Regardless of the optimization method used, model parameter optimization requires a measure for the goodness of model neuron or network activity, i.e. for how well the model produces the desired electrical activity pattern. As an alternative to maximizing the goodness of a model, parameter optimization methods can also minimize the difference between the models activity and the biological target activity as measured by a distance or error function. Because both strategies are in use, this article does not distinguish between maximizing a goodness measure or minimizing an error measure and uses the two optimization strategies interchangeably. The choice of goodness or error measure depends on the purpose of the model neuron or network and can have significant influence on the results and success of model parameter optimization. Examples of goodness or error measures are: ...
Parameter optimization is an important aspect for achieving highest accurate results. This paper investigates different parameters of the one dimensional Log-Gabor filter approach to produce optimal recognition rates. ROC curves are adopted to measure the recognition accuracy. More than 20 million matches have been performed in our experiment. Our experimental results show that optimal wavelength is linear change with the normalized length in angular direction in the polar coordinates. This paper also finds the optimal phase number for pattern encoding, and the optimal radial length ...
Abstract: Recent years have witnessed extensive research activity in modeling biological phenomena as well as in developing intervention strategies for such phenomena. S-systems, which offer a good compromise between accuracy and mathematical flexibility, are a promising framework for modeling the dynamical behavior of biological phenomena. In this paper, two different intervention strategies, namely direct and indirect, are proposed for the S-system model. In the indirect approach, the prespecified desired values for the target variables are used to compute the reference values for the control inputs, and two control algorithms, namely simple sampled-data control and model predictive control (MPC), are developed for transferring the control variables from their initial values to the computed reference ones. In the direct approach, a MPC algorithm is developed that directly guides the target variables to their desired values. The proposed intervention strategies are applied to the ...
EONS modeling platform is a resourceful learning and research tool to study the mechanisms underlying the non-linear dynamics of synaptic transmission with the aid of mathematical models. Mathematical modeling of information processing in CNS pathways, in particular modeling of molecular events and synaptic dynamics, have not been extensively developed owing to the complex computations involved in integrating a multitude of parameters. In this paper, we discuss the development of a strategy to adapt the EONS synaptic modeling platform to a multi-node environment using a parallel computational framework to compute data intensive long simulations in a shorter time frame. We describe how this strategy can be applied to (i) determine the optimal values of the numerous parameters required for fitting experimental data, (ii) determine the impact of all parameters on various aspects of synaptic transmission (under normal conditions or conditions mimicking pathological conditions) and (iii) study the ...
A sequence of measured quantities is determined for a chemical reactor and a data generator generates a curve in normal coordinates from a respective predetermined normal form that describes a type of critical state. Each normal form is imaged onto the sequence of measured quantities by neural networks whereby a respective neural network is allocated to a data generator. The imaging is optimized by applying parameter optimization methods. The neural network that converges best through use of parameter optimization method describes the critical state that lies closest to the actual state of the chemical reactor.
This article investigates the ability of using plasma machining for cutting simultaneously two parallel thin layers at different gap distances. The main aim of this work is to identify whether this technology if mechanized can be more appropriate than using a circular saw to process a three-dimensional structure material such as double layers, box sections or rails. This research is aimed at those working in the automotive industry and converting vehicles. Test models were built for the experiments using 0.7 mm thick steel sheets DCO1 grade, similar material used for some underbody vehicle chassis parts. Serie of cuts were carried out first to analyze the ability of the plasma to perform a simultaneous cutting in two separate sheets with an air gap, followed by tests to minimize the deformation and heat affected zones on the top sheets adopting Taguchi methodology. Parameters analyzed included cutting speed, intensity, pressure, and gap distance between the two sheets. The specimens collected ...
In object-based image analysis (OBIA), the appropriate parametrization of segmentation algorithms is crucial for obtaining satisfactory image classification results. One of the ways this can be done is by unsupervised segmentation parameter optimi...
