University of Notre Dame

About: University of Notre Dame is a education organization based out in Notre Dame, Indiana, United States. It is known for research contribution in the topics: Population & Large Hadron Collider. The organization has 22238 authors who have published 55201 publications receiving 2032925 citations. The organization is also known as: University of Notre Dame du Lac & University of Notre Dame, South Bend.

New perspectives and methods in link prediction

Abstract: This paper examines important factors for link prediction in networks and provides a general, high-performance framework for the prediction task. Link prediction in sparse networks presents a significant challenge due to the inherent disproportion of links that can form to links that do form. Previous research has typically approached this as an unsupervised problem. While this is not the first work to explore supervised learning, many factors significant in influencing and guiding classification remain unexplored. In this paper, we consider these factors by first motivating the use of a supervised framework through a careful investigation of issues such as network observational period, generality of existing methods, variance reduction, topological causes and degrees of imbalance, and sampling approaches. We also present an effective flow-based predicting algorithm, offer formal bounds on imbalance in sparse network link prediction, and employ an evaluation method appropriate for the observed imbalance. Our careful consideration of the above issues ultimately leads to a completely general framework that outperforms unsupervised link prediction methods by more than 30% AUC.

LDPC block and convolutional codes based on circulant matrices

Abstract: A class of algebraically structured quasi-cyclic (QC) low-density parity-check (LDPC) codes and their convolutional counterparts is presented. The QC codes are described by sparse parity-check matrices comprised of blocks of circulant matrices. The sparse parity-check representation allows for practical graph-based iterative message-passing decoding. Based on the algebraic structure, bounds on the girth and minimum distance of the codes are found, and several possible encoding techniques are described. The performance of the QC LDPC block codes compares favorably with that of randomly constructed LDPC codes for short to moderate block lengths. The performance of the LDPC convolutional codes is superior to that of the QC codes on which they are based; this performance is the limiting performance obtained by increasing the circulant size of the base QC code. Finally, a continuous decoding procedure for the LDPC convolutional codes is described.

Global Organization of Metabolic Fluxes in the Bacterium Escherichia coli

Abstract: Cellular metabolism, the integrated interconversion of thousands of metabolic substrates through enzyme-catalysed biochemical reactions, is the most investigated complex intracellular web of molecular interactions. Although the topological organization of individual reactions into metabolic networks is well understood, the principles that govern their global functional use under different growth conditions raise many unanswered questions. By implementing a flux balance analysis of the metabolism of Escherichia coli strain MG1655, here we show that network use is highly uneven. Whereas most metabolic reactions have low fluxes, the overall activity of the metabolism is dominated by several reactions with very high fluxes. E. coli responds to changes in growth conditions by reorganizing the rates of selected fluxes predominantly within this high-flux backbone. This behaviour probably represents a universal feature of metabolic activity in all cells, with potential implications for metabolic engineering.

Molecular Dynamics Study of the Ionic Liquid 1-n-Butyl-3-methylimidazolium Hexafluorophosphate

Abstract: We report the results of a molecular dynamics study of the ionic liquid 1-n-butyl-3-methylimidazolium hexafluorophosphate [bmim][PF6], a widely studied ionic liquid. An all-atom force field is developed using a combination of density functional theory calculations and CHARMM 22 parameter values. Molecular dynamics simulations are carried out in the isothermal−isobaric ensemble at three different temperatures. Quantities computed include infrared frequencies, molar volumes, volume expansivities, isothermal compressibililties, self-diffusivities, cation−anion exchange rates, rotational dynamics, and radial distribution functions. Computed thermodynamic properties are in good agreement with available experimental values.

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Abstract: Background - The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results - In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions - Many current genome assemblers produced useful assemblies, containing a significant representation of their genes, regulatory sequences, and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.