An integrated approach of particle swarm optimization and support vector machine for gene signature selection and cancer prediction

To improve cancer diagnosis and drug development, the classification of tumor types based on genomic information is important. As DNA micro array studies produce a large amount of data, expression data are highly redundant and noisy, and most genes are believed to be uninformative with respect to the studied classes. Only a fraction of genes may present distinct profiles for different classes of samples. Classification tools to deal with these issues are thus important. These tools should learn to robustly identify a subset of informative genes embedded in a large dataset that is contaminated with high dimensional noises. In this paper, an integrated approach of support vector machine (SVM) and particle swarm optimization (PSO) is proposed for this purpose. The proposed approach can simultaneously optimize the selection of feature subset and the classifier through a common solution coding mechanism. As an illustration, the proposed approach is applied to search the combinational gene signatures for predicting histologic response to chemotherapy of osteosarcoma patients. Cross validation results show that the proposed approach outperforms other existing methods in terms of classification accuracy. Further validation using an independent dataset shows misclassification of only one out of fourteen patient samples, suggesting that the selected gene signatures can reflect the chemoresistance in osteosarcoma

Modeling of epoxy dispensing process using a hybrid fuzzy regression approach

In the semiconductor manufacturing industry, epoxy dispensing is a popular process commonly used in die bonding as well as in microchip encapsulation for electronic packaging. Modeling the epoxy dispensing process is important because it enables us to understand the process behavior, as well as determine the optimum operating conditions of the process for a high yield, low cost, and robust operation. Previous studies of epoxy dispensing have mainly focused on the development of analytical models. However, an analytical model for epoxy dispensing is difficult to develop because of its complex behavior and high degree of uncertainty associated with the process in a real-world environment. Previous studies of modeling the epoxy dispensing process have not addressed the development of explicit models involving high-order and interaction terms, as well as fuzziness between process parameters. In this paper, a hybrid fuzzy regression (HFR) method integrating fuzzy regression with genetic programming is proposed to make up the deficiency. Two process models are generated for the two quality characteristics of the process, encapsulation weight and encapsulation thickness based on the HFR, respectively. Validation tests are performed. The performance of the models developed based on the HFR outperforms the performance of those based on statistical regression and fuzzy regression

Design standards for engineered tissues

Traditional technologies are required to meet specific, quantitative standards of safety and performance. In tissue engineering, similar standards will have to be developed to enable routine clinical use and customized tissue fabrication. In this essay, we discuss a framework of concepts leading towards general design standards for tissue-engineering, focusing in particular on systematic design strategies, control of cell behavior, physiological scaling, fabrication modes and functional evaluation

Large Photonic Band Gaps in Certain Periodic and Quasi-Periodic Networks in two and three dimensions

The photonic band structures in certain two- and three-dimensional periodic networks made of one-dimensional waveguides are studied by using the Floquet-Bloch theorem. We find that photonic band gaps exist only in those structures where the fundamental loop exhibits anti-resonant transmission. This is also true for quasi-periodic networks in two and three dimensions, where the photonic band structures are calculated from the spectra of total transmission arising from a source inside the samples. In all the cases we have studied, it is also found that the gap positions in a network are dictated by the frequencies at which the anti-resonance occurs.Comment: 7 pages, 10 figures and 1 table. Published in Phys. Rev. B, 70, 125104 (2004

Somatotopy and movement representation sites following cortical stroke.

Stroke has been associated with many changes in motor system function, but there has been limited study of changes in somatotopic organization. This was examined in a group of patients with cortical stroke affecting primary sensorimotor cortex. In 17 patients with good outcome after cortical stroke involving precentral and/or postcentral gyri, plus 14 controls, four functional MRI evaluations of brain activity were obtained: finger, shoulder, and face motor tasks plus a sensory task, passive finger motion. For each, coordinates for contralateral primary sensorimotor cortex activation site were determined, as was a measure of inter-hemispheric balance. The normal motor somatotopy measured in controls was largely preserved after stroke. The main difference found between controls and patients was that the face was lateral to finger motor activation in all controls, but face was centered medial to finger in 43% of patients. Among patients, smaller infarct volume was associated with more ventral, and larger infarct with more dorsal, contralateral primary sensorimotor cortex activation. On the other hand, better behavioral outcome was associated with a more posterior, and poorer outcome with more anterior, activation. Larger infarct and poorer behavioral outcome were each associated with a change in inter-hemispheric balance towards the non-stroke hemisphere. Shifts in contralateral movement representation site did not correlate with changes in inter-hemispheric balance. Motor somatotopy is generally preserved after injury to primary sensorimotor cortex. Greater injury and larger behavioral deficits are associated with distinct effects on movement representation sites. Changes in motor organization within and between hemispheres arise independently after stroke