Simultaneous identification of models and parameters of scientific simulators

Many scientific models are composed of multiple discrete components, and scien tists often make heuristic decisions about which components to include. Bayesian inference provides a mathematical framework for systematically selecting model components, but defining prior distributions over model components and developing associated inference schemes has been challenging. We approach this problem in an amortized simulation-based inference framework: We define implicit model priors over a fixed set of candidate components and train neural networks to infer joint probability distributions over both, model components and associated parameters from simulations. To represent distributions over model components, we introduce a conditional mixture of multivariate binary distributions in the Grassmann formalism. Our approach can be applied to any compositional stochastic simulator without requiring access to likelihood evaluations. We first illustrate our method on a simple time series model with redundant components and show that it can retrieve joint posterior distribution over a set of symbolic expressions and their parameters while accurately capturing redundancy with strongly correlated posteriors. We then apply our approach to drift-diffusion models, a commonly used model class in cognitive neuroscience. After validating the method on synthetic data, we show that our approach explains experimental data as well as previous methods, but that our fully probabilistic approach can help to discover multiple data-consistent model configurations, as well as reveal non-identifiable model components and parameters. Our method provides a powerful tool for data-driven scientific inquiry which will allow scientists to systematically identify essential model components and make uncertainty-informed modelling decisions

Fovea-like photoreceptor specializations underlie single UV cone driven prey-capture behavior in zebrafish

In the eye, the function of same-type photoreceptors must be regionally adjusted to process a highly asymmetrical natural visual world. Here, we show that UV cones in the larval zebrafish area temporalis are specifically tuned for UV-bright prey capture in their upper frontal visual field, which may use the signal from a single cone at a time. For this, UV-photon detection probability is regionally boosted more than 10-fold. Next, in vivo two-photon imaging, transcriptomics, and computational modeling reveal that these cones use an elevated baseline of synaptic calcium to facilitate the encoding of bright objects, which in turn results from expressional tuning of phototransduction genes. Moreover, the light-driven synaptic calcium signal is regionally slowed by interactions with horizontal cells and later accentuated at the level of glutamate release driving retinal networks. These regional differences tally with variations between peripheral and foveal cones in primates and hint at a common mechanistic origin

Ancestral circuits for vertebrate color vision emerge at the first retinal synapse

For color vision, retinal circuits separate information about intensity and wavelength. In vertebrates that use the full complement of four “ancestral” cone types, the nature and implementation of this computation remain poorly understood. Here, we establish the complete circuit architecture of outer retinal circuits underlying color processing in larval zebrafish. We find that the synaptic outputs of red and green cones efficiently rotate the encoding of natural daylight in a principal components analysis–like manner to yield primary achromatic and spectrally opponent axes, respectively. Blue cones are tuned to capture most remaining variance when opposed to green cones, while UV cone present a UV achromatic axis for prey capture. We note that fruitflies use essentially the same strategy. Therefore, rotating color space into primary achromatic and chromatic axes at the eye’s first synapse may thus be a fundamental principle of color vision when using more than two spectrally well-separated photoreceptor types

Agglutination of benthic foraminifera in relation to mesoscale bathymetric features in the abyssal NE Atlantic (Porcupine Abyssal Plain)

Abyssal hills, small topographic features rising above the abyssal seafloor (< 1000 m altitude), have distinct environmental characteristics compared to abyssal plains, notably the presence of coarser-grained sediments. As a result, they are a major source of habitat heterogeneity in the deep sea. The aim of this study was to investigate whether there is a link between abyssal hills and the test characteristics of selected agglutinated benthic foraminiferal species. We analysed 1) the overall morphometry, and 2) the granulometric and chemical (elemental) characteristics of the agglutinated tests of ten common foraminiferal species (Adercotryma glomerata, Ammobaculites agglutinans, Cribrostomoides subglobosus, Lagenammina sp.1, Nodulina dentaliniformis, Portatrochammina murrayi, three Reophax sp. and Recurvoides sp. 9) at four sites (two on top of abyssal hills and two on the adjacent plain) in the area of the Porcupine Abyssal Plain Sustained Observatory, northeast Atlantic. The foraminiferal test data were compared with the particle size distribution and elemental composition of sediments from the study sites in order to explore possible grain size and mineral selectivity. We found differences in the visual appearance of the tests (i.e. the degree of irregularity in their shape), which was confirmed by morphometric analyses, related to seafloor topography. The agglutinated foraminifera selected different sized particles on hills and plains, reflecting the distinct granulometric characteristics of these settings. These characteristics (incorporation of coarse particles, test morphometry) could provide evidence for the recognition of ancient abyssal hill environments, as well as other palaeoceanographic settings that were characterised by enhanced current flow. Furthermore, analyses of sediment samples from the hill and plain sites using wavelength dispersive X-ray fluorescence (WD-XRF) yielded different elemental profiles from the plains, probably a result of winnowing on the hills, although all samples were carbonate-rich. In contrast, the majority of the agglutinated tests were rich in silica, suggesting a preferential selection for quartz

