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PubMed2001

Ants and agents: a process algebra approach to modelling ant colony behaviour.

Process algebras are widely used in the analysis of distributed computer systems. They allow formal reasoning about how the various components of a system contribute to its overall behaviour. In this paper we show how process algebras can be usefully applied to understanding social insect biology, in particular to studying the relationship between algorithmic behaviour of individual insects and the dynamical behaviour of their colony. We argue that process algebras provide a useful formalism for understanding this relationship, since they combine computer simulation, Markov chain analysis and mean-field methods of analysis. Indeed, process algebras can provide a framework for relating these three methods of analysis to each other and to experiments. We illustrate our approach with a series of graded examples of modelling activity in ant colonies.

Animals↗
PubMed2006

3D volume reconstruction of a mouse brain from histological sections using warp filtering.

Sectioning tissues for optical microscopy often introduces upon the resulting sections distortions that make 3D reconstruction difficult. Here we present an automatic method for producing a smooth 3D volume from distorted 2D sections in the absence of any undistorted references. The method is based on pairwise elastic image warps between successive tissue sections, which can be computed by 2D image registration. Using a Gaussian filter, an average warp is computed for each section from the pairwise warps in a group of its neighboring sections. The average warps deform each section to match its neighboring sections, thus creating a smooth volume where corresponding features on successive sections lie close to each other. The proposed method can be used with any existing 2D image registration method for 3D reconstruction. In particular, we present a novel image warping algorithm based on dynamic programming that extends Dynamic Time Warping in 1D speech recognition to compute pairwise warps between high-resolution 2D images. The warping algorithm efficiently computes a restricted class of 2D local deformations that are characteristic between successive tissue sections. Finally, a validation framework is proposed and applied to evaluate the quality of reconstruction using both real sections and a synthetic volume.

Algorithms↗
PubMed1994

Synthesis of models for excitable membranes, synaptic transmission and neuromodulation using a common kinetic formalism.

Markov kinetic models were used to synthesize a complete description of synaptic transmission, including opening of voltage-dependent channels in the presynaptic terminal, release of neurotransmitter, gating of postsynaptic receptors, and activation of second-messenger systems. These kinetic schemes provide a more general framework for modeling ion channels than the Hodgkin-Huxley formalism, supporting a continuous spectrum of descriptions ranging from the very simple and computationally efficient to the highly complex and biophysically precise. Examples are given of simple kinetic schemes based on fits to experimental data that capture the essential properties of voltage-gated, synaptic and neuromodulatory currents. The Markov formalism allows the dynamics of ionic currents to be considered naturally in the larger context of biochemical signal transduction. This framework can facilitate the integration of a wide range of experimental data and promote consistent theoretical analysis of neural mechanisms from molecular interactions to network computations.

Animals↗
PubMed2002

Computer technology applications in industrial and organizational psychology.

This article reviews computer applications developed and utilized by industrial-organizational (I-O) psychologists, both in practice and in research. A primary emphasis is on applications developed for Internet usage, because this "network of networks" changes the way I-O psychologists work. The review focuses on traditional and emerging topics in I-O psychology. The first topic involves information technology applications in measurement, defined broadly across levels of analysis (persons, groups, organizations) and domains (abilities, personality, attitudes). Discussion then focuses on individual learning at work, both in formal training and in coping with continual automation of work. A section on job analysis follows, illustrating the role of computers and the Internet in studying jobs. Shifting focus to the group level of analysis, we briefly review how information technology is being used to understand and support cooperative work. Finally, special emphasis is given to the emerging "third discipline" in I-O psychology research-computational modeling of behavioral events in organizations. Throughout this review, themes of innovation and dissemination underlie a continuum between research and practice. The review concludes by setting a framework for I-O psychology in a computerized and networked world.

Computer-Assisted Instruction↗
PubMed2002

Using motion planning to study protein folding pathways.

