dataesr/scientific-paragraphs-categorization huggingface dataset:
In a given simulation, all agents implement the same version of the COSMO model: they are either motor, auditory or sensorymotor, as defined in Table  1. Initially, the Gaussian prototypes PðM j O S Þ and PðS j O L Þ encode a complete lack of knowledge, with centered means and large standard deviations 3. A simulation then comprises a series of deictic games. During a deictic game concerning object o i , the simulated environment propagates the proposed motor gesture m according to TransMS, adding a simulated Gaussian noise with standard deviation σ Env , resulting in an acoustic stimulus s. At the end of a deictic game, the speaker and listener agents, respectively, update the parameters of their motor and auditory Gaussian prototypes, according to the observed 〈o i ,m〉 pair for the speaker, and the 〈o i ,s〉 pair for the listener.
Conditions for emergence of a speech code Fig. 7  shows the state of agent societies at the end of three typical simulations, one for each version of the COSMO model. In this first set of simulations, the articulatory-to-acoustic transformation TransMS is linear and the environmental noise σ Env is low. Fig. 7 (top)  shows the results at the end of a simulation of "motor" agents; namely, a simulation whereby agents produce gestures according to the motor production behavior of Table  1. We observe that the motor prototypes of the agents have evolved relatively randomly during the learning process and that the recognition rate stays at the chance level (around 25%). Because the agents do not use auditory knowledge, and therefore have no way to link their productions in front of each object with the auditory inputs they receive from the others, there is no chance that such a society would enable the emergence of a structured and efficient speech code to designate objects.
With respect to quantal behaviors, they are obtained as a consequence of nonlinearities in the articulatory-to-acoustic transformation, for both auditory and sensory-motor agents, and they result in vocal codes that naturally exploit optimal sensorymotor "niches" provided by these nonlinearities, with the consequence that communication is globally favored relative to linear situations. These two theories can therefore be derived from communication in COSMO, provided that parity is ensured by a sensory-motor link in auditory or sensory-motor agents. In this way, a basic level of adequacy is obtained in these simulations. The next section describes how more realistic articulatory-auditory environments constrain adequacy in a richer way, leading to accurate predictions of sound systems for human languages.
Adequacy: realistic predictions of phonological systems We now consider a final series of COSMO simulations, in which we further specify the model and compare its predictions with actual data about sound systems for human languages, as presented in Section 2. This will constitute our third contribution. For this aim, we capitalize on the results of the previous section that showed that motor agents do not let an efficient communication system emerge from deictic games. Furthermore, while both auditory and sensory-motor agents lead to coherent systems, sensory-motor agents are more efficient in terms of dispersion, convergence speed and robustness to noise. We will therefore continue by considering only the sensory-motor version of COSMO, for which the parity requirement is solved most efficiently.
Objectives In this first series of simulations, we consider vowel systems. Changing the unidimensional articulatory-to-acoustic model of the previous section to the multidimensional motor and sensory spaces of VLAM produces a large increase in simulation complexity. Therefore, a preliminary objective is to check that simulations of COSMO agents in the VLAM framework are tractable. We study two types of vowel systems, involving either three or five vowels. Data about human languages presented in Section 2 show that three-vowel systems are most often of the type /i,a,u/, and five-vowel systems are most often of the type /i,e,a,o,u/ (statistics for UPSID,  Maddieson, 1984; Vallée, 1994; Schwartz et al. , 1997b). Therefore, one objective is to check that these systems emerge from COSMO simulations in VLAM.
14, bottom, left). Note that this is not in agreement with data from UPSID. Noise ratios "1-3-6": Because the five-vowel simulations with a noise ratio "1-1-1" are not coherent with the preferred human system /i,e,a,o,u/, we now consider the "1-3-6" noise ratio set. In this experimental condition, the standard deviation σ F1 varies from 0. 1 to 0. 9 Barks in steps of 0. 1, with σ F2 ¼ 3σ F1 and σ F3 ¼ 6σ F1. Typical systems obtained for three-object and five-object simulations are shown in Fig. 15 , for low (σ F1 ¼ 0:1 Bark), medium (σ F1 ¼ 0:4) and high (σ F1 ¼ 0:9) noise values. The distribution of systems obtained over the 10 simulations per condition is reported in Tables  4  and 5. Note that the three-vowel simulations still yield the human-preferred three-vowel system /i,a,u/ for a large range of medium noise values.
