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At least 595 records · Page 33Linked to original sources
PubMed2005

Learning from humans: computational modeling of face recognition.

In this paper, we propose a computational architecture of face recognition based on evidence from cognitive research. Several recent psychophysical experiments have shown that humans process faces by a combination of configural and component information. Using an appearance-based implementation of this architecture based on low-level features and their spatial relations, we were able to model aspects of human performance found in psychophysical studies. Furthermore, results from additional computational recognition experiments show that our framework is able to achieve excellent recognition performance even under large view rotations. Our interdisciplinary study is an example of how results from cognitive research can be used to construct recognition systems with increased performance. Finally, our modeling results also make new experimental predictions that will be tested in further psychophysical studies, thus effectively closing the loop between psychophysical experimentation and computational modeling.

Area Under Curve↗
PubMed1992

Chimeric and humanized antibodies with specificity for the CD33 antigen.

L and H chain cDNAs of M195, a murine mAb that binds to the CD33 Ag on normal and leukemic myeloid cells, were cloned. The cDNAs were used in the construction of mouse/human IgG1 and IgG3 chimeric antibodies. In addition, humanized antibodies were constructed which combined the complementarity-determining regions of the M195 antibody with human framework and constant regions. The human framework was chosen to maximize homology with the M195 V domain sequence. Moreover, a computer model of M195 was used to identify several framework amino acids that are likely to interact with the complementarity-determining regions, and these residues were also retained in the humanized antibodies. Unexpectedly, the humanized IgG1 and IgG3 M195 antibodies, which have reshaped V regions, have higher apparent binding affinity for the CD33 Ag than the chimeric or mouse antibodies.

Amino Acid Sequence↗
PubMed1995

A Bayesian framework for understanding texture segmentation in the primary visual cortex.

This paper presents a mathematical theory for understanding the computations involved in texture segmentation in the primary visual cortex. We propose that texture segmentation is a part of the early visual system's overall strategy to infer surfaces of objects in a visual scene. Based on this insight, we use the Bayesian inference paradigm to formulate the texture segmentation problem into a maximum a posteriori surface inference problem. The dynamical system for finding the optimal solution of this problem can be characterized by two concurrent and interactive processes: a gradual sharpening of the boundary signals and a simultaneous smoothing of the surface signals. The behavior of these dynamical processes was studied using both analytical and computational methods. We present some computational results and mathematical predictions. This theory suggests a novel framework for understanding the functional roles of the complex cells in the primary visual cortex.

Bayes Theorem↗
PubMed2005

Holonomic quantum computation in the presence of decoherence.

We present a scheme to study non-Abelian adiabatic holonomies for open Markovian systems. As an application of our framework, we analyze the robustness of holonomic quantum computation against decoherence. We pinpoint the sources of error that must be corrected to achieve a geometric implementation of quantum computation completely resilient to Markovian decoherence.

Journal Article↗
PubMed2004

Real-time computation at the edge of chaos in recurrent neural networks.

Depending on the connectivity, recurrent networks of simple computational units can show very different types of dynamics, ranging from totally ordered to chaotic. We analyze how the type of dynamics (ordered or chaotic) exhibited by randomly connected networks of threshold gates driven by a time-varying input signal depends on the parameters describing the distribution of the connectivity matrix. In particular, we calculate the critical boundary in parameter space where the transition from ordered to chaotic dynamics takes place. Employing a recently developed framework for analyzing real-time computations, we show that only near the critical boundary can such networks perform complex computations on time series. Hence, this result strongly supports conjectures that dynamical systems that are capable of doing complex computational tasks should operate near the edge of chaos, that is, the transition from ordered to chaotic dynamics.

Animals↗
PubMed2005

Enhancing data sharing in collaborative research projects with DASH.

We describe a software framework, called DASH, that enables the facile access, maintenance, curation and sharing of computational biology data among collaborating research scientists. The DASH event-based framework enables members of team-based research projects to describe the multistep computational processing pipelines frequently required to generate data for sharing, monitors multiple distributed data stores for changes, and will then automatically invoke the appropriate processing pipeline(s). These pipelines can be used to communicate the results of data analyses to collaborators using mechanisms such as Web Services. We describe the overall design of the DASH system and the application of a simple DASH prototype to a collaborative pharmacogenomics research project involving several dozen researchers located at several different sites--the UCSF Pharmacogenetics of Membrane Transporters project.

Automation↗
PubMed2000

Inferring the impact of linguistic boundaries on population differentiation: application to the Afro-Asiatic-Indo-European case.

