dataesr/scientific-paragraphs-categorization huggingface dataset:
Recombinant AhPDF1. 1b is a toxin when applied exogenously All the 12 3D structures of plant defensins available in the RCSB Protein Data Bank (http://www. rcsb. org/pdb/ home/home. do) harbor a globular cysteine-stabilized a-helix b-sheet (CSab) structure with four disulfide bonds  (Cornet et al. 1995). All these defensins which are extracted from plant tissues (seeds or flowers) are fully oxidized and their 3D structures have been solved in this conformation. Although they show a great variability in protein sequence, their 3D structure is highly conserved and gives them a highly resistant scaffold  (Gachomo et al. 2012). To obtain a native-like folded recombinant defensin, we chose the Pichia production system. Indeed, E. coli and P. pastoris are quite different expression systems that produce denatured or fully oxidized folded  defensin, respectively.
Acknowledgments Authors thank  Franc ßois-Xavier Sauvage  ( Head of Biotechnology Platform, UMR Sciences Pour l'Oenologie ) for his valuable assistance and helpful discussions and  Maya Schuldiner  ( Weizmann Institute of Sciences ) for the gift of the UPRE-GFP TEF2-Cherry UPR-reporter system. O. M. was supported by  Institut National de la Recherche Agronomique (INRA) and Montpellier SupAgro funding. O. M. thanks  EIR-A Agreenium  and the  Ecole Doctorale SIBAGHE of University Montpellier 2  for the fellowship granted for of her 3-month visit at D. E. 's laboratory. This visit was also supported by the grant ( RO1-GM56285 ) from  National Institutes of Health  to D. E.
This contribution addresses the problem of extracting some representative data from complex datasets and connecting them in a directed graph. First we define a degree of representativeness (DoR) inspired of the Borda voting procedure. Secondly we present a method to connect pairwise data using neighborhoods and the DoR as an objective function. We then present case studies as illustrative purposes: unsupervised grouping of binary images, analysis of co-authorships in a research team and structuration of a medical patient-oriented database.
Introduction The selection of a small subset from a dataset is a classical way for both reducing the cost of data processing and improving the efficiency of data analysis. In statistics, the process is called sampling. The selection of representative samples is generally based on a randomization process. Unfortunately this approach assumes implicitly or explicitly that data distributions are known. Then the statistical analysis often fails when exploring dataset with unknown distributions. In data mining, the goal is very different. The samples should define interesting patterns and structures to analyse the data set. Then each sample is selected taking into account its own representativeness. These samples are called exemplars  [1]. The extraction of these representative elements presents a significant interest in designing recommendation systems  [2] , selecting leaders or specimens  [3]  for community detection  [4]  or for customer Relationship analysis  [5].
In this context, this paper proposes a new approach for extracting exemplars (i. e. representative elements) from a dataset and for linking data to visualize the structure of the dataset as a forest. In the framework of data mining, the classical ways to determine representative elements refer to the task of clustering  [6]. The representative elements are prototypes selected from a partition of the dataset into clusters. This approach assumes that the number of exemplars is equal to the number of clusters. Unfortunately when exploring a dataset, the number of clusters is unkown. If a cluster contains more than one sub-population, then only one prototype is extracted. But more than one exemplar is expected. Moreover the exemplars are real data extracted from the dataset. But the prototypes are often virtual elements that does not make sense.
First k exemplars are randomly selected from the dataset. Then the algorithm iteratively refines this set of exemplars. The afinity propagation method of Frey and Dueck  [1]  also proposes to extract exemplars by iterative process. Unfortunately the final elements proposed as exemplars are quite sensitive to the initial selection, they depend on input parameters and on the way to stop the iterative process. To circumvent this drawback, this paper proposes a one pass method to extract exemplars from a dataset without any assumption on the shape or the density of data distribution (unlike in  [8] ). The method we propose is only based on a relation that permits a pairwise comparison of data. Using this relation we define a degree of representativeness (DoR). The exemplars are finally chosen as local maxima of the DoR.
