Tree Drawing Research Articles

Treebanks: Building and using parsed corpora (review)

Reviewed by: Treebanks: Building and using parsed corpora ed. by Anne Abeillé Philip Resnik Treebanks: Building and using parsed corpora. Ed. by Anne Abeillé. Dordrecht: Kluwer, 2003. Pp. 440. ISBN 1402013353. $74.95. Annotated corpora have been the fuel for a number of recent advances in the study of language, notably, although not exclusively, in computational linguistics. At the sentence level, corpus annotations range from shallow levels of linguistic representation, such as part-of-speech categories (Francis & Kučera 1982, Leech et al. 1994) or named entities (Strassel et al. 2003), through intermediate levels such as argument structure (Meyers et al. 2004, Palmer et al. 2005), to deeper levels of semantic representation such as semantic roles (Baker et al. 1998), word senses (Landes et al. 1998), events and temporal relations (Pustejovsky et al. 2003), or language-independent meaning representations (Farwell et al. 2004). When it comes to annotating sentences with linguistic representation, the sky is the limit (Meyers 2005). The ‘sweet spot’ in this range of annotations is occupied by treebanks, which is to say parsed (syntactically annotated) corpora. Unlike shallower annotations, syntactic parses capture hierarchical organization, a fundamental notion in virtually any modern theory of sentence structure. But unlike most deeper representations, syntactic parses can be created with high levels of inter-annotator reliability (though see Hovy et al. 2006 and references therein for recent progress in semantic treebanking). With respect to natural language processing applications, the impact of treebanks during the last decade has been remarkable, more than validating Marcus and colleagues’ (1993) premise that ‘significant, rapid progress can be made … by investigating those phenomena that occur most centrally in naturally occurring unconstrained materials and by attempting to automatically extract information about language from very large corpora’ (313). Beyond applications, syntactically annotated corpora have also begun to play an increasingly productive role in psycholinguistics, theoretical syntax, and language pedagogy (e.g. Corley et al. 2001, Jurafsky 2002, Dillon 2005, Meurers 2005, Resnik et al. 2005). In Treebanks: Building and using parsed corpora, Anne Abeille´ draws together a collection of fifteen short pieces focused primarily on the issues that come up in creating treebanks, demonstrated across an impressive variety of languages, along with six chapters on how treebanks are used. Although twenty-one chapters cannot be covered in detail in a short space, I present a brief walk through the chapters, followed by a discussion of the book as a whole. Abeillé’s introduction offers a very concise but clearly written primer on the main issues that come up in choosing representations, annotating corpora, and using treebanks in applications, folding in the obligatory pointers to the chapters that follow. In ‘The Penn Treebank: An overview’, Anne Taylor, Mitchell Marcus, and Beatrice Santorini provide a short, accessible description of the widely used Penn Treebank, extracting and updating the seminal article by Marcus and colleagues (1993) (which still remains the definitive source for in-depth discussion). In ‘Thoughts on two decades of drawing trees’, Geoffrey Sampson offers an engaging, personal discussion that combines elements of corpus description, linguistic analysis, and position paper. Unlike other chapters in the book, Sampson’s chapter offers a high-level look at corpus linguistics as an engineering and scientific discipline, and, contrary to some treebanking work, suggests that corpus annotation should make detail, accuracy, and explicitness a higher priority than the number of sentences annotated. Among the next thirteen chapters, nine provide detailed discussions of treebanking projects for specific languages, following a pattern that generally includes: (1) the goals and historical context of the project, (2) the selection of data to annotate (usually news text), (3) the annotation process (usually automatic analysis followed by human correction using project-specific tools), (4) details of representation (admitting wide variety, but usually an elaboration on syntactic constituency or grammatical dependency representation, with additional features to address language-specific [End Page 876] issues), (5) tools used for manual creation and correction of annotations (again admitting very wide variety), (6) a set of detailed, language-specific annotation choices that illustrate interesting and challenging aspects of the language under consideration, (7) a description of the project’s status, and (8) a brief evaluation and...

