Partially Observable Markov Decision Process Modelling for Assessing Hierarchies

Hierarchical clustering has been shown to be valuable in many scenarios. Despite its usefulness to many situations, there is no agreed methodology on how to properly evaluate the hierarchies produced from different techniques, particularly in the case where ground-truth labels are unavailable. This motivates us to propose a framework for assessing the quality of hierarchical clustering allocations which covers the case of no ground-truth information. This measurement is useful, e.g., to assess the hierarchical structures used by online retailer websites to display their product catalogues. Our framework is one of the few attempts for the hierarchy evaluation from a decision-theoretic perspective. We model the process as a bot searching stochastically for items in the hierarchy and establish a measure representing the degree to which the hierarchy supports this search. We employ Partially Observable Markov Decision Processes (POMDP) to model the uncertainty, the decision making, and the cognitive return for searchers in such a scenario

Seeding for pervasively overlapping communities

In some social and biological networks, the majority of nodes belong to multiple communities. It has recently been shown that a number of the algorithms that are designed to detect overlapping communities do not perform well in such highly overlapping settings. Here, we consider one class of these algorithms, those which optimize a local fitness measure, typically by using a greedy heuristic to expand a seed into a community. We perform synthetic benchmarks which indicate that an appropriate seeding strategy becomes increasingly important as the extent of community overlap increases. We find that distinct cliques provide the best seeds. We find further support for this seeding strategy with benchmarks on a Facebook network and the yeast interactome.Comment: 8 Page

Structural Hole Centrality: Evaluating Social Capital through Strategic Network Formation

Strategic network formation is a branch of network science that takes an economic perspective to the creation of social networks, considering that actors in a network form links in order to maximise some utility that they attain through their connections to other actors in the network. In particular, Jackson’s Connections model, writes an actor’s utility as a sum over all other actors that can be reached along a path in the network of a benefit value that diminishes with the path length. In this paper, we are interested in the “social capital” that an actor retains due to their position in the network. Social capital can be understood as an ability to bond with actors, as well as an ability to form a bridge that connects otherwise disconnected actors. This bridging benefit has previously been modelled in another “structural hole” network formation game, proposed by Kleinberg. In this paper, we develop an approach that generalises the utility of Kleinberg’s game and combines it with that of the Connections model, to create a utility that models both the bonding and bridging capabilities of an actor with social capital. From this utility and its associated formation game, we derive a new centrality measure, which we dub “structural hole centrality”, to identify actors with high social capital. We analyse this measure by applying it to networks of different types, and assessing its correlation to other centrality metrics, using a benchmark dataset of 299 networks, drawn from different domains. Finally, using one social network from the dataset, we illustrate how an actor’s “structural hole centrality profile” can be used to identify their bridging and bonding value to the network.Science Foundation IrelandInsight Research Centre2020-10-06 JG: PDF replaced with correct versio

Posterior Regularization on Bayesian Hierarchical Mixture Clustering

Bayesian hierarchical mixture clustering (BHMC) improves on the traditional Bayesian hierarchical clustering by, with regard to the parent-to-child diffusion in the generative process, replacing the conventional Gaussian-to-Gaussian (G2G) kernels with a Hierarchical Dirichlet Process Mixture Model (HDPMM). However, the drawback of the BHMC lies in the possibility of obtaining trees with comparatively high nodal variance in the higher levels (i.e., those closer to the root node). This can be interpreted as that the separation between the nodes, particularly those in the higher levels, might be weak. We attempt to overcome this drawback through a recent inferential framework named posterior regularization, which facilitates a simple manner to impose extra constraints on a Bayesian model to address its weakness. To enhance the separation of clusters, we apply posterior regularization to impose max-margin constraints on the nodes at every level of the hierarchy. In this paper, we illustrate the modeling detail of applying the PR on BHMC and show that this solution achieves the desired improvements over the BHMC model

Simple, Direct Routes to Polymer Brush Traps and Nanostructures for Studies of Diffusional Transport in Supported Lipid Bilayers

Patterned poly(oligo ethylene glycol) methyl ether methacrylate (POEGMEMA) brush structures may be formed by using a combination of atom-transfer radical polymerization (ATRP) and UV photopatterning. UV photolysis is used to selectively dechlorinate films of 4-(chloromethyl)phenyltrichlorosilane (CMPTS) adsorbed on silica surfaces, by exposure either through a mask or using a two-beam interferometer. Exposure through a mask yields patterns of carboxylic acid-terminated adsorbates. POEGMEMA may be grown from intact Cl initiators that were masked during exposure. Corrals, traps, and other structures formed in this way enable the patterning of proteins, vesicles, and, following vesicle rupture, supported lipid bilayers (SLBs). Bilayers adsorbed on the carboxylic acid-terminated surfaces formed by C–Cl bond photolysis in CMPTS exhibit high mobility. SLBs do not form on POEGMEMA. Using traps consisting of carboxylic acid-functionalized regions enclosed by POEGMEMA structures, electrophoresis may be observed in lipid bilayers containing a small amount of a fluorescent dye. Segregation of dye at one end of the traps was measured by fluorescence microscopy. The increase in the fluorescence intensity was found to be proportional to the trap length, while the time taken to reach the maximum value was inversely proportional to the trap length, indicating uniform, rapid diffusion in all of the traps. Nanostructured materials were formed using interferometric lithography. Channels were defined by exposure of CMPTS films to maxima in the interferogram, and POEGMEMA walls were formed by ATRP. As for the micrometer-scale patterns, bilayers did not form on the POEGMEMA structures, and high lipid mobilities were measured in the polymer-free regions of the channels

The RING-CH ligase K5 antagonizes restriction of KSHV and HIV-1 particle release by mediating ubiquitin-dependent endosomal degradation of tetherin

Tetherin (CD317/BST2) is an interferon-induced membrane protein that inhibits the release of diverse enveloped viral particles. Several mammalian viruses have evolved countermeasures that inactivate tetherin, with the prototype being the HIV-1 Vpu protein. Here we show that the human herpesvirus Kaposi's sarcoma-associated herpesvirus (KSHV) is sensitive to tetherin restriction and its activity is counteracted by the KSHV encoded RING-CH E3 ubiquitin ligase K5. Tetherin expression in KSHV-infected cells inhibits viral particle release, as does depletion of K5 protein using RNA interference. K5 induces a species-specific downregulation of human tetherin from the cell surface followed by its endosomal degradation. We show that K5 targets a single lysine (K18) in the cytoplasmic tail of tetherin for ubiquitination, leading to relocalization of tetherin to CD63-positive endosomal compartments. Tetherin degradation is dependent on ESCRT-mediated endosomal sorting, but does not require a tyrosine-based sorting signal in the tetherin cytoplasmic tail. Importantly, we also show that the ability of K5 to substitute for Vpu in HIV-1 release is entirely dependent on K18 and the RING-CH domain of K5. By contrast, while Vpu induces ubiquitination of tetherin cytoplasmic tail lysine residues, mutation of these positions has no effect on its antagonism of tetherin function, and residual tetherin is associated with the trans-Golgi network (TGN) in Vpu-expressing cells. Taken together our results demonstrate that K5 is a mechanistically distinct viral countermeasure to tetherin-mediated restriction, and that herpesvirus particle release is sensitive to this mode of antiviral inhibition