In this framework, the so-called "motor" and "auditory" theories of speech communication can be seen as simplifications of the general COSMO sensory-motor theory that internalizes the whole communication situation. We show that the internalization hypothesis can be formalized in a Bayesian model that allows a probabilistic expression of the computational issues involved in the main theoretical trends in the speech production and perception literature (see Table  1 ). Our second contribution (Section 5) deals with "parity" in speech communication, by extending the model to include a referential evolutionary bootstrap for studying speech code emergence in societies of interacting COSMO agents. We use deixis as a plausible prelinguistic communicative behavior. A comparison of simulation results based on the three COSMO versions (motor, auditory and sensory-motor), implemented using simplified articulatory-acoustic spaces, confirms previous theoretical propositions about the need to take auditory expectations into account if adequate phonological system predictions  (Schwartz et al.
, 2007; Studdert-Kennedy & Goldstein, 2003)  are to be obtained. We show that within this framework, societies of "pure motor agents" do not allow the emergence of an efficient and structured speech code, unlike auditory and sensory-motor agents. In addition, the sensory-motor COSMO version leads to quicker convergence and "better" speech codes in terms of sound distinctiveness. Furthermore, Lindblom's Dispersion Theory and Stevens' Quantal Theory appear to be grounded in more general principles of communication, in the sense that neither distance optimization nor nonlinearity detection processes were included explicitly in the computational architecture. Our third contribution (Section 6) deals with "adequacy" in speech communication and is based on realistic predictions about the phonological systems of human languages in the "sensory-motor" COSMO model.
Acknowledgments The research leading to these results has received funding from the  European Research Council  under the European Community's  Seventh Framework Programme  (FP7/2007-2013 Grant Agreement no. 339152  -"Speech Unit(e)s"). A secondary source of founding was the  ERC Starting Grant   EXPLORERS 240 007  which partially financed the first author during the revision process. The authors would also like to thank  Louis-Jean Boë ,  Raphaël Laurent  and  Pascal Perrier  for countless helpful discussions, as well as the  Explora-Doc program  of the  French Rhône-Alpes region.
SHS parameter estimation for snow Using the closed form expression C SHS (k|φ 2 , d, τ ) for the correlation function from Eq. (  34 ) we are now able to objectively estimate optimal SHS parameters d and τ for a given snow sample by fitting the expression to the angularaveraged experimental data C(k). The volume fraction φ 2 is prescribed by the value obtained from the µCT image. We used the same fit interval k = [0, k max /3] for all samples. The number of points in this interval and the maximum wavevector k max = 2π/l vox however varies from sample to sample due to variations in voxelsize l vox and sample size L of the cubic µCT image. The regression on d, τ was carried out using MATLAB's nonlinear, least-squares fitting tools to minimize the sum of squared differences between model and measurement.
This is generally valid for any two-phase system with a smooth interface, and also present in the experimental data (Fig. 3 ). The Porod law is mathematically equivalent to the existence www. the-cryosphere. net/9/2101/2015/ The Cryosphere, 9, 2101-2117, 2015 of a cusp singularity of the real-space correlation function C(r) at the origin, i. e. , the existence of a small-r expansion of the form C(r)/C(0) = 1 -sr/4 + O(r 3 ). However the limit lim k→∞ k 4 C(k) does not exist for Eq. (  34 ). This is a known, subtle problem and a consequence of monodispersity  (Tomita, 1986). Thus the monodisperse SHS model bears some mathematical peculiarities which have to be examined with care. If, however, the present method of µCT-based parameter estimation were to be generalized to polydisperse SHS, some additional effort would be required.
4B ). For each section, we extracted the velocity distribution (Fig. 4B ), and analyzed it with NVDA to extract v 0 j. Note that we did not estimate the channel height in the fitting procedure, because this parameter was not precisely assessed for strongly deformed channels (a/h~0. 05< < 1). As the offset pressure increased, we noticed an acceleration of the flow, which was maximal and symmetric about the channel centerline (Fig. 4B , left panel). We then wished to estimate the channel height, and used Poiseuille law to relate it to the maximum flow velocity in each section j: = ∆ × μ × ( ) ( ) v P L h 1 2 3 j j 0 2 After normalization of Eq. (3) to the velocity measured for j = 1 at P offset = 0 mbar (datasets in Fig. 4C ), we inverted Eq. (  3 ) and deduced the relative variations of h j , which compared well with fluorescein intensity ratiometric measurements (gray lines in Fig.
