3D time series analysis of cell shape using Laplacian approaches

Background: Fundamental cellular processes such as cell movement, division or food uptake critically depend on cells being able to change shape. Fast acquisition of three-dimensional image time series has now become possible, but we lack efficient tools for analysing shape deformations in order to understand the real three-dimensional nature of shape changes. Results: We present a framework for 3D+time cell shape analysis. The main contribution is three-fold: First, we develop a fast, automatic random walker method for cell segmentation. Second, a novel topology fixing method is proposed to fix segmented binary volumes without spherical topology. Third, we show that algorithms used for each individual step of the analysis pipeline (cell segmentation, topology fixing, spherical parameterization, and shape representation) are closely related to the Laplacian operator. The framework is applied to the shape analysis of neutrophil cells. Conclusions: The method we propose for cell segmentation is faster than the traditional random walker method or the level set method, and performs better on 3D time-series of neutrophil cells, which are comparatively noisy as stacks have to be acquired fast enough to account for cell motion. Our method for topology fixing outperforms the tools provided by SPHARM-MAT and SPHARM-PDM in terms of their successful fixing rates. The different tasks in the presented pipeline for 3D+time shape analysis of cells can be solved using Laplacian approaches, opening the possibility of eventually combining individual steps in order to speed up computations

The Importance of Forgetting: Limiting Memory Improves Recovery of Topological Characteristics from Neural Data

We develop of a line of work initiated by Curto and Itskov towards understanding the amount of information contained in the spike trains of hippocampal place cells via topology considerations. Previously, it was established that simply knowing which groups of place cells fire together in an animal's hippocampus is sufficient to extract the global topology of the animal's physical environment. We model a system where collections of place cells group and ungroup according to short-term plasticity rules. In particular, we obtain the surprising result that in experiments with spurious firing, the accuracy of the extracted topological information decreases with the persistence (beyond a certain regime) of the cell groups. This suggests that synaptic transience, or forgetting, is a mechanism by which the brain counteracts the effects of spurious place cell activity

Dynamic PRA: an Overview of New Algorithms to Generate, Analyze and Visualize Data

State of the art PRA methods, i.e. Dynamic PRA (DPRA) methodologies, largely employ system simulator codes to accurately model system dynamics. Typically, these system simulator codes (e.g., RELAP5 ) are coupled with other codes (e.g., ADAPT, RAVEN that monitor and control the simulation. The latter codes, in particular, introduce both deterministic (e.g., system control logic, operating procedures) and stochastic (e.g., component failures, variable uncertainties) elements into the simulation. A typical DPRA analysis is performed by: 1. Sampling values of a set of parameters from the uncertainty space of interest 2. Simulating the system behavior for that specific set of parameter values 3. Analyzing the set of simulation runs 4. Visualizing the correlations between parameter values and simulation outcome Step 1 is typically performed by randomly sampling from a given distribution (i.e., Monte-Carlo) or selecting such parameter values as inputs from the user (i.e., Dynamic Event Tre

Consistent SDNs through Network State Fuzzing

The conventional wisdom is that a software-defined network (SDN) operates under the premise that the logically centralized control plane has an accurate representation of the actual data plane state. Nevertheless, bugs, misconfigurations, faults or attacks can introduce inconsistencies that undermine correct operation. Previous work in this area, however, lacks a holistic methodology to tackle this problem and thus, addresses only certain parts of the problem. Yet, the consistency of the overall system is only as good as its least consistent part. Motivated by an analogy of network consistency checking with program testing, we propose to add active probe-based network state fuzzing to our consistency check repertoire. Hereby, our system, PAZZ, combines production traffic with active probes to continuously test if the actual forwarding path and decision elements (on the data plane) correspond to the expected ones (on the control plane). Our insight is that active traffic covers the inconsistency cases beyond the ones identified by passive traffic. PAZZ prototype was built and evaluated on topologies of varying scale and complexity. Our results show that PAZZ requires minimal network resources to detect persistent data plane faults through fuzzing and localize them quickly

Consistent SDNs through Network State Fuzzing

The conventional wisdom is that a software-defined network (SDN) operates under the premise that the logically centralized control plane has an accurate representation of the actual data plane state. Unfortunately, bugs, misconfigurations, faults or attacks can introduce inconsistencies that undermine correct operation. Previous work in this area, however, lacks a holistic methodology to tackle this problem and thus, addresses only certain parts of the problem. Yet, the consistency of the overall system is only as good as its least consistent part. Motivated by an analogy of network consistency checking with program testing, we propose to add active probe-based network state fuzzing to our consistency check repertoire. Hereby, our system, PAZZ, combines production traffic with active probes to periodically test if the actual forwarding path and decision elements (on the data plane) correspond to the expected ones (on the control plane). Our insight is that active traffic covers the inconsistency cases beyond the ones identified by passive traffic. PAZZ prototype was built and evaluated on topologies of varying scale and complexity. Our results show that PAZZ requires minimal network resources to detect persistent data plane faults through fuzzing and localize them quickly while outperforming baseline approaches.Comment: Added three extra relevant references, the arXiv later was accepted in IEEE Transactions of Network and Service Management (TNSM), 2019 with the title "Towards Consistent SDNs: A Case for Network State Fuzzing

Bi-velocity discrete particle swarm optimization and its application to multicast routing problem in communication networks

This paper proposes a novel bi-velocity discrete particle swarm optimization (BVDPSO) approach and extends its application to the NP-complete multicast routing problem (MRP). The main contribution is the extension of PSO from continuous domain to the binary or discrete domain. Firstly, a novel bi-velocity strategy is developed to represent possibilities of each dimension being 1 and 0. This strategy is suitable to describe the binary characteristic of the MRP where 1 stands for a node being selected to construct the multicast tree while 0 stands for being otherwise. Secondly, BVDPSO updates the velocity and position according to the learning mechanism of the original PSO in continuous domain. This maintains the fast convergence speed and global search ability of the original PSO. Experiments are comprehensively conducted on all of the 58 instances with small, medium, and large scales in the OR-library (Operation Research Library). The results confirm that BVDPSO can obtain optimal or near-optimal solutions rapidly as it only needs to generate a few multicast trees. BVDPSO outperforms not only several state-of-the-art and recent heuristic algorithms for the MRP problems, but also algorithms based on GA, ACO, and PSO