11 Search Results for "Liu, Tian"


Document
Polynomial Pass Semi-Streaming Lower Bounds for K-Cores and Degeneracy

Authors: Sepehr Assadi, Prantar Ghosh, Bruno Loff, Parth Mittal, and Sagnik Mukhopadhyay

Published in: LIPIcs, Volume 300, 39th Computational Complexity Conference (CCC 2024)


Abstract
The following question arises naturally in the study of graph streaming algorithms: Is there any graph problem which is "not too hard", in that it can be solved efficiently with total communication (nearly) linear in the number n of vertices, and for which, nonetheless, any streaming algorithm with Õ(n) space (i.e., a semi-streaming algorithm) needs a polynomial n^Ω(1) number of passes? Assadi, Chen, and Khanna [STOC 2019] were the first to prove that this is indeed the case. However, the lower bounds that they obtained are for rather non-standard graph problems. Our first main contribution is to present the first polynomial-pass lower bounds for natural "not too hard" graph problems studied previously in the streaming model: k-cores and degeneracy. We devise a novel communication protocol for both problems with near-linear communication, thus showing that k-cores and degeneracy are natural examples of "not too hard" problems. Indeed, previous work have developed single-pass semi-streaming algorithms for approximating these problems. In contrast, we prove that any semi-streaming algorithm for exactly solving these problems requires (almost) Ω(n^{1/3}) passes. The lower bound follows by a reduction from a generalization of the hidden pointer chasing (HPC) problem of Assadi, Chen, and Khanna, which is also the basis of their earlier semi-streaming lower bounds. Our second main contribution is improved round-communication lower bounds for the underlying communication problems at the basis of these reductions: - We improve the previous lower bound of Assadi, Chen, and Khanna for HPC to achieve optimal bounds for this problem. - We further observe that all current reductions from HPC can also work with a generalized version of this problem that we call MultiHPC, and prove an even stronger and optimal lower bound for this generalization. These two results collectively allow us to improve the resulting pass lower bounds for semi-streaming algorithms by a polynomial factor, namely, from n^{1/5} to n^{1/3} passes.

Cite as

Sepehr Assadi, Prantar Ghosh, Bruno Loff, Parth Mittal, and Sagnik Mukhopadhyay. Polynomial Pass Semi-Streaming Lower Bounds for K-Cores and Degeneracy. In 39th Computational Complexity Conference (CCC 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 300, pp. 7:1-7:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


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@InProceedings{assadi_et_al:LIPIcs.CCC.2024.7,
  author =	{Assadi, Sepehr and Ghosh, Prantar and Loff, Bruno and Mittal, Parth and Mukhopadhyay, Sagnik},
  title =	{{Polynomial Pass Semi-Streaming Lower Bounds for K-Cores and Degeneracy}},
  booktitle =	{39th Computational Complexity Conference (CCC 2024)},
  pages =	{7:1--7:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-331-7},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{300},
  editor =	{Santhanam, Rahul},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CCC.2024.7},
  URN =		{urn:nbn:de:0030-drops-204035},
  doi =		{10.4230/LIPIcs.CCC.2024.7},
  annote =	{Keywords: Graph streaming, Lower bounds, Communication complexity, k-Cores and degeneracy}
}
Document
Improved Cut Strategy for Tensor Network Contraction Orders

Authors: Christoph Staudt, Mark Blacher, Julien Klaus, Farin Lippmann, and Joachim Giesen

Published in: LIPIcs, Volume 301, 22nd International Symposium on Experimental Algorithms (SEA 2024)


Abstract
In the field of quantum computing, simulating quantum systems on classical computers is crucial. Tensor networks are fundamental in simulating quantum systems. A tensor network is a collection of tensors, that need to be contracted into a result tensor. Tensor contraction is a generalization of matrix multiplication to higher order tensors. The contractions can be performed in different orders, and the order has a significant impact on the number of floating point operations (flops) needed to get the result tensor. It is known that finding an optimal contraction order is NP-hard. The current state-of-the-art approach for finding efficient contraction orders is to combinine graph partitioning with a greedy strategy. Although heavily used in practice, the current approach ignores so-called free indices, chooses node weights without regarding previous computations, and requires numerous hyperparameters that need to be tuned at runtime. In this paper, we address these shortcomings by developing a novel graph cut strategy. The proposed modifications yield contraction orders that significantly reduce the number of flops in the tensor contractions compared to the current state of the art. Moreover, by removing the need for hyperparameter tuning at runtime, our approach converges to an efficient solution faster, which reduces the required optimization time by at least an order of magnitude.

