Smoothed Analysis of the Minimum-Mean Cycle Canceling Algorithm and the Network Simplex Algorithm

The minimum-cost flow (MCF) problem is a fundamental optimization problem with many applications and seems to be well understood. Over the last half century many algorithms have been developed to solve the MCF problem and these algorithms have varying worst-case bounds on their running time. However, these worst-case bounds are not always a good indication of the algorithms' performance in practice. The Network Simplex (NS) algorithm needs an exponential number of iterations for some instances, but it is considered the best algorithm in practice and performs best in experimental studies. On the other hand, the Minimum-Mean Cycle Canceling (MMCC) algorithm is strongly polynomial, but performs badly in experimental studies. To explain these differences in performance in practice we apply the framework of smoothed analysis. We show an upper bound of $O(mn^2\log(n)\log(\phi))$ for the number of iterations of the MMCC algorithm. Here $n$ is the number of nodes, $m$ is the number of edges, and $\phi$ is a parameter limiting the degree to which the edge costs are perturbed. We also show a lower bound of $\Omega(m\log(\phi))$ for the number of iterations of the MMCC algorithm, which can be strengthened to $\Omega(mn)$ when $\phi=\Theta(n^2)$. For the number of iterations of the NS algorithm we show a smoothed lower bound of $\Omega(m \cdot \min \{ n, \phi \} \cdot \phi)$.Comment: Extended abstract to appear in the proceedings of COCOON 201

Mod/Resc Parsimony Inference

We address in this paper a new computational biology problem that aims at understanding a mechanism that could potentially be used to genetically manipulate natural insect populations infected by inherited, intra-cellular parasitic bacteria. In this problem, that we denote by \textsc{Mod/Resc Parsimony Inference}, we are given a boolean matrix and the goal is to find two other boolean matrices with a minimum number of columns such that an appropriately defined operation on these matrices gives back the input. We show that this is formally equivalent to the \textsc{Bipartite Biclique Edge Cover} problem and derive some complexity results for our problem using this equivalence. We provide a new, fixed-parameter tractability approach for solving both that slightly improves upon a previously published algorithm for the \textsc{Bipartite Biclique Edge Cover}. Finally, we present experimental results where we applied some of our techniques to a real-life data set.Comment: 11 pages, 3 figure

Dynamic hierarchies in temporal directed networks

The outcome of interactions in many real-world systems can be often explained by a hierarchy between the participants. Discovering hierarchy from a given directed network can be formulated as follows: partition vertices into levels such that, ideally, there are only forward edges, that is, edges from upper levels to lower levels. In practice, the ideal case is impossible, so instead we minimize some penalty function on the backward edges. One practical option for such a penalty is agony, where the penalty depends on the severity of the violation. In this paper we extend the definition of agony to temporal networks. In this setup we are given a directed network with time stamped edges, and we allow the rank assignment to vary over time. We propose 2 strategies for controlling the variation of individual ranks. In our first variant, we penalize the fluctuation of the rankings over time by adding a penalty directly to the optimization function. In our second variant we allow the rank change at most once. We show that the first variant can be solved exactly in polynomial time while the second variant is NP-hard, and in fact inapproximable. However, we develop an iterative method, where we first fix the change point and optimize the ranks, and then fix the ranks and optimize the change points, and reiterate until convergence. We show empirically that the algorithms are reasonably fast in practice, and that the obtained rankings are sensible

Longitudinal Changes in Physical Caregiving for Parents of Children with Cerebral Palsy.

Aims: To determine changes in physical caregiving for parents of children with cerebral palsy (CP) over a two-year period based on children’s gross motor function level and age. Methods: 153 parents of children with CP rated their physical caregiving using the Ease of Caregiving for Children three times over two years. Parents and assessors classified children’s gross motor function using the Gross Motor Function Classification System (GMFCS). Physical caregiving was compared at three test times among parents of children grouped by GMFCS level (I, II–III, and IV–V) and age (1.7–5.9 and 6–11 years) using a three-way mixed ANOVA. Results: Among all analyses, a two-way interaction was found between children’s GMFCS level and test time on ease of caregiving, p \u3c 0.01. Change over two-year period was found for parents of children in level I and II–III, p \u3c 0.01, but not parents of children in levels IV–V. At each test time, parents of children in level I reported the greatest ease of caregiving followed by parents of children in levels II–III, and levels IV–V, who reported the lowest ease of caregiving, p \u3c 0.001. Conclusions: Findings support evaluation and monitoring of physical caregiving for parents of children with CP over time

