Theoretically Efficient Parallel Graph Algorithms Can Be Fast and Scalable

There has been significant recent interest in parallel graph processing due to the need to quickly analyze the large graphs available today. Many graph codes have been designed for distributed memory or external memory. However, today even the largest publicly-available real-world graph (the Hyperlink Web graph with over 3.5 billion vertices and 128 billion edges) can fit in the memory of a single commodity multicore server. Nevertheless, most experimental work in the literature report results on much smaller graphs, and the ones for the Hyperlink graph use distributed or external memory. Therefore, it is natural to ask whether we can efficiently solve a broad class of graph problems on this graph in memory. This paper shows that theoretically-efficient parallel graph algorithms can scale to the largest publicly-available graphs using a single machine with a terabyte of RAM, processing them in minutes. We give implementations of theoretically-efficient parallel algorithms for 20 important graph problems. We also present the optimizations and techniques that we used in our implementations, which were crucial in enabling us to process these large graphs quickly. We show that the running times of our implementations outperform existing state-of-the-art implementations on the largest real-world graphs. For many of the problems that we consider, this is the first time they have been solved on graphs at this scale. We have made the implementations developed in this work publicly-available as the Graph-Based Benchmark Suite (GBBS).Comment: This is the full version of the paper appearing in the ACM Symposium on Parallelism in Algorithms and Architectures (SPAA), 201

Characterization of Highly Mucus-Adherent Non-GMO Derivatives of Lacticaseibacillus rhamnosus GG

Lacticaseibacillus rhamnosusGG is one of the best studied lactic acid bacteria in the context of probiotic effects.L. rhamnosusGG has been shown to prevent diarrhea in children and adults and has been implicated to have mitigating or preventive effects in several disorders connected to microbiota dysbiosis. The probiotic effects are largely attributed to its adhesive heterotrimeric sortase-dependent pili, encoded by thespaCBA-srtC1gene cluster. Indeed, the strain-specific SpaCBA pili have been shown to contribute to adherence, biofilm formation and host signaling. In this work we set out to generate non-GMO derivatives ofL. rhamnosusGG that adhere stronger to mucus compared to the wild-type strain using chemical mutagenesis. We selected 13 derivatives that showed an increased mucus-adherent phenotype. Deep shotgun resequencing of the strains enabled division of the strains into three classes, two of which revealed SNPs (single nucleotide polymorphisms) in thespaAandspaCgenes encoding the shaft and tip adhesive pilins, respectively. Strikingly, the other class derivatives demonstrated less clear genotype - phenotype relationships, illustrating that pili biogenesis and structure is also affected by other processes. Further characterization of the different classes of derivatives was performed by PacBio SMRT sequencing and RNAseq analysis, which resulted in the identification of molecular candidates driving pilin biosynthesis and functionality. In conclusion, we report on the generation and characterization of three classes of strongly adherentL. rhamnosusGG derivatives that show an increase in adhesion to mucus. These are of special interest as they provide a window on processes and genes driving piliation and its control inL. rhamnosusGG and offer a variety of non-GMO derivatives of this key probiotic strain that are applicable in food products.Peer reviewe

Parallel Graph Decompositions Using Random Shifts

We show an improved parallel algorithm for decomposing an undirected unweighted graph into small diameter pieces with a small fraction of the edges in between. These decompositions form critical subroutines in a number of graph algorithms. Our algorithm builds upon the shifted shortest path approach introduced in [Blelloch, Gupta, Koutis, Miller, Peng, Tangwongsan, SPAA 2011]. By combining various stages of the previous algorithm, we obtain a significantly simpler algorithm with the same asymptotic guarantees as the best sequential algorithm

A novel consortium of Lactobacillus rhamnosus and Streptococcus thermophilus for increased access to functional fermented foods

Background: The lactic acid bacterium Lactobacillus rhamnosus GG is the most studied probiotic bacterium with proven health benefits upon oral intake, including the alleviation of diarrhea. The mission of the Yoba for Life foundation is to provide impoverished communities in Africa increased access to Lactobacillus rhamnosus GG under the name Lactobacillus rhamnosus yoba 2012, world's first generic probiotic strain. We have been able to overcome the strain's limitations to grow in food matrices like milk, by formulating a dried starter consortium with Streptococcus thermophilus that enables the propagation of both strains in milk and other food matrices. The affordable seed culture is used by people in resource-poor communities. Results: We used S. thermophilus C106 as an adjuvant culture for the propagation of L. rhamnosus yoba 2012 in a variety of fermented foods up to concentrations, because of its endogenous proteolytic activity, ability to degrade lactose and other synergistic effects. Subsequently, L. rhamnosus could reach final titers of 1E+09 CFU ml(-1), which is sufficient to comply with the recommended daily dose for probiotics. The specific metabolic interactions between the two strains were derived from the full genome sequences of L. rhamnosus GG and S. thermophilus C106. The piliation of the L. rhamnosus yoba 2012, required for epithelial adhesion and inflammatory signaling in the human host, was stable during growth in milk for two rounds of fermentation. Sachets prepared with the two strains, yoba 2012 and C106, retained viability for at least 2 years. Conclusions: A stable dried seed culture has been developed which facilitates local and low-cost production of a wide range of fermented foods that subsequently act as delivery vehicles for beneficial bacteria to communities in east Africa.Peer reviewe