Brief Report: Human Figure Drawings by Children with Asperger’s Syndrome

Twenty-nine children with Asperger's syndrome and 28 typically developing children, matched on gender, chronological age and nonverbal IQ, were asked to produce a free drawing, then requested to draw a person, a house and a tree. The drawings were scored using standardized procedures for assessing accuracy, detail and complexity. There were no differences between the diagnostic groups on the tree or house drawing scores. The human figure drawing scores of children with Asperger's syndrome were significantly lower than those of the typically developing children, and there was a positive correlation between human figure drawing scores and communication sub-scores on the Vineland Adaptive Behaviour Scales, for the Asperger's group. These results suggest that the selective deficit in generating human figure representations may derive from a relative lack of interest in the social world, and/or limited practice in drawing people.

A Study on the Elderly's Ego Integrity and their Reactions to the Tree Drawing

A Study on the Elderly's Ego Integrity and their Reactions to the Tree Drawing

On Balloon Drawings of Rooted Trees

Among various styles of tree drawing, balloon drawing, where each subtree is enclosed in a circle, enjoys a desirable feature of displaying tree structures in a rather balanced fashion. We first design an efficient algorithm to optimize angular resolution and aspect ratio for the balloon drawing of rooted unordered trees. For the case of ordered trees for which the center of the enclosing circle of a subtree need not coincide with the root of the subtree, flipping the drawing of a subtree (along the axis from the parent to the root of the subtree) might change both the aspect ratio and the angular resolution of the drawing. We show that optimizing the angular resolution as well as the aspect ratio with respect to this type of rooted ordered trees is reducible to the perfect matching problem for bipartite graphs, which is solvable in polynomial time. Aside from studying balloon drawing from an algorithmic viewpoint, we also propose a local magnetic spring model for producing dynamic balloon drawings with applications to the drawings of galaxy systems, H-trees, and sparse graphs, which are of practical interest.

Tgp: AnRPackage for Bayesian Nonstationary, Semiparametric Nonlinear Regression and Design by Treed Gaussian Process Models

The tgp package for R is a tool for fully Bayesian nonstationary, semiparametric nonlinear regression and design by treed Gaussian processes with jumps to the limiting linear model. Special cases also implemented include Bayesian linear models, linear CART, stationary separable and isotropic Gaussian processes. In addition to inference and posterior prediction, the package supports the (sequential) design of experiments under these models paired with several objective criteria. 1-d and 2-d plotting, with higher dimension projection and slice capabilities, and tree drawing functions (requiring maptree and combinat packages), are also provided for visualization of tgp objects.

Smashing Peacocks Further: Drawing Quasi-Trees from Biconnected Components

Quasi-trees, namely graphs with tree-like structure, appear in many application domains, including bioinformatics and computer networks. Our new SPF approach exploits the structure of these graphs with a two-level approach to drawing, where the graph is decomposed into a tree of biconnected components. The low-level biconnected components are drawn with a force-directed approach that uses a spanning tree skeleton as a starting point for the layout. The higher-level structure of the graph is a true tree with meta-nodes of variable size that contain each biconnected component. That tree is drawn with a new area-aware variant of a tree drawing algorithm that handles high-degree nodes gracefully, at the cost of allowing edge-node overlaps. SPF performs an order of magnitude faster than the best previous approaches, while producing drawings of commensurate or improved quality.