We present here a quantitative way to assess the impact of language-family boundaries on population differentiation and to evaluate the homogeneity of the genetic processes along these boundaries. Our estimator (delta a) of the impact of the boundary is based on an isolation by distance (IBD) model and measures the added genetic distance between populations located on different sides of the boundary. We compare this statistic with another estimator of group differentiation (F(CT)) computed under an analysis of variance framework that does not assume any particular spatial structure of the populations. Monte Carlo simulations are used to study the behaviour of these statistics under a two-dimensional stepping-stone model. Simulations show that F(CT) can suggest the existence of a frontier when populations only differ because of IBD. This spurious behaviour is much less frequent for the delta a statistic. However, the large variance associated with the delta a statistic, and the fact that it should only be computed in the presence of IBD, may limit the use of this statistic. Overall, the origin and the effect of the boundary is best understood by comparing different statistics and by testing for the presence of IBD on each side of the boundary as well as across the boundary. We illustrate our approach by examining the boundary between Afro-Asiatic and Indo-European populations. These populations are globally genetically differentiated, but the effect of the linguistic boundary on gene flow seems geographically very heterogeneous. This boundary appears to be the result of a secondary contact between two differentiation centres rather than an enhancer of population differentiation.

Africa↗
PubMed2002

Source-detector calibration in three-dimensional Bayesian optical diffusion tomography.

Optical diffusion tomography is a method for reconstructing three-dimensional optical properties from light that passes through a highly scattering medium. Computing reconstructions from such data requires the solution of a nonlinear inverse problem. The situation is further complicated by the fact that while reconstruction algorithms typically assume exact knowledge of the optical source and detector coupling coefficients, these coupling coefficients are generally not available in practical measurement systems. A new method for estimating these unknown coupling coefficients in the three-dimensional reconstruction process is described. The joint problem of coefficient estimation and three-dimensional reconstruction is formulated in a Bayesian framework, and the resulting estimates are computed by using a variation of iterative coordinate descent optimization that is adapted for this problem. Simulations show that this approach is an accurate and efficient method for simultaneous reconstruction of absorption and diffusion coefficients as well as the coupling coefficients. A simple experimental result validates the approach.

Bayes Theorem↗
PubMed2003

A framework for classifying decision support systems.

BACKGROUND: Computer-based clinical decision support systems (CDSSs) vary greatly in design and function. A taxonomy for classifying CDSS structure and function would help efforts to describe and understand the variety of CDSSs in the literature, and to explore predictors of CDSS effectiveness and generalizability. OBJECTIVE: To define and test a taxonomy for characterizing the contextual, technical, and workflow features of CDSSs. METHODS: We retrieved and analyzed 150 English language articles published between 1975 and 2002 that described computer systems designed to assist physicians and/or patients with clinical decision making. We identified aspects of CDSS structure or function and iterated our taxonomy until additional article reviews did not result in any new descriptors or taxonomic modifications. RESULTS: Our taxonomy comprises 95 descriptors along 24 descriptive axes. These axes are in 5 categories: Context, Knowledge and Data Source, Decision Support, Information Delivery, and Workflow. The axes had an average of 3.96 coded choices each. 75% of the descriptors had an inter-rater agreement kappa of greater than 0.6. CONCLUSIONS: We have defined and tested a comprehensive, multi-faceted taxonomy of CDSSs that shows promising reliability for classifying CDSSs reported in the literature.

Classification↗
PubMed2004

Virtual Reality by Cerec inLab Framework.

Virtual Reality--meaning the visualization of abstract computer processes--is gaining increasing significance in the everyday routine of the dental laboratory working with CAD/CAM technology. This is indispensable especially when processing the new high-strength materials such as ZrO2. The average maximum chewing forces previously permitted a bridge in the posterior region only when metal ceramics were used. With the aid of modern computer technology, it is now possible to use the all-ceramic material of zirconium dioxide for these indications. The technical procedure in the dental laboratory corresponds largely to the production techniques that are known from use with aluminum oxide. VITA VM 9 (Vita Zahnfabrik, Bad Säckingen, Germany) is available as veneer material. Its coefficient of thermal expansion is perfectly matched to the ceramic.

Bite Force↗
PubMed2004

Adapting the Lagrangian speckle model estimator for endovascular elastography: theory and validation with simulated radio-frequency data.

Intravascular ultrasound (IVUS) is known to be the reference tool for preoperative vessel lesion assessments and for endovascular therapy planning. Nevertheless, IVUS echograms only provide subjective information about vessel wall lesions. Since changes in the vascular tissue stiffness are characteristic of vessel pathologies, catheter-based endovascular ultrasound elastography (EVE) has been proposed in the literature as a method for outlining the elastic properties of vessel walls. In this paper, the Lagrangian Speckle Model Estimator (LSME) is formulated for investigations in EVE, i.e., using a polar coordinate system. The method was implemented through an adapted version of the Levenberg-Marquardt minimization algorithm, using the optical flow equations to compute the Jacobbian matrix. The theoretical framework was validated with simulated ultrasound rf data of mechanically complex vessel wall pathologies. The results, corroborated with Ansys finite element software, demonstrated the potential of EVE to provide useful information about the heterogeneous nature of atherosclerotic plaques.