Competency based assessment of speech pathology students' performance in the workplace

Ensuring that speech pathology students are sufficiently competent to practise their profession is of critical importance to the speech pathology profession, students, their future employers, and clients/patients. This thesis describes the development and validation of a competency based assessment of speech pathology students’ performance in the workplace and their readiness to enter the profession. Development involved an extensive literature review regarding the nature of competency and its relationship to professional practice, the purpose and nature of assessment, and the validation of performance assessments. An online and hard copy assessment tool (paper) was designed through integrating multiple sources of information regarding speech pathology and assessment of workplace performance. Sources included research, theory, expert opinion, current practice, and focus group consultations with clinical educators and speech pathology students. The resulting assessment tool and resource material included four generic components of competency (clinical reasoning, professional communication, lifelong learning, and professional role) and seven occupational competencies previously developed by the speech pathology profession. The tool comprised an assessment format, either in a booklet or online, for clinical educators to rate students’ performances on the competencies at mid and end placement using a visual analogue scale. Behavioural descriptors and an assessment resource booklet informed and supported clinical educators’ judgement. The validity of the assessment tool was evaluated through a national field trial and using Messick’s six interrelated validity criteria which address content, substantive, structural, generalisability, external, and consequential aspects of validity (Messick, 1996). The validity of the assessment tool and its use with speech pathology students was evaluated through Rasch analysis, parametric statistical evaluation of relationships existing between information yielded by the Rasch analysis and other factors, and student and clinical educator feedback. The assessment tool was found to have strong validity characteristics across all validity components. Item Fit statistics generated through Rasch analysis ranged from .81 to 1.17 strongly upholding that the assessment items sampled a unidimensional construct of workplace competency for speech pathology students and confirming that generic and occupational competencies are both necessary for competent practice of speech pathology. High Item and Person Reliabilities (analogous to Cronbach’s alpha) were found (.98 and .97 respectively) and a wide range of person measures (-14.2 to 13.1) were generated. This indicated that a large spread of ability and a clear hierarchy of development on the construct was identified and that the assessment tool was highly reliable. This was further confirmed by high Intra Class Correlation coefficients for a small group of paired clinical educators rating the same student in the same workplace (.87) or in different workplaces concurrently (.82). Rasch analysis of the visual analogue scale used to rate student performance on 11 items of competence identified that clinical educators were able to reliably discriminate 7 categories or levels of student performance. This, in combination with careful calibration procedures, has resulted in an assessment tool that Australian Speech Pathology pre-professional preparation programs can use with confidence to place their students’ level of workplace competence into 7 zones of competency, with the seventh representing sufficient competence to enter the profession. The assessment tool also showed strong potential for identifying marginal students and for future use in promoting quality teaching and learning of professional competence. Limitations to the research and the tool validity were discussed, and recommendations made regarding future research. First, the clinical educator, who has dual and possibly conflicting roles as facilitator and assessor of student learning, made the assessment. Second, situating the assessment in the real workplace limits the students’ opportunities to demonstrate competence to those that naturally arise in the workplace. Paradoxically, both these factors also contributed to the validity of the assessment tool. It was recommended that the assessment tool be revised on the basis of the information gathered from the field trial, that further data be collected to ensure a broader proportional representation of speech pathology programs, to investigate possible threats to validity as well as those areas for which the tool showed promise. This research developed the first prototype of a validated assessment of entry level speech pathology competence that is grounded in a unified theoretical conception of entry level competence to the profession of speech pathology and the developmental progression required to reach this competence. This research will assist the profession of speech pathology by ensuring that speech pathologists enter the workplace well equipped to provide quality care to their future clients, the ultimate goal of any professional preparation program. Messick, S. (1996). Validity of performance assessments. In G. W. Phillips (Ed.), Technical Issues in Large-Scale Performance Assessment (pp. 1-18). Washington: National Centre for Education Statistics

Competency based assessment of speech pathology students' performance in the workplace

