Autonomous Algorithms for Centralized and Distributed Interference Coordination: A Virtual Layer Based Approach

Interference mitigation techniques are essential for improving the performance of interference limited wireless networks. In this paper, we introduce novel interference mitigation schemes for wireless cellular networks with space division multiple access (SDMA). The schemes are based on a virtual layer that captures and simplifies the complicated interference situation in the network and that is used for power control. We show how optimization in this virtual layer generates gradually adapting power control settings that lead to autonomous interference minimization. Thereby, the granularity of control ranges from controlling frequency sub-band power via controlling the power on a per-beam basis, to a granularity of only enforcing average power constraints per beam. In conjunction with suitable short-term scheduling, our algorithms gradually steer the network towards a higher utility. We use extensive system-level simulations to compare three distributed algorithms and evaluate their applicability for different user mobility assumptions. In particular, it turns out that larger gains can be achieved by imposing average power constraints and allowing opportunistic scheduling instantaneously, rather than controlling the power in a strict way. Furthermore, we introduce a centralized algorithm, which directly solves the underlying optimization and shows fast convergence, as a performance benchmark for the distributed solutions. Moreover, we investigate the deviation from global optimality by comparing to a branch-and-bound-based solution.Comment: revised versio

Algorithms for Analysis of Heterogeneous Cancer and Viral Populations Using High-Throughput Sequencing Data

Next-generation sequencing (NGS) technologies experienced giant leaps in recent years. Short read samples reach millions of reads, and the number of samples has been growing enormously in the wake of the COVID-19 pandemic. This data can expose essential aspects of disease transmission and development and reveal the key to its treatment. At the same time, single-cell sequencing saw the progress of getting from dozens to tens of thousands of cells per sample. These technological advances bring new challenges for computational biology and require the development of scalable, robust methods to deal with a wide range of problems varying from epidemiology to cancer studies. The first part of this work is focused on processing virus NGS data. It proposes algorithms that can facilitate the initial data analysis steps by filtering genetically related sequencing and the tool investigating intra-host virus diversity vital for biomedical research and epidemiology. The second part addresses single-cell data in cancer studies. It develops evolutionary cancer models involving new quantitative parameters of cancer subclones to understand the underlying processes of cancer development better

Homeostatic plasticity and external input shape neural network dynamics

In vitro and in vivo spiking activity clearly differ. Whereas networks in vitro develop strong bursts separated by periods of very little spiking activity, in vivo cortical networks show continuous activity. This is puzzling considering that both networks presumably share similar single-neuron dynamics and plasticity rules. We propose that the defining difference between in vitro and in vivo dynamics is the strength of external input. In vitro, networks are virtually isolated, whereas in vivo every brain area receives continuous input. We analyze a model of spiking neurons in which the input strength, mediated by spike rate homeostasis, determines the characteristics of the dynamical state. In more detail, our analytical and numerical results on various network topologies show consistently that under increasing input, homeostatic plasticity generates distinct dynamic states, from bursting, to close-to-critical, reverberating and irregular states. This implies that the dynamic state of a neural network is not fixed but can readily adapt to the input strengths. Indeed, our results match experimental spike recordings in vitro and in vivo: the in vitro bursting behavior is consistent with a state generated by very low network input (< 0.1%), whereas in vivo activity suggests that on the order of 1% recorded spikes are input-driven, resulting in reverberating dynamics. Importantly, this predicts that one can abolish the ubiquitous bursts of in vitro preparations, and instead impose dynamics comparable to in vivo activity by exposing the system to weak long-term stimulation, thereby opening new paths to establish an in vivo-like assay in vitro for basic as well as neurological studies.Comment: 14 pages, 8 figures, accepted at Phys. Rev.

Live media production: multicast optimization and visibility for clos fabric in media data centers

Media production data centers are undergoing a major architectural shift to introduce digitization concepts to media creation and media processing workflows. Content companies such as NBC Universal, CBS/Viacom and Disney are modernizing their workflows to take advantage of the flexibility of IP and virtualization. In these new environments, multicast is utilized to provide point-to-multi-point communications. In order to build point-to-multi-point trees, Multicast has an established set of control protocols such as IGMP and PIM. The existing multicast protocols do not optimize multicast tree formation for maximizing network throughput which lead to decreased fabric utilization and decreased total number of admitted flows. In addition, existing multicast protocols are not bandwidth-aware and could cause links to over-subscribe leading to packet loss and lower video quality. TV production traffic patterns are unique due to ultra high bandwidth requirements and high sensitivity to packet loss that leads to video impairments. In such environments, operators need monitoring tools that are able to proactively monitor video flows and provide actionable alerts. Existing network monitoring tools are inadequate because they are reactive by design and perform generic monitoring of flows with no insights into video domain. The first part of this dissertation includes a design and implementation of a novel Intelligent Rendezvous Point algorithm iRP for bandwidth-aware multicast routing in media DC fabrics. iRP utilizes a controller-based architecture to optimize multicast tree formation and to increase bandwidth availability in the fabric. The system offers up to 50\% increase in fabric capacity to handle multicast flows passing through the fabric. In the second part of this dissertation, DiRP algorithm is presented. DiRP is based on a distributed decision-making approach to achieve multicast tree capacity optimization while maintaining low multicast tree setup time. DiRP algorithm is tested using commercially available data center switches. DiRP algorithm offers substantially lower path setup time compared to centralized systems while maintaining bandwidth awareness when setting up the fabric. The third part of this dissertation studies the utilization of machine learning algorithms to improve on multicast efficiency in the fabric. The work includes implementation and testing of LiRP algorithm to increase iRP\u27s fabric efficiency by implementing k-fold cross validation method to predict future multicast group memberships for time-series analysis. Testing results confirm that LiRP system increases the efficiency of iRP by up to 40\% through prediction of multicast group memberships with online arrival. In the fourth part of this dissertation, The problem of live video monitoring is studied. Existing network monitoring tools are either reactive by design or perform generic monitoring of flows with no insights into video domain. MediaFlow is a robust system for active network monitoring and reporting of video quality for thousands of flows simultaneously using a fraction of the cost of traditional monitoring solutions. MediaFlow is able to detect and report on integrity of video flows at a granularity of 100 mSec at line rate for thousands of flows. The system increases video monitoring scale by a thousand-fold compared to edge monitoring solutions

