Advanced computing for systems biology

Systems biology is based on computational modelling and simulation of large networks of interacting components. Models may be intended to capture processes, mechanisms, components and interactions at different levels of fidelity. Input data are often large and geographically disperse, and may require the computation to be moved to the data, not vice versa. In addition, complex system-level problems require collaboration across institutions and disciplines. Grid computing can offer robust, scaleable solutions for distributed data, compute and expertise. We illustrate some of the range of computational and data requirements in systems biology with three case studies: one requiring large computation but small data (orthologue mapping in comparative genomics), a second involving complex terabyte data (the Visible Cell project) and a third that is both computationally and data-intensive (simulations at multiple temporal and spatial scales). Authentication, authorisation and audit systems are currently not well scalable and may present bottlenecks for distributed collaboration particularly where outcomes may be commercialised. Challenges remain in providing lightweight standards to facilitate the penetration of robust, scalable grid-type computing into diverse user communities to meet the evolving demands of systems biology.

Discovering user access pattern based on probabilistic latent factor model

There has been an increased demand for characterizing user access patterns using web mining techniques since the informative knowledge extracted from web server log files can not only offer benefits for web site structure improvement but also for better understanding of user navigational behavior. In this paper, we present a web usage mining method, which utilize web user usage and page linkage information to capture user access pattern based on Probabilistic Latent Semantic Analysis (PLSA) model. A specific probabilistic model analysis algorithm, EM algorithm, is applied to the integrated usage data to infer the latent semantic factors as well as generate user session clusters for revealing user access patterns. Experiments have been conducted on real world data set to validate the effectiveness of the proposed approach. The results have shown that the presented method is capable of characterizing the latent semantic factors and generating user profile in terms of weighted page vectors, which may reflect the common access interest exhibited by users among same session cluster.

Towards user profiling for web recommendation

Collaborative recommendation is one of widely used recommendation systems, which recommend items to visitor on a basis of referring other's preference that is similar to current user. User profiling technique upon Web transaction data is able to capture such informative knowledge of user task or interest. With the discovered usage pattern information, it is likely to recommend Web users more preferred content or customize the Web presentation to visitors via collaborative recommendation. In addition, it is helpful to identify the underlying relationships among Web users, items as well as latent tasks during Web mining period. In this paper, we propose a Web recommendation framework based on user profiling technique. In this approach, we employ Probabilistic Latent Semantic Analysis (PLSA) to model the co-occurrence activities and develop a modified k-means clustering algorithm to build user profiles as the representatives of usage patterns. Moreover, the hidden task model is derived by characterizing the meaningful latent factor space. With the discovered user profiles, we then choose the most matched profile, which possesses the closely similar preference to current user and make collaborative recommendation based on the corresponding page weights appeared in the selected user profile. The preliminary experimental results performed on real world data sets show that the proposed approach is capable of making recommendation accurately and efficiently.