Incompatibility boundaries for properties of community partitions

We prove the incompatibility of certain desirable properties of community partition quality functions. Our results generalize the impossibility result of [Kleinberg 2003] by considering sets of weaker properties. In particular, we use an alternative notion to solve the central issue of the consistency property. (The latter means that modifying the graph in a way consistent with a partition should not have counterintuitive effects). Our results clearly show that community partition methods should not be expected to perfectly satisfy all ideally desired properties. We then proceed to show that this incompatibility no longer holds when slightly relaxed versions of the properties are considered, and we provide in fact examples of simple quality functions satisfying these relaxed properties. An experimental study of these quality functions shows a behavior comparable to established methods in some situations, but more debatable results in others. This suggests that defining a notion of good partition in communities probably requires imposing additional properties.Comment: 17 pages, 3 figure

Incompatibility boundaries for properties of community partitions

We prove the incompatibility of certain desirable properties of community partition quality functions. Our results generalize the impossibility result of [Kleinberg 2003] by considering sets of weaker properties. In particular, we use an alternative notion to solve the central issue of the consistency property. (The latter means that modifying the graph in a way consistent with a partition should not have counterintuitive effects). Our results clearly show that community partition methods should not be expected to perfectly satisfy all ideally desired properties. We then proceed to show that this incompatibility no longer holds when slightly relaxed versions of the properties are considered, and we provide examples of simple quality functions satisfying these relaxed properties. An experimental study of these quality functions shows a behavior comparable to established methods in some situations, but more debatable results in others. This suggests that defining a notion of good partition in communities probably requires imposing additional properties

Different approaches to community detection

A precise definition of what constitutes a community in networks has remained elusive. Consequently, network scientists have compared community detection algorithms on benchmark networks with a particular form of community structure and classified them based on the mathematical techniques they employ. However, this comparison can be misleading because apparent similarities in their mathematical machinery can disguise different reasons for why we would want to employ community detection in the first place. Here we provide a focused review of these different motivations that underpin community detection. This problem-driven classification is useful in applied network science, where it is important to select an appropriate algorithm for the given purpose. Moreover, highlighting the different approaches to community detection also delineates the many lines of research and points out open directions and avenues for future research.Comment: 14 pages, 2 figures. Written as a chapter for forthcoming Advances in network clustering and blockmodeling, and based on an extended version of The many facets of community detection in complex networks, Appl. Netw. Sci. 2: 4 (2017) by the same author

Partitioned Compressive Sensing with Neighbor-Weighted Decoding

Compressive sensing has gained momentum in recent years as an exciting new theory in signal processing with several useful applications. It states that signals known to have a sparse representation may be encoded and later reconstructed using a small number of measurements, approximately proportional to the signal s sparsity rather than its size. This paper addresses a critical problem that arises when scaling compressive sensing to signals of large length: that the time required for decoding becomes prohibitively long, and that decoding is not easily parallelized. We describe a method for partitioned compressive sensing, by which we divide a large signal into smaller blocks that may be decoded in parallel. However, since this process requires a signi cant increase in the number of measurements needed for exact signal reconstruction, we focus on mitigating artifacts that arise due to partitioning in approximately reconstructed signals. Given an error-prone partitioned decoding, we use large magnitude components that are detected with highest accuracy to in uence the decoding of neighboring blocks, and call this approach neighbor-weighted decoding. We show that, for applications with a prede ned error threshold, our method can be used in conjunction with partitioned compressive sensing to improve decoding speed, requiring fewer additional measurements than unweighted or locally-weighted decoding.Engineering and Applied Science

A Conceptualist View in the Metaphysics of Species

The species concept is one of the central concepts in biological science. Although modern systematics speculates about the existence of a complex hierarchy of nested taxa, biological species are considered particularly important for the active role they play in evolution. However, neither theoretical biologists nor philosophers of biology have come to an agreement about what a species is. In this chapter, we address two questions pertaining to biological species: (1) are they individuals or universals? and (2) are they bona fide or fiat entities? In section The Species-as-Individuals View, we illustrate the reasons that have led many scholars to support the view that species are individuals. In the next two sections, we show that the relational concepts of species – on which the species-as-individuals view is based – provide neither necessary nor sufficient conditions for species membership. This seriously undermines the species-as-individuals view. In the section A Conceptualist Model for the Metaphysics of Species, we advance the proposal that species are fiat concepts (and thus, universal entities partially dependent on the human mind) carved in a multi-dimensional space representing the properties that the biological organisms possess. The final section concludes

The imperfect hiding : some introductory concepts and preliminary issues on modularity