Cite as

Christoph Staudt, Mark Blacher, Julien Klaus, Farin Lippmann, and Joachim Giesen. Improved Cut Strategy for Tensor Network Contraction Orders. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 27:1-27:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


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@InProceedings{staudt_et_al:LIPIcs.SEA.2024.27,
  author =	{Staudt, Christoph and Blacher, Mark and Klaus, Julien and Lippmann, Farin and Giesen, Joachim},
  title =	{{Improved Cut Strategy for Tensor Network Contraction Orders}},
  booktitle =	{22nd International Symposium on Experimental Algorithms (SEA 2024)},
  pages =	{27:1--27:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-325-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{301},
  editor =	{Liberti, Leo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2024.27},
  URN =		{urn:nbn:de:0030-drops-203924},
  doi =		{10.4230/LIPIcs.SEA.2024.27},
  annote =	{Keywords: tensor network, contraction order, graph partitioniong, quantum simulation}
}
Document
JuMP2start: Time-Aware Stop-Start Technology for a Software-Defined Vehicle System

Authors: Anam Farrukh and Richard West

Published in: LIPIcs, Volume 298, 36th Euromicro Conference on Real-Time Systems (ECRTS 2024)


Abstract
Software-defined vehicle (SDV) systems replace traditional ECU architectures with software tasks running on centralized multicore processors in automotive-grade PCs. However, PC boot delays to cold-start an integrated vehicle management system (VMS) are problematic for time-critical functions, which must process sensor and actuator data within specific time bounds. To tackle this challenge, we present JuMP2start: a time-aware multicore stop-start approach for SDVs. JuMP2start leverages PC-class suspend-to-RAM techniques to capture a system snapshot when the vehicle is stopped. Upon restart, critical services are resumed-from-RAM within order of milliseconds compared to normal cold-start times. This work showcases how JuMP2start manages global suspension and resumption mechanisms for a state-of-the-art dual-domain vehicle management system comprising real-time OS (RTOS) and Linux SMP guests. JuMP2start models automotive tasks as continuable or restartable to ensure timing- and safety-critical function pipelines are reactively resumed with low latency, while discarding stale task state. Experiments with the VMS show that critical CAN traffic processing resumes within 500 milliseconds of waking the RTOS guest, and reaches steady-state throughput in under 7ms.

Cite as

Anam Farrukh and Richard West. JuMP2start: Time-Aware Stop-Start Technology for a Software-Defined Vehicle System. In 36th Euromicro Conference on Real-Time Systems (ECRTS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 298, pp. 1:1-1:27, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


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@InProceedings{farrukh_et_al:LIPIcs.ECRTS.2024.1,
  author =	{Farrukh, Anam and West, Richard},
  title =	{{JuMP2start: Time-Aware Stop-Start Technology for a Software-Defined Vehicle System}},
  booktitle =	{36th Euromicro Conference on Real-Time Systems (ECRTS 2024)},
  pages =	{1:1--1:27},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-324-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{298},
  editor =	{Pellizzoni, Rodolfo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECRTS.2024.1},
  URN =		{urn:nbn:de:0030-drops-203046},
  doi =		{10.4230/LIPIcs.ECRTS.2024.1},
  annote =	{Keywords: Time-aware stop-start, Real-time power management, Suspend-to-RAM, Partitioning hypervisor, Vehicle management system, Vehicle-OS, Software-defined vehicles (SDV)}
}
Document
The Omnivisor: A Real-Time Static Partitioning Hypervisor Extension for Heterogeneous Core Virtualization over MPSoCs

Authors: Daniele Ottaviano, Francesco Ciraolo, Renato Mancuso, and Marcello Cinque

Published in: LIPIcs, Volume 298, 36th Euromicro Conference on Real-Time Systems (ECRTS 2024)