We present a framework for studying protein folding pathways and potential landscapes which is based on techniques recently developed in the robotics motion planning community. Our focus in this work is to study the protein folding mechanism assuming we know the native fold. That is, instead of performing fold prediction, we aim to study issues related to the folding process, such as the formation of secondary and tertiary structure, and the dependence of the folding pathway on the initial denatured conformation. Our work uses probabilistic roadmap (PRM) motion planning techniques which have proven successful for problems involving high-dimensional configuration spaces. A strength of these methods is their efficiency in rapidly covering the planning space without becoming trapped in local minima. We have applied our PRM technique to several small proteins (~60 residues) and validated the pathways computed by comparing the secondary structure formation order on our paths to known hydrogen exchange experimental results. An advantage of the PRM framework over other simulation methods is that it enables one to easily and efficiently compute folding pathways from any denatured starting state to the (known) native fold. This aspect makes our approach ideal for studying global properties of the protein's potential landscape, most of which are difficult to simulate and study with other methods. For example, in the proteins we study, the folding pathways starting from different denatured states sometimes share common portions when they are close to the native fold, and moreover, the formation order of the secondary structure appears largely independent of the starting denatured conformation. Another feature of our technique is that the distribution of the sampled conformations is correlated with the formation of secondary structure and, in particular, appears to differentiate situations in which secondary structure clearly forms first and those in which the tertiary structure is obtained more directly. Overall, our results applying PRM techniques are very encouraging and indicate the promise of our approach for studying proteins for which experimental results are not available.

Computational Biology↗
PubMed2002

Horses for courses: facilitating postgraduate research students' choice of Computer Assisted Qualitative Data Analysis System (CAQDAS).

Supervisors of postgraduate students are increasingly likely to find themselves discussing whether or not the student should use a CAQDAS (computer assisted qualitative data analysis system) in their research. This paper discusses Weitzman and Miles (1995) framework for decision-making about CAQDAS and then reports the experiences of five postgraduate students, each of whom made a different decision. (These were variously: not to use a CAQDAS, using Atlas-Ti, Ethnograph, N. VIVO and N5). It explores the fit between Weitzman's and Miles' principles and the students' experiences then suggests some modifications of the principles and strategies for advising students.

Choice Behavior↗
PubMed1996

RETAIN--an ATM pilot project for applications in health care.

The availability of ATM-based broadband wide-area networks facilitates a range of new applications in health care, especially the performance of videoconferences combined with software for computer-supported cooperative discussion and diagnosis of digital medical images. This report about a research project for applications of the 'European ATM pilot network' in radiology describes the technical, economic and structural framework for the application of broadband technology in health care.

Computer Communication Networks↗
PubMed1993

Ratio estimates, the delta method, and quantal response tests for increased carcinogenicity.

This paper demonstrates the use of the delta method for estimating the variance of ratio statistics derived from animal carcinogenicity experiments. The Cochran-Armitage test (Cochran, 1954, Biometrika 10, 417-451; and Armitage, 1955, Biometrics 11, 375-386) is routinely applied to carcinogenicity data as a test for linear trend in lifetime tumor incidence rates. The computing formula for this test derives from the assumption that the denominators of the quantal response rates are fixed. However, when time-at-risk weights are introduced to correct for treatment-related differences in survival, the denominators of the quantal response rates are subject to random variation. The delta method and weighted least squares techniques are applied here to approximate the variance of such ratio statistics and test for a linear dose-response relationship among treatments. This technique is compared to that of Bailer and Portier (1988, Biometrics 44, 417-431), who introduced a survival-adjusted quantal response test for trend in lifetime tumor incidence rates. Their test modifies the usual Cochran-Armitage computing formula by weighting the denominators of the response rates to reflect less-than-whole-animal contributions to risk. Within the framework of a weighted least squares linear regression model that underlies the Cochran-Armitage test, the time-at-risk weights of Bailer and Portier are incorporated using the delta method. Although the delta method approach is slightly more computationally intensive, small-sample simulations indicate that it has superior operating characteristics over the Poly-3 trend test of Bailer and Portier when background tumor incidence rates are low (under 3%) and survival patterns differ markedly across treatments.(ABSTRACT TRUNCATED AT 250 WORDS)

Analysis of Variance↗
PubMed1995

Using a pen-based computer to collect health-related quality of life and utilities information.

We have developed a system that uses the Newton MessagePad technology as part of a client-client-server paradigm to collect health-related quality of life information from breast cancer patients attending an outpatient clinic at the Dana-Farber Cancer Institute. Patients are asked to fill out an electronic questionnaire on the Newton, which then uploads the information into the institution's Oracle database. The program consists of a separate questionnaire engine and question base, facilitating questionnaire design and allowing us to give different questionnaires to different patients dynamically. The results of a preliminary trial show excellent user-acceptance of the device. Finally, we present a general framework for such systems and discuss issues that developers must consider when implementing a pen-based computer project.

Adult↗
PubMed1998

Decision Accuracy in Computer-Mediated versus Face-to-Face Decision-Making Teams.