Abstract. As one of the drinking water sources for Xuzhou city, Yuquan River has been polluted seriously in recent years. In this paper, enhanced coagulation t
We invite submissions that apply mathematical modeling to the study of biological processes in microorganisms, mammalian cells, tissues, organs, and whole organisms. Suggested topics include, but are not limited to, metabolism, reaction and diffusion in biofilms, quorum sensing, signal transduction, protein trafficking, and gene regulation. Preference will be given to submissions that describe novel modeling approaches and directly link mathematical modeling with experimental data.. ...
The formation of filaments from naturally occurring protein molecules is a process at the core of a range of functional and aberrant biological phenomena, such as the assembly of the cytoskeleton or the appearance of aggregates in Alzheimers disease. The macroscopic behaviour associated with such processes
In order to study a complex biological phenomenon such as tumor cell metastasis, one must focus on examining discrete aspects of the process which are amenable to experimentation. In this thesis, I made use of xenograft ...
IEEE is a leader in engineering and technology education, providing resources for pre-university, university, and continuing professional education. IEEE offers innovative STEM and university education and recognition programs for students and their teachers, facilitates the accreditation of engineering programs at the university level, and offers ongoing continuing professional education for practitioners and engineering faculty through platforms such as the IEEE Learning Network (ILN). Explore education programs and offerings from IEEE below ...
materials with novel chemical, physical, mechanical, or intelligent properties, produced through processes that employ or mimic biological phenomena. ...
012492543X: Biochemistry, 2 Vol. Set, Metzler D.E. - |p align=justify|Biochemistry: The Chemical Reactions of Living Cells is a well-integrated, up-to-date reference for basic biochemistry, associated chemistry, and underlying biological phenomena. Bioche
Aging process is a biological phenomenon, which everyone has to undergo at a certain point of life. It is accentuated by a few factors, details of which are explained in the article below.
In this paper a new genetic algorithm called the Breeder Genetic Algorithm (BGA) is introduced. The BGA is based on artificial selection similar to that used by human breeders. A predictive model for the BGA is presented that is derived from quantitative genetics. The model is used to predict the behavior of the BGA for simple test functions. Different mutation schemes are compared by computing the expected progress to the solution. The numerical performance of the BGA is demonstrated on a test suite of multimodal functions. The number of function evaluations needed to locate the optimum scales only as n ln(n) where n is the number of parameters. Results up to n = 1000 are reported.. ...
JC just returned from two back-to-back meetings in Snowmass, CO. He presented work on small-helix partitioning in membranes at the first meeting on Free Energy Methods and structures of BamA and a new complex between SecY and a nascent chain at the second meeting on Membrane Proteins. Not all the time was spent in front of a screen though, as the picture to the right clearly shows!. ...
Fit biologically meaningful distribution functions to time-sequence data (phenology), estimate parameters to draw the cumulative distribution function and probability density function and calculate standard statistical moments and percentiles.
The work presented has highlighted the many disadvantages of parameter optimisation. Whilst significant improvements in the r.m.s.e were achieved in some areas, this was only after extensive testing and regeneration of the same model. The large number of strategy parameters used in OrthoMAX means that to test every parameter combination would be an enormous undertaking and clearly impracticable in normal circumstances. The data and results from the study prove the extreme variability of the software in certain areas, and the importance and criticality of the strategy parameters. Whilst the parameters have proved to have a significant effect in certain areas, the data has shown that manipulation of the parameters has little if any effect in areas well suited to the matching algorithm. Improvements in the accuracy of these areas are likely to be marginal through manipulation of the strategy parameters. The tests in this study were all carried out on data with checkpoint information. If this data ...
Role: lead data analyst. Carnegie Learning, Inc. has accumulated a large body of data on student learning in Cognitive Tutor Algebra® in the order of hundreds of schools, tens of thousands of students, and tens of millions of student problem-solving steps. This project is focusing on harnessing the Big Data to set up a close the loop workflow for iterative improvement of the Cognitive Tutor®. The improvement is driven by using machine learning to tune the parameters of the Bayesian cognitive model that tracks students progress and controls problem selection.. First results (Yudelson, et al., 2014a) show that only a subset of the Big Data - the Better Data - needs to be utilized to drive the optimization. Preliminary investigation of the Bayesian model parameter optimization effects for college-level math courses shows that students could save up to 37% of their time spent in Cognitive Tutor ® (in preparation).. ...