Then we show how to build a directed graph to visualize the organization of dataset around the exemplars as trees. By fitting the locality parameter called scale factor we determine the exemplars at each scale that the user needs. The new method we propose is deterministic. Thus each dataset leads to one specific set of exemplars. Some properties can indicate the ability of the method to reveal intrinsic structures of the dataset. Thus the paper study the stability and the robustness of our method to indicate this ability. When data is corrupted with noise or outliers, the selection of exemplars should be robust against such corruptions. When resampling the dataset, the stability of exemplars (i. e. the exemplars do not change when resampling) is another indication of the ability of the method to reveal dataset structures.
Moreover our deterministic method gives one result at each scale. When the scale increase, we also study the variation of the set of exemplars and the forest we build on the dataset. To sum up this paper proposes a new method for exemplar selection and it studies some of properties of the method. It is organized as follows. In the first section we introduce the context and expose our method. We present the formal definition of degree of representativeness (DoR) used to extract exemplars. The notion of standard is defined when only one exemplar is selected from the dataset. Then we show how to build a directed graph (more precisely a forest) to visualize the inherent structure of the dataset. For each definition we present some interesting and remarkable properties (robustness and stability).
Method Let Ω be a set of n elements in a multidimensional space. Let us describe the way we use to extract the exemplars from Ω for structuring this set as a forest. In this paper, the n elements are called objects. They consist of qualitative, quantitative or mixed data. We assume that Ω is only a relational dataset. We do not need for any assumption on underlying distribution of data. We only use the relation for comparisons between objects.
e. ∀x ∈ Ω, R(x, x) = 0) Unlike a distance, the relation does not necessarily respect the property of symmetry. R(x, y) may be different from R(y, x). For instance, if the cost from a point x to a point y is the time to go from x to y, then the cost from y to x could differ from the first one because of the slope, wind, flow, etc. Moreover, the relation does not respect the triangle inequality. A dissimilarity index gives a classical example of such a relation which does not respect the triangle inequality. x is dissimilar from y with R(x, y) and y is dissimilar from z with R(y, z) but x could be dissimilar from z with R(x, z) > R(x, y) + R(y, z). Such a relation can lead to a vote to designate exemplars within the dataset. Specifically, we can rank the objets of Ω taking into account the relation to set up votes between the objects themselves.
Computing all relative scores, each object x receives n scores corresponding to the votes of all objects of Ω (i. e. the n values Sc y (x) with y ∈ Ω). Then the relative scores are aggregated to define the degree of representativeness (DoR) of data. The DoR is finally used as an objective function to choose the winner of the voting procedure. The aggregate score is defined by: DoR : Ω → R + x → Aggreg y∈Ω (Sc y (x)) In this paper, the aggregation function is the mean function. Let us observe the DoR in a simulated dataset. Figure  1  displays an example of a dataset with 120 two dimensional random samples (A). Euclidean distance is used as the pairwise valued relation between samples. The respective DoR (B) confirm that the score increases when the sample approaches the center of the dataset, i.
Standard The object with highest DoR is called standard. The standard is usefull when only one exemplar is expected for resuming the dataset Ω. Let us observe some properties of the standard. When resampling the dataset using the bootstrap technique  [14] , the standard could change. If it does not change, the extraction of this standard is robust against the resampling. We propose to quantify the robustness of the standard by bootstraping the extraction of the standard. We claim that the frequency of the extracted standards indicates the stability of the standard when resampling. This frequency characterizes the robustness of the standard. Our experiments using simulated data and real data show that the standard depends very weakly on the resampling. We have simulated three random datasets (let us call them A B and C) of 100 elements.