Continuous gas processing without bubbles using thin liquid film bioreactors containing biocomposite biocatalysts

Continuous microbial gas processing without bubbles is possible with thin liquid film, plug flow bioreactors. We have demonstrated that power input can be minimized by using a falling liquid film operating under laminar wavy flow conditions (Re \u3c200) in contact with highly concentrated living, non-growing microbes stabilized in a porous biocomposite biocatalyst. This composite materials approach to continuous gas processing can dramatically increase mass transfer rates \u3e100 fold compared to bubble aeration, decrease process volume, significantly decrease gas-liquid mass transfer energy input, decrease water use, and increase secreted product concentration. We have shown that this approach can also increase microbial specific activity for some organisms compared to microbes suspended in liquid media. Paper-based biocomposite biocatalysts provide a rough hydrophilic surface resulting in uniform ~300 μm thick falling liquid films. Paper roughness enhances gas-liquid-microbe mass transfer. This mass transfer enhancement has been simulated using a finite element (FEM) CFD model. The paper structure also functions as a separation device - the secreted products are released into the falling liquid film and continuously removed from the reactor. We are investigating biocomposite biocatalyst design and stabilization using a 0.05 m2 prototype cylindrical paper falling film bioreactor (FFBR). This approach can be used for continuous gas processing with either non-photosynthetic or photosynthetic microorganisms. Current experimental model systems we are investigating include Clostridium ljungdahlii OTA1 for absorbing CO from syn-gas, Methylomycrobium alkaliphilum 20Z for absorbing CH4 in air, and Chlamydomonas renhardtii for CO2 emissions. Critical to biocomposite biocatalyst design are generation of nanoporous coating microstructure, microbe adhesion to paper during film formation (which may include engineering the surface of the microbes), surviving osmotic shock in coating formulations, as well as desiccation tolerance to drying and prolonged dry storage. Spatially correlated Raman microspectroscopy and hyperspectral imaging techniques have been developed as a non-destructive method to monitor the distribution of residual water surrounding and within the cells. The distribution of vitrified residual water may contribute to desiccation resistance. Other types of thin liquid film reactors, such as a spinning disk bioreactor (SDBR), that enhance mass transfer by reducing liquid film thickness to \u3c100 μm with wave induced turbulent flow using centrifugal force (1000 x g) can be used in the future to further intensify continuous gas processing rates using biocomposite biocatalysts

Visual-to-auditory sensory substitution alters language asymmetry in both sighted novices and experienced visually impaired users

Visual-to-auditory sensory substitution devices (SSDs) provide improved access to the visual environment for the visually impaired by converting images into auditory information. Research is lacking on the mechanisms involved in processing data that is perceived through one sensory modality, but directly associated with a source in a different sensory modality. This is important because SSDs that use auditory displays could involve binaural presentation requiring both ear canals, or monaural presentation requiring only one – but which ear would be ideal? SSDs may be similar to reading, as an image (printed word) is converted into sound (when read aloud). Reading, and language more generally, are typically lateralised to the left cerebral hemisphere. Yet, unlike symbolic written language, SSDs convert images to sound based on visuospatial properties, with the right cerebral hemisphere potentially having a role in processing such visuospatial data. Here we investigated whether there is a hemispheric bias in the processing of visual-to-auditory sensory substitution information and whether that varies as a function of experience and visual ability. We assessed the lateralization of auditory processing with two tests: a standard dichotic listening test and a novel dichotic listening test created using the auditory information produced by an SSD, The vOICe. Participants were tested either in the lab or online with the same stimuli. We did not find a hemispheric bias in the processing of visual-to-auditory information in visually impaired, experienced vOICe users. Further, we did not find any difference between visually impaired, experienced vOICe users and sighted novices in the hemispheric lateralization of visual-to-auditory information processing. Although standard dichotic listening is lateralised to the left hemisphere, the auditory processing of images in SSDs is bilateral, possibly due to the increased influence of right hemisphere processing. Auditory SSDs might therefore be equally effective with presentation to either ear if a monaural, rather than binaural, presentation were necessary