Automating Requirements Traceability: Two Decades of Learning from KDD

This paper summarizes our experience with using Knowledge Discovery in Data (KDD) methodology for automated requirements tracing, and discusses our insights.Comment: The work of the second author has been supported in part by NSF grants CCF-1511117 and CICI 1642134; 4 pages; in Proceedings of IEEE Requirements Engineering 201

A dynamic mode of mitotic bookmarking by transcription factors.

During mitosis, transcription is shut off, chromatin condenses, and most transcription factors (TFs) are reported to be excluded from chromosomes. How do daughter cells re-establish the original transcription program? Recent discoveries that a select set of TFs remain bound on mitotic chromosomes suggest a potential mechanism for maintaining transcriptional programs through the cell cycle termed mitotic bookmarking. Here we report instead that many TFs remain associated with chromosomes in mouse embryonic stem cells, and that the exclusion previously described is largely a fixation artifact. In particular, most TFs we tested are significantly enriched on mitotic chromosomes. Studies with Sox2 reveal that this mitotic interaction is more dynamic than in interphase and is facilitated by both DNA binding and nuclear import. Furthermore, this dynamic mode results from lack of transcriptional activation rather than decreased accessibility of underlying DNA sequences in mitosis. The nature of the cross-linking artifact prompts careful re-examination of the role of TFs in mitotic bookmarking

Speeding up Permutation Testing in Neuroimaging

Multiple hypothesis testing is a significant problem in nearly all neuroimaging studies. In order to correct for this phenomena, we require a reliable estimate of the Family-Wise Error Rate (FWER). The well known Bonferroni correction method, while simple to implement, is quite conservative, and can substantially under-power a study because it ignores dependencies between test statistics. Permutation testing, on the other hand, is an exact, non-parametric method of estimating the FWER for a given $\alpha$-threshold, but for acceptably low thresholds the computational burden can be prohibitive. In this paper, we show that permutation testing in fact amounts to populating the columns of a very large matrix ${\bf P}$. By analyzing the spectrum of this matrix, under certain conditions, we see that ${\bf P}$ has a low-rank plus a low-variance residual decomposition which makes it suitable for highly sub--sampled --- on the order of $0.5\%$ --- matrix completion methods. Based on this observation, we propose a novel permutation testing methodology which offers a large speedup, without sacrificing the fidelity of the estimated FWER. Our evaluations on four different neuroimaging datasets show that a computational speedup factor of roughly $50\times$ can be achieved while recovering the FWER distribution up to very high accuracy. Further, we show that the estimated $\alpha$-threshold is also recovered faithfully, and is stable.Comment: NIPS 1

EEG signals analysis using multiscale entropy for depth of anesthesia monitoring during surgery through artificial neural networks

In order to build a reliable index to monitor the depth of anesthesia (DOA), many algorithms have been proposed in recent years, one of which is sample entropy (SampEn), a commonly used and important tool to measure the regularity of data series. However, SampEn only estimates the complexity of signals on one time scale. In this study, a new approach is introduced using multiscale entropy (MSE) considering the structure information over different time scales. The entropy values over different time scales calculated through MSE are applied as the input data to train an artificial neural network (ANN) model using bispectral index (BIS) or expert assessment of conscious level (EACL) as the target. To test the performance of the new index's sensitivity to artifacts, we compared the results before and after filtration by multivariate empirical mode decomposition (MEMD). The new approach via ANN is utilized in real EEG signals collected from 26 patients before and after filtering by MEMD, respectively; the results show that is a higher correlation between index from the proposed approach and the gold standard compared with SampEn. Moreover, the proposed approach is more structurally robust to noise and artifacts which indicates that it can be used for monitoring the DOA more accurately.This research was financially supported by the Center for Dynamical Biomarkers and Translational Medicine, National Central University, Taiwan, which is sponsored by Ministry of Science and Technology (Grant no. MOST103-2911-I-008-001). Also, it was supported by National Chung-Shan Institute of Science & Technology in Taiwan (Grant nos. CSIST-095-V301 and CSIST-095-V302) and National Natural Science Foundation of China (Grant no. 51475342)

Two dimensional bulge disk decomposition

We propose a two dimensional galaxy fitting algorithm to extract parameters of the bulge, disk, and a central point source from broad band images of galaxies. We use a set of realistic galaxy parameters to construct a large number of model galaxy images which we then use as input to our galaxy fitting program to test it. We find that our approach recovers all structural parameters to a fair degree of accuracy. We elucidate our procedures by extracting parameters for 3 real galaxies -- NGC 661, NGC 1381, and NGC 1427.Comment: 23 pages, LaTeX, AASTEX macros used, 7 Postscript figures, submitted to Ap