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A New Framework for Analysis of Coevolutionary Systems-Directed Graph Representation and Random Walks

Chong SY, Tiňo P, He J, Yao X

Evol Comput, 2019;27(2):195-228.
PMID: 29155606 DOI: 10.1162/evco_a_00218

Studying coevolutionary systems in the context of simplified models (i.e., games with pairwise interactions between coevolving solutions modeled as self plays) remains an open challenge since the rich underlying structures associated with pairwise-comparison-based fitness measures are often not taken fully into account. Although cyclic dynamics have been demonstrated in several contexts (such as intransitivity in coevolutionary problems), there is no complete characterization of cycle structures and their effects on coevolutionary search. We develop a new framework to address this issue. At the core of our approach is the directed graph (digraph) representation of coevolutionary problems that fully captures structures in the relations between candidate solutions. Coevolutionary processes are modeled as a specific type of Markov chains-random walks on digraphs. Using this framework, we show that coevolutionary problems admit a qualitative characterization: a coevolutionary problem is either solvable (there is a subset of solutions that dominates the remaining candidate solutions) or not. This has an implication on coevolutionary search. We further develop our framework that provides the means to construct quantitative tools for analysis of coevolutionary processes and demonstrate their applications through case studies. We show that coevolution of solvable problems corresponds to an absorbing Markov chain for which we can compute the expected hitting time of the absorbing class. Otherwise, coevolution will cycle indefinitely and the quantity of interest will be the limiting invariant distribution of the Markov chain. We also provide an index for characterizing complexity in coevolutionary problems and show how they can be generated in a controlled manner.

Matched MeSH terms: Computer Graphics*
Cytopathology whole slide images and adaptive tutorials for postgraduate pathology trainees: a randomized crossover trial

Van Es SL, Kumar RK, Pryor WM, Salisbury EL, Velan GM

Hum Pathol, 2015 Sep;46(9):1297-305.
PMID: 26093936 DOI: 10.1016/j.humpath.2015.05.009

To determine whether cytopathology whole slide images and virtual microscopy adaptive tutorials aid learning by postgraduate trainees, we designed a randomized crossover trial to evaluate the quantitative and qualitative impact of whole slide images and virtual microscopy adaptive tutorials compared with traditional glass slide and textbook methods of learning cytopathology. Forty-three anatomical pathology registrars were recruited from Australia, New Zealand, and Malaysia. Online assessments were used to determine efficacy, whereas user experience and perceptions of efficiency were evaluated using online Likert scales and open-ended questions. Outcomes of online assessments indicated that, with respect to performance, learning with whole slide images and virtual microscopy adaptive tutorials was equivalent to using traditional methods. High-impact learning, efficiency, and equity of learning from virtual microscopy adaptive tutorials were strong themes identified in open-ended responses. Participants raised concern about the lack of z-axis capability in the cytopathology whole slide images, suggesting that delivery of z-stacked whole slide images online may be important for future educational development. In this trial, learning cytopathology with whole slide images and virtual microscopy adaptive tutorials was found to be as effective as and perceived as more efficient than learning from glass slides and textbooks. The use of whole slide images and virtual microscopy adaptive tutorials has the potential to provide equitable access to effective learning from teaching material of consistently high quality. It also has broader implications for continuing professional development and maintenance of competence and quality assurance in specialist practice.

Matched MeSH terms: Computer Graphics
Mechanism diagrams and abstraction-by-aggregation

Tee SH

Stud Hist Philos Biol Biomed Sci, 2018 Oct;71:17-25.
PMID: 30318277 DOI: 10.1016/j.shpsc.2018.10.003

Mechanism diagrams exhibit visually the organized parts and operations of a biological mechanism. A mechanism diagram can facilitate mechanistic research by providing a mechanistic explanation of the phenomenon of interest. Much research has been focusing on the mechanistic explanation and the explanatory mechanistic models. As a specific type of scientific diagram, a simple mechanism diagram can be explanatory by drawing on the rich explanatory resources of non-depicted background knowledge. The relationship between the visually depicted and the background knowledge is underexplored. It is unclear how the non-depicted background knowledge of a mechanism diagram contributes to providing a better-informed explanation of the phenomenon of interest in biological sciences. With the aim to explore this relationship, I articulate that a mechanism diagram provides a mechanistic explanation by a process called abstraction-by-aggregation. Through visual cues, the unified relevant background knowledge provides an epistemic access to a better-informed explanation.

