Defining Bonferroni means over lattices

In the face of mass amounts of information and the need for transparent and fair decision processes, aggregation functions are essential for summarizing data and providing overall evaluations. Although families such as weighted means and medians have been well studied, there are still applications for which no existing aggregation functions can capture the decision makers' preferences. Furthermore, extensions of aggregation functions to lattices are often needed to model operations on L-fuzzy sets, interval-valued and intuitionistic fuzzy sets. In such cases, the aggregation properties need to be considered in light of the lattice structure, as otherwise counterintuitive or unreliable behavior may result. The Bonferroni mean has recently received attention in the fuzzy sets and decision making community as it is able to model useful notions such as mandatory requirements. Here, we consider its associated penalty function to extend the generalized Bonferroni mean to lattices. We show that different notions of dissimilarity on lattices can lead to alternative expressions.

Using linear programming for weights identification of generalized bonferroni means in R

The generalized Bonferroni mean is able to capture some interaction effects between variables and model mandatory requirements. We present a number of weights identification algorithms we have developed in the R programming language in order to model data using the generalized Bonferroni mean subject to various preferences. We then compare its accuracy when fitting to the journal ranks dataset.

A generalization of the Bonferroni mean based on partitions

The mean defined by Bonferroni in 1950 (known by the same name) averages all non-identical product pairs of the inputs. Its generalizations to date have been able to capture unique behavior that may be desired in some decision-making contexts such as the ability to model mandatory requirements. In this paper, we propose a composition that averages conjunctions between the respective means of a designated subset-size partition. We investigate the behavior of such a function and note the relationship within a given family as the subset size is changed. We found that the proposed function is able to more intuitively handle multiple mandatory requirements or mandatory input sets.

On some properties of weighted averaging with variable weights

Density-based means have been recently proposed as a method for dealing with outliers in the stream processing of data. Derived from a weighted arithmetic mean with variable weights that depend on the location of all data samples, these functions are not monotonic and hence cannot be classified as aggregation functions. In this article we establish the weak monotonicity of this class of averaging functions and use this to establish robust generalisations of these means. Specifically, we find that as proposed, the density based means are only robust to isolated outliers. However, by using penalty based formalisms of averaging functions and applying more sophisticated and robust density estimators, we are able to define a broader family of density based means that are more effective at filtering both isolated and clustered outliers. © 2014 Elsevier Inc. All rights reserved.

Can indices of ecological evenness be used to measure consensus?

In the context of group decision making with fuzzy preferences, consensus measures are employed to provide feedback and help guide automatic or semi-automatic decision reaching processes. These measures attempt to capture the intuitive notion of how much inputs, individuals or groups agree with one another. Meanwhile, in ecological studies there has been an ongoing research effort to define measures of community evenness based on how evenly the proportional abundances of species are distributed. The question hence arises as to whether there can be any cross-fertilization from developments in these fields given their intuitive similarity. Here we investigate some of the models used in ecology toward their potential use in measuring consensus. We found that although many consensus characteristics are exhibited by evenness indices, lack of reciprocity and a tendency towards a minimum when a single input is non-zero would make them undesirable for inputs expressed on an interval scale. On the other hand, we note that some of the general frameworks could still be useful for other types of inputs like ranking profiles and that in the opposite direction consensus measures have the potential to provide new insights in ecology.

Characterizing compactness of geometrical clusters using fuzzy measures

Certain tasks in image processing require the preservation of fine image details, while applying a broad operation to the image, such as image reduction, filtering, or smoothing. In such cases, the objects of interest are typically represented by small, spatially cohesive clusters of pixels which are to be preserved or removed, depending on the requirements. When images are corrupted by the noise or contain intensity variations generated by imaging sensors, identification of these clusters within the intensity space is problematic as they are corrupted by outliers. This paper presents a novel approach to accounting for spatial organization of the pixels and to measuring the compactness of pixel clusters based on the construction of fuzzy measures with specific properties: monotonicity with respect to the cluster size; invariance with respect to translation, reflection, and rotation; and discrimination between pixel sets of fixed cardinality with different spatial arrangements. We present construction methods based on Sugeno-type fuzzy measures, minimum spanning trees, and fuzzy measure decomposition. We demonstrate their application to generating fuzzy measures on real and artificial images.

