Algorithms for spatial collocation pattern mining in a limited memory environment: a summary of results

Rapid growth of spatial datasets requires methods to find (semi-)automatically spatial knowledge from these sets. Spatial collocation patterns represent subsets of spatial features whose instances are frequently located together in a spatial neighborhood. In recent years, efficient methods for collocation discovery have been developed, however, none of them assume limited size of the operational memory or limited access to memory with short access times. Such restrictions are especially important in the context of the large size of the data structures required for efficient identification of collocation instances. In this work we present and compare three algorithms for collocation pattern mining in a limited memory environment. The first algorithm is based on the well-known joinless method introduced by Shekhar and Yoo. The second and third algorithms are inspired by a tree structure (iCPI-tree) presented by Wang et al. In our experimental evaluation, we have compared the efficiency of the algorithms, both on synthetic and real world datasets.     

Cryo-EM image alignment based on nonuniform fast Fourier transform

In single particle analysis, two-dimensional (2-D) alignment is a fundamental step intended to put into register various particle projections of biological macromolecules collected at the electron microscope. The efficiency and quality of three-dimensional (3-D) structure reconstruction largely depends on the computational speed and alignment accuracy of this crucial step. In order to improve the performance of alignment, we introduce a new method that takes advantage of the highly accurate interpolation scheme based on the gridding method, a version of the nonuniform fast Fourier transform, and utilizes a multi-dimensional optimization algorithm for the refinement of the orientation parameters. Using simulated data, we demonstrate that by using less than half of the sample points and taking twice the runtime, our new 2-D alignment method achieves dramatically better alignment accuracy than that based on quadratic interpolation. We also apply our method to image to volume registration, the key step in the single particle EM structure refinement protocol. We find that in this case the accuracy of the method not only surpasses the accuracy of the commonly used real-space implementation, but results are achieved in much shorter time, making gridding-based alignment a perfect candidate for efficient structure determination in single particle analysis.     

Segmentation of microscope images of living cells

This paper describes a segmentation method combining a texture based technique with a contour based method. The technique is designed to enable the study of cell behaviour over time by segmenting brightfield microscope image sequences. The technique was tested on artificial images, based on images of living cells and on real sequences acquired from microscope observations of neutrophils and lymphocytes as well as on a sequence of MRI images. The results of the segmentation are compared with the results of the watershed and snake segmentation methods. The results show that the method is both effective and practical.

An empirical analysis of heuristics for solving the two-machine flow shop problem with job release times

The theoretical analysis of heuristics for solving intractable optimization problems has many well-known drawbacks. Constructed instances demonstrating an exceptionally poor worst-case performance of heuristics are typically too peculiar to occur in practice. Theoretical results on the average-case performance of most heuristics could not be established due to the difficulty with the use of probabilistic analysis. Moreover, the heuristics for which some type of asymptotic optimality has been proven are likely to perform questionably in practice. The purpose of this paper is to confront known theoretical results with our empirical results concerning heuristics for solving the strongly NP-hard problem of minimizing the makespan in a two-machine flow shop with job release times. The heuristics' performance is examined with respect to their average and maximum relative errors, as well as their optimality rate, that is, the probability of being optimal. In particular, this allows us to observe that the asymptotic optimality rate of so called “almost surely asymptotically optimal” heuristic can be zero. We also present a new heuristic with short worst-case running time and statistically prove that it outperforms all heuristics known so far. However, our empirical experiments reveal that the heuristic is on average slower that its competitors with much longer worst-case running times.     

Application of Sensitivity Analysis to Discover Potential Molecular Drug Targets

Mathematical modeling of signaling pathways and regulatory networks has been supporting experimental research for some time now. Sensitivity analysis, aimed at finding model parameters whose changes yield significantly altered cellular responses, is an important part of modeling work. However, sensitivity methods are often directly transplanted from analysis of technical systems, and thus, they may not serve the purposes of analysis of biological systems. This paper presents a novel sensitivity analysis method that is particularly suited to the task of searching for potential molecular drug targets in signaling pathways. Using two sample models of pathways, p53/Mdm2 regulatory module and IFN-β-induced JAK/STAT signaling pathway, we show that the method leads to biologically relevant conclusions, identifying processes suitable for targeted pharmacological inhibition, represented by the reduction of kinetic parameter values. That, in turn, facilitates subsequent search for active drug components.     

