Abnormal Pedestrian Trajectory analysis based on arbitrary-length clustering

This papers examines the use of trajectory distance measures and clustering techniques to define normal
and abnormal trajectories in the context of pedestrian tracking in public spaces. In order to detect abnormal
trajectories, what is meant by a normal trajectory in a given scene is firstly defined. Then every trajectory
that deviates from this normality is classified as abnormal. By combining Dynamic Time Warping and a
modified K-Means algorithms for arbitrary-length data series, we have developed an algorithm for trajectory
clustering and abnormality detection. The final system performs with an overall accuracy of 83% and 75%
when tested in two different standard datasets.

Respiratory virus-associated severe acute respiratory illness (SARI) and viral clustering in Malawian children in a setting with a high prevalence of HIV, malaria and malnutrition

BACKGROUND:  We used four years of paediatric severe acute respiratory illness (SARI) sentinel surveillance in Blantyre, Malawi to identify factors associated with clinical severity and co-viral clustering.

METHODS:  From January 2011 to December 2014, 2363 children aged 3 months to 14 years presenting to hospital with SARI were enrolled. Nasopharyngeal aspirates were tested for influenza and other respiratory viruses. We assessed risk factors for clinical severity and conducted clustering analysis to identify viral clusters in children with co-viral detection.

RESULTS:  Hospital-attended influenza-positive SARI incidence was 2.0 cases per 10,000 children annually; it was highest children aged under 1 year (6.3 cases per 10,000), and HIV-infected children aged 5 to 9 years (6.0 cases per 10,000). 605 (26.8%) SARI cases had warning signs, which were positively associated with HIV infection (adjusted risk ratio [aRR]: 2.4, 95% CI: 1.4, 3.9), RSV infection (aRR: 1.9, 95% CI: 1.3, 3.0) and rainy season (aRR: 2.4, 95% CI: 1.6, 3.8). We identified six co-viral clusters; one cluster was associated with SARI with warning signs.

CONCLUSIONS:  Influenza vaccination may benefit young children and HIV infected children in this setting. Viral clustering may be associated with SARI severity; its assessment should be included in routine SARI surveillance.

Clustering-based Query Routing in Cooperative Semi-structured Peer to Peer Networks

We consider the problem of resource selection in clustered Peer-to-Peer Information Retrieval (P2P IR) networks with cooperative peers. The clustered P2P IR framework presents a significant departure from general P2P IR architectures by employing clustering to ensure content coherence between resources at the resource selection layer, without disturbing document allocation. We propose that such a property could be leveraged in resource selection by adapting well-studied and popular inverted lists for centralized document retrieval. Accordingly, we propose the Inverted PeerCluster Index (IPI), an approach that adapts the inverted lists, in a straightforward manner, for resource selection in clustered P2P IR. IPI also encompasses a strikingly simple peer-specific scoring mechanism that exploits the said index for resource selection. Through an extensive empirical analysis on P2P IR testbeds, we establish that IPI competes well with the sophisticated state-of-the-art methods in virtually every parameter of interest for the resource selection task, in the context of clustered P2P IR.

LDA-TM : A two-step approach to twitter topic data clustering

The Twitter System is the biggest social network in the world, and everyday millions of tweets are posted and talked about, expressing various views and opinions. A large variety of research activities have been conducted to study how the opinions can be clustered and analyzed, so that some tendencies can be uncovered. Due to the inherent weaknesses of the tweets - very short texts and very informal styles of writing - it is rather hard to make an investigation of tweet data analysis giving results with good performance and accuracy. In this paper, we intend to attack the problem from another aspect - using a two-layer structure to analyze the twitter data: LDA with topic map modelling. The experimental results demonstrate that this approach shows a progress in twitter data analysis. However, more experiments with this method are expected in order to ensure that the accurate analytic results can be maintained.

A New Clustering Methodology for the Analysis of Sorted or Categorized Stimuli

This paper introduces a new stochastic clustering methodology devised for the analysis of categorized or sorted data. The methodology reveals consumers' common category knowledge as well as individual differences in using this knowledge for classifying brands in a designated product class. A small study involving the categorization of 28 brands of U.S. automobiles is presented where the results of the proposed methodology are compared with those obtained from KMEANS clustering. Finally, directions for future research are discussed.

Search Based Clustering for Protecting Software with Diversified Updates

Reverse engineering is usually the stepping stone of a variety of at-tacks aiming at identifying sensitive information (keys, credentials, data, algo-rithms) or vulnerabilities and flaws for broader exploitation. Software applica-tions are usually deployed as identical binary code installed on millions of com-puters, enabling an adversary to develop a generic reverse-engineering strategy that, if working on one code instance, could be applied to crack all the other in-stances. A solution to mitigate this problem is represented by Software Diversity, which aims at creating several structurally different (but functionally equivalent) binary code versions out of the same source code, so that even if a successful attack can be elaborated for one version, it should not work on a diversified ver-sion. In this paper, we address the problem of maximizing software diversity from a search-based optimization point of view. The program to protect is subject to a catalogue of transformations to generate many candidate versions. The problem of selecting the subset of most diversified versions to be deployed is formulated as an optimisation problem, that we tackle with different search heuristics. We show the applicability of this approach on some popular Android apps.