Changes in the way organizations are structured and advances in communication technologies are two factors that have altered the conditions under which group decisions are made. Decisions are increasingly made by teams that have a hierarchical structure and whose members have different areas of expertise. In addition, many decisions are no longer made via strictly face-to-face interaction. The present study examines the effects of two modes of communication (face-to-face or computer-mediated) on the accuracy of teams' decisions. The teams are characterized by a hierarchical structure and their members differ in expertise consistent with the framework outlined in the Multilevel Theory of team decision making presented by Hollenbeck, Ilgen, Sego, Hedlund, Major, and Phillips (1995). Sixty-four four-person teams worked for 3 h on a computer simulation interacting either face-to-face (FtF) or over a computer network. The communication mode had mixed effects on team processes in that members of FtF teams were better informed and made recommendations that were more predictive of the correct team decision, but leaders of CM teams were better able to differentiate staff members on the quality of their decisions. Controlling for the negative impact of FtF communication on staff member differentiation increased the beneficial effect of the FtF mode on overall decision making accuracy. Copyright 1998 Academic Press.

Journal Article↗
PubMed2025

ScITree: Scalable Bayesian inference of transmission tree from epidemiological and genomic data.

Phylodynamic models capture joint epidemiological-evolutionary dynamics during an outbreak, providing a powerful tool to enhance understanding and management of disease transmission. Existing phylodynamic approaches, however, mostly rely on various non-mechanistic or semi-mechanistic approximations of the underlying epidemiological-evolutionary process. Previous work by Lau and colleagues has shown that full Bayesian mechanistic models, without relying on these approximations, can enable highly accurate joint inference of the epidemiological-evolutionary dynamics including the unobserved transmission tree. However, the Lau method faces major computational bottlenecks. As the volume of genomic data collected during outbreaks continues to grow, it is crucial to develop scalable yet accurate phylodynamic methods. Here we propose a new Bayesian phylodynamic model, overcoming the major scalability issue in the previous method and enabling a readily deployable, yet accurate, phylodynamic modeling framework. Specifically, we develop a scalable spatio-temporal phylodynamic framework for inferring the transmission tree (ScITree) and other key epidemiological parameters considering the infinite sites assumption in modeling mutation on the sequence level, in contrast to the Lau method in which mutation was modeled explicitly on the nucleotide level. Our approach features full Bayesian implementation utilizing an exact likelihood to mechanistically integrate epidemiological and evolutionary processes. We develop a computationally-efficient data-augmentation Markov Chain Monte Carlo algorithm, inferring key model parameters and unobserved dynamics including the transmission tree. We assess performance of our method using multiple simulated outbreak datasets. Our results indicate that our method can achieve high inference accuracy, comparable to the performance of the Lau method. Additionally, our method scales significantly more efficiently for large outbreaks, with computing time increasing linearly with outbreak size, compared to the exponential scaling of the Lau method. We also demonstrate our method's utility by applying our validated modeling framework to a dataset describing a foot-and-mouth disease outbreak in the UK. Our results show that our method is able to generate estimates of the transmission dynamics consistent with those from the prior method, further demonstrating the robustness of our new approach. In summary, our method provides a computationally-efficient, highly scalable, accurate modeling framework for inferring the joint spatio-temporal dynamics of epidemiological and evolutionary processes, facilitating timely and effective outbreak responses in space and time. Our method is implemented in our R package ScITree.

Bayes Theorem↗
PubMed2004

Modeling signal and background components of electrosensory scenes.

Weakly electric fish are able to detect and localize prey based on microvolt-level perturbations in the fish's self-generated electric field. In natural environments, weak prey-related signals are embedded in much stronger electrosensory background noise. To better characterize the signal and background components associated with natural electrolocation tasks, we recorded transdermal voltage modulations in restrained Apteronotus albifrons in response to moving spheres, tail bends, and large nonconducting boundaries. Spherical objects give rise to ipsilateral images with center-surround structure and contralateral images that are weak and diffuse. Tail bends and laterally placed nonconducting boundaries induce relatively strong ipsilateral and contralateral modulations of opposite polarity. We present a computational model of electric field generation and electrosensory image formation that is able to reproduce the key features of these empirically measured signal and background components in a unified framework. The model comprises an array of point sources and sinks distributed along the midline of the fish, which can conform to arbitrary body bends. The model is computationally fast and can be used to estimate the spatiotemporal pattern of activation across the entire electroreceptor array of the fish during natural behaviors.

Animals↗
PubMed1985

Crystallographic structure of an active, sequence-engineered ribonuclease.