Abstract
Following the needs of industrial applications, virtualization has emerged as one of the most effective approaches for the consolidation of mixed-criticality systems while meeting tight constraints in terms of space, weight, power, and cost (SWaP-C). In embedded platforms with homogeneous processors, a wealth of works have proposed designs and techniques to enforce spatio-temporal isolation by leveraging well-understood virtualization support. Unfortunately, achieving the same goal on heterogeneous MultiProcessor Systems-on-Chip (MPSoCs) has been largely overlooked. Modern hypervisors are designed to operate exclusively on main cores, with little or no consideration given to other co-processors within the system, such as small microcontroller-level CPUs or soft-cores deployed on programmable logic (FPGA). Typically, hypervisors consider co-processors as I/O devices allocated to virtual machines that run on primary cores, yielding full control and responsibility over them. Nevertheless, inadequate management of these resources can lead to spatio-temporal isolation issues within the system. In this paper, we propose the Omnivisor model as a paradigm for the holistic management of heterogeneous platforms. The model generalizes the features of real-time static partitioning hypervisors to enable the execution of virtual machines on processors with different Instruction Set Architectures (ISAs) within the same MPSoC. Moreover, the Omnivisor ensures temporal and spatial isolation between virtual machines by integrating and leveraging a variety of hardware and software protection mechanisms. The presented approach not only expands the scope of virtualization in MPSoCs but also enhances the overall system reliability and real-time performance for mixed-criticality applications. A full open-source reference implementation of the Omnivisor based on the Jailhouse hypervisor is provided, targeting ARM real-time processing units and RISC-V soft-cores on FPGA. Experimental results on real hardware show the benefits of the solution, including enabling the seamless launch of virtual machines on different ISAs and extending spatial/temporal isolation to heterogenous cores with enhanced regulation policies.

Cite as

Daniele Ottaviano, Francesco Ciraolo, Renato Mancuso, and Marcello Cinque. The Omnivisor: A Real-Time Static Partitioning Hypervisor Extension for Heterogeneous Core Virtualization over MPSoCs. In 36th Euromicro Conference on Real-Time Systems (ECRTS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 298, pp. 7:1-7:27, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


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@InProceedings{ottaviano_et_al:LIPIcs.ECRTS.2024.7,
  author =	{Ottaviano, Daniele and Ciraolo, Francesco and Mancuso, Renato and Cinque, Marcello},
  title =	{{The Omnivisor: A Real-Time Static Partitioning Hypervisor Extension for Heterogeneous Core Virtualization over MPSoCs}},
  booktitle =	{36th Euromicro Conference on Real-Time Systems (ECRTS 2024)},
  pages =	{7:1--7:27},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-324-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{298},
  editor =	{Pellizzoni, Rodolfo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECRTS.2024.7},
  URN =		{urn:nbn:de:0030-drops-203107},
  doi =		{10.4230/LIPIcs.ECRTS.2024.7},
  annote =	{Keywords: Mixed-Criticality, Embedded Virtualization, Real-Time Systems, MPSoCs}
}
Document
DeepTrust^RT: Confidential Deep Neural Inference Meets Real-Time!

Authors: Mohammad Fakhruddin Babar and Monowar Hasan

Published in: LIPIcs, Volume 298, 36th Euromicro Conference on Real-Time Systems (ECRTS 2024)


Abstract
Deep Neural Networks (DNNs) are becoming common in "learning-enabled" time-critical applications such as autonomous driving and robotics. One approach to protect DNN inference from adversarial actions and preserve model privacy/confidentiality is to execute them within trusted enclaves available in modern processors. However, running DNN inference inside limited-capacity enclaves while ensuring timing guarantees is challenging due to (a) large size of DNN workloads and (b) extra switching between "normal" and "trusted" execution modes. This paper introduces new time-aware scheduling schemes - DeepTrust^RT - to securely execute deep neural inferences for learning-enabled real-time systems. We first propose a variant of EDF (called DeepTrust^RT-LW) that slices each DNN layer and runs them sequentially in the enclave. However, due to extra context switch overheads of individual layer slices, we further introduce a novel layer fusion technique (named DeepTrust^RT-FUSION). Our proposed scheme provides hard real-time guarantees by fusing multiple layers of DNN workload from multiple tasks; thus allowing them to fit and run concurrently within the enclaves while maintaining real-time guarantees. We implemented and tested DeepTrust^RT ideas on the Raspberry Pi platform running OP-TEE+DarkNet-TZ DNN APIs and three DNN workloads (AlexNet-squeezed, Tiny Darknet, YOLOv3-tiny). Compared to the layer-wise partitioning approach (DeepTrust^RT-LW), DeepTrust^RT-FUSION can schedule up to 3x more tasksets and reduce context switches by up to 11.12x. We further demonstrate the efficacy of DeepTrust^RT using a flight controller (ArduPilot) case study and find that DeepTrust^RT-FUSION retains real-time guarantees where DeepTrust^RT-LW becomes unschedulable.