Extension of bivariate means to weighted means of several arguments by using binary trees

ABSTRACTAveraging aggregation functions are valuable in building decision making and fuzzy logic systems and in handling uncertainty. Some interesting classes of averages are bivariate and not easily extended to the multivariate case. We propose a generic method for extending bivariate symmetric means to n-variate weighted means by recursively applying the specified bivariate mean in a binary tree construction. We prove that the resulting extension inherits many desirable properties of the base mean and design an efficient numerical algorithm by pruning the binary tree. We show that the proposed method is numerically competitive to the explicit analytical formulas and hence can be used in various computational intelligence systems which rely on aggregation functions.

Improving tenants' trust in SaaS applications using dynamic security monitors

It is almost impossible to prove that a given software system achieves an absolute security level. This becomes more complicated when addressing multi-tenant cloud-based SaaS applications. Developing practical security properties and metrics to monitor, verify, and assess the behavior of such software systems is a feasible alternative to such problem. However, existing efforts focus either on verifying security properties or security metrics but not both. Moreover, they are either hard to adopt, in terms of usability, or require design-time preparation to support monitoring of such security metrics and properties which is not feasible for SaaS applications. In this paper, we introduce, to the best of our knowledge, the first unified monitoring platform that enables SaaS application tenants to specify, at run-time, security metrics and properties without design-time preparation and hence increases tenants’ trust of their cloud-assets security. The platform automatically converts security metrics and properties specifications into security probes and integrates them with the target SaaS application at run-time. Probes-generated measurements are fed into an analysis component that verifies the specified properties and calculates security metrics’ values using aggregation functions. This is then reported to SaaS tenants and cloud platform security engineers. We evaluated our platform expressiveness and usability, soundness, and performance overhead.

Learning stable weights for data of varying dimension

In this paper we develop a data-driven weight learning method for weighted quasi-arithmetic means where the observed data may vary in dimension.

Distinguishing between mechanisms of cell aggregation using pair-correlation functions

Many cell types form clumps or aggregates when cultured in vitro through a variety of mechanisms including rapid cell proliferation, chemotaxis, or direct cell-to-cell contact. In this paper we develop an agent-based model to explore the formation of aggregates in cultures where cells are initially distributed uniformly, at random, on a two-dimensional substrate. Our model includes unbiased random cell motion, together with two mechanisms which can produce cell aggregates: (i) rapid cell proliferation, and (ii) a biased cell motility mechanism where cells can sense other cells within a finite range, and will tend to move towards areas with higher numbers of cells. We then introduce a pair-correlation function which allows us to quantify aspects of the spatial patterns produced by our agent-based model. In particular, these pair-correlation functions are able to detect differences between domains populated uniformly at random (i.e. at the exclusion complete spatial randomness (ECSR) state) and those where the proliferation and biased motion rules have been employed - even when such differences are not obvious to the naked eye. The pair-correlation function can also detect the emergence of a characteristic inter-aggregate distance which occurs when the biased motion mechanism is dominant, and is not observed when cell proliferation is the main mechanism of aggregate formation. This suggests that applying the pair-correlation function to experimental images of cell aggregates may provide information about the mechanism associated with observed aggregates. As a proof of concept, we perform such analysis for images of cancer cell aggregates, which are known to be associated with rapid proliferation. The results of our analysis are consistent with the predictions of the proliferation-based simulations, which supports the potential usefulness of pair correlation functions for providing insight into the mechanisms of aggregate formation.