We have computed the frequencies of the standards obtained with 200 bootstraps. The extracted standards remain in the center of the three datatsets. The frequencies of the most frequent standards when resampling the 100 initial samples are respectively equal to 40%, 32%, 36%. These frequencies assess the stability of the standard with respect to the samples. Respectively 90%, 88%, and 90% of the dataset elements are never extracted as q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q -15 -10 q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q -10 0 10 0 10 20 30 x y 30 40 50 60 70 DoR q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q -10 0 standards when resampling.
Thus we assume that a standard gives a clue on the center of the dataset. Because the standard is a real element, it avoids the nonsense that the classical averages could produce with a virtual out-of-scope element outside of the data distribution. Note that the stability of the standard (i. e. the frequency of the most frequent standard) increases when the number of objects increases. Let us now examine the stability of the standard when outliers are feared. We simulate outliers that we append to an initial dataset. We consider that the standard extraction is robust against outliers when the extracted standard remains one of three most frequent standards of the initial dataset. In this paper we describe the study of robustness (see  [15]  for more details about the concept of robustness) using the datasets A, B and C of Figure  2.
The outliers are random elements out of the range of the initial data domain. In this section, the domain is defined by elements of coordinates (x, y) where -10 ≤ x ≤ 40 and -15 ≤ y ≤ 15. Outliers are simulated in a larger domain defined by -10000 ≤ x ≤ 40000 and -15000 ≤ y ≤ 15000 (the initial limits are multiplied by 1000) excluding the elements that are too close from the initial domain by keeping the elements (x, y) where x ≤ -1000 or 4000 ≤ x and y ≤ -1500 or 1500 ≤ y (the limits of initial domain are multiplied by 100). We add such random outliers to an initial dataset until the extracted standards changes (i. e. until the extracted standard from the new dataset with outliers will not be one of the three most frequent standards of the initial dataset). When outliers are randomly generated in a such very large domain, the percentage of outliers could be higher than 200% without changing the initial standard.
Exemplars and forest The standard is the only exemplar extracted from a dataset. But the dataset may be complex and it could require more than one exemplar to represent the whole set. This section describes how the dataset can be structured to retrieve these exemplars from the set. The first step consists in defining the neighborhood of each object within Ω. Let x be one of the n objects of Ω. Let k be a value between 0 and n. The k-nearest neighbors of x are defined using the ranks relative to x. Then the k-neighborhood of x in Ω is defined by: ∀x ∈ Ω, ∀k ∈ {1,. , n}, N k (x) = {y ∈ Ω/Rk x (y) ≤ k} Thus N k (x) is the set of k nearest objects of x. In a second step, each object x is associated with the neighbor having the highest DoR. Thus we define a link from x to its preferred neighbor.
Each object x is linked to an object y. The links are defined by: ∀x ∈ Ω, x → y = argmax z∈N k (x) DoR(z) In this definition, x is linked to y and y is generally different from x when DoR(y) > DoR(x). If Sc(x) is maximal inside N k (x), then y = x and x is linked to x itself. These self-linked objects are simply called exemplars of Ω. Using the links, the dataset becomes a forest where the nodes are the objects. The exemplars become the terminal nodes of this forest. The exemplars depend on the value of k which influences the forest configuration. In this paper, k is the size of the neighborhood we use. This parameter is called scale factor. Figure  3  displays four forests obtained from the simulated dataset of Figure  1 (A). The dataset has the 120 samples (n = 120). The four forests are configured using the scale factors 5, 10, 20, and 40.
Therefore the number of exemplars necessarily decreases when the scale factor increases. Increasing the scale factor, some exemplars could disappear among those who were extracted. But an object never appears as an exemplar if it was not extracted at lower scale factor. Figure  4  displays the duration of each exemplar when increasing the scale factor. The exemplars are extracted from Figure  1  dataset (n = 100). When the scale factor is equal to 1, all the objects are exemplars. When the scale factor increases, some exemplars disappear and their duration is shortened. Only the standard is kept from scale 1 to the scale n. It has the longest duration equal to n. At the scale k, we assume that the numbers of exemplars is smaller than n -(k -1) where k is the scale factor and n is the number of objects of the dataset.