5A ), and observed a peaked shape toward high velocity states in comparison to the prediction of the model with a uniform density of particles (black line in Fig. 5A ). We hypothesized that frequent high-velocity events were associated to the accumulation of tracers at the channel centerline, and that depletion from the walls reduced the occurrence of low-velocity events. Therefore the ratio of the experimental velocity distribution to that predicted by the model (that is, with tracers evenly dispersed over the channel height) appeared to be proportional to the vertical repartition of particles. We computed the repartition of particles derived from the velocimetry distribution (datasets in Fig. 5B ), and compared it to that directly inferred from the simulation (solid lines in Fig. 5B ). The excellent consistency of these two curves showed that NVDA could be used to measure particle spatial distribution across a Poiseuille flow in a confined channel.
5D, E ). For 200 nm tracers, depletion from the walls was marginal for shear rates lower than 500 s -1 (Fig. 5D ), and particles appeared to accumulate away from the middle of the channel at 500 nm from the walls for the maximal shear rate of 2000 s -1 (red dataset in Fig. 5D ). Due to this bimodal repartition, which showed that particles were repelled from channel centerline where the shear was null, the relative difference in average velocity between 100 and 200 nm tracers Δv/v 0 decreased from 9% to 4% for a shear rate of 1000 s -1 and 2000 s -1 , respectively. This result suggested that efficient separation conditions of 100 and 200 nm particles should be obtained at γ  ~1000 s -1. Altogether NVDA is a versatile tool for the characterization of inhomogeneous concentrations of flowing particles through shallow channels.
(C) Experimental velocity distributions were obtained with 2a = 200 nm particles transported in a 1. 6 μ m thick channel. The fluid composed of 2% PVP 360 kDa was visco-elastic. The inset shows the linearity of the maximal velocity as a function of the pressure drop for 200 and 100 nm tracers (green and red datasets, respectively). (C-D) The plots show the repartition of tracers of 100 and 200 nm across the channel half-height for a range of pressure drops.
Data simulation All DNA methylation simulations were performed on the human Chromosome 10 using a Beta-Binomial approach implemented in R (R Core Team 2013) to simulate both biological methylation and the sequencing step. The simulated data that were used for the benchmarks are available at http://www. bioinf. uni-leipzig. de/Software/metilene/. The scripts and parameters to simulate these data from scratch can also be found in the Supplemental Material. We simulated two different backgrounds to account for promoter and nonpromoter differences. Since the overall sequence composition in promoters is expected to be different from nonpromoter regions, and to do the simulation in a more realistic fashion, we used the ENCODE chromatin state segmentation of a lymphoblastoid cell line (GM12878)  (Ernst and Kellis 2010; Ernst et al.
Acknowledgments This publication is supported by the  German Bundesministerium für Bildung und Forschung  (BMBF; PTJ grant HNPCCSys  031 6065A  and ICGC MMML-Seq  01KU1002J ), the  European Union  in the framework of the  BLUEPRINT  ( HEALTH-F5-2011-282510 ) project, and by  LIFE: Leipzig Research Center for Civilization Diseases, University of Leipzig. LIFE is funded by means of the  European Union , by the  European Regional Development Fund (ERDF) , the  European Social Fund (ESF) , and by means of the  Free State of Saxony  within the framework of the excellence initiative. Author contributions: F. J. , H. K. , P. F. S. , and S. H. conceived the project. F. J. and S. H. implemented metilene. H. K. , F. J. , C. O. , and S. H. B. tested metilene on artificial and biological data. F. J. , H.
Analysis of ICN systems Recently, the ICN has gained attention in various research initiatives, e. g. , ALICANTE  [3] , COMET  [4] , PSIRP/ PURSUIT  [5, 6] , 4WARD/SAIL  [9] , DONA  [17]. Also some ICN-based mechanisms have been proposed in other ICT fields (e. g. , Internet of Things  [18] ). Each of them follows new design paradigms, which treat the content as the primary citizen of the network. The investigated approaches differ in particularities, but all of them support: (1) ubiquitous and location independent content identifiers, (2) content aware routing of requests towards selected content server, (3) innetwork caching and content storage, (4) flexible data plane allowing for anycast and point-to-multipoint connections, and (5) application and location agnostic content access. In this way, the ICN becomes a sophisticated content access and delivery system instead of a simple host-to-host communication network.