Despite recent advances in the field of image-guided interventions (IGI), the bottleneck for Angiography/X-ray guided procedures in particular is accurate and robust 2D-3D image alignment. The conventional, straight-forward parameter optimisation approach is known to be ill-posed and less efficient. Retrieval-based approaches may be of superior choice here. However, this requires salient and robust image features, which can handle the difficulties of Angiographic images such as high level of noise and contrast variance. In this paper, we investigate state-of-the-art features of the field of computer vision regarding the applicability and reliability in the challenging scenario of Angiography ...
Polymeric thin films coated on non-wettable substrates undergo film-instabilities, which are usually manifested as surface deformation in the form of dewetting or wrinkling. The former takes place in fluidic films, whereas the latter occurs in solid films. Therefore, there have rarely been reports of systems
Mathematical models have helped shape our current understanding of the way most of our world works, especially in the physical and macromolecular world where classical physics and Newtonian mechanics has dominated for several centuries. However, there is a strong drive to seek mathematical models to explain biological phenomena. Well established engineering fields such as electrical engineering or mechanical engineering have relied on mathematical models, but due to the dynamic nature of biological systems, modeling them is more difficult. The health care industry has grown over the past decade, and the US alone spends over $2 trillion per annum and is expected to double by 2015. With an increasing population, advancements in health care, and under changing health care consumer demands, the medical industry can no long afford to wait for serendipitous events to occur such as the discovery of the small pox vaccine or the discovery of penicillin. By creating and building on simple mathematical ...
The Journal of Mathematical Biology focuses on mathematical biology - work that uses mathematical approaches to gain biological understanding or explain biological phenomena.Papers should either provide biological insight as a ...
Cocoa is a dense annotator for biological text. It annotates macromolecules, chemicals, protein/DNA parts, organisms, processes, anatomical parts, locations, physiological terms, parameters, values, experimental techniques, and foods. It should be noted that Cocoas coverage of general biological phenomena (i.e. evolution) tends to be poor. Cocoa provides a RESTful API that returns information in JSON.
At the onset of our experiments with gemcitabine in pancreatic cancer cells, we were surprised to find that there was a large inconsistency in the published results (Fig. 1B and SI Appendix, Table S1). The same cell lines in different studies were reported as sensitive or resistant, and this was true in all 15 cell lines tested. We found that differences in sensitivity depended very strongly on the cell density (Fig. 1D), and this stands as the most likely explanation for these findings and perhaps for others in drug-profiling efforts (6). Discrepancy in experimental findings is often blamed on sloppiness and has been excoriated as part of an epidemic of irreproducible scientific experiments (51). A fairer lesson is that inconsistency may reflect the extreme sensitivity of some biological phenomena to experimental conditions. History has shown that trying to resolve these can inspire discovery, as we believe has happened here. The resolution to the discrepant findings with gemcitabine is in ...
Calpain represents a family of Ca(2+)-dependent cytosolic cysteine proteases found in almost all eukaryotes and some bacteria, and is involved in a variety of biological phenomena, including brain function. Several substrates of calpain are aggressively proteolyzed under pathological conditions, e.g …
New series in which each volume is dedicated to a single biological phenomenon and summarizes its genetic and molecular underpinnings. Emphasis is placed on comparing the approaches and results in several model systems, including bioinformatics where appropriate.
Programmed cell death or apoptosis is a widespread biological phenomenon. Apoptosis is characterized by typical cell features such as membrane blebbing, chromatin condensation, and DNA fragmentation....
Malvern MicroCal microcalorimeters enable characterization of biomolecular interactions in solution measurements of binding affinity thermodynamics and stability.