PHY·FI: fast and easy online creation and manipulation of phylogeny color figures

BackgroundThe need to depict a phylogeny, or some other kind of abstract tree, is very frequently experienced by researchers from a broad range of biological and computational disciplines. Thousands of papers and talks include phylogeny figures, and often during everyday work, one would like to quickly get a graphical display of, e.g., the phylogenetic relationship between a set of sequences as calculated by an alignment program such as ClustalW or the phylogenetic package Phylip. A wealth of software tools capable of tree drawing exists; most are comprehensive packages that also perform various types of analysis, and hence they are available only for download and installing. Some online tools exist, too.ResultsThis paper presents an online tool, PHY·FI, which encompasses all the qualities of existing online programs and adds functionality to hopefully eliminate the need for post-processing the phylogeny figure in some other general-purpose graphics program. PHY·FI is versatile, easy-to-use and fast, and supports comprehensive graphical control, several download image formats, and the possibility of dynamically collapsing groups of nodes into named subtrees (e.g. "Primates"). The user can create a color figure from any phylogeny, or other kind of tree, represented in the widely used parenthesized Newick format.ConclusionPHY·FI is fast and easy to use, yet still offers full color control, tree manipulation, and several image formats. It does not require any downloading and installing, and thus any internet user regardless of computer skills, and computer platform, can benefit from it. PHY·FI is free for all and is available from this web address:

Relaxing the Clock Brings Time Back into Phylogenetics

The hypothesis of a “molecular clock”—a constant rate of mutation over evolutionary time—revolutionized phylogenetics, the study of evolutionary relationships among organisms. Using the assumption of this constant rate, one can determine the time since two organisms diverged from a common ancestor simply by toting up the number of DNA sequence differences between them. Thus, the molecular clock provided an important tool for constructing phylogenies, “trees” of relatedness, for organisms as diverse as primates and protists. However, the constancy of the mutation rate, both between different groups and within a single group over time, has been repeatedly challenged. As a result, the molecular clock has been largely abandoned in recent years for constructing phylogenetic trees. In its place has arisen a model that accepts that each branch may have its own rate of mutation. Relatedness between two organisms can still be determined and trees can still be drawn, but without a constant mutation rate, no estimate can be made of the time since divergence, and thus the position in time of the last common ancestor—the “root” of the tree—cannot be calculated. An alternative approach, termed a “relaxed molecular clock,” has been developed to overcome the difficulties of both the molecular clock and unrooted phylogeny models. In a new study, Alexei Drummond, Andrew Rambaut, and colleagues describe a new approach to relaxed-clock analysis, showing that it can be used to simultaneously construct accurate trees and infer times of divergence. Previous attempts to reintroduce a molecular clock into relaxed phylogenetics have posited differing, but correlated, rates of mutation along different branches. But filling in these rates requires specifying the topology of the tree—knowing who's related to whom—beforehand. This is often poorly known, and may be the very question phylogeneticists are trying to answer. Drummond et al. took a different approach. Using a set of artificial DNA sequences generated and mutated to form a rooted tree, they tested five different models of rate variations to determine which most accurately modeled the simulated evolution of this group. The five models included a strict molecular clock, in which mutation rates were the same on all branches at all times, as well as various modifications in which rates were correlated or uncorrelated among the branches. Using the phylogenetic analysis program called BEAST, they found that the most robust model—the one that did best under various starting conditions—was neither the strict molecular clock nor the correlated models, but the “uncorrelated relaxed-clock” models, in which the mutation rates in each branch are allowed to vary but within particular constraints. They then tested their models in several real sets of data, including viruses, marsupials, plants, bacteria, and yeast. In the plant dataset, which was known to have the most “clock-like” evolution, the strict molecular clock model did best, not surprisingly. But the relaxed-clock model performed best overall among all the datasets, drawing trees that were closest to known relationships with the fewest missteps. And, unlike in the unrooted phylogenic approach, they were able to assign times of divergence to each branch on the tree. The model developed by the authors promises to bring the very important question of time back into phylogenetic analysis. The ability of the model to create accurate trees may also make it of use even to scientists whose main interests are in understanding phylogenetic relationships, rather than the timing of evolutionary divergence.

