A new linear initialization in SOM for biomolecular data

In the past decade, the amount of data in biological field has become larger and larger; Bio-techniques for analysis of biological data have been developed and new tools have been introduced. Several computational methods are based on unsupervised neural network algorithms that are widely used for multiple purposes including clustering and visualization, i.e. the Self Organizing Maps (SOM). Unfortunately, even though this method is unsupervised, the performances in terms of quality of result and learning speed are strongly dependent from the neuron weights initialization. In this paper we present a new initialization technique based on a totally connected undirected graph, that report relations among some intersting features of data input. Result of experimental tests, where the proposed algorithm is compared to the original initialization techniques, shows that our technique assures faster learning and better performance in terms of quantization error.

High performance subgraph mining in molecular compounds

Structured data represented in the form of graphs arises in several fields of the science and the growing amount of available data makes distributed graph mining techniques particularly relevant. In this paper, we present a distributed approach to the frequent subgraph mining problem to discover interesting patterns in molecular compounds. The problem is characterized by a highly irregular search tree, whereby no reliable workload prediction is available. We describe the three main aspects of the proposed distributed algorithm, namely a dynamic partitioning of the search space, a distribution process based on a peer-to-peer communication framework, and a novel receiver-initiated, load balancing algorithm. The effectiveness of the distributed method has been evaluated on the well-known National Cancer Institute’s HIV-screening dataset, where the approach attains close-to linear speedup in a network of workstations.

Design for design: support for creative practice in computer-supported collaborative work (CSCW) in design

This paper describes a novel methodology for observing and analysing collaborative design by using the concepts of cognitive dimensions related to concept-based misfit analysis. The study aims at gaining an insight into support for creative practice of graphical communication in collaborative design processes of designers while sketching within a shared white board and audio conferencing environment. Empirical data on design processes have been obtained from observation of groups of student designers solving an interior space-planning problem of a lounge-diner in a shared virtual environment. The results of the study provide recommendations for the design and development of interactive systems to support such collaborative design activities.

Automated pre-processing strategies for species occurrence data used in biodiversity modelling

To construct Biodiversity richness maps from Environmental Niche Models (ENMs) of thousands of species is time consuming. A separate species occurrence data pre-processing phase enables the experimenter to control test AUC score variance due to species dataset size. Besides, removing duplicate occurrences and points with missing environmental data, we discuss the need for coordinate precision, wide dispersion, temporal and synonymity filters. After species data filtering, the final task of a pre-processing phase should be the automatic generation of species occurrence datasets which can then be directly ’plugged-in’ to the ENM. A software application capable of carrying out all these tasks will be a valuable time-saver particularly for large scale biodiversity studies.

Integrating constructive feedback in personalised e-learning

When using e-learning material some students progress readily, others have difficulties. In a traditional classroom the teacher would identify those with difficulties and direct them to additional resources. This support is not easily available within e-learning. A new approach to providing constructive feedback is developed that will enable an e-learning system to identify areas of weakness and provide guidance on further study. The approach is based on the tagging of learning material with appropriate keywords that indicate the contents. Thus if a student performs poorly on an assessment on topic X, there is a need to suggest further study of X and participation in activities related to X such as forums. As well as supporting the learner this type of constructive feedback can also inform other stakeholders. For example a tutor can monitor the progress of a cohort; an instructional designer can monitor the quality of learning objects in facilitating the appropriate knowledge across many learners.

A peer-to-peer approach to content dissemination and search in collaborative networks

There are three key driving forces behind the development of Internet Content Management Systems (CMS) - a desire to manage the explosion of content, a desire to provide structure and meaning to content in order to make it accessible, and a desire to work collaboratively to manipulate content in some meaningful way. Yet the traditional CMS has been unable to meet the latter of these requirements, often failing to provide sufficient tools for collaboration in a distributed context. Peer-to-Peer (P2P) systems are networks in which every node is an equal participant (whether transmitting data, exchanging content, or invoking services) and there is an absence of any centralised administrative or coordinating authorities. P2P systems are inherently more scalable than equivalent client-server implementations as they tend to use resources at the edge of the network much more effectively. This paper details the rationale and design of a P2P middleware for collaborative content management.

A Design for Generating Personalised Feedback in Knowledge Construction

As the learning paradigm shifts to a more personalised learning process, users need dynamic feedback from their knowledge path. Learning Management Systems (LMS) offer customised feedback dependent on questions and the answers given. However these LMSs are not designed to generate personalised feedback for an individual learner, tutor and instructional designer. This paper presents an approach for generating constructive feedback for all stakeholders during a personalised learning process. The dynamic personalised feedback model generates feedback based on the learning objectives for the Learning Object. Feedback can be generated at Learning Object level and the Information Object level for both the individual learner and the group. The group feedback is meant for the tutors and instructional designer to improve the learning process.

Significance tests in climate science

A large fraction of papers in the climate literature includes erroneous uses of significance tests. A Bayesian analysis is presented to highlight the meaning of significance tests and why typical misuse occurs. The significance statistic is not a quantitative measure of how confident we can be of the ‘reality’ of a given result. It is concluded that a significance test very rarely provides useful quantitative information.

Efficient on the fly calculation of time correlation functions in computer simulations

Time correlation functions yield profound information about the dynamics of a physical system and hence are frequently calculated in computer simulations. For systems whose dynamics span a wide range of time, currently used methods require significant computer time and memory. In this paper, we discuss the multiple-tau correlator method for the efficient calculation of accurate time correlation functions on the fly during computer simulations. The multiple-tau correlator is efficacious in terms of computational requirements and can be tuned to the desired level of accuracy. Further, we derive estimates for the error arising from the use of the multiple-tau correlator and extend it for use in the calculation of mean-square particle displacements and dynamic structure factors. The method described here, in hardware implementation, is routinely used in light scattering experiments but has not yet found widespread use in computer simulations.