Matched MeSH terms: Computer Graphics
Fulltext Realistic real-time outdoor rendering in augmented reality

Kolivand H, Sunar MS

PLoS One, 2014;9(9):e108334.
PMID: 25268480 DOI: 10.1371/journal.pone.0108334

Realistic rendering techniques of outdoor Augmented Reality (AR) has been an attractive topic since the last two decades considering the sizeable amount of publications in computer graphics. Realistic virtual objects in outdoor rendering AR systems require sophisticated effects such as: shadows, daylight and interactions between sky colours and virtual as well as real objects. A few realistic rendering techniques have been designed to overcome this obstacle, most of which are related to non real-time rendering. However, the problem still remains, especially in outdoor rendering. This paper proposed a much newer, unique technique to achieve realistic real-time outdoor rendering, while taking into account the interaction between sky colours and objects in AR systems with respect to shadows in any specific location, date and time. This approach involves three main phases, which cover different outdoor AR rendering requirements. Firstly, sky colour was generated with respect to the position of the sun. Second step involves the shadow generation algorithm, Z-Partitioning: Gaussian and Fog Shadow Maps (Z-GaF Shadow Maps). Lastly, a technique to integrate sky colours and shadows through its effects on virtual objects in the AR system, is introduced. The experimental results reveal that the proposed technique has significantly improved the realism of real-time outdoor AR rendering, thus solving the problem of realistic AR systems.

Matched MeSH terms: Computer Graphics
Fulltext A Method for Quantifying, Visualising, and Analysing Gastropod Shell Form

Liew TS, Schilthuizen M

PLoS One, 2016;11(6):e0157069.
PMID: 27280463 DOI: 10.1371/journal.pone.0157069

Quantitative analysis of organismal form is an important component for almost every branch of biology. Although generally considered an easily-measurable structure, the quantification of gastropod shell form is still a challenge because many shells lack homologous structures and have a spiral form that is difficult to capture with linear measurements. In view of this, we adopt the idea of theoretical modelling of shell form, in which the shell form is the product of aperture ontogeny profiles in terms of aperture growth trajectory that is quantified as curvature and torsion, and of aperture form that is represented by size and shape. We develop a workflow for the analysis of shell forms based on the aperture ontogeny profile, starting from the procedure of data preparation (retopologising the shell model), via data acquisition (calculation of aperture growth trajectory, aperture form and ontogeny axis), and data presentation (qualitative comparison between shell forms) and ending with data analysis (quantitative comparison between shell forms). We evaluate our methods on representative shells of the genera Opisthostoma and Plectostoma, which exhibit great variability in shell form. The outcome suggests that our method is a robust, reproducible, and versatile approach for the analysis of shell form. Finally, we propose several potential applications of our methods in functional morphology, theoretical modelling, taxonomy, and evolutionary biology.

Matched MeSH terms: Computer Graphics*
Fulltext The effectiveness of interactive learning in manufacturing engineering

Nadia Abdul Rani, Faieza Abdul Aziz, Rohidatun M,W.