Animals↗
PubMed1998

Biological computation.

It is argued that biological systems can be viewed as special computing devices. This view emerges from considerations of how information is stored in and retrieved from the genes. Genes can only specify the properties of the proteins they code for, and any integrative properties of the system must be 'computed' by their interactions. This provides a framework for analysis by simulation and sets practical bounds on what can be achieved by reductionist models.

Computational Biology↗
PubMedDate not supplied

Using ICPC in a computer-based primary care information system.

INTRODUCTION: Although the framework of the episode of care offers much promise in examining the process of primary health care, the development of episode-oriented, automated data sources has proceeded slowly. Experience with the International Classification of Primary Care (ICPC) in the European Community has confirmed its usefulness in creating and analyzing episodes of care, but it has seen little use in the United States. We describe the development of a Primary Care Information System (PCIS), which employs ICPC to create episodes of care from routinely collected clinical data. METHODS: The PCIS is a partially computerized medical information system running on a standard Macintosh microcomputer. The PCIS integrates ICPC, ICD-9-CM, and CPT-4 coding structures to provide episode-oriented data for clinical, administrative, research, and reimbursement needs. The performance of the PCIS was assessed based on five major issues: clinician cooperation, data-entry accuracy, validity of episode data, cost, and perceived value to users. RESULTS: The data collection and entry process required minimal additional effort from clinicians and data-entry personnel, and data-entry accuracy exceeded published estimates for other primary care data sources. Data management costs of about $1 per encounter compare favorably to published estimates for other office-based clinical information systems. The major problem seen during pilot testing was inaccurate tracking of episode boundaries through changes in providers and consequent changes in labels for problems and diagnoses. This problem has been addressed in development of the second-generation PCIS. CONCLUSION: The combination of an episode-oriented framework such as ICPC and a flexible medical information system provides a promising platform for the study of the content and process of primary health care.

Family Practice↗
PubMed2001

From paper-based to electronic guidelines: application to French guidelines.

In order to develop an internet-based decision support system, making available for French general practitioners several prevention guidelines is was necessary to implement paper based guideline. We propose a framework allowing to transform paper based practice guideline into their electronic form. Three different problems were identified: computability (e.g. determinism of the eCPG), logic (e.g. ambiguities when combining Booleans operators) and external validity (i.e. stability of decision for variations around thresholds and proportion of subjects classified in the various terminal nodes). The last problem concerned documentation of evidence: the level of evidence was associated only with the terminal decision node and not with the pathway through the decision tree. We concluded that computerisation of guidelines is not possible without expertise or authors advice. To improve computability it is necessary to provide authors with a framework that checks ambiguities, and logical errors.

Algorithms↗
PubMed2005

Clustered blockwise PCA for representing visual data.

Principal Component Analysis (PCA) is extensively used in computer vision and image processing. Since it provides the optimal linear subspace in a least-square sense, it has been used for dimensionality reduction and subspace analysis in various domains. However, its scalability is very limited because of its inherent computational complexity. We introduce a new framework for applying PCA to visual data which takes advantage of the spatio-temporal correlation and localized frequency variations that are typically found in such data. Instead of applying PCA to the whole volume of data (complete set of images), we partition the volume into a set of blocks and apply PCA to each block. Then, we group the subspaces corresponding to the blocks and merge them together. As a result, we not only achieve greater efficiency in the resulting representation of the visual data, but also successfully scale PCA to handle large data sets. We present a thorough analysis of the computational complexity and storage benefits of our approach. We apply our algorithm to several types of videos. We show that, in addition to its storage and speed benefits, the algorithm results in a useful representation of the visual data.

Algorithms↗
PubMed2004

Quantitative analysis of gated SPECT images using an efficient physical deformation model.

In this paper, we present quantitative analysis of cardiac images using an efficient physical deformation model to evaluate ventricular function. By using this model we can accurately and efficiently compute ventricular volume, myocardial mass, endo- and epi-cardial wall motions and wall thickness over a full cardiac cycle. Patients with cardiac diseases were studied in our modeling and measurement framework using gated single-photon emission computed tomographic images. The results show that quantitative analysis using the model is very useful for the assessment of the extent and severity of myocardial ischemia or infarction. And it could be helpful to improve the decision-making process in the treatment of patients with cardiac diseases.

