Compact Floor-Planning via Orderly Spanning Trees

Floor-planning is a fundamental step in VLSI chip design. Based upon the concept of orderly spanning trees, we present a simple O(n)-time algorithm to construct a floor-plan for any n-node plane triangulation. In comparison with previous floor-planning algorithms in the literature, our solution is not only simpler in the algorithm itself, but also produces floor-plans which require fewer module types. An equally important aspect of our new algorithm lies in its ability to fit the floor-plan area in a rectangle of size (n-1)x(2n+1)/3. Lower bounds on the worst-case area for floor-planning any plane triangulation are also provided in the paper.Comment: 13 pages, 5 figures, An early version of this work was presented at 9th International Symposium on Graph Drawing (GD 2001), Vienna, Austria, September 2001. Accepted to Journal of Algorithms, 200

Planar Induced Subgraphs of Sparse Graphs

We show that every graph has an induced pseudoforest of at least $n-m/4.5$ vertices, an induced partial 2-tree of at least $n-m/5$ vertices, and an induced planar subgraph of at least $n-m/5.2174$ vertices. These results are constructive, implying linear-time algorithms to find the respective induced subgraphs. We also show that the size of the largest $K_h$-minor-free graph in a given graph can sometimes be at most $n-m/6+o(m)$.Comment: Accepted by Graph Drawing 2014. To appear in Journal of Graph Algorithms and Application

Py-Tetrad and RPy-Tetrad: A New Python Interface with R Support for Tetrad Causal Search

We give novel Python and R interfaces for the (Java) Tetrad project for causal modeling, search, and estimation. The Tetrad project is a mainstay in the literature, having been under consistent development for over 30 years. Some of its algorithms are now classics, like PC and FCI; others are recent developments. It is increasingly the case, however, that researchers need to access the underlying Java code from Python or R. Existing methods for doing this are inadequate. We provide new, up-to-date methods using the JPype Python-Java interface and the Reticulate Python-R interface, directly solving these issues. With the addition of some simple tools and the provision of working examples for both Python and R, using JPype and Reticulate to interface Python and R with Tetrad is straightforward and intuitive.Comment: Causal Analysis Workshop Series (CAWS) 2023, 12 pages, 4 Figures, 2 Table

FORG3D: Force-directed 3D graph editor for visualization of integrated genome scale data

<p>Abstract</p> <p>Background</p> <p>Genomics research produces vast amounts of experimental data that needs to be integrated in order to understand, model, and interpret the underlying biological phenomena. Interpreting these large and complex data sets is challenging and different visualization methods are needed to help produce knowledge from the data.</p> <p>Results</p> <p>To help researchers to visualize and interpret integrated genomics data, we present a novel visualization method and bioinformatics software tool called FORG3D that is based on real-time three-dimensional force-directed graphs. FORG3D can be used to visualize integrated networks of genome scale data such as interactions between genes or gene products, signaling transduction, metabolic pathways, functional interactions and evolutionary relationships. Furthermore, we demonstrate its utility by exploring gene network relationships using integrated data sets from a <it>Caenorhabditis elegans </it>Parkinson's disease model.</p> <p>Conclusion</p> <p>We have created an open source software tool called FORG3D that can be used for visualizing and exploring integrated genome scale data.</p

Метод описания топологической структуры вычислительных кластеров, основанный на операциях произведений подграфов

Topological structure of communication networks in supercomputers with grow in size and complexity of installation, respectively becomes more difficult. There are many methods to describe it, but such descriptions are cumbersome, which makes them difficult to manipulate. The article proposes an approach to describing the communication environment of a supercomputer, when the communication network is described as a constructor. The elements of the constructor are typical topological structures often found in various computing systems. For this purpose, a language for describing the topological structure has been developed. It based on the operation products of subgraphs. The language is ideologically similar in its principles to the NetML and OMNeT++ languages. Special attention is paid to exceptions in the regularity of networks of real supercomputers; in order to add the possibility of describing this fact, special constructions have been introduced into the language. A library has been developed in the C programming language with purpose to facilitate work with the language intoduced in this article. Also a special wrapper over C library has been written in Python3, which then can be used to visualize graphs described by the language. The expressive power of language has been demonstrated in the description computing clusters: Tianhe-2A, AI Bridging Cloud Infrastructure and Lomonosov-2. The method has been tested and compared with GraphViz DOT it is showed multiple reductions in the Record volume required to save topology for some of the major Top500 systems.Топологическая структура коммуникационных сетей суперкомпьютерных систем при увеличении размера и сложности суперкомпьютеров соответственно усложняется. Для ее описания существует множество методов, однако такие описания являются громоздкими, что усложняет манипулирование ими. В статье предложен подход к описанию коммуникационной среды суперкомпьютера, когда коммуникационная сеть описывается как конструктор, где элементами конструктора являются типовые топологические структуры, часто встречающиеся в различных вычислительных системах. С этой целью разработан язык описания топологической структуры, основанный на операции произведения подграфов. Язык идейно схож в своих принципах с языками NetML и OMNeT++. Отдельное внимание в работе уделяется исключениям в регулярности сетей реальных суперкомпьютеров; с целью добавления возможности описания данного факта в язык внесены специальные конструкции. Для поддержки работы с языком описания разработана библиотека на языке программирования Си и специальная оболочка над ней написанная на языке Python3, которая затем может использоваться для визуализации описываемых языком графов. Выразительная мощность языка была продемонстрирована на описании вычислительных кластеров: Tianhe-2A, AI Bridging Cloud Infrastructure и Ломоносов-2. Метод был проверен и сравнен с GraphViz DOT показано многократное сокращение необходимых объема записи для некоторых крупных систем из Top500