Clustering through post inhibitory rebound in synaptically coupled neurons

Post inhibitory rebound is a nonlinear phenomenon present in a variety of nerve cells. Following a period of hyper-polarization this effect allows a neuron to fire a spike or packet of spikes before returning to rest. It is an important mechanism underlying central pattern generation for heartbeat, swimming and other motor patterns in many neuronal systems. In this paper we consider how networks of neurons, which do not intrinsically oscillate, may make use of inhibitory synaptic connections to generate large scale coherent rhythms in the form of cluster states. We distinguish between two cases i) where the rebound mechanism is due to anode break excitation and ii) where rebound is due to a slow T-type calcium current. In the former case we use a geometric analysis of a McKean type model to obtain expressions for the number of clusters in terms of the speed and strength of synaptic coupling. Results are found to be in good qualitative agreement with numerical simulations of the more detailed Hodgkin-Huxley model. In the second case we consider a particular firing rate model of a neuron with a slow calcium current that admits to an exact analysis. Once again existence regions for cluster states are explicitly calculated. Both mechanisms are shown to prefer globally synchronous states for slow synapses as long as the strength of coupling is sufficiently large. With a decrease in the duration of synaptic inhibition both systems are found to break into clusters. A major difference between the two mechanisms for cluster generation is that anode break excitation can support clusters with several groups, whilst slow T-type calcium currents predominantly give rise to clusters of just two (anti-synchronous) populations.

Hierarchical clustering with multiple-height branch-cut applied to short time-series gene expression data.

Rigid adherence to pre-specified thresholds and static graphical representations can lead to incorrect decisions on merging of clusters. As an alternative to existing automated or semi-automated methods, we developed a visual analytics approach for performing hierarchical clustering analysis of short time-series gene expression data. Dynamic sliders control parameters such as the similarity threshold at which clusters are merged and the level of relative intra-cluster distinctiveness, which can be used to identify "weak-edges" within clusters. An expert user can drill down to further explore the dendrogram and detect nested clusters and outliers. This is done by using the sliders and by pointing and clicking on the representation to cut the branches of the tree in multiple-heights. A prototype of this tool has been developed in collaboration with a small group of biologists for analysing their own datasets. Initial feedback on the tool has been positive.

Neuropsychiatric disease (NPD) clustering in families with Autism Spectrum Disorder (ASD): genetic, epigenetic and environmental issues

Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder characterized by deficits in social communication/interaction and by unusual repetitive and restricted behaviors and interests. ASD often co-occurs in the same families with other neuropsychiatric diseases (NPD), such as intellectual disability, schizophrenia, epilepsy, depression and attention deficit hyperactivity disorder. Genetic factors have an important role in ASD etiology. Multiple copy number variants (CNVs) and single nucleotide variants (SNVs) in candidate genes have been associated with an increased risk to develop ASD. Nevertheless, recent heritability estimates and the high genotypic and phenotypic heterogeneity characteristic of ASD indicate a role of environmental and epigenetic factors, such as long noncoding RNA (lncRNA) and microRNA (miRNA), as modulators of genetic expression and further clinical presentation. Both miRNA and lncRNA are functional RNA molecules that are transcribed from DNA but not translated into proteins, instead they act as powerful regulators of gene expression. While miRNA are small noncoding RNAs with 22-25 nucleotides in length that act at the post-transcriptional level of gene expression, the lncRNA are bigger molecules (>200 nucleotides in length) that are capped, spliced, and polyadenylated, similar to messenger RNA. Although few lncRNA were well characterized until date, there is a great evidence that they are implicated in several levels of gene expression (transcription/post-transcription/post-translation, organization of protein complexes, cell– cell signaling as well as recombination) as shown in figure 1.