Journal of Engineering and Science Research, 2018;2(6):10-16.
MyJurnal

Interactive learning is a pedagogical model that encourages students to be part of the lesson instead of passive observers, quietly sitting at a desk taking notes or memorizing information. Students interact with the material, each other and the teacher in an active way. The new emerging technologies that can overcome some of the potential difficulties in this area includes computer graphics, augmented reality, computational dynamics, and virtual worlds. Therefore, the manufacturing industry relies on new design concepts and methods undertake the challenges in integrating technologies to expedite the march towards industrial revolution 4.0.This paper reviews and investigates the current context of the use of interactive learning such as Virtual Reality(VR),Augmented Reality(AR),Computer aided design and manufacturing(CADCAM), computer graphics, computational dynamics and new emerging technologies that effect on students and lectures in learning and teaching environments for Manufacturing Engineering. Interactive learning is part of the factors that could influence the self-learning and regulations environments.

Matched MeSH terms: Computer Graphics
Fulltext Graphery: interactive tutorials for biological network algorithms

Zeng H, Zhang J, Preising GA, Rubel T, Singh P, Ritz A

Nucleic Acids Res, 2021 07 02;49(W1):W257-W262.
PMID: 34037782 DOI: 10.1093/nar/gkab420

Networks have been an excellent framework for modeling complex biological information, but the methodological details of network-based tools are often described for a technical audience. We have developed Graphery, an interactive tutorial webserver that illustrates foundational graph concepts frequently used in network-based methods. Each tutorial describes a graph concept along with executable Python code that can be interactively run on a graph. Users navigate each tutorial using their choice of real-world biological networks that highlight the diverse applications of network algorithms. Graphery also allows users to modify the code within each tutorial or write new programs, which all can be executed without requiring an account. Graphery accepts ideas for new tutorials and datasets that will be shaped by both computational and biological researchers, growing into a community-contributed learning platform. Graphery is available at https://graphery.reedcompbio.org/.

Matched MeSH terms: Computer Graphics
Fulltext Preventing shoulder-surfing attack with the concept of concealing the password objects' information

Ho PF, Kam YH, Wee MC, Chong YN, Por LY

ScientificWorldJournal, 2014;2014:838623.
PMID: 24991649 DOI: 10.1155/2014/838623

Traditionally, picture-based password systems employ password objects (pictures/icons/symbols) as input during an authentication session, thus making them vulnerable to "shoulder-surfing" attack because the visual interface by function is easily observed by others. Recent software-based approaches attempt to minimize this threat by requiring users to enter their passwords indirectly by performing certain mental tasks to derive the indirect password, thus concealing the user's actual password. However, weaknesses in the positioning of distracter and password objects introduce usability and security issues. In this paper, a new method, which conceals information about the password objects as much as possible, is proposed. Besides concealing the password objects and the number of password objects, the proposed method allows both password and distracter objects to be used as the challenge set's input. The correctly entered password appears to be random and can only be derived with the knowledge of the full set of password objects. Therefore, it would be difficult for a shoulder-surfing adversary to identify the user's actual password. Simulation results indicate that the correct input object and its location are random for each challenge set, thus preventing frequency of occurrence analysis attack. User study results show that the proposed method is able to prevent shoulder-surfing attack.

Matched MeSH terms: Computer Graphics/standards*
Fulltext Computers in health education

Krishnan R, Kueh ST, Lin YM, Samsuri MF, Seng OC, Mahadavan M, et al.

World Health Forum, 1990;11(3):310-1.
PMID: 2291796
Matched MeSH terms: Computer Graphics*
A low-cost, high-quality method for remote recording of presentations

Tan LK, Wong JH, Ng KH

AJR Am J Roentgenol, 2006 Mar;186(3):898-901.
PMID: 16498128

The purpose of this article was to develop a low-cost method for high-quality remote capturing and recording of multimedia presentations.

Matched MeSH terms: Computer Graphics*
Fulltext A novel state space reduction algorithm for team formation in social networks

Rehman MZ, Zamli KZ, Almutairi M, Chiroma H, Aamir M, Kader MA, et al.