Extraction of exemplars from a set of binary images In this first application we consider a set of binary images contained in a database. The goal is to extract exemplar images from this database. The interest could be providing a set of resuming images or distinguishing subsets of images according to their content. In a first step we construct the matrix of the relation by using the Asymetric Haussdorff Distance. Classical methods of clustering have to work with symmetric distance. They are inapplicable when distance from an image A to image B is not equal to distance from image B to image A. As we wrote at the beginning of this paper, the symmetry property is not required in our method. Firstly, we compute the score of each image of the database. In a second step we build the associated directed graph presented in Figure  6  and representing the exemplars network (with a scale factor of 4).
Exploration of co-authoring network The second application of our concept deals with publication data inside a laboratory, a research team or any other group of researchers. Co-authoring informations can be considered as relational data (  [16] ,  [17] ). In this work, we consider that the value of the relation from a researcher named Alice to a researcher named Bob is computed as the sum for each common publication of the product of the number of coauthor on the publication and the number of publication of Alice. This relation is not symmetric. In fact, generally, Alice can be the "preferred" co-author of Bob, but Bob is not necessarily the "preferred" co-author of Alice. This valued relation characterizes the "quality" of links between the members and takes where k is the scale factor and 100 is the number of objects of the dataset.
The grouping index (bottom) (the difference between 100 -(k -1) (gray line) and the number of extracted exemplars (red points)) is maximal when the scale factor is equal to 9 circle). account of their publication activity. The dataset we used is the set of publications of the CReSTIC Laboratory (University of Reims, France)  [18]. This information is extracted from the web site of the laboratory. The graph of the Figure  7 (Left) represents this dataset. Each node is a lab member and each edge between two members represents one common publication. Different colors are used to represents Figure  6. Network of the binary images where each image is connected to one exemplar. This directed graph exhibits three connected components forming three clusters coinciding with the content of images the different teams that compose the laboratory (but this information is not used in the computation of the exemplars).
Therefore the scale factor is not used in this application because the size of the neighborhood is implicitly fixed in the dataset (according to the number of co-author of each member of the team). After computing the scores, we built the exemplars forest represented on the Figure  7 (Right). The size of the node is proportional to its score. This graph is displayed using the same position for the nodes. The graphs presented in the Figure  7  show several interests of our method. The first interests is the simplification of the graph of the Figure  7  (Left). When the numbers of vertices and edges are growing the graph becomes more unreadable. For big data, resuming and simplifying is a necessary task. The second interest is to exhibit such a sub-structure of the team (this task is called community detection in a network  [19] ).
Structuration of a medical database In this case study, we consider a dataset of 71 diabetic patients described by 10 variables. This dataset was constitued by the endocrinology service of the University Hospital Center (CHU) of Reims. Our goal is to exhibit how the medical cases could be linked. After computing the distance matrix between patients with the Chebyshev distance  [20] , we obtain the forest shown in the figure  8  according to the DoR of patients. The resulting forest structures the raw database as a network of medical cases. We can see this graph as a knowledge representation extracted from data and could be view as a first step for building a medical case based reasoning system.
Conclusion In the framework of data mining, this paper describes a new way for extracting exemplars from a relational dataset. The method we propose is based on a pairwise comparison assuming a coarse relation on the dataset. This approach is particularly adapted when no distance is available or meaningful in the data domain. Moreover the coarse relation between data does not need symmetry or transitivity properties. Thus the method is useful for any kinds of relational data. The DoR is defined from these pairwise comparisons. The paper defines the standard which is the sample with the highest score. Simulations show the robustness of the standard against outliers and the stability of the standard when resampling dataset. Thus these results confirm the standard as a robust location estimator.