Energy consumption in networks on chip : efficiency and scaling

Computer architecture design is in a new era where performance is increased by replicating processing cores on a chip rather than making CPUs larger and faster. This design strategy is motivated by the superior energy efficiency of the multi-core architecture compared to the traditional monolithic CPU. If the trend continues as expected, the number of cores on a chip is predicted to grow exponentially over time as the density of transistors on a die increases. A major challenge to the efficiency of multi-core chips is the energy used for communication among cores over a Network on Chip (NoC). As the number of cores increases, this energy also increases, imposing serious constraints on design and performance of both applications and architectures. Therefore, understanding the impact of different design choices on NoC power and energy consumption is crucial to the success of the multi- and many-core designs. This dissertation proposes methods for modeling and optimizing energy consumption in multi- and many-core chips, with special focus on the energy used for communication on the NoC. We present a number of tools and models to optimize energy consumption and model its scaling behavior as the number of cores increases. We use synthetic traffic patterns and full system simulations to test and validate our methods. Finally, we take a step back and look at the evolution of computer hardware in the last 40 years and, using a scaling theory from biology, present a predictive theory for power-performance scaling in microprocessor systems

Segment Routing: a Comprehensive Survey of Research Activities, Standardization Efforts and Implementation Results

Fixed and mobile telecom operators, enterprise network operators and cloud providers strive to face the challenging demands coming from the evolution of IP networks (e.g. huge bandwidth requirements, integration of billions of devices and millions of services in the cloud). Proposed in the early 2010s, Segment Routing (SR) architecture helps face these challenging demands, and it is currently being adopted and deployed. SR architecture is based on the concept of source routing and has interesting scalability properties, as it dramatically reduces the amount of state information to be configured in the core nodes to support complex services. SR architecture was first implemented with the MPLS dataplane and then, quite recently, with the IPv6 dataplane (SRv6). IPv6 SR architecture (SRv6) has been extended from the simple steering of packets across nodes to a general network programming approach, making it very suitable for use cases such as Service Function Chaining and Network Function Virtualization. In this paper we present a tutorial and a comprehensive survey on SR technology, analyzing standardization efforts, patents, research activities and implementation results. We start with an introduction on the motivations for Segment Routing and an overview of its evolution and standardization. Then, we provide a tutorial on Segment Routing technology, with a focus on the novel SRv6 solution. We discuss the standardization efforts and the patents providing details on the most important documents and mentioning other ongoing activities. We then thoroughly analyze research activities according to a taxonomy. We have identified 8 main categories during our analysis of the current state of play: Monitoring, Traffic Engineering, Failure Recovery, Centrally Controlled Architectures, Path Encoding, Network Programming, Performance Evaluation and Miscellaneous...Comment: SUBMITTED TO IEEE COMMUNICATIONS SURVEYS & TUTORIAL

EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data

Recovery of ribosomal small subunit genes by assembly of short read community DNA sequence data generally fails, making taxonomic characterization difficult. Here, we solve this problem with a novel iterative method, based on the expectation maximization algorithm, that reconstructs full-length small subunit gene sequences and provides estimates of relative taxon abundances. We apply the method to natural and simulated microbial communities, and correctly recover community structure from known and previously unreported rRNA gene sequences. An implementation of the method is freely available at https://github.com/csmiller/EMIRGE

Existing and Potential Statistical and Computational Approaches for the Analysis of 3D CT Images of Plant Roots

Scanning technologies based on X-ray Computed Tomography (CT) have been widely used in many scientific fields including medicine, nanosciences and materials research. Considerable progress in recent years has been made in agronomic and plant science research thanks to X-ray CT technology. X-ray CT image-based phenotyping methods enable high-throughput and non-destructive measuring and inference of root systems, which makes downstream studies of complex mechanisms of plants during growth feasible. An impressive amount of plant CT scanning data has been collected, but how to analyze these data efficiently and accurately remains a challenge. We review statistical and computational approaches that have been or may be effective for the analysis of 3D CT images of plant roots. We describe and comment on different approaches to aspects of the analysis of plant roots based on images, namely, (1) root segmentation, i.e., the isolation of root from non-root matter; (2) root-system reconstruction; and (3) extraction of higher-level phenotypes. As many of these approaches are novel and have yet to be applied to this context, we limit ourselves to brief descriptions of the methodologies. With the rapid development and growing use of X-ray CT scanning technologies to generate large volumes of data relevant to root structure, it is timely to review existing and potential quantitative and computational approaches to the analysis of such data. Summaries of several computational tools are included in the Appendix