PLoS One, 2021;16(12):e0259786.
PMID: 34855771 DOI: 10.1371/journal.pone.0259786

Team formation (TF) in social networks exploits graphs (i.e., vertices = experts and edges = skills) to represent a possible collaboration between the experts. These networks lead us towards building cost-effective research teams irrespective of the geolocation of the experts and the size of the dataset. Previously, large datasets were not closely inspected for the large-scale distributions & relationships among the researchers, resulting in the algorithms failing to scale well on the data. Therefore, this paper presents a novel TF algorithm for expert team formation called SSR-TF based on two metrics; communication cost and graph reduction, that will become a basis for future TF's. In SSR-TF, communication cost finds the possibility of collaboration between researchers. The graph reduction scales the large data to only appropriate skills and the experts, resulting in real-time extraction of experts for collaboration. This approach is tested on five organic and benchmark datasets, i.e., UMP, DBLP, ACM, IMDB, and Bibsonomy. The SSR-TF algorithm is able to build cost-effective teams with the most appropriate experts-resulting in the formation of more communicative teams with high expertise levels.

Matched MeSH terms: Computer Graphics
ProLysED: an integrated database and meta-server of bacterial protease systems

Firdaus Raih M, Ahmad HA, Sharum MY, Azizi N, Mohamed R

Appl. Bioinformatics, 2005;4(2):147-50.
PMID: 16128617

Bacterial proteases are an important group of enzymes that have very diverse biochemical and cellular functions. Proteases from prokaryotic sources also have a wide range of uses, either in medicine as pathogenic factors or in industry and therapeutics. ProLysED (Prokaryotic Lysis Enzymes Database), our meta-server integrated database of bacterial proteases, is a useful, albeit very niche, resource. The features include protease classification browsing and searching, organism-specific protease browsing, molecular information and visualisation of protease structures from the Protein Data Bank (PDB) as well as predicted protease structures.

Matched MeSH terms: Computer Graphics
The Suffering Pictogram: Measuring Suffering in Palliative Care

Beng TS, Ann YH, Guan NC, Chin LE, Loong LC, Ying NT, et al.

J Palliat Med, 2017 08;20(8):869-874.
PMID: 28410449 DOI: 10.1089/jpm.2016.0448

BACKGROUND: Measuring suffering objectively presents a challenge because suffering is a unique and subjective experience. However, objective tools are of profound importance in the detection and management of suffering in clinical practice for optimal patient care.
OBJECTIVE: The objective of the study is to assess the psychometric properties of the Suffering Pictogram, a new suffering assessment instrument on a population of palliative care patients.
DESIGN AND SETTING: This is a validation study conducted at University of Malaya Medical Centre, Kuala Lumpur, Malaysia. Ninety one palliative care patients were recruited. Patients were interviewed with the Suffering Pictogram and FACIT-Sp.
RESULTS: The median completion time for the Suffering Pictogram was five minutes. The Suffering Pictogram showed good internal consistency, with a Cronbach's alpha of 0.836. The total scores of the Suffering Pictogram correlated strongly and negatively with FACIT-Sp total score (Spearman's Rho = -0.625, p

Matched MeSH terms: Computer Graphics*
Orderings a class of unicyclic graphs with respect to Hosoya dan Merrifield-Simmons index

Wang Yan-feng, Ma Ning

Sains Malaysiana, 2016;45:55-58.

Hosoya and Merrifield-Simmons index were the two valuable topological indices in chemical graph theory. The Hosoya and Merrifield-Simmons index of the class of unicyclic graphs G(k) were investigated, according to the distance between u and v on Cm, their orderings with respect to these two topological indices were obtained.