Redundancy analysis was performed on the results from all REVEALS-model runs using the groups within (i) and (ii) separately, and on the results from all runs using the groups within (ii) together. The explanatory power and significance of the variables were identified using forward selection and Monte Carlo permutation tests. The results show that (a) although the REVEALS model was designed for pollen data from large lakes, it also performs well with pollen data from multiple small sites in reconstructing the percentage cover of groups of plant taxa (e. g. open land taxa, summer-green trees, evergreen trees) or individual plant taxa; however, in the case of this study area, the reconstruction of the percentage cover of Calluna vulgaris, Cyperaceae, and Betula may be problematic when using small bogs; (b) standard errors of multiple small-site REVEALS estimates will generally be larger than those obtained using pollen records from large lakes, and they will decrease with increasing size of pollen counts and increasing number of small sites; (c) small lakes are better to use than small bogs if the total number of small sites is low; and (d) the size of small sites and the distance between them do not play a major role, but the distance between the small sites and landscape/vegetation boundaries is a determinant factor for the accuracy of the vegetation reconstructions.
2001 ) with an anthropogenic land-cover change scenario (KK10;  Kaplan et al. 2009 ). These maps (or datasets) of past land-cover can now potentially be used as alternative land-cover descriptions in climate modelling. The REVEALS model was developed to reconstruct past vegetation composition in percentage cover at a scale of 100 by 100 km using pollen data from large lakes. It has been tested with numerous simulations  (Sugita 2007a ) and empirical studies in southern Sweden  (Hellman et al. 2008a, b) , on the Swiss Plateau  (Soepboer et al. 2010) , in Denmark  (Nielsen et al. 2012)  and in northern America (N Michigan and NW Wisconsin;  Sugita et al. 2010). All the empirical studies except one-NW Wisconsin where pollen records from small forest hollows were the only data available-used pollen data from large lakes.
e. the study of the effect of anthropogenic land-cover change on climate. We also used the same chronologies for the pollen records as those applied in the LANDCLIM project  (Mazier et al. 2012; Trondman et al. 2015)  except for the sites Ekena ¨s and Ska ¨rsgo ¨larna. For those two sites, new age-depth models were established using the computer program clam version 2. 1  (Blaauw 2010 ) that implements the IntCal09 calibration curve of  Reimer et al. (2009). A smoothing spline was applied for both Ekena ¨s (four radiocarbon dates ? core top age) and Ska ¨rsgo ¨larna (five radiocarbon dates ? core top age) (not shown here). c Fig. 2  RDA analyses of RUNS 1 REVEALS estimates for the temperate zone, for all five time windows (see text for more explanations). The eigenvalues of axes one and two for all RUNS 1 (this Figure and Fig.
Multivariate analyses Multivariate analysis implemented by the computer program CANOCO 4. 5  (Ter Braak and S ˇmilauer 2002)  was applied on the REVEALS RUNS 1-5 (see above) to evaluate the influence of a set of selected environmental/explanatory variables on the REVEALS estimates of regional vegetation composition. The explanatory variables include basin size, number and type (bog or lake) of sites, b Fig. 3  RDA analyses of RUNS 1 REVEALS estimates for the hemiboreal/southern boreal zone, for all five time windows (see text for more explanations). The scores of the nominal variables ''Trummen'' and ''Kansjo ¨n'' (large lakes) and ''Kan ? Tru'' (midpoint of a segment joining the centers of lakes Trummen and Kansjo ¨n)'' are shown with black circles. For other interpretation of the figure, see the caption of Fig.
2  the distance between small sites and large site(s), and vegetation characteristics (vegetation zone and vegetation openness; see also below). The length of the gradient in a detrended correspondence analysis (DCA) of the REVEALS dataset was short (\2. 0 SD units) for all tested RUNS, which motivated the choice of a linear ordination method, e. g. redundancy analysis (RDA) for further analysis  (Leps ˇand S ˇmilauer 2003). RDA was applied on the REVEALS estimates from (i) each of the RUNS 1-5 separately, and (ii) all RUNS 2-5 together as one dataset, resulting in six RDAs. For RUNS 1 we selected four environmental variables for the analysis, i. e. number of sites, type of site (entered as a dummy variable (0, 1): lake, bog, or lake ? bog; note that a group of small sites may consist of both bogs and lakes, therefore the variable ''lake ? bog''), proportion of open land (nonforested land expressed in percentage cover as estimated by REVEALS in each RUNS), and basin size (mean radius expressed in metres).
