Finding groups in data: Cluster analysis with ants

Wepresent in this paper a modification of Lumer and Faieta’s algorithm for data clustering. This approach mimics the clustering behavior observed in real ant colonies. This algorithm discovers automatically clusters in numerical data without prior knowledge of possible number of clusters. In this paper we focus on ant-based clustering algorithms, a particular kind of a swarm intelligent system, and on the effects on the final clustering by using during the classification differentmetrics of dissimilarity: Euclidean, Cosine, and Gower measures. Clustering with swarm-based algorithms is emerging as an alternative to more conventional clustering methods, such as e.g. k-means, etc. Among the many bio-inspired techniques, ant clustering algorithms have received special attention, especially because they still require much investigation to improve performance, stability and other key features that would make such algorithms mature tools for data mining. As a case study, this paper focus on the behavior of clustering procedures in those new approaches. The proposed algorithm and its modifications are evaluated in a number of well-known benchmark datasets. Empirical results clearly show that ant-based clustering algorithms performs well when compared to another techniques

Fast training of self organizing maps for the visual exploration of molecular compounds

Visual exploration of scientific data in life science area is a growing research field due to the large amount of available data. The Kohonen’s Self Organizing Map (SOM) is a widely used tool for visualization of multidimensional data. In this paper we present a fast learning algorithm for SOMs that uses a simulated annealing method to adapt the learning parameters. The algorithm has been adopted in a data analysis framework for the generation of similarity maps. Such maps provide an effective tool for the visual exploration of large and multi-dimensional input spaces. The approach has been applied to data generated during the High Throughput Screening of molecular compounds; the generated maps allow a visual exploration of molecules with similar topological properties. The experimental analysis on real world data from the National Cancer Institute shows the speed up of the proposed SOM training process in comparison to a traditional approach. The resulting visual landscape groups molecules with similar chemical properties in densely connected regions

Multi-membership gene regulation in pathway based microarray analysis

This article is available through the Brunel Open Access Publishing Fund. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Background: Gene expression analysis has been intensively researched for more than a decade. Recently, there has been elevated interest in the integration of microarray data analysis with other types of biological knowledge in a holistic analytical approach. We propose a methodology that can be facilitated for pathway based microarray data analysis, based on the observation that a substantial proportion of genes present in biochemical pathway databases are members of a number of distinct pathways. Our methodology aims towards establishing the state of individual pathways, by identifying those truly affected by the experimental conditions based on the behaviour of such genes. For that purpose it considers all the pathways in which a gene participates and the general census of gene expression per pathway. Results: We utilise hill climbing, simulated annealing and a genetic algorithm to analyse the consistency of the produced results, through the application of fuzzy adjusted rand indexes and hamming distance. All algorithms produce highly consistent genes to pathways allocations, revealing the contribution of genes to pathway functionality, in agreement with current pathway state visualisation techniques, with the simulated annealing search proving slightly superior in terms of efficiency. Conclusions: We show that the expression values of genes, which are members of a number of biochemical pathways or modules, are the net effect of the contribution of each gene to these biochemical processes. We show that by manipulating the pathway and module contribution of such genes to follow underlying trends we can interpret microarray results centred on the behaviour of these genes.The work was sponsored by the studentship scheme of the School of Information Systems, Computing and Mathematics, Brunel Universit

Multi-Level Visual Alphabets

A central debate in visual perception theory is the argument for indirect versus direct perception; i.e., the use of intermediate, abstract, and hierarchical representations versus direct semantic interpretation of images through interaction with the outside world. We present a content-based representation that combines both approaches. The previously developed Visual Alphabet method is extended with a hierarchy of representations, each level feeding into the next one, but based on features that are not abstract but directly relevant to the task at hand. Explorative benchmark experiments are carried out on face images to investigate and explain the impact of the key parameters such as pattern size, number of prototypes, and distance measures used. Results show that adding an additional middle layer improves results, by encoding the spatial co-occurrence of lower-level pattern prototypes

Transfer Learning via Contextual Invariants for One-to-Many Cross-Domain Recommendation

The rapid proliferation of new users and items on the social web has aggravated the gray-sheep user/long-tail item challenge in recommender systems. Historically, cross-domain co-clustering methods have successfully leveraged shared users and items across dense and sparse domains to improve inference quality. However, they rely on shared rating data and cannot scale to multiple sparse target domains (i.e., the one-to-many transfer setting). This, combined with the increasing adoption of neural recommender architectures, motivates us to develop scalable neural layer-transfer approaches for cross-domain learning. Our key intuition is to guide neural collaborative filtering with domain-invariant components shared across the dense and sparse domains, improving the user and item representations learned in the sparse domains. We leverage contextual invariances across domains to develop these shared modules, and demonstrate that with user-item interaction context, we can learn-to-learn informative representation spaces even with sparse interaction data. We show the effectiveness and scalability of our approach on two public datasets and a massive transaction dataset from Visa, a global payments technology company (19% Item Recall, 3x faster vs. training separate models for each domain). Our approach is applicable to both implicit and explicit feedback settings.Comment: SIGIR 202

Latent class analysis for segmenting preferences of investment bonds

Market segmentation is a key component of conjoint analysis which addresses consumer preference heterogeneity. Members in a segment are assumed to be homogenous in their views and preferences when worthing an item but distinctly heterogenous to members of other segments. Latent class methodology is one of the several conjoint segmentation procedures that overcome the limitations of aggregate analysis and a-priori segmentation. The main benefit of Latent class models is that market segment membership and regression parameters of each derived segment are estimated simultaneously. The Latent class model presented in this paper uses mixtures of multivariate conditional normal distributions to analyze rating data, where the likelihood is maximized using the EM algorithm. The application focuses on customer preferences for investment bonds described by four attributes; currency, coupon rate, redemption term and price. A number of demographic variables are used to generate segments that are accessible and actionable.peer-reviewe