A dynamic call admission scheme for VBR traffic in ATM networks

The role of call admission control (CAC) in high-speed networks is to maintain the network utilization at a high level, while ensuring that the quality of service (QoS) requirements of the individual calls are met. We use the term static CAC to describe schemes that always allocate the same bandwidth to a specific group of multiplexed calls, independent of the other traffic sharing the link. Dynamic CAC, on the other hand, denotes a scheme in which the bandwidth allocation to a group of calls sharing a queue is influenced by the traffic in other queues destined for the same outgoing link. We propose a generic dynamic call admission scheme for VBR and ABR traffic whose aim is to reduce the blocking rate for VBR calls at the expense of a higher blocking rate for ABR calls. Our scheme is generic because it builds up on a pre-existing static scheme, e.g., one based on a simple notion of effective bandwidth. Our simple approach results in a significant reduction of the blocking rate for VBR traffic (several orders of magnitude), if the bandwidth requirements of a single call are a reasonably small fraction of the link capacity. At the same time, the deterioration of service for ABR traffic can be contained. This revised version was published online in August 2006 with corrections to the Cover Date.     

Photolithographic patterning of organic photodetectors with a non-fluorinated photoresist system

We report on the fabrication of organic photodetectors (OPD) based on isolated islands of P3HT:PCBM. Pattern transfer to the active material was done with photolithography based on non-fluorinated solvents and the excessive organic semiconductor was removed with oxygen plasma reactive ion etching. The photoresist system used was found to be benign to the P3HT:PCBM layer as confirmed by absorption, thickness and roughness measurements. Current–voltage characteristics and external quantum efficiency (EQE) remained unchanged after the patterning process. It was demonstrated that it is possible to photolithographically pattern isolated islands with 200 μm edge length with the same dark current density (<10⁻⁵ A/cm² at −2 V bias voltage) and photocurrent density (>5 × 10⁻³ A/cm² at −2 V). Furthermore, concerning the solar cell performance, the patterned, small-area devices showed power conversion efficiency of 2.1% and fill-factor of 60%. Dark current was observed to depend on the size of the remaining semiconductor island, which was demonstrated on OPDs with diameter of 50 μm. The presented results show the feasibility of fabrication of isolated devices based on organic semiconductors patterned with non-fluorinated photolithography.     

Simulations for the Development of Thermoelectric Measurements

In thermoelectricity, continuum theoretical equations are usually used for the calculation of the characteristics and performance of thermoelectric elements, modules or devices as a function of external parameters (material, geometry, temperatures, current, flow, load, etc.). An increasing number of commercial software packages aimed at applications, such as COMSOL and ANSYS, contain vkernels using direct thermoelectric coupling. Application of these numerical tools also allows analysis of physical measurement conditions and can lead to specifically adapted methods for developing special test equipment required for the determination of TE material and module properties. System-theoretical and simulation-based considerations of favorable geometries are taken into account to create draft sketches in the development of such measurement systems. Particular consideration is given to the development of transient measurement methods, which have great advantages compared with the conventional static methods in terms of the measurement duration required. In this paper the benefits of using numerical tools in designing measurement facilities are shown using two examples. The first is the determination of geometric correction factors in four-point probe measurement of electrical conductivity, whereas the second example is focused on the so-called combined thermoelectric measurement (CTEM) system, where all thermoelectric material properties (Seebeck coefficient, electrical and thermal conductivity, and Harman measurement of zT) are measured in a combined way. Here, we want to highlight especially the measurement of thermal conductivity in a transient mode. Factors influencing the measurement results such as coupling to the environment due to radiation, heat losses via the mounting of the probe head, as well as contact resistance between the sample and sample holder are illustrated, analyzed, and discussed. By employing the results of the simulations, we have developed an improved sample head that allows for measurements over a larger temperature interval with enhanced accuracy.     

Highly Stretchable Conducting SIBS‐P3HT Fibers

Poly(styrene‐β‐isobutylene‐β‐styrene)‐poly(3‐hexylthiophene) (SIBS‐P3HT) conducting composite fibers are successfully produced using a continuous flow approach. Composite fibers are stiffer than SIBS fibers and able to withstand strains of up 975% before breaking. These composite fibers exhibit interesting reversible mechanical and electrical characteristics, which are applied to demonstrate their strain gauging capabilities. This will facilitate their potential applications in strain sensing or elastic electrodes. Here, the fabrication and characterization of highly stretchable electrically conducting SIBS‐P3HT fibers using a solvent/non‐solvent wet‐spinning technique is reported. This fabrication method combines the processability of conducting SIBS‐P3HT blends with wet‐spinning, resulting in fibers that could be easily spun up to several meters long. The resulting composite fiber materials exhibit an increased stiffness (higher Young’s modulus) but lower ductility compared to SIBS fibers. The fibers’ reversible mechanical and electrical characteristics are applied to demonstrate their strain gauging capabilities.