A Ligand predication tool based on modeling and reasoning with imprecise probabilistic knowledge

Ligand prediction has been driven by a fundamental desire to understand more about how biomolecules recognize their ligands and by the commercial imperative to develop new drugs. Most of the current available software systems are very complex and time-consuming to use. Therefore, developing simple and efficient tools to perform initial screening of interesting compounds is an appealing idea. In this paper, we introduce our tool for very rapid screening for likely ligands (either substrates or inhibitors) based on reasoning with imprecise probabilistic knowledge elicited from past experiments. Probabilistic knowledge is input to the system via a user-friendly interface showing a base compound structure. A prediction of whether a particular compound is a substrate is queried against the acquired probabilistic knowledge base and a probability is returned as an indication of the prediction. This tool will be particularly useful in situations where a number of similar compounds have been screened experimentally, but information is not available for all possible members of that group of compounds. We use two case studies to demonstrate how to use the tool.

The Essential Role of Human Databases for Learning in and Validation of Affectively Competent Agents.

This output is an invited and refereed chapter in the second of the two book length outputs resulting from the EU HUMAINE grant and follow-on grants. The book is in the OUP Affective Science Series and is intended to provide a theoretically oriented state of the art model for those working in the area of affective computing. Each chapter provides a synthesis of a specific area and presents new data/findings/approaches developed by the author(s) which take the area further. This chapter is in the section on ‘Approaches to developing expression corpora and databases.’ The chapter provides a critical synthesis of the issues involved in databases for affective computing and introduces the SEMAINE SAL Database, developed as an integral part of the EU SEMAINE Project (The Sensitive Agent Project 2008-2011) which is an interdisciplinary project. The project aimed to develop a computer interface that would allow a human to interact with an artificial agent in an emotional manner.

Identifying functional stakeholder clusters to maximise communication for the ecosystem approach to fisheries management

Interaction with ecological models can improve stakeholder participation in fisheries management. Problems exist in efficiently communicating outputs to stakeholders and an objective method of structuring stakeholder differences is lacking. This paper aims to inform the design of a multi-user communication interface for fisheries management by identifying functional stakeholder groups. Intuitive categorisation of stakeholders, derived from survey responses, is contrasted with an Evidence-Based method derived from analysis of stakeholder literature. Intuitive categorisation relies on interpretation and professional judgement when categorising stakeholders among conventional stakeholder groups. Evidence-Based categorisation quantitatively characterises each stakeholder with a vector of four management objective interest-strength values (Yield, Employment, Profit and Ecosystem Preservation). Survey respondents agreed little in forming intuitive groups and the groups were poorly defined and heterogeneous in interests. In contrast the Evidence-Based clusters were well defined and largely homogeneous, so more useful for identifying functional relations with model outputs. The categorisations lead to two different clusterings of stakeholders and suggest unhelpful stereotyping of stakeholders may occur with the Intuitive categorisation method. Stakeholder clusters based on literature-evidence show a high degree of common interests among clusters and is encouraging for those seeking to maximise dialogue and consensus forming. © 2013 Elsevier Ltd.

Adaptive Fusion Of Particle Filtering And Spatio-Temporal Motion Energy For Human Tracking

Object tracking is an active research area nowadays due to its importance in human computer interface, teleconferencing and video surveillance. However, reliable tracking of objects in the presence of occlusions, pose and illumination changes is still a challenging topic. In this paper, we introduce a novel tracking approach that fuses two cues namely colour and spatio-temporal motion energy within a particle filter based framework. We conduct a measure of coherent motion over two image frames, which reveals the spatio-temporal dynamics of the target. At the same time, the importance of both colour and motion energy cues is determined in the stage of reliability evaluation. This determination helps maintain the performance of the tracking system against abrupt appearance changes. Experimental results demonstrate that the proposed method outperforms the other state of the art techniques in the used test datasets.

Learning about probability from text and tables: Do color coding and labeling through an interactive-user interface help?

Learning from visual representations is enhanced when learners appropriately integrate corresponding visual and verbal information. This study examined the effects of two methods of promoting integration, color coding and labeling, on learning about probabilistic reasoning from a table and text. Undergraduate students (N = 98) were randomly assigned to learn about probabilistic reasoning from one of 4 computer-based lessons generated from a 2 (color coding/no color coding) by 2 (labeling/no labeling) between-subjects design. Learners added the labels or color coding at their own pace by clicking buttons in a computer-based lesson. Participants' eye movements were recorded while viewing the lesson. Labeling was beneficial for learning, but color coding was not. In addition, labeling, but not color coding, increased attention to important information in the table and time with the lesson. Both labeling and color coding increased looks between the text and corresponding information in the table. The findings provide support for the multimedia principle, and they suggest that providing labeling enhances learning about probabilistic reasoning from text and tables

