Structural Agnostic Modeling: Adversarial Learning of Causal Graphs

A new causal discovery method, Structural Agnostic Modeling (SAM), is presented in this paper. Leveraging both conditional independencies and distributional asymmetries in the data, SAM aims at recovering full causal models from continuous observational data along a multivariate non-parametric setting. The approach is based on a game between $d$ players estimating each variable distribution conditionally to the others as a neural net, and an adversary aimed at discriminating the overall joint conditional distribution, and that of the original data. An original learning criterion combining distribution estimation, sparsity and acyclicity constraints is used to enforce the end-to-end optimization of the graph structure and parameters through stochastic gradient descent. Besides the theoretical analysis of the approach in the large sample limit, SAM is extensively experimentally validated on synthetic and real data

INTERNET REPRESENTATIONS OF DIALECTAL ENGLISH

International audienceThis paper presents an account of how alternative spellings found online can be linked to phonetic and phonological roots, especially in settings where dialects are encouraged. These spellings are part of Netspeak uses, and dialectal spellings are influenced by official, lexicographical sources and a personal desire to spell words as they are pronounced. Consonants and vowels are affected by these choices, and this paper will mainly discuss consonantal changes and the limits of vocalic alternations. The first research question focuses on how non-traditional spellings aim at showing an alteration of the same type of sound, irrespective of the dialect, to see if there are common underlying mechanisms between very different dialects of English. Exposure to the Internet culture, and forum-specific uses may account for neography. Limits reached by these respellings (homophony, semantic ambiguity) will also be discussed. The corpus of this study is composed of written productions found in African American and Scottish online communities, Black Planet and Scotster, to examine the parallel development of alternative spellings in two dialects that contravene the rhoticity of the variety of English spoken in their country. The wider ecological 1 context of writing online is the first focal point: Netspeak influences alternative written practices, and censorship is a peculiarity of this environment. The typology of alternative spellings will be defined: they are not limited to simple deletion or doubling of letters, and their difference with spelling mistakes will be specified. The stance of linguistic studies on spelling and lexical differences with standard English will shed light on the official stances regarding these two dialects, and which rules alternative forms found on the forums are supposed to follow. While Scots spelling is seen with a little more prescriptivism, works on African American Vernacular describe forms and sanitize them (there is very little profanity in dictionaries). Bearing in mind these specificities and the wider online context, consonantal substitutions will be tackled, both generally, and then more specifically when they are applied to grammatical words. Vowel changes and limits created by homophony will be the point of the last subsection.Les graphies alternatives en ligne peuvent être attribuées à des causes phonétiques et phonologiques, surtout dans des contextes où l’utilisation d’un dialecte est encouragée. Je m’intéresse ici surtout aux changements consonantiques dans les graphies utilisées par des membres de forums afro-américains et écossais.Ces graphies peuvent être contraintes par la culture internet, et par celle des forums fréquentés. Après une typologie des phénomènes rencontrés, et des strates linguistiques (Netspeak, graphies alternatives idiolectales…), j’étudierai dans la seconde partie les points de vue des organismes officiels qui édictent des règles pour ces deux langues minoritaires. Si l’attitude écossaise est plus prescriptiviste, les lexicographes afro-américains décrivent en censurant les lexèmes qu’ils recensent. La dernière partie examinera les substitutions consonantales, notamment dans les mots grammaticaux, puis les substitutions vocaliques et les problèmes d’homophonie qu’elles peuvent provoquer

Role of the small subunit of Rubisco in the green algal phylogeny and Carbon Concentrating Mechanism expression

Photoautotrophic organisms globally fix 111-117x1015 grams of carbon per year and around half of this global net primary production is aquatic (Behrenfeld et al., 2001; Field et al., 1998), with green algae a major contributor to this global carbon fixation. However, aquatic environments have some limitations The concentration of CO2 is often 2,200 times lower in water than in air, and diffusion is also 8,000 times slower. In addition, Rubisco, which catalyses the first major step of carbon fixation, converting atmospheric CO2 into precursors of energy-rich molecules, exhibits slow catalytic rates, low affinity for CO2 and competition from O2 for the active sites. Therefore, most green algae have developed a Carbon Concentrating Mechanism (CCM). In eukaryotic micro-algae, the Rubisco micro-compartment is called the pyrenoid and together with active inorganic carbon transporters and strategically located carbonic anhydrases, elevated CO2 within the pyrenoid improves photosynthetic efficiency. Most photosynthetic organisms have an hexadecameric Rubisco holoenzyme (L8S8), composed of eight ~55-kDa large subunit (LSU), encoded by a chloroplast gene (rbcL) and eight ~15-kDa small subunit (SSU), encoded by a nuclear gene family (RbcS) in Form I Rubisco. The CCM has been particularly well-defined in the model unicellular chlorophyte Chlamydomonas reinhardtii and recent studies showed that for full CCM induction, a key protein linker EPYC1 and its interaction with Rubisco SSU were necessary. The overall goal of this study was to use a phylogenetic approach, firstly to investigate SSU structure across the green algal phylogeny, and also to explore CCM diversity in two specific groups of species. This study used a variety of methodologies combining physiological experiments, biochemistry, imaging and bioinformatic analyses. The results firstly showed the presence of two different Rubisco SSU structures within the green algae. Secondly, the Rubisco catalytic properties found in streptophyte algae closely related to land plants (streptophytes) reflect the strength of any CCM and pyrenoid leakiness, whereas Rubisco in extant land plants reflects more recent selective pressures associated with the terrestrial atmospheric environment. This research also provides evidence for diversity of CCM expression in two closely related genera (Chlamydomonas and Chloromonas), ranging from species expressing a CCM and pyrenoid, or a CCM without a pyrenoid, to neither pyrenoid or CCM. This study provides the first preliminary analyses of five different genomes confirming multiple independent origins of the pyrenoid in green algae but has also allowed an initial comparison of the molecular components essential for pyrenoid formation across these species.Natural Environment Research Council (grant number NE/L002507/1 to Howard Griffiths) and resources associated with BBSRC-BB/M007693/1, BB/I024518/1 as part of the Combining Algal and Plant Photosynthesis (CAPP), supported by BBSRC and NSF. We are grateful for a Cambridge Trust Vice Chancellor’s award and Lucy Cavendish College, Cambridge, for supporting the PhD scholarship of Myriam Goudet. Doug Orr and Elizabete Carmo-Silva acknowledge support from the UK Biotechnology and Biological Sciences Research Council (BBSRC; grant number BB/I024488/1)