Moreover the DoR is used to extract exemplars which are real objects. Then our approach of location estimator avoids the drawbacks of average objects which are meaningless when processing qualitative data. Using a score based on the pairwise comparison, we define the k nearest neighbors of each datum. This approach permits us to extract exemplars depending on this k value. We state that the number of local exemplars decreases from n to 1 (n is the number of data samples) when k value increases from 1 to n. Thus k is considered as a scale factor. The method we propose allows us to explore the dataset through different scales. We can adjust the k value for extracting a reduced number of exemplars. An automated approach is proposed to determine an optimal number of exemplars. On top of the extraction of exemplars, the method proposes to design a forest.
The paper shows that the forest is reconfigured when the scale factor changes. The forest eases the explanation of the exemplar roles in the dataset. When the scale factor increases, some exemplars could disappear keeping the most important ones (i. e. the exemplars which are important nodes for connecting some data). In future works we propose to use the fuzzy set theory as in  [21]  to generalize our framework in the case of fuzzy relation, when ranking data is not easy. The major way we would to explore is the area of Social Network Analysis. We are convinced that our concept of exemplar could be a significant tool for extracting leaders or mentors in social network and improve recommendation systems. Our concept of degree of representativeness should be compared to the different definitions of centrality in a network  [22].
6 F. Figure 5. 65 Figure 5. Number of Exemplars (top) from Figure 1 (A) dataset and Scale Factor : The number of exemplar is smaller than 100-(k -1)where k is the scale factor and 100 is the number of objects of the dataset. The grouping index (bottom) (the difference between 100 -(k -1) (gray line) and the number of extracted exemplars (red points)) is maximal when the scale factor is equal to 9 circle).
However, as  Schmidt et al. (2011)  point out, the choice of one particular configuration from a range of plausible boundary conditions and forcings is often arbitrary and does not account for uncertainties in the data used for developing the forcings/boundary conditions. Moreover, in designing the PMIP last deglaciation experiment, we have attempted to strike a balance between establishing a framework within which to assess model differences and performance, and taking the opportunity to utilise the full range of PMIP climate models (Earth System, General Circulation and Intermediate Complexity) to examine uncertainties in deglacial forcings, trigger-mechanisms and dynamic feedbacks. Consequently, forcings/boundary conditions that are relatively well established (atmospheric trace gases and orbital parameters) are tightly constrained in the Core experiment design.
These data will be provided with the ice -Global ocean salinity should be +1 psu, compared to preindustrial, to account for the increased terrestrial ice mass at the LGM (PMIP LGM Working Group, 2015). -Any other boundary conditions should be set to be consistent with the Core transient simulation to follow (Sects. 2. 2-2. 7). On the freshwater budget, PMIP advises groups to "carefully check the fresh water budget in their LGM experiments in order to avoid unnecessary drifts of the ocean salinity. It can be necessary to route the snow which has fallen in excess on the ice sheets to the ocean. Given the change in coastlines, it is also sometimes necessary to relocate the large river estuaries on the coast" (PMIP LGM Working Group, 2015). Tarasov and Peltier (2006)  provides a glaciological example of the possible re-routings for North America.
Tarasov, personal communication, 2014). The topography in the global combined solution was adjusted in Patagonia and Iceland following ICE-5G  (Peltier, 2004) , but the changes in these ice caps are not reflected in the ice mask. Both datasets include ice extent and topography at intervals of 1000 years or less through the deglaciation. Ice extent is provided as a fractional ice mask for ICE-6G_C and a binary ice mask in GLAC-1D. The two reconstructions incorporate similar constraints for North American ice sheet extent (i. e. Dyke, 2004). For Eurasia, ICE-6G_C follows the ice extent provided by  Gyllencreutz et al. (2007) , whereas GLAC-1D uses data from  Hughes et al. (2015). The reconstructions only differ slightly in their ice extent evolution (Figs. 2  and 4 ), for example the Barents Sea deglaciates earlier in GLAC-1D than in ICE-6G_C (Fig.