death is unknown. Verbal autopsy is an interim solution for estimating the cause of death distribution at the population level in the absence of medical certification. A Verbal Autopsy (VA) consists of an interview with the relative or the caregiver of the deceased. The VA includes both Closed Questions (CQs) with structured answer options, and an Open Response (OR) consisting of a free narrative of the events expressed in natural language and without any pre-determined structure. There are a number of automated systems to analyze the CQs to obtain cause specific mortality fractions with limited performance. We hypothesize that the incorporation of the text provided by the OR might convey relevant information to discern the CoD. The experimental layout compares existing Computer Coding Verbal Autopsy methods such as Tariff 2.0 with other approaches well suited to the processing of structured inputs as is the case of the CQs. Next, alternative approaches based on language models are employed to analyze the OR. Finally, we propose a new method with a bi-modal input that combines the CQs and the OR. Empirical results corroborated that the CoD prediction capability of the Tariff 2.0 algorithm is outperformed by our method taking into account the valuable information conveyed by the OR. As an added value, with this work we made available the software to enable the reproducibility of the results attained with a version implemented in R to make the comparison with Tariff 2.0 evident

Persistence in complex systems

Persistence is an important characteristic of many complex systems in nature, related to how long the system remains at a certain state before changing to a different one. The study of complex systems’ persistence involves different definitions and uses different techniques, depending on whether short-term or long-term persistence is considered. In this paper we discuss the most important definitions, concepts, methods, literature and latest results on persistence in complex systems. Firstly, the most used definitions of persistence in short-term and long-term cases are presented. The most relevant methods to characterize persistence are then discussed in both cases. A complete literature review is also carried out. We also present and discuss some relevant results on persistence, and give empirical evidence of performance in different detailed case studies, for both short-term and long-term persistence. A perspective on the future of persistence concludes the work.This research has been partially supported by the project PID2020-115454GB-C21 of the Spanish Ministry of Science and Innovation (MICINN). This research has also been partially supported by Comunidad de Madrid, PROMINT-CM project (grant ref: P2018/EMT-4366). J. Del Ser would like to thank the Basque Government for its funding support through the EMAITEK and ELKARTEK programs (3KIA project, KK-2020/00049), as well as the consolidated research group MATHMODE (ref. T1294-19). GCV work is supported by the European Research Council (ERC) under the ERC-CoG-2014 SEDAL Consolidator grant (grant agreement 647423)

Persistence in complex systems

Persistence is an important characteristic of many complex systems in nature, related to how long the system remains at a certain state before changing to a different one. The study of complex systems' persistence involves different definitions and uses different techniques, depending on whether short-term or long-term persistence is considered. In this paper we discuss the most important definitions, concepts, methods, literature and latest results on persistence in complex systems. Firstly, the most used definitions of persistence in short-term and long-term cases are presented. The most relevant methods to characterize persistence are then discussed in both cases. A complete literature review is also carried out. We also present and discuss some relevant results on persistence, and give empirical evidence of performance in different detailed case studies, for both short-term and long-term persistence. A perspective on the future of persistence concludes the work.This research has been partially supported by the project PID2020-115454GB-C21 of the Spanish Ministry of Science and Innovation (MICINN). This research has also been partially supported by Comunidad de Madrid, PROMINT-CM project (grant ref: P2018/EMT-4366). J. Del Ser would like to thank the Basque Government for its funding support through the EMAITEK and ELKARTEK programs (3KIA project, KK-2020/00049), as well as the consolidated research group MATHMODE (ref. T1294-19). GCV work is supported by the European Research Council (ERC) under the ERC-CoG-2014 SEDAL Consolidator grant (grant agreement 647423)

Corrigendum to: Drosophila Evolution over Space and Time (DEST): a New Population Genomics Resource

Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome datasets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate datasets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in > 20 countries on four continents. Several of these locations have been sampled at different seasons across multiple years. This dataset, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental meta-data. A web-based genome browser and web portal provide easy access to the SNP dataset. We further provide guidelines on how to use Pool-Seq data for model-based demographic inference. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan dataset. Our resource will enable population geneticists to analyze spatio-temporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.DrosEU is funded by a Special Topic Networks (STN) grant from the European Society for Evolutionary Biology (ESEB). MK (M. Kapun) was supported by the Austrian Science Foundation (grant no. FWF P32275); JG by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (H2020-ERC-2014-CoG-647900) and by the Spanish Ministry of Science and Innovation (BFU-2011-24397); TF by the Swiss National Science Foundation (SNSF grants PP00P3_133641, PP00P3_165836, and 31003A_182262) and a Mercator Fellowship from the German Research Foundation (DFG), held as a EvoPAD Visiting Professor at the Institute for Evolution and Biodiversity, University of Münster; AOB by the National Institutes of Health (R35 GM119686); MK (M. Kankare) by Academy of Finland grant 322980; VL by Danish Natural Science Research Council (FNU) grant 4002-00113B; FS Deutsche Forschungsgemeinschaft (DFG) grant STA1154/4-1, Project 408908608; JP by the Deutsche Forschungsgemeinschaft Projects 274388701 and 347368302; AU by FPI fellowship (BES-2012-052999); ET Israel Science Foundation (ISF) grant 1737/17; MSV, MSR and MJ by a grant from the Ministry of Education, Science and Technological Development of the Republic of Serbia (451-03-68/2020-14/200178); AP, KE and MT by a grant from the Ministry of Education, Science and Technological Development of the Republic of Serbia (451-03-68/2020-14/200007); and TM NSERC grant RGPIN-2018-05551.Peer reviewe