Bose-Einstein Correlations of Three Charged Pions in Hadronic Z^0 Decays

Bose-Einstein Correlations (BEC) of three identical charged pions were studied in 4 x 10^6 hadronic Z^0 decays recorded with the OPAL detector at LEP. The genuine three-pion correlations, corrected for the Coulomb effect, were separated from the known two-pion correlations by a new subtraction procedure. A significant genuine three-pion BEC enhancement near threshold was observed having an emitter source radius of r_3 = 0.580 +/- 0.004 (stat.) +/- 0.029 (syst.) fm and a strength of \lambda_3 = 0.504 +/- 0.010 (stat.) +/- 0.041 (syst.). The Coulomb correction was found to increase the \lambda_3 value by \~9% and to reduce r_3 by ~6%. The measured \lambda_3 corresponds to a value of 0.707 +/- 0.014 (stat.) +/- 0.078 (syst.) when one takes into account the three-pion sample purity. A relation between the two-pion and the three-pion source parameters is discussed.Comment: 19 pages, LaTeX, 5 eps figures included, accepted by Eur. Phys. J.

Conversos y librepensamiento. A la búsqueda de algunas huellas (ss. XVI y XVII)

In the 16th and 17th centuries, among Iberian New Christians there can be detected some radical manifestations of religious disruption. Following the research of Yitzhak Baer, Carl Gebhardt and most notably Israël S. Révah, these phenomena repeatedly have been linked both to late medieval Jewish «averroism» and the Spinozistic philosophy of the 17th century. However, more perspectives are possible. Here, we would like to present the trends of converso unbelieve with their academic background and in the European context, paying special attention to a group of five New Christian physicians, who, about 1630, together studied at the University of Alcalá de Henares.En los siglos XVI y XVII, en el entorno de los cristianos nuevos ibéricos se detectan algunas manifestaciones radicales de desvinculación religiosa. Prosiguiendo las investigaciones de Yitzhak Baer, Carl Gebhardt y sobre todo de Israël S. Révah, esos fenómenos han sido repetidamente vinculados tanto con el «averroísmo» judío bajomedieval como con la filosofía spinoziana del seiscientos. Sin embargo, nos parecen posibles más enfoques. Aquí, queremos presentar esas corrientes de incredulidad conversa sobre su trasfondo académico y enmarcadas en el contexto europeo, prestando una atención particular a un grupo de cinco médicos cristianos nuevos que, alrededor de 1630, estudiaron juntos en la Universidad de Alcalá de Henares

A new multi-proxy investigation of Late Quaternary palaeoenvironments along the north-western Barents Sea (Storfjorden Trough Mouth Fan)

A new integrated micropalaeontological study on planktonic and benthic foraminifera, calcareous nannofossils and diatoms was performed on three sediment cores from the Storfjorden Trough Mouth Fan to reconstruct the Late Quaternary palaeoenvironmental and climatic history. Two main intervals were discussed: the last deglaciation (16.2\u201311.7 ka BP) and the Holocene. The age model relies on palaeomagnetic parameters together with 10 radiocarbon dates. Deglacial sediments had largely diluted the biogenic content which was scarce and poorly preserved. The first occurrence of Cibicidoides wuellerstorfi (benthic foraminifer), together with Turborotalita quinqueloba (planktonic foraminifer) and Coscinodiscus spp. (diatoms) at 11.3 ka BP followed the end of the Younger Dryas cold event and marked the beginning of the early Holocene warm period. Diatoms and planktonic foraminifers indicated a warming of the surface water from 10.5 to 9.2 ka BP, identifying the Holocene Thermal Maximum event. Bottom water fauna registered these warming conditions less clearly. Cooling events were identified during the Holocene, in particular the 8.2 ka BP event and the Neoglacial between 3.2 and 2 ka BP, as shown by the presence of cold-water taxa such as Gephyrocapsa muellerae (nannoplankton) and Neogloboquadrina pachyderma (planktonic foraminifer). These events were influenced by sea ice extent, cold or relatively warm current influxes

The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima.

Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history.This work was supported by the following grants: NHGRIU54HG003273 to R.A.G; EU Marie Curie ITN #215781 “Evonet” to M.A.; a Wellcome Trust Value in People (VIP) award to C.B. and Wellcome Trust graduate studentship WT089615MA to J.E.G; Marine rhythms of Life” of the University of Vienna, an FWF (http://www.fwf.ac.at/) START award (#AY0041321) and HFSP (http://www.hfsp.org/) research grant (#RGY0082/2010) to KT-­‐R; MFPL Vienna International PostDoctoral Program for Molecular Life Sciences (funded by Austrian Ministry of Science and Research and City of Vienna, Cultural Department -­‐Science and Research to T.K; Direct Grant (4053034) of the Chinese University of Hong Kong to J.H.L.H.; NHGRI HG004164 to G.M.; Danish Research Agency (FNU), Carlsberg Foundation, and Lundbeck Foundation to C.J.P.G.; U.S. National Institutes of Health R01AI55624 to J.H.W.; Royal Society University Research fellowship to F.M.J.; P.D.E. was supported by the BBSRC via the Babraham Institute;This is the final version of the article. It first appeared from PLOS via http://dx.doi.org/10.1371/journal.pbio.100200