Mathematical models for cellular aggregation: the chemotactic instability and clustering formation

In this thesis we present a mathematical formulation of the interaction between microorganisms such as bacteria or amoebae and chemicals, often produced by the organisms themselves. This interaction is called chemotaxis and leads to cellular aggregation. We derive some models to describe chemotaxis. The first is the pioneristic Keller-Segel parabolic-parabolic model and it is derived by two different frameworks: a macroscopic perspective and a microscopic perspective, in which we start with a stochastic differential equation and we perform a mean-field approximation. This parabolic model may be generalized by the introduction of a degenerate diffusion parameter, which depends on the density itself via a power law. Then we derive a model for chemotaxis based on Cattaneo's law of heat propagation with finite speed, which is a hyperbolic model. The last model proposed here is a hydrodynamic model, which takes into account the inertia of the system by a friction force. In the limit of strong friction, the model reduces to the parabolic model, whereas in the limit of weak friction, we recover a hyperbolic model. Finally, we analyze the instability condition, which is the condition that leads to aggregation, and we describe the different kinds of aggregates we may obtain: the parabolic models lead to clusters or peaks whereas the hyperbolic models lead to the formation of network patterns or filaments. Moreover, we discuss the analogy between bacterial colonies and self gravitating systems by comparing the chemotactic collapse and the gravitational collapse (Jeans instability).

Clustering of tau-immunoreactive pathology in chronic traumatic encephalopathy

Chronic traumatic encephalopathy (CTE) is a neurodegenerative disorder which may result from repetitive brain injury. A variety of tau-immunoreactive pathologies are present, including neurofibrillary tangles (NFT), neuropil threads (NT), dot-like grains (DLG), astrocytic tangles (AT), and occasional neuritic plaques (NP). In tauopathies, cellular inclusions in the cortex are clustered within specific laminae, the clusters being regularly distributed parallel to the pia mater. To determine whether a similar spatial pattern is present in CTE, clustering of the tau-immunoreactive pathology was studied in the cortex, hippocampus, and dentate gyrus in 11 cases of CTE and 7 cases of Alzheimer’s disease neuropathologic change (ADNC) without CTE. In CTE: (1) all aspects of tau-immunoreactive pathology were clustered and the clusters were frequently regularly distributed parallel to the tissue boundary, (2) clustering was similar in two CTE cases with minimal co-pathology compared with cases with associated ADNC or TDP-43 proteinopathy, (3) in a proportion of cortical gyri, estimated cluster size was similar to that of cell columns of the cortico-cortical pathways, and (4) clusters of the tau-immunoreactive pathology were infrequently spatially correlated with blood vessels. The NFT and NP in ADNC without CTE were less frequently randomly or uniformly distributed and more frequently in defined clusters than in CTE. Hence, the spatial pattern of the tau-immunoreactive pathology observed in CTE is typical of the tauopathies but with some distinct differences compared to ADNC alone. The spread of pathogenic tau along anatomical pathways could be a factor in the pathogenesis of the disease.

Clustering of Rab11 vesicles in influenza A virus infected cells creates hotspots containing the 8 viral ribonucleoproteins

Influenza A virus is an important human pathogen causative of yearly epidemics and occasional pandemics. The ability to replicate within the host cell is a determinant of virulence, amplifying viral numbers for host-to-host transmission. This process requires multiple rounds of entering permissive cells, replication, and virion assembly at the plasma membrane, the site of viral budding and release. The assembly of influenza A virus involves packaging of several viral (and host) proteins and of a segmented genome, composed of 8 distinct RNAs in the form of viral ribonucleoproteins (vRNPs). The selective assembly of the 8-segment core remains one of the most interesting unresolved problems in virology. The recycling endosome regulatory GTPase Rab11 was shown to contribute to the process, by transporting vRNPs to the periphery, giving rise to enlarged cytosolic puncta rich in Rab11 and the 8 vRNPs. We recently reported that vRNP hotspots were formed of clustered vesicles harbouring protruding electron-dense structures that resembled vRNPs. Mechanistically, vRNP hotspots were formed as vRNPs outcompeted the cognate effectors of Rab11, the Rab11-Family-Interacting-Proteins (FIPs) for binding, and as a consequence impair recycling sorting at an unknown step. Here, we speculate on the impact that such impairment might have in host immunity, membrane architecture and viral assembly.

Travelers’ use of social media: A clustering approach

Research regarding the use of social media among travelers has mainly focused on its impact on travelers’ travel planning process and there is consensus that travel decisions are highly influenced by social media. Yet, little attention has been paid to the differences among travelers regarding their use of social media for travel purposes. Based on the use of travel social media, cluster analysis was employed to identify different segments among travelers. Furthermore, the study profiles the clusters based on demographic and other travel related characteristics. The findings of this study are important to online marketers to better understand traveler’s use of social media and their characteristics, in order to adapt online marketing strategies according to the profile of each segment.

Travelers’ use of social media: A clustering approach

Research regarding the use of social media among travelers has mainly focused on its impact on travelers’ travel planning process and there is consensus that travel decisions are highly influenced by social media. Yet, little attention has been paid to the differences among travelers regarding their use of social media for travel purposes. Based on the use of travel social media, cluster analysis was employed to identify different segments among travelers. Furthermore, the study profiles the clusters based on demographic and other travel related characteristics. The findings of this study are important to online marketers to better understand traveler’s use of social media and their characteristics, in order to adapt online marketing strategies according to the profile of each segment.