Infant and young children's nutritional health and feeding practices in relation to flooding in Bangladesh

Bangladesh is one of the poorest developing countries in the world where infant and young children (IYC) suffer from extremely high levels of malnutrition resulting in high morbidity and mortality rates. IYC are defined here as birth to 3 years old. Due to the double burden of climate variability and urbanisation, longer and more severe floods affect people living in urban slums, with IYC being highly vulnerable. Insufficient research exists into understanding the mechanisms leading to poor nutritional child health related to flooding in urban slums. Maternal nutritional status associated with infant and child health has been established previously, but rarely in the aftermath of a flood. This study explores, 1) whether maternal nutritional status measured soon after a flood can predict the current nutritional status and the risk for future deterioration of nutritional status of their children, 2) the impact of flooding on IYC feeding practices during flooding compared to non-flooding and the coping strategies developed by caretakers in urban slums, 3) the perceptions of root causes of malnutrition including flooding for IYC living in urban slums and 4) develops a pilot study for an intervention to tackle malnutrition in IYC living in urban slums. The research uses 1) quantitative data (n=143, secondary analysis of data collected after the 1998 flood in Bangladesh) to answer the first research question, and 2) a mixed method approach of qualitative data (participant observation n=24, semi-structured interviews n=23 (18 mothers, 5 community health workers), and focus group discussions n=10) and quantitative data (household questionnaire n=23 and anthropometric measurements n=55 for IYC and n=23 for mothers and community health workers) collected in slums in Dhaka to answer the second and third research questions. A new technique is used to answer question three. This technique is based on existing methods for the building of a causal model combined with a pile sorting of photographs to understand the root causes and processes leading to malnutrition. The participants of the mixed method were mothers, pregnant women and Bangladesh Rural Advancement Committee (BRAC) community health workers living and working in the slums. The key findings are: 1) maternal nutritional status measured soon after a flood can predict the current nutritional status and the risk for future deterioration of nutritional status of their children, 2) feeding practices for IYC deteriorate during flooding in Dhaka slums, 3) the coping strategies of IYC caretakers are limited and their resilience capacity to floods is low, 4) there is a good perception of the root causes of malnutrition by participants living in Dhaka slums but feeding practices are not meeting the WHO guidelines due to barriers, limitations and poor knowledge, and 5) there is a need for a pilot project to test the feasibility of an intervention aiming at improving IYC nutritional health and feeding practices. This research deepens the understanding of coping strategies for feeding practices and perceived roots of malnutrition for IYC living in urban slums exposed to flooding. It brings evidence of the interactions between coping strategies and nutritional health in relation to flooding. It also casts new anthropological light onto the series of existing studies and previous research essentially focused on the flood event itself. As a result, the research leads to recommendations for risk reduction strategies and nutrition promotion for flood exposed populations with infants and young children

On the study of the Beran estimator for generalized censoring indicators

Along with the analysis of time-to-event data, it is common to assume that only partial information is given at hand. In the presence of right-censored data with covariates, the conditional Kaplan-Meier estimator (also referred as the Beran estimator) is known to propose a consistent estimate for the lifetimes conditional survival function. However, a necessary condition is the clear knowledge of whether each individual is censored or not, although, this information might be incomplete or even totally absent in practice. We thus propose a study on the Beran estimator when the censoring indicator is not clearly specified. From this, we provide a new estimator for the conditional survival function and establish its asymptotic normality under mild conditions. We further study the supervised learning problem where the conditional survival function is to be predicted with no censorship indicators. To this aim, we investigate various approaches estimating the conditional expectation for the censoring indicator. Along with the theoretical results, we illustrate how the estimators work for small samples by means of a simulation study and show their practical applicability with the analysis of synthetic data and the study of real data for the prognosis of monoclonal gammopathy

Experimental evidence of inbreeding avoidance in the hermaphroditic snail Physa acuta

Inbreeding depression should select for inbreeding avoidance behaviours. Here we test this hypothesis in two populations of the simultaneous hermaphroditic freshwater snail Physa acuta. We recorded the copulatory behaviour of 288 pairs of sib-mates, non-kin mates from the same population, or non-kin mates from two different populations. We find that kin discriminatory behaviours exist in this species, exclusively expressed by individuals playing the female role. We discuss the relevance of our finding in the context of the evolution of recognition systems and the consequences of such a behaviour in natural population