Results Redundancy analysis (RDA): the effects of environmental variables on the mean REVEALS estimates based on multiple small sites The results of the RDA are presented in Table  3  and in triplots for the different runs and time windows. In this paper we chose to present only the tri-plots for RUNS 1 (Figs. 2,  3) and RUNS 2-5 together as one dataset (Figs. 4, 5; Online Resource 2 Figs. 1, 2 ). In all tri-plots, the first axis contrasts taxa indicators of open land on the right with forested vegetation on the left, and the second axis contrasts Poaceae and indicator taxa of cultivated and ruderal land (e. g. Cerealia-type, Secale, Rumex acetosa-type, Artemisia) with Calluna vulgaris, Cyperaceae and Filipendula; in RUNS 2-5, axis 2 also contrasts Pinus and Betula with broadleaved trees and Alnus.
Discussion Redundant analysis (RDA): the effect of site characteristics on the multiple small-sites REVEALS estimates The results from the RDA analyses of RUNS 1 can be explained by the following characteristics of the dataset: (a) Filipendula and Cyperaceae are associated with bogs, (b) the number of bogs in the REVEALS runs is larger than the number of lakes, (c) a majority of the studied lakes are located in the open landscapes of the temperate zone and therefore have a tendency to be characterised by the occurrence of broadleaved trees in their surroundings and (d) lakes are generally larger than bogs in the temperate zone. The RDA analyses of RUNS 1 suggest that the type of basin (lake or bog) influences significantly the REVEALS estimates in this study for the reasons above. Further, the RDA analyses of RUNS 2-5 suggest that a few small sites located in another vegetation zone than the majority of the sites in a multi-site group can affect the mean REVEALS estimates significantly (see RUNS 2-5 for sites within 150 and 200 km of the large lakes).
The Monte Carlo permutation tests show that, after ''open land'', ''number of sites'' has the stronger explanatory power (except for RUNS 2) and is always a significant variable, either when it is implemented on RUNS 1 and on RUNS 2-5 separately, or on RUNS 2-5 together (Table  3 ). ''Open land'' has the stronger explanatory power in all RUNS 1-5, which is a common feature of the results from numerical analyses of pollen data with a strong gradient in values of non-arboreal pollen (NAP) (or arboreal pollen AP), axis one generally contrasting pollen assemblages with high NAP (or low AP) with pollen assemblages with low NAP (or high AP) (e. g. Gaillard et al. 1994; Mazier et al. 2006 ). The ''site size'' either is not significant or has a very low explanatory power. The latter suggests that, although the dataset in this study includes a higher number of small bogs than small lakes, and although the small lakes are generally larger than the small bogs, the ''type of site'' (bog or lake) explains the REVEALS estimates better than the site size.
Acknowledgments The  LANDCLIM  project and research network were sponsored in 2009-2011 by the  Swedish [VR] and Nordic [NordForsk] Research Councils , respectively, and coordinated by  Marie-Jose  ´Gaillard ( Linnaeus University, Sweden ). The two initiatives are a contribution to the IGBP-PAGES-Focus 4 programme (http://pages-igbp. org/science/foci/focus-4),and to the  Swedish Strategic Research Area ''ModElling the Regional and Global Earth system-MERGE''  (http://www. merge. lu. se). LANDCLIM has been supported financially by MERGE since 2010. The authors are also very grateful to the members of LANDCLIM for valuable discussions and advice. Other funding sources include the  Faculty of Health and Life Sciences of Linnaeus University (Kalmar and Va ¨xjo ¨, Sweden)  for  A-K Trondman  and  M-J Gaillard , the  French CNRS  and the  LUCCI  project ( Lund University , Grant Number:  VR 349-2007-8705 ) for  F Mazier , and the '' King of Sweden professorship in Environmental Science '' (2011)(2012) at  Linnaeus University for S Sugita.