Extracting cause of death from verbal autopsy with deep learning interpretable methods

The international standard to ascertain the cause of death is medical certification. However, in many low and middle-income countries, the majority of deaths occur outside of health facilities. In these cases, Verbal Autopsy (VA), the narrative provided by a family member or friend together with a questionnaire is designed by the World Health Organization as the main information source. Until now technology allowed us to automatically analyze the responses of the VA questionnaire with the narrative captured by the interviewer excluded. Our work addresses this gap by developing a set of models for automatic Cause of Death (CoD) ascertainment in VAs with a focus on the textual information. Empirical results show that the open response conveys valuable information towards the ascertainment of the Cause of Death, and the combination of the closed-ended questions and the open response lead to the best results. Model interpretation capabilities position the Deep Learning models as the most encouraging choice

High resolution optical experimental technique for computing pulsed laser-induced cavitation bubble dynamics in a single shot

The experiments conducted in this study consisted of a series of plasma generated cavitation bubbles in water, obtained by focusing a 532-nm Q-switched Nd:YAG nanosecond-pulsed laser. For the purpose of detection of such cavitation bubbles, a novel direct light transmission technique is used, referred to as spatial transmission modulation (STM), consisting of a nearly collimated beam of light passing through the sample at the point where the cavitation bubble is formed. The presence of the cavitation bubble modifies the direct light transmission, which is detected with a photodiode located at the opposite end. This is observed as an electrical signal response with an oscilloscope. A 1-megapixel high-speed video camera simultaneously records the cavitation event. The video was taken in an orthogonal direction with respect to the STM optical axis and was triggered simultaneously with an oscilloscope using the electronic synchronization signal from the pulsed laser. Data from the highspeed video was used to show that a computational spatial energetic analysis from the continuous laser probe beam is a valid method to directly obtain the cavitation bubble evolution from a single shot pulse. © 2013 by Begell House, Inc

High resolution optical experimental technique for computing pulsed laser-induced cavitation bubble dynamics in a single shot

The experiments conducted in this study consisted of a series of plasma generated cavitation bubbles in water, obtained by focusing a 532-nm Q-switched Nd:YAG nanosecond-pulsed laser. For the purpose of detection of such cavitation bubbles, a novel direct light transmission technique is used, referred to as spatial transmission modulation (STM), consisting of a nearly collimated beam of light passing through the sample at the point where the cavitation bubble is formed. The presence of the cavitation bubble modifies the direct light transmission, which is detected with a photodiode located at the opposite end. This is observed as an electrical signal response with an oscilloscope. A 1-megapixel high-speed video camera simultaneously records the cavitation event. The video was taken in an orthogonal direction with respect to the STM optical axis and was triggered simultaneously with an oscilloscope using the electronic synchronization signal from the pulsed laser. Data from the highspeed video was used to show that a computational spatial energetic analysis from the continuous laser probe beam is a valid method to directly obtain the cavitation bubble evolution from a single shot pulse. © 2013 by Begell House, Inc

Analysis, Characterization, Prediction and Attribution of Extreme Atmospheric Events with Machine Learning: a Review

Atmospheric Extreme Events (EEs) cause severe damages to human societies and ecosystems. The frequency and intensity of EEs and other associated events are increasing in the current climate change and global warming risk. The accurate prediction, characterization, and attribution of atmospheric EEs is therefore a key research field, in which many groups are currently working by applying different methodologies and computational tools. Machine Learning (ML) methods have arisen in the last years as powerful techniques to tackle many of the problems related to atmospheric EEs. This paper reviews the ML algorithms applied to the analysis, characterization, prediction, and attribution of the most important atmospheric EEs. A summary of the most used ML techniques in this area, and a comprehensive critical review of literature related to ML in EEs, are provided. A number of examples is discussed and perspectives and outlooks on the field are provided.This research has been partially supported by the European Union, through H2020 Project “CLIMATE INTELLIGENCE Extreme events detection, attribution and adaptation design using machine learning (CLINT)”, Ref: 101003876-CLINT. This research has also been partially supported by the project PID2020-115454GB-C21 of the Spanish Ministry of Science and Innovation (MICINN). J. Del Ser also acknowledges support by the Basque Government through EMAITEK and ELKARTEK funds (ref. KK-2020/00049), as well as the consolidated research group MATHMODE (IT1294-19)

Analysis and Prediction of Dammed Water Level in a Hydropower Reservoir Using Machine Learning and Persistence-Based Techniques

This paper presents long- and short-term analyses and predictions of dammed water level in a hydropower reservoir. The long-term analysis was carried out by using techniques such as detrended fluctuation analysis, auto-regressive models, and persistence-based algorithms. On the other hand, the short-term analysis of the dammed water level in the hydropower reservoir was modeled as a prediction problem, where machine learning regression techniques were studied. A set of models, including different types of neural networks, Support Vector regression, or Gaussian processes was tested. Real data from a hydropower reservoir located in Galicia, Spain, qwew considered, together with predictive variables from upstream measuring stations. We show that the techniques presented in this paper offer an excellent tool for the long- and short-term analysis and prediction of dammed water level in reservoirs for hydropower purposes, especially important for the management of water resources in areas with hydrology stress, such as Spain