The Tree Drawing Test of Children with School Refusal and Orthostatic Dysregulation

The Tree Drawing Test of Children with School Refusal and Orthostatic Dysregulation

On the complexity of drawing trees nicely: corrigendum

In this journal, Supowit and Reingold [1] have given a proof that it is NP-complete to decide whether a binary tree can be drawn on a grid with width 24 if certain aesthetic requirements are obeyed. We identify and repair a mistake in their proof.

PATHWIDTH AND LAYERED DRAWINGS OF TREES

An h-layer drawing of a graph G is a planar drawing of G in which each vertex is placed on one of h parallel lines and each edge is drawn as a straight line between its end-vertices. In such a drawing, we say that an edge is proper if its endpoints lie on adjacent layers, flat if they lie on the same layer and long otherwise. Thus, a proper h-layer drawing contains only proper edges, a short h-layer drawing contains no long edges, an upright h-layer drawing contains no flat edges, and an unconstrained h-layer drawing contains any type of edge. In this paper, we derive upper and lower bounds on the number of layers required by proper, short, upright, and unconstrained layered drawings of trees. We prove that these bounds are optimal with respect to the pathwidth of the tree being drawn. Finally, we give linear-time algorithms for obtaining layered drawings that match these upper bounds.

Proximity drawings in polynomial area and volume

We introduce a novel technique for drawing proximity graphs in polynomial area and volume. Previously known algorithms produce representations whose size increases exponentially with the size of the graph. This holds even when we restrict ourselves to binary trees. Our method is quite general and yields the first algorithms to construct (a) polynomial area weak Gabriel drawings of ternary trees, (b) polynomial area weak β-proximity drawing of binary trees for any 0⩽ β<∞, and (c) polynomial volume weak Gabriel drawings of unbounded degree trees. Notice that, in general, the above graphs do not admit a strong proximity drawing. Finally, we give evidence of the effectiveness of our technique by showing that a class of graph requiring exponential area even for weak Gabriel drawings, admits a linear-volume strong β- proximity drawing and a relative neighborhood drawing. All described algorithms run in linear time.

Proximity drawings in polynomial area and volume*1

We introduce a novel technique for drawing proximity graphs in polynomial area and volume. Previously known algorithms produce representations whose size increases exponentially with the size of the graph. This holds even when we restrict ourselves to binary trees. Our method is quite general and yields the first algorithms to construct (a) polynomial area weak Gabriel drawings of ternary trees , (b) polynomial area weak β -proximity drawing of binary trees for any 0⩽ β <∞, and (c) polynomial volume weak Gabriel drawings of unbounded degree trees. Notice that, in general, the above graphs do not admit a strong proximity drawing. Finally, we give evidence of the effectiveness of our technique by showing that a class of graph requiring exponential area even for weak Gabriel drawings, admits a linear-volume strong β - proximity drawing and a relative neighborhood drawing. All described algorithms run in linear time.

Order-preserving, upward drawing of binary trees using fewer bends

For a binary tree with n nodes, we present a planar, polyline, order-preserving, upward, grid drawing that has O(n/ log n) bends and matches the previously best area O(n log n) . This is an improvement over the O(n log n) area drawing, which has O( n) bends.

A Learning Tool For The Visualization Of GeneralDirected Or Undirected Rooted Trees

This paper presents a new learning tool developed for the visualization of general directed and undirected rooted trees. This visualization tool for teaching graph and network algorithms provides an interactive view of the subject being taught to the students. The tool is designed for three different groups of users: developers, instructors and students. It could be used for the visualization of any algorithm that generates a sequence of trees. This new tool minimizes the instructor’s effort and gives him the possibility of drawing trees easily with many different properties. It can be used efficiently in courses like Graph Theory or Network Programming or in an introductory course like Algorithms and Data Structures. We believe that this tool will be an effective supplement to traditional classroom education. It is a commonly accepted fact that teaching can be vastly amplified when it is done visually and interactively instead of in the traditional way. Therefore, a summary of other educational tools concerning tree drawing is presented. Benefits and drawbacks are thoroughly described in order to support the efficiency of modern learning technology.