Predicting protein functions from PPI networks using functional aggregation

Predicting protein functions computationally from massive protein–protein interaction (PPI) data generated by high-throughput technology is one of the challenges and fundamental problems in the post-genomic era. Although there have been many approaches developed for computationally predicting protein functions, the mutual correlations among proteins in terms of protein functions have not been thoroughly investigated and incorporated into existing prediction methods, especially in voting based prediction methods. In this paper, we propose an innovative method to predict protein functions from PPI data by aggregating the functional correlations among relevant proteins using the Choquet-Integral in fuzzy theory. This functional aggregation measures the real impact of each relevant protein function on the final prediction results, and reduces the impact of repeated functional information on the prediction. Accordingly, a new protein similarity and a new iterative prediction algorithm are proposed in this paper. The experimental evaluations on real PPI datasets demonstrate the effectiveness of our method.

Quantifying spatial structure in experimental observations and agent-based simulations using pair-correlation functions

We define a pair-correlation function that can be used to characterize spatiotemporal patterning in experimental images and snapshots from discrete simulations. Unlike previous pair-correlation functions, the pair-correlation functions developed here depend on the location and size of objects. The pair-correlation function can be used to indicate complete spatial randomness, aggregation or segregation over a range of length scales, and quantifies spatial structures such as the shape, size and distribution of clusters. Comparing pair-correlation data for various experimental and simulation images illustrates their potential use as a summary statistic for calibrating discrete models of various physical processes.

Scalable Preference Aggregation in Social Networks

In social choice theory, preference aggregation refers to computing an aggregate preference over a set of alternatives given individual preferences of all the agents. In real-world scenarios, it may not be feasible to gather preferences from all the agents. Moreover, determining the aggregate preference is computationally intensive. In this paper, we show that the aggregate preference of the agents in a social network can be computed efficiently and with sufficient accuracy using preferences elicited from a small subset of critical nodes in the network. Our methodology uses a model developed based on real-world data obtained using a survey on human subjects, and exploits network structure and homophily of relationships. Our approach guarantees good performance for aggregation rules that satisfy a property which we call expected weak insensitivity. We demonstrate empirically that many practically relevant aggregation rules satisfy this property. We also show that two natural objective functions in this context satisfy certain properties, which makes our methodology attractive for scalable preference aggregation over large scale social networks. We conclude that our approach is superior to random polling while aggregating preferences related to individualistic metrics, whereas random polling is acceptable in the case of social metrics.

Novel Functions of (p)ppGpp and Cyclic di-GMP in Mycobacterial Physiology Revealed by Phenotype Microarray Analysis of Wild-Type and Isogenic Strains of Mycobacterium smegmatis

The bacterial second messengers (p)ppGpp and bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) regulate important functions, such as transcription, virulence, biofilm formation, and quorum sensing. In mycobacteria, they regulate long-term survival during starvation, pathogenicity, and dormancy. Recently, a Pseudomonas aeruginosa strain lacking (p) ppGpp was shown to be sensitive to multiple classes of antibiotics and defective in biofilm formation. We were interested to find out whether Mycobacterium smegmatis strains lacking the gene for either (p)ppGpp synthesis (Delta rel(Msm)) or c-di-GMP synthesis (Delta dcpA) would display similar phenotypes. We used phenotype microarray technology to compare the growth of the wild-type and the knockout strains in the presence of several antibiotics. Surprisingly, the Delta rel(Msm) and Delta dcpA strains showed enhanced survival in the presence of many antibiotics, but they were defective in biofilm formation. These strains also displayed altered surface properties, like impaired sliding motility, rough colony morphology, and increased aggregation in liquid cultures. Biofilm formation and surface properties are associated with the presence of glycopeptidolipids (GPLs) in the cell walls of M. smegmatis. Thin-layer chromatography analysis of various cell wall fractions revealed that the levels of GPLs and polar lipids were reduced in the knockout strains. As a result, the cell walls of the knockout strains were significantly more hydrophobic than those of the wild type and the complemented strains. We hypothesize that reduced levels of GPLs and polar lipids may contribute to the antibiotic resistance shown by the knockout strains. Altogether, our data suggest that (p)ppGpp and c-di-GMP may be involved in the metabolism of glycopeptidolipids and polar lipids in M. smegmatis.