In this work we present a critical assessment of some problems and open questions on the debated notion of modularity. Modularity is greatly in fashion nowadays, being often proposed as the new approach to complex artefact production that enables to combine fast innovation pace, enhanced product variety and reduced need for co-ordination. In line with recent critical assessments of the managerial literature on modularity, we sustain that modularity is only one among several arrangements to cope with the complexity inherent in most high-technology artefact production, and by no means the best one. We first discuss relations between modularity and the broader (and much older within economics) notion of division of labour. Then we sustain that a modular approach to labour division aimed at eliminating technological interdependencies between components or phases of a complex production process may have, as a by-product, the creation of other types of interdependencies which may subsequently result in inefficiencies of various types. Hence, the choice of a modular design strategy implies the resolution of various tradeoffs. Depending on how such tradeoffs are solved, different organisational arrangements may be created to cope with ‘residual’ interdependencies. Hence, there is no need to postulate a perfect isomorphism, as some recent literature has proposed, between modularity at the product level and modularity at the organisational level

A Peer-to-Peer Middleware Framework for Resilient Persistent Programming

The persistent programming systems of the 1980s offered a programming model that integrated computation and long-term storage. In these systems, reliable applications could be engineered without requiring the programmer to write translation code to manage the transfer of data to and from non-volatile storage. More importantly, it simplified the programmer's conceptual model of an application, and avoided the many coherency problems that result from multiple cached copies of the same information. Although technically innovative, persistent languages were not widely adopted, perhaps due in part to their closed-world model. Each persistent store was located on a single host, and there were no flexible mechanisms for communication or transfer of data between separate stores. Here we re-open the work on persistence and combine it with modern peer-to-peer techniques in order to provide support for orthogonal persistence in resilient and potentially long-running distributed applications. Our vision is of an infrastructure within which an application can be developed and distributed with minimal modification, whereupon the application becomes resilient to certain failure modes. If a node, or the connection to it, fails during execution of the application, the objects are re-instantiated from distributed replicas, without their reference holders being aware of the failure. Furthermore, we believe that this can be achieved within a spectrum of application programmer intervention, ranging from minimal to totally prescriptive, as desired. The same mechanisms encompass an orthogonally persistent programming model. We outline our approach to implementing this vision, and describe current progress.Comment: Submitted to EuroSys 200

MITOCHONDRIAL AND NUCLEAR PATTERNS OF CONFLICT AND CONCORDANCE AT THE GENE, GENOME, AND BEHAVIORAL SCALES IN \u3cem\u3eDESMOGNATHUS\u3c/em\u3e SALAMANDERS

Advancements in molecular sequencing have revealed unexpected cryptic genetic diversity and contrasting evolutionary histories within genes and between genomes of many organisms; often in disagreement with recognized taxonomy. Incongruent patterns between the mitochondrial and nuclear evolutionary history can have several plausible explanations, but widespread systematic conflict inevitably challenges our conceptions of species boundaries when there is discordance between coevolving and coinherited genomes. It is unknown to what degree mitonuclear conflict drives the process of divergence, or how ubiquitous these patterns are across the tree of life. To understand the evolutionary relevance of intergenomic discordance we must identify the conflicting patterns that exist in natural systems by generating robust estimates of the underlying species history, quantify support for alternative hypotheses of lineage formation, and describe patterns of genetic variation present in robust nuclear genomic datasets. Empirically testing correlations between mitonuclear genomic conflict and reduced gene flow at the organism level will contribute toward a better understanding of lineage boundaries and how intergenomic interactions shape the process of divergence. Mitochondrial introgression has been inferred in many salamander systems with limited perspective from nuclear sequence data. Within dusky salamanders (Desmognathus), these patterns have been observed between morphologically and geographically disparate populations. I sequenced regions throughout the nuclear genome to reconstruct species trees, performed population-level analyses testing concordance between the mitochondrial, nuclear datasets, and nuclear genes with mitochondrial functions with the expectation that coevolutionary interactions among genomes are more likely to manifest in these regions. I also estimated migration rates between populations that may have experienced historical mitochondrial introgression to evaluate phylogeographic patterns. Using these data we definitively reject species models in which genetic boundaries are based solely on mitochondrial data, favoring geographic models instead. Furthermore, analyses soundly reject current taxonomic models based on morphological characteristics, suggesting there is greater lineage diversity than is currently recognized. I also used empirical assays of pre-zygotic reproductive mating behavior within and among populations containing diverse mitochondrial lineages to test metrics of reproductive isolation, and to determine if introgression shapes the evolution of complex traits directly influencing rates of divergence. These results may explain incongruent patterns observed between the mitochondrial and nuclear data as a function of inheritance and population dynamics rather than directly functioning to suppress nuclear gene flow. This research builds upon recent studies suggesting that speciation is a highly complex and often non-bifurcating process in which introgression can have a profound and lasting signature on the nuclear evolutionary history. Mechanisms responsible for divergence with gene flow challenge evolutionary biologists to reevaluate our notions and definitions of species boundaries to accommodate seemingly conflicted genomic patterns within and between genomes