Straight-line Drawings of Binary Trees with Linear Area and Arbitrary Aspect Ratio

Trees are usually drawn planar, i.e. without any crossings. In this paper, we investigate the area requirement of (non-upward) planar straight-line grid drawings of binary trees. Let T be a binary tree with n nodes. We show that T admits a planar straight-line grid drawing with area O(n) and with any pre-specified aspect ratio in the range [1,n α ], where a is a constant such that 0 < a < 1. We also show that such a drawing can be constructed in O(n log n) time.

The Late Triassic Schilderia Adamanica and Woodworthia Arizonica Trees of the Petrified Forest National Park, Arizona, Usa

Two fossil tree species, both with unusual characteristics, occur in the Upper Triassic of the Petrified Forest National Park, Arizona, USA and adjacent areas. The first, Schilderia adamanica, has a highly idiosyncratic secondary xylem structure which contains normal uniseriate and broad complex multiseriate ‘herring‐bone’ rays. The trunk cross‐section of the secondary xylem may be either of a normal pycnoxylic type with a central pith and rays radiating from that or it may consist of appressed ‘xylem masses’ with rays curving towards one another at their extremities. The second, Woodworthia arizonica, has narrow, horizontal vascular traces traversing the entire radial width of the secondary xylem. By analogy with extant tree species, these traces would have terminated on preventitious buds deeply embedded in the bark which, in the case of these fossil trunks, have failed to be silicified. Such buds have the capacity to develop into epicormic shoots when the crown foliage of the tree is damaged. A further specimen of W. arizonica is recorded for the first time from the Permian of southern Brazil. Reconstruction drawings of both trees are produced.

Drawing Trees Symmetrically in Three Dimensions

Symmetric graph drawing enables a clear understanding of the structure of the graph. Previous work on symmetric graph drawing has focused on two dimensions. Symmetry in three dimensions is much richer than that of two dimensions. This is the first paper to extend symmetric graph drawing into three dimensions. More specifically, the paper investigates the problem of drawing trees symmetrically in three dimensions. First, we suggest a model for drawing trees symmetrically in three dimensions. Based on this model, we present a linear time algorithm for finding the maximum number of three-dimensional symmetries in trees. We also present a three-dimensional symmetric drawing algorithm for trees.

A clustering algorithm for huge trees

We present a new tree clustering algorithm based on combinatorial statistics on trees. Using well-known measures on trees giving the number of leaves of a subtree or the number of siblings of a node, we design a parameter that can be used to detect irregularities in a tree. We obtain a clustering approach for trees by implementing classical statistical tests on this parameter, thus providing well balanced drawings of trees offering better aspect ratios which can be useful when dealing with large, irregular hierarchical data. Our algorithm is linear in time and can thus be applied to large data structures. Moreover the larger the structure is the better the precision of the statistical tools.

Space-Optimized Tree: A Connection+Enclosure Approach for the Visualization of Large Hierarchies

This paper describes a new approach, space-optimized tree, for the visualization and navigation of tree-structured relational data. This technique can be used especially for the display of very large hierarchies in a two-dimensional space. We discuss the advantages and limitations of current techniques of tree visualization. Our strategy is to optimize the drawing of trees in a geometrical plane and maximize the utilization of display space by allowing more nodes and links to be displayed at a limited screen resolution. Space-optimized tree is a connection+ enclosure visualization approach that recursively positions children of a subtree into polygon areas and still uses a node–link diagram to present the entire hierarchical structure. To be able to handle the navigation of large hierarchies, we use a new hybrid viewing technique that combines two viewing methods, the modified semantic zooming and a focus+ context technique. While the semantic zooming technique can enlarge a particular viewing area by filtering out the rest of tree structure from the visualization, the focus+context technique allows the user to interactively focus, view and browse the entire visual structure with a reasonable high-density display.