Male Pedigree Toolbox:A Versatile Software for Y-STR Data Analyses

Y-chromosomal short tandem repeats (Y-STRs) are widely used in forensic, genealogical, and population genetics. With the recent increase in the number of rapidly mutating (RM) Y-STRs, an unprecedented level of male differentiation can be achieved, widening and improving the applications of Y-STRs in various fields, including forensics. The growing complexity of Y-STR data increases the need for automated data analyses, but dedicated software tools are scarce. To address this, we present the Male Pedigree Toolbox (MPT), a software tool for the automated analysis of Y-STR data in the context of patrilineal genealogical relationships. The MPT can estimate mutation rates and male relative differentiation rates from input Y-STR pedigree data. It can aid in determining ancestral haplotypes within a pedigree and visualize the genetic variation within pedigrees in all branches of family trees. Additionally, it can provide probabilistic classifications using machine learning, helping to establish or prove the structure of the pedigree and the level of relatedness between males, even for closely related individuals with highly similar haplotypes. The tool is flexible and easy to use and can be adjusted to any set of Y-STR markers by modifying the intuitive input file formats. We introduce the MPT software tool v1.0 and make it publicly available with the goal of encouraging and supporting forensic, genealogical, and other geneticists in utilizing the full potential of Y-STRs for both research purposes and practical applications, including criminal casework.</p

Crossing-number critical graphs have bounded path-width

AbstractThe crossing number of a graph G, denoted by cr(G), is defined as the smallest possible number of edge-crossings in a drawing of G in the plane. A graph G is crossing-critical if cr(G−e)<cr(G) for all edges e of G. We prove that crossing-critical graphs have “bounded path-width” (by a function of the crossing number), which roughly means that such graphs are made up of small pieces joined in a linear way on small cut-sets. Equivalently, a crossing-critical graph cannot contain a subdivision of a “large” binary tree. This assertion was conjectured earlier by Salazar (J. Geelen, B. Richter, G. Salazar, Embedding grids on surfaces, manuscript, 2000)

TAF6δ orchestrates an apoptotic transcriptome profile and interacts functionally with p53

<p>Abstract</p> <p>Background</p> <p>TFIID is a multiprotein complex that plays a pivotal role in the regulation of RNA polymerase II (Pol II) transcription owing to its core promoter recognition and co-activator functions. TAF6 is a core TFIID subunit whose splice variants include the major TAF6α isoform that is ubiquitously expressed, and the inducible TAF6δ. In contrast to TAF6α, TAF6δ is a pro-apoptotic isoform with a 10 amino acid deletion in its histone fold domain that abolishes its interaction with TAF9. TAF6δ expression can dictate life versus death decisions of human cells.</p> <p>Results</p> <p>Here we define the impact of endogenous TAF6δ expression on the global transcriptome landscape. TAF6δ was found to orchestrate a transcription profile that included statistically significant enrichment of genes of apoptotic function. Interestingly, gene expression patterns controlled by TAF6δ share similarities with, but are not equivalent to, those reported to change following TAF9 and/or TAF9b depletion. Finally, because TAF6δ regulates certain p53 target genes, we tested and demonstrated a physical and functional interaction between TAF6δ and p53.</p> <p>Conclusion</p> <p>Together our data define a TAF6δ-driven apoptotic gene expression program and show crosstalk between the p53 and TAF6δ pathways.</p