Cite as

Mohammad Fakhruddin Babar and Monowar Hasan. DeepTrust^RT: Confidential Deep Neural Inference Meets Real-Time!. In 36th Euromicro Conference on Real-Time Systems (ECRTS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 298, pp. 13:1-13:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


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@InProceedings{babar_et_al:LIPIcs.ECRTS.2024.13,
  author =	{Babar, Mohammad Fakhruddin and Hasan, Monowar},
  title =	{{DeepTrust^RT: Confidential Deep Neural Inference Meets Real-Time!}},
  booktitle =	{36th Euromicro Conference on Real-Time Systems (ECRTS 2024)},
  pages =	{13:1--13:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-324-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{298},
  editor =	{Pellizzoni, Rodolfo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECRTS.2024.13},
  URN =		{urn:nbn:de:0030-drops-203161},
  doi =		{10.4230/LIPIcs.ECRTS.2024.13},
  annote =	{Keywords: DNN, TrustZone, Real-Time Systems}
}
Document
Track A: Algorithms, Complexity and Games
Non-Linear Paging

Authors: Ilan Doron-Arad and Joseph (Seffi) Naor

Published in: LIPIcs, Volume 297, 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)


Abstract
We formulate and study non-linear paging - a broad model of online paging where the size of subsets of pages is determined by a monotone non-linear set function of the pages. This model captures the well-studied classic weighted paging and generalized paging problems, and also submodular and supermodular paging, studied here for the first time, that have a range of applications from virtual memory to machine learning. Unlike classic paging, the cache threshold parameter k does not yield good competitive ratios for non-linear paging. Instead, we introduce a novel parameter 𝓁 that generalizes the notion of cache size to the non-linear setting. We obtain a tight deterministic 𝓁-competitive algorithm for general non-linear paging and a o(log²𝓁)-competitive lower bound for randomized algorithms. Our algorithm is based on a new generic LP for the problem that captures both submodular and supermodular paging, in contrast to LPs used for submodular cover settings. We finally focus on the supermodular paging problem, which is a variant of online set cover and online submodular cover, where sets are repeatedly requested to be removed from the cover. We obtain polylogarithmic lower and upper bounds and an offline approximation algorithm.

Cite as

Ilan Doron-Arad and Joseph (Seffi) Naor. Non-Linear Paging. In 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 297, pp. 57:1-57:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


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@InProceedings{doronarad_et_al:LIPIcs.ICALP.2024.57,
  author =	{Doron-Arad, Ilan and Naor, Joseph (Seffi)},
  title =	{{Non-Linear Paging}},
  booktitle =	{51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)},
  pages =	{57:1--57:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-322-5},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{297},
  editor =	{Bringmann, Karl and Grohe, Martin and Puppis, Gabriele and Svensson, Ola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2024.57},
  URN =		{urn:nbn:de:0030-drops-202000},
  doi =		{10.4230/LIPIcs.ICALP.2024.57},
  annote =	{Keywords: paging, competitive analysis, non-linear paging, submodular and supermodular functions}
}
Document
Track A: Algorithms, Complexity and Games
Cut Sparsification and Succinct Representation of Submodular Hypergraphs

Authors: Yotam Kenneth and Robert Krauthgamer

Published in: LIPIcs, Volume 297, 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)