Matched MeSH terms: Computer Graphics
Fulltext Soft bilateral filtering volumetric shadows using cube shadow maps

Ali HH, Sunar MS, Kolivand H

PLoS One, 2017;12(6):e0178415.
PMID: 28632740 DOI: 10.1371/journal.pone.0178415

Volumetric shadows often increase the realism of rendered scenes in computer graphics. Typical volumetric shadows techniques do not provide a smooth transition effect in real-time with conservation on crispness of boundaries. This research presents a new technique for generating high quality volumetric shadows by sampling and interpolation. Contrary to conventional ray marching method, which requires extensive time, this proposed technique adopts downsampling in calculating ray marching. Furthermore, light scattering is computed in High Dynamic Range buffer to generate tone mapping. The bilateral interpolation is used along a view rays to smooth transition of volumetric shadows with respect to preserving-edges. In addition, this technique applied a cube shadow map to create multiple shadows. The contribution of this technique isreducing the number of sample points in evaluating light scattering and then introducing bilateral interpolation to improve volumetric shadows. This contribution is done by removing the inherent deficiencies significantly in shadow maps. This technique allows obtaining soft marvelous volumetric shadows, having a good performance and high quality, which show its potential for interactive applications.

Matched MeSH terms: Computer Graphics*
Fulltext Invariant Feature Matching for Image Registration Application Based on New Dissimilarity of Spatial Features

Mousavi Kahaki SM, Nordin MJ, Ashtari AH, J Zahra S

PLoS One, 2016;11(3):e0149710.
PMID: 26985996 DOI: 10.1371/journal.pone.0149710

An invariant feature matching method is proposed as a spatially invariant feature matching approach. Deformation effects, such as affine and homography, change the local information within the image and can result in ambiguous local information pertaining to image points. New method based on dissimilarity values, which measures the dissimilarity of the features through the path based on Eigenvector properties, is proposed. Evidence shows that existing matching techniques using similarity metrics--such as normalized cross-correlation, squared sum of intensity differences and correlation coefficient--are insufficient for achieving adequate results under different image deformations. Thus, new descriptor's similarity metrics based on normalized Eigenvector correlation and signal directional differences, which are robust under local variation of the image information, are proposed to establish an efficient feature matching technique. The method proposed in this study measures the dissimilarity in the signal frequency along the path between two features. Moreover, these dissimilarity values are accumulated in a 2D dissimilarity space, allowing accurate corresponding features to be extracted based on the cumulative space using a voting strategy. This method can be used in image registration applications, as it overcomes the limitations of the existing approaches. The output results demonstrate that the proposed technique outperforms the other methods when evaluated using a standard dataset, in terms of precision-recall and corner correspondence.

Matched MeSH terms: Computer Graphics
Fulltext Geometric feature descriptor and dissimilarity-based registration of remotely sensed imagery

Kahaki SMM, Arshad H, Nordin MJ, Ismail W

PLoS One, 2018;13(7):e0200676.
PMID: 30024921 DOI: 10.1371/journal.pone.0200676

Image registration of remotely sensed imagery is challenging, as complex deformations are common. Different deformations, such as affine and homogenous transformation, combined with multimodal data capturing can emerge in the data acquisition process. These effects, when combined, tend to compromise the performance of the currently available registration methods. A new image transform, known as geometric mean projection transform, is introduced in this work. As it is deformation invariant, it can be employed as a feature descriptor, whereby it analyzes the functions of all vertical and horizontal signals in local areas of the image. Moreover, an invariant feature correspondence method is proposed as a point matching algorithm, which incorporates new descriptor's dissimilarity metric. Considering the image as a signal, the proposed approach utilizes a square Eigenvector correlation (SEC) based on the Eigenvector properties. In our experiments on standard test images sourced from "Featurespace" and "IKONOS" datasets, the proposed method achieved higher average accuracy relative to that obtained from other state of the art image registration techniques. The accuracy of the proposed method was assessed using six standard evaluation metrics. Furthermore, statistical analyses, including t-test and Friedman test, demonstrate that the method developed as a part of this study is superior to the existing methods.

