8 Search Results for "Liu, Han"


Document
Abstract
Quartets Enable Statistically Consistent Estimation of Cell Lineage Trees Under an Unbiased Error and Missingness Model (Abstract)

Authors: Yunheng Han and Erin K. Molloy

Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)


Abstract
Cancer progression and treatment can be informed by reconstructing its evolutionary history from tumor cells [Lim et al., 2020]. Although many methods exist to estimate evolutionary trees (called phylogenies) from molecular sequences, traditional approaches assume the input data are error-free and the output tree is fully resolved. These assumptions are challenged in tumor phylogenetics because single-cell sequencing produces sparse, error-ridden data and because tumors evolve clonally [Jahn et al., 2016; Schwartz and Schäffer, 2017]. Here, we study the theoretical utility of methods based on quartets (four-leaf, unrooted phylogenetic trees) and triplets (three-leaf, rooted phylogenetic trees), in light of these barriers. Quartets and triplets have long been used as the building blocks for reconstructing the evolutionary history of species [Wilkinson et al., 2005]. The reason triplet-based methods (e.g., MP-EST [Liu et al., 2010]) and quartet-based methods (e.g., ASTRAL [Mirarab et al., 2014]) have garnered such success in species phylogenetics is their good statistical properties under the Multi-Species Coalescent (MSC) model [Pamilo and Nei, 1988; Rannala and Yang, 2003]; see Allman et al. (2011) and Degnan (2006) for identifiability results under the MSC model for quartets and triplets, respectively. Inspired by these efforts, we study the utility of quartets and triplets for estimating cell lineage trees under a popular tumor phylogenetics model [Jahn et al., 2016; Ross and Markowetz, 2016; Wu, 2019; Kizilkale et al., 2022] with two phases. First, mutations arise on a (highly unresolved) cell lineage tree according to the infinite sites model, and second, errors (false positives and false negatives) and missing values are introduced to the resulting mutation data in an unbiased fashion, mimicking data produced by single-cell sequencing protocols. This infinite sites plus unbiased error and missingness (IS+UEM) model generates mutations (rather than gene genealogies like the MSC model). However, a quartet (with leaves bijectively labeled by four cells) is implied by a mutation being present in two cells and absent from two cells [Molloy et al., 2021; Springer et al., 2019]; similarly, a triplet (on three cells) is implied by a mutation being present in two cells and absent from one cell. Our main result is that under the IS+UEM, the most probable quartet identifies the unrooted model cell lineage tree on four cells, with a mild assumption: the probability of false negatives and the probability of false positives must not sum to one. Somewhat surprisingly, our identifiability result for quartets does not extend to triplets, with more restrictive assumptions being required for identifiability. These results motivate seeking an unrooted cell lineage tree such that the number of quartets shared between it and the input mutations is maximized. We prove an optimal solution to this problem is a consistent estimator of the unrooted cell lineage tree under the IS+UEM model; this guarantee includes the case where the model tree is highly unresolved, provided that tree error is defined as the number of false negative branches. We therefore conclude by outlining how quartet-based methods might be employed for tumor phylogenetics given other important challenges like copy number aberrations and doublets.

Cite as

Yunheng Han and Erin K. Molloy. Quartets Enable Statistically Consistent Estimation of Cell Lineage Trees Under an Unbiased Error and Missingness Model (Abstract). In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 8:1-8:2, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)


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@InProceedings{han_et_al:LIPIcs.WABI.2023.8,
  author =	{Han, Yunheng and Molloy, Erin K.},
  title =	{{Quartets Enable Statistically Consistent Estimation of Cell Lineage Trees Under an Unbiased Error and Missingness Model}},
  booktitle =	{23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
  pages =	{8:1--8:2},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-294-5},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{273},
  editor =	{Belazzougui, Djamal and Ouangraoua, A\"{i}da},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.8},
  URN =		{urn:nbn:de:0030-drops-186347},
  doi =		{10.4230/LIPIcs.WABI.2023.8},
  annote =	{Keywords: Tumor Phylogenetics, Cell Lineage Trees, Quartets, Supertrees, ASTRAL}
}
Document
A Hybrid Programming Language for Formal Modeling and Verification of Hybrid Systems

Authors: Eduard Kamburjan, Stefan Mitsch, and Reiner Hähnle

Published in: LITES, Volume 8, Issue 2 (2022): Special Issue on Distributed Hybrid Systems. Leibniz Transactions on Embedded Systems, Volume 8, Issue 2


Abstract
Designing and modeling complex cyber-physical systems (CPS) faces the double challenge of combined discrete-continuous dynamics and concurrent behavior. Existing formal modeling and verification languages for CPS expose the underlying proof search technology. They lack high-level structuring elements and are not efficiently executable. The ensuing modeling gap renders formal CPS models hard to understand and to validate. We propose a high-level programming-based approach to formal modeling and verification of hybrid systems as a hybrid extension of an Active Objects language. Well-structured hybrid active programs and requirements allow automatic, reachability-preserving translation into differential dynamic logic, a logic for hybrid (discrete-continuous) programs. Verification is achieved by discharging the resulting formulas with the theorem prover KeYmaera X. We demonstrate the usability of our approach with case studies.