Coronary Artery Disease↗
PubMed2003

Syntheses, crystallographic/computational characterizations, and reactions of the first 10-vertex arachno- and nido-phosphamonocarbaboranes.

A synthetic sequence involving the initial reaction of a substituted phosphorus dihalide (RPCl(2), R = CH(3), C(6)H(5)) with the arachno-CB(8)H(13)(-) (1-) monoanion followed by an in situ dehydrohalogenation reaction initiated by Proton Sponge, resulted in phosphorus cage insertion to yield the first 10-vertex arachno- and nido-phosphamonocarbaboranes, exo-6-R-arachno-6,7-PCB(8)H(12) (2a, 2b) and PSH(+)6-R-nido-6,9-PCB(8)H(9)(-) (PSH+3a-, PSH+3b-) (R = C(6)H(5) (a), CH(3) (b)). Alternatively, 2a and 2b were synthesized in high yield as the sole product of the reaction of the arachno-4-CB(8)H(12)(2-) (1(2-)) dianion with RPCl(2). Crystallographic determinations of PSH+3a- and PSH+3b- in conjunction with DFT/GIAO computational studies of the anions have confirmed the expected nido cage framework based on an octadecahedron missing the six-coordinate vertex. DFT/GIAO computational studies have also shown that while the gross cage geometries of the exo-6-R-arachno-6,7-PCB(8)H(12) compounds 2a and 2b resemble the known isoelectronic arachno-6,9-SCB(8)H(12), the phosphorus and carbon atoms are in thermodynamically unfavorable adjacent positions on the six-membered puckered face. They also each have an endo-hydrogen at the P6-position arising from proton transfer to the basic phosphorus during the cage-insertion reaction. Possible stepwise reaction pathways that can account for the formation of both the arachno and nido products are discussed. Deprotonation of 2a and 2b resulted in the formation of their corresponding conjugate monoanions, 6-R-arachno-6,7-PCB(8)H(11)(-) (2a-, 2b-), in which the proton that had been attached to the P6 atom was removed. Reactions of 2a- with O(2), S(8), BH(3).THF, or Br(2) further demonstrated the basicity of the P6-phosphorus yielding the new arachno-substituted compounds, endo-6-O-exo-6-(C(6)H(5))-arachno-6,7-PCB(8)H(11)(-) (4a-), endo-6-S-exo-6-(C(6)H(5))-arachno-6,7-PCB(8)H(11)(-) (5a-), endo-6-BH(3)-exo-6-(C(6)H(5))-arachno-6,7-PCB(8)H(11)(-) (6a-), and endo-6-Br-exo-6-(C(6)H(5))-arachno-6,7-PCB(8)H(11) (7a), respectively, in which the O, S, BH(3), and Br substituents are bound to the phosphorus at the endo position.

Journal Article↗
PubMed1996

A comparison of two murine monoclonal antibodies humanized by CDR-grafting and variable domain resurfacing.

The variable domain resurfacing and CDR-grafting approaches to antibody humanization were compared directly on the two murine monoclonal antibodies N901 (anti-CD56) and anti-B4 (anti-CD19). Resurfacing replaces the set of surface residues of a rodent variable region with a human set of surface residues. The method of CDR-grafting conceptually consists of transferring the CDRs from a rodent antibody onto the Fv framework of a human antibody. Computer-aided molecular modeling was used to design the initial CDR-grafted and resurfaced versions of these two antibodies. The initial versions of resurfaced N901 and resurfaced anti-B4 maintained the full binding affinity of the original murine parent antibodies and further refinements to these versions described herein generated five new resurfaced antibodies that contain fewer murine residues at surface positions, four of which also have the full parental binding affinity. A mutational study of three surface positions within 5 A of the CDRs of resurfaced anti-B4 revealed a remarkable ability of the resurfaced antibodies to maintain binding affinity despite dramatic changes of charges near their antigen recognition surfaces, suggesting that the resurfacing approach can be used with a high degree of confidence to design humanized antibodies that maintain the full parental binding affinity. By comparison CDR-grafted anti-B4 antibodies with parental affinity were produced only after seventeen versions were attempted using two different strategies for selecting the human acceptor frameworks. For both the CDR-grafted anti-B4 and N901 antibodies, full restoration of antigen binding affinity was achieved when the most identical human acceptor frameworks were selected. The CDR-grafted anti-B4 antibodies that maintained high affinity binding for CD19 had more murine residues at surface positions than any of the three versions of the resurfaced anti-B4 antibody. This observation suggests that the resurfacing approach can be used to produce humanized antibodies with reduced antigenic potential relative to their corresponding CDR-grafted versions.

Amino Acid Sequence↗