Matched MeSH terms: Computer Graphics
Determining level of postural control in young adults using force-sensing resistors

Gopalai AA, Senanayake SM, Gouwanda D

IEEE Trans Inf Technol Biomed, 2011 Jul;15(4):608-14.
PMID: 21478080 DOI: 10.1109/TITB.2011.2140378

A force-sensing platform (FSP), sensitive to changes of the postural control system was designed. The platform measured effects of postural perturbations in static and dynamic conditions. This paper describes the implementation of an FSP using force-sensing resistors as sensing elements. Real-time qualitative assessment utilized a rainbow color scale to identify areas with high force concentration. Postprocessing of the logged data provided end-users with quantitative measures of postural control. The objective of this research was to establish the feasibility of using an FSP to test and gauge human postural control. Tests were conducted in eye open and eye close states. Readings obtained were tested for repeatability using a one-way analysis of variance test. The platform gauged postural sway by measuring the area of distribution for the weighted center of applied pressure at the foot. A fuzzy clustering algorithm was applied to identify regions of the foot with repetitive pressure concentration. Potential application of the platform in a clinical setting includes monitoring rehabilitation progress of stability dysfunction. The platform functions as a qualitative tool for initial, on-the-spot assessment, and quantitative measure for postacquisition assessment on balance abilities.

Matched MeSH terms: Computer Graphics
Glove-based approach to online signature verification

Kamel NS, Sayeed S, Ellis GA

IEEE Trans Pattern Anal Mach Intell, 2008 Jun;30(6):1109-13.
PMID: 18421114 DOI: 10.1109/TPAMI.2008.32

Utilizing the multiple degrees of freedom offered by the data glove for each finger and the hand, a novel on-line signature verification system using the Singular Value Decomposition (SVD) numerical tool for signature classification and verification is presented. The proposed technique is based on the Singular Value Decomposition in finding r singular vectors sensing the maximal energy of glove data matrix A, called principal subspace, so the effective dimensionality of A can be reduced. Having modeled the data glove signature through its r-principal subspace, signature authentication is performed by finding the angles between the different subspaces. A demonstration of the data glove is presented as an effective high-bandwidth data entry device for signature verification. This SVD-based signature verification technique is tested and its performance is shown to be able to recognize forgery signatures with a false acceptance rate of less than 1.2%.

Matched MeSH terms: Computer Graphics
Fulltext Design and development of a spatial immersive track cycling simulator

Yap, H.J., Tan, C.H., Sivadas, C.S., Wan, W.L., Taha, Z., Chang, S.W.

Movement Health & Exercise, 2018;7(2):39-52.
MyJurnal

Virtual Reality (VR) is a technology that makes use of computer graphics,
algorithms and special hardware to simulate the real world in real time. There
are four main elements required to make a VR system a success, namely
virtual world, immersion, sensory feedback and interactivity. The virtual
world created must be as real as possible. Users should have a sense of
immersion in the virtual world. Position tracking is usually incorporated into
a VR system for visual, sound and force feedback on the users and the virtual
objects in the VR world must be interact-able with the users. VR has proven
to be effective in training and widely used in many areas, for example medical
surgery, dental treatment, psychology treatment for phobia, engineering
design, maintenance and repair, sports and many more. By implementing VR
technology in training, users are able to reduce the training cost and time. VR
training is also safer for users, as harsh environments can be simulated despite
the environment and/or human factors. On the other hand, the physical
facilities and infrastructures of the track cycling are very costly. In track
cycling, the game field, known as a velodrome, requires a large space of area.
It requires a huge budget and professional manpower to maintain these
facilities. Therefore, the proposed spatial immersive track cycling simulator
is invented to overcome these issues. The aim of this study is to simulate the
velodrome track cycling in VR environment and synchronize with a 6 degreeof-freedom
motion platform. The simulator is aimed to be low cost and
minimal space requirement compared to actual velodrome. A trainee who
undergoes VR track cycling simulator training wears a head-mounted-display (HMD) to visualize the VR environment. An actual bike will be mounted on
the 6-DOF motion platform, which the platform will synchronize with the VR
environment to simulate the track condition for the training purposes. An
encoder is placed at the bicycle wheel to feedback the moving speed and
synchronize the visualize feedback to the HMD.

Matched MeSH terms: Computer Graphics

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