X-ray diffraction methods were used to test a synthetic-modeling approach to the sequence engineering of bovine pancreatic ribonuclease. A model of RNase S-peptide (residues 1-20), having a simplified amino acid sequence but retaining elements deduced to be essential for conformation and function, was previously synthesized and found to form a catalytically active and stable complex with native S-protein (residues 21-24). We have now obtained a 3-A-resolution electron density map of this semisynthetic complex which reveals that the conformation of model peptide closely mimics that of native S-peptide, as intended by sequence design. Some small differences from the native structure are observed: Glu-2 and Arg-10 of the model complex are not close enough to form a salt bridge, the position of the His-12 imidazole ring is slightly shifted in the active site, and the peptide's amino terminus is reoriented. Nonetheless, the major structural features predicted to be essential by computer-aided peptide-design analysis are preserved in the model peptide portion of the complex. These include (i) the alpha-helical framework involving residues 3-13, (ii) the catalytically competent orientation of His-12, and (iii) complex-stabilizing non-bonding interactions involving Phe-8 and Met-13 of S-peptide and hydrophobic residues in the cleft region of S-protein. Further, sequence simplification has not introduced any non-native, potentially stabilizing contacts between the model peptide and S-protein. The results emphasize the usefulness, in redesigning native proteins, of categorizing sequence into residues providing conformational framework and those determining intra-and intermolecular surface recognition.

Amino Acid Sequence↗
PubMed2003

Key-string algorithm--novel approach to computational analysis of repetitive sequences in human centromeric DNA.

AIM: To use a novel computational approach, Key-string Algorithm (KSA), for the identification and analysis of arbitrarily large repetitive sequences and higher-order repeats (HORs) in noncoding DNA. This approach is based on the use of key string that plays a role of an arbitrarily constructed "computer enzyme". METHOD: A cluster of novel KSA-related methods was introduced and developed on the basis of a combination of computations on a very modest scale, by eye inspection and graphical display of results of analysis. Sequence analysis software was developed, containing seven programs for KSA-related analyses. This approach was demonstrated in the case study of alpha satellites and HORs in the human genetic sequence AC017075.8 (193277 bp) from the centromeric region of human chromosome 7. The KSA segmentation method was applied by using DCCGTTT, GTA, and TTTC key strings. RESULTS: Fifty-five copies of 2734-bp 16mer HORs were identified and investigated, and a start-string TTTTTTAAAAA was identified. The HOR-matrix was constructed and employed for graphical display of mutations. KSA identification of HORs in AC017075.8 was compared with that of RepeatMasker and Tandem Repeat Finder, which identified alpha monomers in AC017075.8, but not the HORs. On the basis of KSA study, the centromere folding was described as an effect of HORs and super-HORs (3 x 2734 bp) in AC017075.8. The following novel computational KSA-based methods, easy-to-use and intended for computational "pedestrians", were demonstrated: color-HOR diagram, KSA-divergence method, 171-bp subsequence-convergence diagram, and total frequency distribution of the key-string subsequence lengths. The results were supplemented by Fast Fourier Transform, employing a novel mapping of symbolic genomic sequence into a numerical sequence. CONCLUSION: The KSA approach offers a simple and robust framework for a wide range of investigations of large repetitive sequences and HORs, involving a very modest scope of computations that can be carried out by using a PC. As the KSA method is HOR-oriented, the identification of HORs is even easier than the identification of underlying alpha monomer itself. This approach provides an easy identification of point mutations, insertions, and deletions, with respect to consensus. This may be useful in a wide range of investigations and applied in forensic medicine, medical diagnosis of malignant diseases, biological evolution, and paleontology.

Algorithms↗
PubMed2006

Integral invariants for shape matching.

For shapes represented as closed planar contours, we introduce a class of functionals which are invariant with respect to the Euclidean group and which are obtained by performing integral operations. While such integral invariants enjoy some of the desirable properties of their differential counterparts, such as locality of computation (which allows matching under occlusions) and uniqueness of representation (asymptotically), they do not exhibit the noise sensitivity associated with differential quantities and, therefore, do not require presmoothing of the input shape. Our formulation allows the analysis of shapes at multiple scales. Based on integral invariants, we define a notion of distance between shapes. The proposed distance measure can be computed efficiently and allows warping the shape boundaries onto each other; its computation results in optimal point correspondence as an intermediate step. Numerical results on shape matching demonstrate that this framework can match shapes despite the deformation of subparts, missing parts and noise. As a quantitative analysis, we report matching scores for shape retrieval from a database.

Algorithms↗