Abstract
In cut sparsification, all cuts of a hypergraph H = (V,E,w) are approximated within 1±ε factor by a small hypergraph H'. This widely applied method was generalized recently to a setting where the cost of cutting each hyperedge e is provided by a splitting function g_e: 2^e → ℝ_+. This generalization is called a submodular hypergraph when the functions {g_e}_{e ∈ E} are submodular, and it arises in machine learning, combinatorial optimization, and algorithmic game theory. Previous work studied the setting where H' is a reweighted sub-hypergraph of H, and measured the size of H' by the number of hyperedges in it. In this setting, we present two results: (i) all submodular hypergraphs admit sparsifiers of size polynomial in n = |V| and ε^{-1}; (ii) we propose a new parameter, called spread, and use it to obtain smaller sparsifiers in some cases. We also show that for a natural family of splitting functions, relaxing the requirement that H' be a reweighted sub-hypergraph of H yields a substantially smaller encoding of the cuts of H (almost a factor n in the number of bits). This is in contrast to graphs, where the most succinct representation is attained by reweighted subgraphs. A new tool in our construction of succinct representation is the notion of deformation, where a splitting function g_e is decomposed into a sum of functions of small description, and we provide upper and lower bounds for deformation of common splitting functions.

Cite as

Yotam Kenneth and Robert Krauthgamer. Cut Sparsification and Succinct Representation of Submodular Hypergraphs. In 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 297, pp. 97:1-97:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


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@InProceedings{kenneth_et_al:LIPIcs.ICALP.2024.97,
  author =	{Kenneth, Yotam and Krauthgamer, Robert},
  title =	{{Cut Sparsification and Succinct Representation of Submodular Hypergraphs}},
  booktitle =	{51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)},
  pages =	{97:1--97:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-322-5},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{297},
  editor =	{Bringmann, Karl and Grohe, Martin and Puppis, Gabriele and Svensson, Ola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2024.97},
  URN =		{urn:nbn:de:0030-drops-202406},
  doi =		{10.4230/LIPIcs.ICALP.2024.97},
  annote =	{Keywords: Cut Sparsification, Submodular Hypergraphs, Succinct Representation}
}
Document
Track A: Algorithms, Complexity and Games
Better Sparsifiers for Directed Eulerian Graphs

Authors: Sushant Sachdeva, Anvith Thudi, and Yibin Zhao

Published in: LIPIcs, Volume 297, 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)


Abstract
Spectral sparsification for directed Eulerian graphs is a key component in the design of fast algorithms for solving directed Laplacian linear systems. Directed Laplacian linear system solvers are crucial algorithmic primitives to fast computation of fundamental problems on random walks, such as computing stationary distributions, hitting and commute times, and personalized PageRank vectors. While spectral sparsification is well understood for undirected graphs and it is known that for every graph G, (1+ε)-sparsifiers with O(nε^{-2}) edges exist [Batson-Spielman-Srivastava, STOC '09] (which is optimal), the best known constructions of Eulerian sparsifiers require Ω(nε^{-2}log⁴ n) edges and are based on short-cycle decompositions [Chu et al., FOCS '18]. In this paper, we give improved constructions of Eulerian sparsifiers, specifically: 1) We show that for every directed Eulerian graph G→, there exists an Eulerian sparsifier with O(nε^{-2} log² n log²log n + nε^{-4/3}log^{8/3} n) edges. This result is based on combining short-cycle decompositions [Chu-Gao-Peng-Sachdeva-Sawlani-Wang, FOCS '18, SICOMP] and [Parter-Yogev, ICALP '19], with recent progress on the matrix Spencer conjecture [Bansal-Meka-Jiang, STOC '23]. 2) We give an improved analysis of the constructions based on short-cycle decompositions, giving an m^{1+δ}-time algorithm for any constant δ > 0 for constructing Eulerian sparsifiers with O(nε^{-2}log³ n) edges.