!%Plexera LLC%! has launched the PlexArray HT system, a high-throughput, label-free, surface plasmon resonance-based biomolecular interaction detecti
Pterygium is a common ocular surface disease characterized by fibrovascular invasion of the cornea and is sight-threatening due to astigmatism, tear film disturbance, or occlusion of the visual axis. However, the mechanisms for formation and post-surgical recurrence of pterygium are not understood, and a valid animal model does not exist. Here, we investigated the possible mechanisms of pterygium pathogenesis and recurrence. First we performed a genome wide expression analysis (human Affymetrix Genechip, |22000 genes) with principal component analysis and clustering techniques, and validated expression of key molecules with PCR. The controls for this study were the un-involved conjunctival tissue of the same eye obtained during the surgical resection of the lesions. Interesting molecules were further investigated with immunohistochemistry, Western blots, and comparison with tear proteins from pterygium patients. Principal component analysis in pterygium indicated a signature of matrix-related structural
Just about everyone on this planet would dearly love to honor any research scientist who can find a cure for cancer. Despite all the money and time already poured into extensive research efforts in labs and hospitals, the goal of curing this devastating clinical disease still remains elusive; about 589,000 cancer patients are expected to die from cancer in 2015 [1]. A big question thus arises, What good is all the research and money spent on trying to conquer cancer, if a cure still has not been found after all these years? The more you know about cancer as a biological phenomenon, the better will you be able to understand why attaining a general cure is so very, very difficult. This brief essay will teach you about the reasons for this frustrating situation that seems to damn the efforts of dedicated researchers in both basic and clinical science.. A brief background of essentials about cancer. At its most fundamental level, the biological phenomenon of cancer takes place in our cells. All ...
Just about everyone on this planet would dearly love to honor any research scientist who can find a cure for cancer. Despite all the money and time already poured into extensive research efforts in labs and hospitals, the goal of curing this devastating clinical disease still remains elusive; about 589,000 cancer patients are expected to die from cancer in 2015 [1]. A big question thus arises, What good is all the research and money spent on trying to conquer cancer, if a cure still has not been found after all these years? The more you know about cancer as a biological phenomenon, the better will you be able to understand why attaining a general cure is so very, very difficult. This brief essay will teach you about the reasons for this frustrating situation that seems to damn the efforts of dedicated researchers in both basic and clinical science.. A brief background of essentials about cancer. At its most fundamental level, the biological phenomenon of cancer takes place in our cells. All ...
PubMed comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
Cad Dynamic Freeware - Free Software Listing (Page3). Companion Software for the Dynamic Modeling and Control of Engineering Systems, 2e book by J. This book starts with a review of parameter optimization and then treats dynamic optimization, first with fixed final time and no constraints, next with terminal contraints, and finally with terminal constraints and open final time.
The paper that has been most influential to my career is most certainly Johnston, P. R., and D. H. Pilgrim (1976), Parameter optimization for watershed models, Water Resources Research, 12(3), 477-486. I read this paper during my graduate work in the early 1980s and was intrigued by their report that A true optimum set of (parameter) values was not found in over 2 years of full-time work concentrated on one watershed, although many apparent optimum sets were readily obtained.. On the one hand this paper clearly identified an important problem that needed to be addressed. On the other (as I often remark during talks on the subject), I think it was remarkable as an example of a paper reporting the apparent failure of the researchers to achieve their goals … how often do we see people reporting their failures in the literature these days :-). More of this kind of work - reporting a scientific study and accurately reporting both successes and failures … but especially failures … is ...
For statistical modeling, the model parameters are usually estimated by maximizing a probability measure, such as the likelihood or the posterior. In contrast, a variational Bayesian method threats the parameters of the model as probability distributions and computes optimal distributions for them rather than values. It has been shown that this approach effectively avoids the overfitting problem, which is common with other parameter optimization methods. This paper applies a variational Bayesian technique to surface fitting for height field data. Then, we propose point cloud denoising based on the basic surface fitting technique. Validation experiments and further tests with scan data verify the robustness of the proposed method. ...
CHANG Hung-Jen , FREEMAN Walter J. , BURKE Brian C. Neural networks : the official journal of the International Neural Network Society 11(3), 449-466, 1998-04-01 参考文献21件 被引用文献1件 ...
Recent advances in the use of plasmonic metamaterials to improve absorption of light in thin-film solar photovoltaic devices has created a demand for a scalable method of patterning large areas with metal nanostructures deposited in an ordered array. This article describes two methods of fabricating ordered 2D nanosphere colloidal films: spin coating and interface coating. The two methods are compared and parameter optimization discussed. The study reveals that: ...
