SCIP-Jack—a solver for STP and variants with parallelization extensions

This is the author accepted manuscript. The final version is available from Springer Verlag via the DOI in this record The Steiner tree problem in graphs is a classical problem that commonly arises in practical applications as one of many variants. While often a strong relationship between different Steiner tree problem variants can be observed, solution approaches employed so far have been prevalently problemspecific. In contrast, this paper introduces a general-purpose solver that can be used to solve both the classical Steiner tree problem and many of its variants without modification. This versatility is achieved by transforming various problem variants into a general form and solving them by using a state-ofthe-art MIP-framework. The result is a high-performance solver that can be employed in massively parallel environments and is capable of solving previously unsolved instances.German Federal Ministry of Education and Researc

Inference of single-cell phylogenies from lineage tracing data using Cassiopeia.

The pairing of CRISPR/Cas9-based gene editing with massively parallel single-cell readouts now enables large-scale lineage tracing. However, the rapid growth in complexity of data from these assays has outpaced our ability to accurately infer phylogenetic relationships. First, we introduce Cassiopeia-a suite of scalable maximum parsimony approaches for tree reconstruction. Second, we provide a simulation framework for evaluating algorithms and exploring lineage tracer design principles. Finally, we generate the most complex experimental lineage tracing dataset to date, 34,557 human cells continuously traced over 15 generations, and use it for benchmarking phylogenetic inference approaches. We show that Cassiopeia outperforms traditional methods by several metrics and under a wide variety of parameter regimes, and provide insight into the principles for the design of improved Cas9-enabled recorders. Together, these should broadly enable large-scale mammalian lineage tracing efforts. Cassiopeia and its benchmarking resources are publicly available at www.github.com/YosefLab/Cassiopeia

Optimization in Telecommunication Networks

Network design and network synthesis have been the classical optimization problems intelecommunication for a long time. In the recent past, there have been many technologicaldevelopments such as digitization of information, optical networks, internet, and wirelessnetworks. These developments have led to a series of new optimization problems. Thismanuscript gives an overview of the developments in solving both classical and moderntelecom optimization problems.We start with a short historical overview of the technological developments. Then,the classical (still actual) network design and synthesis problems are described with anemphasis on the latest developments on modelling and solving them. Classical results suchas Menger’s disjoint paths theorem, and Ford-Fulkerson’s max-flow-min-cut theorem, butalso Gomory-Hu trees and the Okamura-Seymour cut-condition, will be related to themodels described. Finally, we describe recent optimization problems such as routing andwavelength assignment, and grooming in optical networks.operations research and management science;

EFFICIENT IMPLEMENTATION OF BRANCH-AND-BOUND METHOD ON DESKTOP GRIDS

The Berkeley Open Infrastructure for Network Computing (BOINC) is an opensource middleware system for volunteer and desktop grid computing. In this paper we propose BNBTEST, a BOINC version of distributed branch and bound method. The crucial issues of distributed branch-and-bound method are traversing the search tree and loading balance. We developed subtaskspackaging method and three dierent subtasks' distribution strategies to solve these

Graphics Processing Unit-Based Computer-Aided Design Algorithms for Electronic Design Automation

The electronic design automation (EDA) tools are a specific set of software that play important roles in modern integrated circuit (IC) design. These software automate the design processes of IC with various stages. Among these stages, two important EDA design tools are the focus of this research: floorplanning and global routing. Specifically, the goal of this study is to parallelize these two tools such that their execution time can be significantly shortened on modern multi-core and graphics processing unit (GPU) architectures. The GPU hardware is a massively parallel architecture, enabling thousands of independent threads to execute concurrently. Although a small set of EDA tools can benefit from using GPU to accelerate their speed, most algorithms in this field are designed with the single-core paradigm in mind. The floorplanning and global routing algorithms are among the latter, and difficult to render any speedup on the GPU due to their inherent sequential nature. This work parallelizes the floorplanning and global routing algorithm through a novel approach and results in significant speedups for both tools implemented on the GPU hardware. Specifically, with a complete overhaul of solution space and design space exploration, a GPU-based floorplanning algorithm is able to render 4-166X speedup, while achieving similar or improved solutions compared with the sequential algorithm. The GPU-based global routing algorithm is shown to achieve significant speedup against existing state-of-the-art routers, while delivering competitive solution quality. Importantly, this parallel model for global routing renders a stable solution that is independent from the level of parallelism. In summary, this research has shown that through a design paradigm overhaul, sequential algorithms can also benefit from the massively parallel architecture. The findings of this study have a positive impact on the efficiency and design quality of modern EDA design flow

Design of Overlay Networks for Internet Multicast - Doctoral Dissertation, August 2002

Multicast is an efficient transmission scheme for supporting group communication in networks. Contrasted with unicast, where multiple point-to-point connections must be used to support communications among a group of users, multicast is more efficient because each data packet is replicated in the network – at the branching points leading to distinguished destinations, thus reducing the transmission load on the data sources and traffic load on the network links. To implement multicast, networks need to incorporate new routing and forwarding mechanisms in addition to the existing are not adequately supported in the current networks. The IP multicast are not adequately supported in the current networks. The IP multicast solution has serious scaling and deployment limitations, and cannot be easily extended to provide more enhanced data services. Furthermore, and perhaps most importantly, IP multicast has ignored the economic nature of the problem, lacking incentives for service providers to deploy the service in wide area networks. Overlay multicast holds promise for the realization of large scale Internet multicast services. An overlay network is a virtual topology constructed on top of the Internet infrastructure. The concept of overlay networks enables multicast to be deployed as a service network rather than a network primitive mechanism, allowing deployment over heterogeneous networks without the need of universal network support. This dissertation addresses the network design aspects of overlay networks to provide scalable multicast services in the Internet. The resources and the network cost in the context of overlay networks are different from that in conventional networks, presenting new challenges and new problems to solve. Our design goal are the maximization of network utility and improved service quality. As the overall network design problem is extremely complex, we divide the problem into three components: the efficient management of session traffic (multicast routing), the provisioning of overlay network resources (bandwidth dimensioning) and overlay topology optimization (service placement). The combined solution provides a comprehensive procedure for planning and managing an overlay multicast network. We also consider a complementary form of overlay multicast called application-level multicast (ALMI). ALMI allows end systems to directly create an overlay multicast session among themselves. This gives applications the flexibility to communicate without relying on service provides. The tradeoff is that users do not have direct control on the topology and data paths taken by the session flows and will typically get lower quality of service due to the best effort nature of the Internet environment. ALMI is therefore suitable for sessions of small size or sessions where all members are well connected to the network. Furthermore, the ALMI framework allows us to experiment with application specific components such as data reliability, in order to identify a useful set of communication semantic for enhanced data services

SCIP-Jack - A solver for STP and variants with parallelization extensions

The Steiner tree problem in graphs is a classical problem that commonly arises in practical applications as one of many variants. While often a strong relationship between different Steiner tree problem variants can be observed, solution approaches employed so far have been prevalently problem-specific. In contrast, this paper introduces a general-purpose solver that can be used to solve both the classical Steiner tree problem and many of its variants without modification. This versatility is achieved by transforming various problem variants into a general form and solving them by using a state-of-the-art MIP-framework. The result is a high-performance solver that can be employed in massively parallel environments and is capable of solving previously unsolved instances