Cite as

Sushant Sachdeva, Anvith Thudi, and Yibin Zhao. Better Sparsifiers for Directed Eulerian Graphs. In 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 297, pp. 119:1-119:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


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@InProceedings{sachdeva_et_al:LIPIcs.ICALP.2024.119,
  author =	{Sachdeva, Sushant and Thudi, Anvith and Zhao, Yibin},
  title =	{{Better Sparsifiers for Directed Eulerian Graphs}},
  booktitle =	{51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)},
  pages =	{119:1--119:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-322-5},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{297},
  editor =	{Bringmann, Karl and Grohe, Martin and Puppis, Gabriele and Svensson, Ola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2024.119},
  URN =		{urn:nbn:de:0030-drops-202628},
  doi =		{10.4230/LIPIcs.ICALP.2024.119},
  annote =	{Keywords: Graph algorithms, Linear algebra and computation, Discrepancy theory}
}
Document
Vertex Sparsifiers for Hyperedge Connectivity

Authors: Han Jiang, Shang-En Huang, Thatchaphol Saranurak, and Tian Zhang

Published in: LIPIcs, Volume 244, 30th Annual European Symposium on Algorithms (ESA 2022)


Abstract
Recently, Chalermsook et al. {[}SODA'21{]} introduces a notion of vertex sparsifiers for c-edge connectivity, which has found applications in parameterized algorithms for network design and also led to exciting dynamic algorithms for c-edge st-connectivity {[}Jin and Sun FOCS'22{]}. We study a natural extension called vertex sparsifiers for c-hyperedge connectivity and construct a sparsifier whose size matches the state-of-the-art for normal graphs. More specifically, we show that, given a hypergraph G = (V,E) with n vertices and m hyperedges with k terminal vertices and a parameter c, there exists a hypergraph H containing only O(kc³) hyperedges that preserves all minimum cuts (up to value c) between all subset of terminals. This matches the best bound of O(kc³) edges for normal graphs by [Liu'20]. Moreover, H can be constructed in almost-linear O(p^{1+o(1)} + n(rclog n)^{O(rc)}log m) time where r = max_{e ∈ E}|e| is the rank of G and p = ∑_{e ∈ E}|e| is the total size of G, or in poly(m, n) time if we slightly relax the size to O(kc³log^{1.5}(kc)) hyperedges.

Cite as

Han Jiang, Shang-En Huang, Thatchaphol Saranurak, and Tian Zhang. Vertex Sparsifiers for Hyperedge Connectivity. In 30th Annual European Symposium on Algorithms (ESA 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 244, pp. 70:1-70:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)


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@InProceedings{jiang_et_al:LIPIcs.ESA.2022.70,
  author =	{Jiang, Han and Huang, Shang-En and Saranurak, Thatchaphol and Zhang, Tian},
  title =	{{Vertex Sparsifiers for Hyperedge Connectivity}},
  booktitle =	{30th Annual European Symposium on Algorithms (ESA 2022)},
  pages =	{70:1--70:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-247-1},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{244},
  editor =	{Chechik, Shiri and Navarro, Gonzalo and Rotenberg, Eva and Herman, Grzegorz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2022.70},
  URN =		{urn:nbn:de:0030-drops-170081},
  doi =		{10.4230/LIPIcs.ESA.2022.70},
  annote =	{Keywords: Vertex sparsifier, hypergraph, connectivity}
}
Document
Faster Pan-Genome Construction for Efficient Differentiation of Naturally Occurring and Engineered Plasmids with Plaster

Authors: Qi Wang, R. A. Leo Elworth, Tian Rui Liu, and Todd J. Treangen

Published in: LIPIcs, Volume 143, 19th International Workshop on Algorithms in Bioinformatics (WABI 2019)


Abstract
As sequence databases grow, characterizing diversity across extremely large collections of genomes requires the development of efficient methods that avoid costly all-vs-all comparisons [Marschall et al., 2018]. In addition to exponential increases in the amount of natural genomes being sequenced, improved techniques for the creation of human engineered sequences is ushering in a new wave of synthetic genome sequence databases that grow alongside naturally occurring genome databases. In this paper, we analyze the full diversity of available sequenced natural and synthetic plasmid genome sequences. This diversity can be represented by a data structure that captures all presently available nucleotide sequences, known as a pan-genome. In our case, we construct a single linear pan-genome nucleotide sequence that captures this diversity. To process such a large number of sequences, we introduce the plaster algorithmic pipeline. Using plaster we are able to construct the full synthetic plasmid pan-genome from 51,047 synthetic plasmid sequences as well as a natural pan-genome from 6,642 natural plasmid sequences. We demonstrate the efficacy of plaster by comparing its speed against another pan-genome construction method as well as demonstrating that nearly all plasmids align well to their corresponding pan-genome. Finally, we explore the use of pan-genome sequence alignment to distinguish between naturally occurring and synthetic plasmids. We believe this approach will lead to new techniques for rapid characterization of engineered plasmids. Applications for this work include detection of genome editing, tracking an unknown plasmid back to its lab of origin, and identifying naturally occurring sequences that may be of use to the synthetic biology community. The source code for fully reconstructing the natural and synthetic plasmid pan-genomes as well for plaster are publicly available and can be downloaded at https://gitlab.com/qiwangrice/plaster.git.