EJBQL 3.0 Quick Reference Guide Parameters Optimizations …
Lipids are a different and ubiquitous cluster of compounds having key biological functions like structural constituents of cell membranes, aiding as energy storage bases and play a part in cell signaling pathways. Compound research in structural diversity of lipids benefits developments in the field of membrane lipids which in turn explains biological phenomena at the nanoscale sphere. Multiple roles can be performed by Phospholipids in cells by creating the permeability blockade for cells and cell organelles and by providing the matrix for the association and utility of a wide diversity of catalytic developments, also by substitute as donors in the production of macromolecules, and by keenly inducing the functional properties of membrane-associated developments.. ...
The Cell Systems Science Group conducts research in measurements and models that support the understanding of complex biological phenomena at the cellular and subcellular level.
If you have a question about this talk, please contact Lorena Escudero.. Location matters in biology. Both the inner workings of tissues and organs and their dysregulation, which leads to disease, depend on the tight web of relationships between different cell populations, and on the concerted regulation of their function mediated by genetic and environmental effects. In the last 10 years and more, it has become clear that many biological phenomena cannot be studied by analyzing cells in bulk and outside of their natural environment, but their underlying mechanisms can only be mechanistically investigated if observed both at the single-cell level and in situ. While technologies allowing either the former or the latter of these features are now available, combining both is extremely challenging, at least with the throughput necessary to obtain reliable results. In our laboratory, we have recently launched a project, named IMAXT (Imaging and Molecular Annotation of Xenografts and Tumours), that ...
Location matters in biology. Both the inner workings of tissues and organs and their dysregulation, which leads to disease, depend on the tight web of relationships between different cell populations, and on the concerted regulation of their function mediated by genetic and environmental effects. In the last 10 years and more, it has become clear that many biological phenomena cannot be studied by analyzing cells in bulk and outside of their natural environment, but their underlying mechanisms can only be mechanistically investigated if observed both at the single-cell level and in situ. While technologies allowing either the former or the latter of these features are now available, combining both is extremely challenging, at least with the throughput necessary to obtain reliable results. In our laboratory, we have recently launched a project, named IMAXT (Imaging and Molecular Annotation of Xenografts and Tumours), that aims to produce a comprehensive tri-dimensional map of breast tumours in ...
Bioengineering applies engineering principles and methodologies to biological and medical sciences to better understand biological phenomena, to devel...
Bioengineering applies engineering principles and methodologies to biological and medical sciences to better understand biological phenomena, to devel...
Calpains are intracellular Ca(2+)-dependent Cys proteases that play important roles in a wide range of biological phenomena via the limited proteolysis of their substrates. Genetic defects in calpain genes cause lethality and/or functional deficits in many organisms, including humans. Despite their …
A STRESSFUL life in the womb is known to affect adult behaviour in both animals and humans. But stress is a complex biological phenomenon, so scientists have found it hard to pin down the mechanism for this link. Now a team of researchers in France says that the stress hormone corticosterone is to blame. They …
to achieve the student with the theoretical skills that allow an adequate knowledge of physical and biological phenomena at the base of radioimmunoassay techniques.. ...
Transcription factor NF-κB: Nuclear factor κB (NF-κB) was initially identified as a transcription factor that binds to the κ-light-chain-enhancer of immunoglobulins expressed selectively in B cells, but it has since been shown to be expressed by almost all cells, including the cells of invertebrates, such as urchins and fruit flies, as well as higher animals. In mammals in particular, five molecules that belong to the NF-κB family, also called as the Rel family, are known. Members of the NF-κB family are involved in various biological phenomena, such as the immune response and cell viability, through induction of expression of inflammatory cytokines, antiapoptotic factors, etc. In addition, NF-κB activation is dysregulated in various diseases, including inflammatory and autoimmune diseases, and cancer, and attention is therefore being given to NF-κB as target molecules for treatment of various diseases ...
We use the tools of Structural Biology to investigate the key biomolecular interactions that underpin the molecular mechanisms of life and disease.. Read More ». ...