A pseudo-transient solution strategy for the analysis of delamination by means of interface elements

Recent efforts in the finite element modelling of delamination have concentrated on the development of cohesive interface elements. These are characterised by a bilinear constitutive law, where there is an initial high positive stiffness until a threshold stress level is reached, followed by a negative tangent stiffness representing softening (or damage evolution). Complete decohesion occurs when the amount of work done per unit area of crack surface is equal to a critical strain energy release rate. It is difficult to achieve a stable, oscillation-free solution beyond the onset of damage, using standard implicit quasi-static methods, unless a very refined mesh is used. In the present paper, a new solution strategy is proposed based on a pseudo-transient formulation and demonstrated through the modelling of a double cantilever beam undergoing Mode I delamination. A detailed analysis into the sensitivity of the user-defined parameters is also presented. Comparisons with other published solutions using a quasi-static formulation show that the pseudo-transient formulation gives improved accuracy and oscillation-free results with coarser meshes

Surface alloying and mixing at the Mn/Fe(001) interface: Real-time photoelectron spectroscopy and modified embedded atom simulations

Structural and magnetic properties of thin Mn films on the Fe(001) surface have been investigated by a combination of photoelectron spectroscopy and computer simulation in the temperature range 300 Kless than or equal toTless than or equal to750 K. Room-temperature as deposited Mn overlayers are found to be ferromagnetic up to 2.5-monolayer (ML) coverage, with a magnetic moment parallel to that of the iron substrate. The Mn atomic moment decreases with increasing coverage, and thicker samples (4-ML and 4.5-ML coverage) are antiferromagnetic. Photoemission measurements performed while the system temperature is rising at constant rate (dT/dtsimilar to0.5 K/s) detect the first signs of Mn-Fe interdiffusion at T=450 K, and reveal a broad temperature range (610 Kless than or equal toTless than or equal to680 K) in which the interface appears to be stable. Interdiffusion resumes at Tgreater than or equal to680 K. Molecular dynamics and Monte Carlo simulations allow us to attribute the stability plateau at 610 Kless than or equal toTless than or equal to680 K to the formation of a single-layer MnFe surface alloy with a 2x2 unit cell and a checkerboard distribution of Mn and Fe atoms. X-ray-absorption spectroscopy and analysis of the dichroic signal show that the alloy has a ferromagnetic spin structure, collinear with that of the substrate. The magnetic moments of Mn and Fe atoms in the alloy are estimated to be 0.8mu(B) and 1.1mu(B), respectively.

An experimental investigation into the influence of user state and environment on fading characteristics in wireless body area networks at 2.45 GHz

Using seven strategically placed, time-synchronized bodyworn receivers covering the head, upper front and back torso, and the limbs, we have investigated the effect of user state: stationary or mobile and local environment: anechoic chamber, open office area and hallway upon first and second order statistics for on-body fading channels. Three candidate models were considered: Nakagami, Rice and lognormal. Using maximum likelihood estimation and the Akaike information criterion it was established that the Nakagami-m distribution best described small-scale fading for the majority of on-body channels over all the measurement scenarios. When the user was stationary, Nakagami-m parameters were found to be much greater than 1, irrespective of local surroundings. For mobile channels, Nakagami-m parameters significantly decreased, with channels in the open office area and hallway experiencing the worst fading conditions.

Systolic VLSI compiler (SVC) for high performance vector quantisation chips

An overview is given of a systolic VLSI compiler (SVC) tool currently under development for the automated design of high performance digital signal processing (DSP) chips. Attention is focused on the design of systolic vector quantization chips for use in both speech and image coding systems. The software in question consists of a cell library, silicon assemblers, simulators, test pattern generators, and a specially designed graphics shell interface which makes it expandable and user friendly. It allows very high performance digital coding systems to be rapidly designed in VLSI.

yambo: An ab initio tool for excited state calculations

yambo is an ab initio code for calculating quasiparticle energies and optical properties of electronic systems within the framework of many-body perturbation theory and time-dependent density functional theory. Quasiparticle energies are calculated within the GW approximation for the self-energy. Optical properties are evaluated either by solving the Bethe-Salpeter equation or by using the adiabatic local density approximation. yambo is a plane-wave code that, although particularly suited for calculations of periodic bulk systems, has been applied to a large variety of physical systems. yambo relies on efficient numerical techniques devised to treat systems with reduced dimensionality, or with a large number of degrees of freedom. The code has a user-friendly command-line based interface, flexible 110 procedures and is interfaced to several publicly available density functional ground-state codes.