Cite as

Qi Wang, R. A. Leo Elworth, Tian Rui Liu, and Todd J. Treangen. Faster Pan-Genome Construction for Efficient Differentiation of Naturally Occurring and Engineered Plasmids with Plaster. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 19:1-19:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


Copy BibTex To Clipboard

@InProceedings{wang_et_al:LIPIcs.WABI.2019.19,
  author =	{Wang, Qi and Elworth, R. A. Leo and Liu, Tian Rui and Treangen, Todd J.},
  title =	{{Faster Pan-Genome Construction for Efficient Differentiation of Naturally Occurring and Engineered Plasmids with Plaster}},
  booktitle =	{19th International Workshop on Algorithms in Bioinformatics (WABI 2019)},
  pages =	{19:1--19:12},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-123-8},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{143},
  editor =	{Huber, Katharina T. and Gusfield, Dan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2019.19},
  URN =		{urn:nbn:de:0030-drops-110492},
  doi =		{10.4230/LIPIcs.WABI.2019.19},
  annote =	{Keywords: comparative genomics, sequence alignment, pan-genome, engineered plasmids}
}
Document
A (1.4 + epsilon)-Approximation Algorithm for the 2-Max-Duo Problem

Authors: Yao Xu, Yong Chen, Guohui Lin, Tian Liu, Taibo Luo, and Peng Zhang

Published in: LIPIcs, Volume 92, 28th International Symposium on Algorithms and Computation (ISAAC 2017)


Abstract
The maximum duo-preservation string mapping (Max-Duo) problem is the complement of the well studied minimum common string partition (MCSP) problem, both of which have applications in many fields including text compression and bioinformatics. k-Max-Duo is the restricted version of Max-Duo, where every letter of the alphabet occurs at most k times in each of the strings, which is readily reduced into the well known maximum independent set (MIS) problem on a graph of maximum degree \Delta \le 6(k-1). In particular, 2-Max-Duo can then be approximated arbitrarily close to 1.8 using the state-of-the-art approximation algorithm for the MIS problem. 2-Max-Duo was proved APX-hard and very recently a (1.6 + \epsilon)-approximation was claimed, for any \epsilon > 0. In this paper, we present a vertex-degree reduction technique, based on which, we show that 2-Max-Duo can be approximated arbitrarily close to 1.4.

Cite as

Yao Xu, Yong Chen, Guohui Lin, Tian Liu, Taibo Luo, and Peng Zhang. A (1.4 + epsilon)-Approximation Algorithm for the 2-Max-Duo Problem. In 28th International Symposium on Algorithms and Computation (ISAAC 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 92, pp. 66:1-66:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)


Copy BibTex To Clipboard

@InProceedings{xu_et_al:LIPIcs.ISAAC.2017.66,
  author =	{Xu, Yao and Chen, Yong and Lin, Guohui and Liu, Tian and Luo, Taibo and Zhang, Peng},
  title =	{{A (1.4 + epsilon)-Approximation Algorithm for the 2-Max-Duo Problem}},
  booktitle =	{28th International Symposium on Algorithms and Computation (ISAAC 2017)},
  pages =	{66:1--66:12},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-054-5},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{92},
  editor =	{Okamoto, Yoshio and Tokuyama, Takeshi},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2017.66},
  URN =		{urn:nbn:de:0030-drops-82120},
  doi =		{10.4230/LIPIcs.ISAAC.2017.66},
  annote =	{Keywords: Approximation algorithm, duo-preservation string mapping, string partition, independent set}
}
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