Ensuring that speech pathology students are sufficiently competent to practise their profession is of critical importance to the speech pathology profession, students, their future employers, and clients/patients. This thesis describes the development and validation of a competency based assessment of speech pathology students’ performance in the workplace and their readiness to enter the profession. Development involved an extensive literature review regarding the nature of competency and its relationship to professional practice, the purpose and nature of assessment, and the validation of performance assessments. An online and hard copy assessment tool (paper) was designed through integrating multiple sources of information regarding speech pathology and assessment of workplace performance. Sources included research, theory, expert opinion, current practice, and focus group consultations with clinical educators and speech pathology students. The resulting assessment tool and resource material included four generic components of competency (clinical reasoning, professional communication, lifelong learning, and professional role) and seven occupational competencies previously developed by the speech pathology profession. The tool comprised an assessment format, either in a booklet or online, for clinical educators to rate students’ performances on the competencies at mid and end placement using a visual analogue scale. Behavioural descriptors and an assessment resource booklet informed and supported clinical educators’ judgement. The validity of the assessment tool was evaluated through a national field trial and using Messick’s six interrelated validity criteria which address content, substantive, structural, generalisability, external, and consequential aspects of validity (Messick, 1996). The validity of the assessment tool and its use with speech pathology students was evaluated through Rasch analysis, parametric statistical evaluation of relationships existing between information yielded by the Rasch analysis and other factors, and student and clinical educator feedback. The assessment tool was found to have strong validity characteristics across all validity components. Item Fit statistics generated through Rasch analysis ranged from .81 to 1.17 strongly upholding that the assessment items sampled a unidimensional construct of workplace competency for speech pathology students and confirming that generic and occupational competencies are both necessary for competent practice of speech pathology. High Item and Person Reliabilities (analogous to Cronbach’s alpha) were found (.98 and .97 respectively) and a wide range of person measures (-14.2 to 13.1) were generated. This indicated that a large spread of ability and a clear hierarchy of development on the construct was identified and that the assessment tool was highly reliable. This was further confirmed by high Intra Class Correlation coefficients for a small group of paired clinical educators rating the same student in the same workplace (.87) or in different workplaces concurrently (.82). Rasch analysis of the visual analogue scale used to rate student performance on 11 items of competence identified that clinical educators were able to reliably discriminate 7 categories or levels of student performance. This, in combination with careful calibration procedures, has resulted in an assessment tool that Australian Speech Pathology pre-professional preparation programs can use with confidence to place their students’ level of workplace competence into 7 zones of competency, with the seventh representing sufficient competence to enter the profession. The assessment tool also showed strong potential for identifying marginal students and for future use in promoting quality teaching and learning of professional competence. Limitations to the research and the tool validity were discussed, and recommendations made regarding future research. First, the clinical educator, who has dual and possibly conflicting roles as facilitator and assessor of student learning, made the assessment. Second, situating the assessment in the real workplace limits the students’ opportunities to demonstrate competence to those that naturally arise in the workplace. Paradoxically, both these factors also contributed to the validity of the assessment tool. It was recommended that the assessment tool be revised on the basis of the information gathered from the field trial, that further data be collected to ensure a broader proportional representation of speech pathology programs, to investigate possible threats to validity as well as those areas for which the tool showed promise. This research developed the first prototype of a validated assessment of entry level speech pathology competence that is grounded in a unified theoretical conception of entry level competence to the profession of speech pathology and the developmental progression required to reach this competence. This research will assist the profession of speech pathology by ensuring that speech pathologists enter the workplace well equipped to provide quality care to their future clients, the ultimate goal of any professional preparation program. Messick, S. (1996). Validity of performance assessments. In G. W. Phillips (Ed.), Technical Issues in Large-Scale Performance Assessment (pp. 1-18). Washington: National Centre for Education Statistics

Inequality and Network Formation Games

This paper addresses the matter of inequality in network formation games. We employ a quantity that we are calling the Nash Inequality Ratio (NIR), defined as the maximal ratio between the highest and lowest costs incurred to individual agents in a Nash equilibrium strategy, to characterize the extent to which inequality is possible in equilibrium. We give tight upper bounds on the NIR for the network formation games of Fabrikant et al. (PODC '03) and Ehsani et al. (SPAA '11). With respect to the relationship between equality and social efficiency, we show that, contrary to common expectations, efficiency does not necessarily come at the expense of increased inequality.Comment: 27 pages. 4 figures. Accepted to Internet Mathematics (2014

OutFlank Routing: Increasing Throughput in Toroidal Interconnection Networks

We present a new, deadlock-free, routing scheme for toroidal interconnection networks, called OutFlank Routing (OFR). OFR is an adaptive strategy which exploits non-minimal links, both in the source and in the destination nodes. When minimal links are congested, OFR deroutes packets to carefully chosen intermediate destinations, in order to obtain travel paths which are only an additive constant longer than the shortest ones. Since routing performance is very sensitive to changes in the traffic model or in the router parameters, an accurate discrete-event simulator of the toroidal network has been developed to empirically validate OFR, by comparing it against other relevant routing strategies, over a range of typical real-world traffic patterns. On the 16x16x16 (4096 nodes) simulated network OFR exhibits improvements of the maximum sustained throughput between 14% and 114%, with respect to Adaptive Bubble Routing.Comment: 9 pages, 5 figures, to be presented at ICPADS 201