Cite as

Eduard Kamburjan, Stefan Mitsch, and Reiner Hähnle. A Hybrid Programming Language for Formal Modeling and Verification of Hybrid Systems. In LITES, Volume 8, Issue 2 (2022): Special Issue on Distributed Hybrid Systems. Leibniz Transactions on Embedded Systems, Volume 8, Issue 2, pp. 04:1-04:34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2022)


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@Article{kamburjan_et_al:LITES.8.2.4,
  author =	{Kamburjan, Eduard and Mitsch, Stefan and H\"{a}hnle, Reiner},
  title =	{{A Hybrid Programming Language for Formal Modeling and Verification of Hybrid Systems}},
  booktitle =	{LITES, Volume 8, Issue 2 (2022): Special Issue on Distributed Hybrid Systems},
  pages =	{04:1--04:34},
  journal =	{Leibniz Transactions on Embedded Systems},
  ISSN =	{2199-2002},
  year =	{2022},
  volume =	{8},
  number =	{2},
  editor =	{Kamburjan, Eduard and Mitsch, Stefan and H\"{a}hnle, Reiner},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LITES.8.2.4},
  doi =		{10.4230/LITES.8.2.4},
  annote =	{Keywords: Active Objects, Differential Dynamic Logic, Hybrid Systems}
}
Document
Introduction
Introduction to the Special Issue on Embedded Systems for Computer Vision

Authors: Samarjit Chakraborty and Qing Rao

Published in: LITES, Volume 8, Issue 1 (2022): Special Issue on Embedded Systems for Computer Vision. Leibniz Transactions on Embedded Systems, Volume 8, Issue 1


Abstract
We provide a broad overview of some of the current research directions at the intersection of embedded systems and computer vision, in addition to introducing the papers appearing in this special issue. Work at this intersection is steadily growing in importance, especially in the context of autonomous and cyber-physical systems design. Vision-based perception is almost a mandatory component in any autonomous system, but also adds myriad challenges like, how to efficiently implement vision processing algorithms on resource-constrained embedded architectures, and how to verify the functional and timing correctness of these algorithms. Computer vision is also crucial in implementing various smart functionality like security, e.g., using facial recognition, or monitoring events or traffic patterns. Some of these applications are reviewed in this introductory article. The remaining articles featured in this special issue dive into more depth on a few of them.

Cite as

LITES, Volume 8, Issue 1: Special Issue on Embedded Systems for Computer Vision, pp. 0:i-0:viii, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2022)


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@Article{chakraborty_et_al:LITES.8.1.0,
  author =	{Chakraborty, Samarjit and Rao, Qing},
  title =	{{Introduction to the Special Issue on Embedded Systems for Computer Vision}},
  booktitle =	{LITES, Volume 8, Issue 1 (2022): Special Issue on Embedded Systems for Computer Vision},
  pages =	{00:1--00:8},
  journal =	{Leibniz Transactions on Embedded Systems},
  ISSN =	{2199-2002},
  year =	{2022},
  volume =	{8},
  number =	{1},
  editor =	{Chakraborty, Samarjit and Rao, Qing},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LITES.8.1.0},
  doi =		{10.4230/LITES.8.1.0},
  annote =	{Keywords: Embedded systems, Computer vision, Cyber-physical systems, Computer architecture}
}
Document
HW-Flow: A Multi-Abstraction Level HW-CNN Codesign Pruning Methodology

Authors: Manoj-Rohit Vemparala, Nael Fasfous, Alexander Frickenstein, Emanuele Valpreda, Manfredi Camalleri, Qi Zhao, Christian Unger, Naveen-Shankar Nagaraja, Maurizio Martina, and Walter Stechele

Published in: LITES, Volume 8, Issue 1 (2022): Special Issue on Embedded Systems for Computer Vision. Leibniz Transactions on Embedded Systems, Volume 8, Issue 1


Abstract
Convolutional neural networks (CNNs) have produced unprecedented accuracy for many computer vision problems in the recent past. In power and compute-constrained embedded platforms, deploying modern CNNs can present many challenges. Most CNN architectures do not run in real-time due to the high number of computational operations involved during the inference phase. This emphasizes the role of CNN optimization techniques in early design space exploration. To estimate their efficacy in satisfying the target constraints, existing techniques are either hardware (HW) agnostic, pseudo-HW-aware by considering parameter and operation counts, or HW-aware through inflexible hardware-in-the-loop (HIL) setups. In this work, we introduce HW-Flow, a framework for optimizing and exploring CNN models based on three levels of hardware abstraction: Coarse, Mid and Fine. Through these levels, CNN design and optimization can be iteratively refined towards efficient execution on the target hardware platform. We present HW-Flow in the context of CNN pruning by augmenting a reinforcement learning agent with key metrics to understand the influence of its pruning actions on the inference hardware. With 2× reduction in energy and latency, we prune ResNet56, ResNet50, and DeepLabv3 with minimal accuracy degradation on the CIFAR-10, ImageNet, and CityScapes datasets, respectively.

Cite as

Manoj-Rohit Vemparala, Nael Fasfous, Alexander Frickenstein, Emanuele Valpreda, Manfredi Camalleri, Qi Zhao, Christian Unger, Naveen-Shankar Nagaraja, Maurizio Martina, and Walter Stechele. HW-Flow: A Multi-Abstraction Level HW-CNN Codesign Pruning Methodology. In LITES, Volume 8, Issue 1 (2022): Special Issue on Embedded Systems for Computer Vision. Leibniz Transactions on Embedded Systems, Volume 8, Issue 1, pp. 03:1-03:30, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2022)


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@Article{vemparala_et_al:LITES.8.1.3,
  author =	{Vemparala, Manoj-Rohit and Fasfous, Nael and Frickenstein, Alexander and Valpreda, Emanuele and Camalleri, Manfredi and Zhao, Qi and Unger, Christian and Nagaraja, Naveen-Shankar and Martina, Maurizio and Stechele, Walter},
  title =	{{HW-Flow: A Multi-Abstraction Level HW-CNN Codesign Pruning Methodology}},
  booktitle =	{LITES, Volume 8, Issue 1 (2022): Special Issue on Embedded Systems for Computer Vision},
  pages =	{03:1--03:30},
  journal =	{Leibniz Transactions on Embedded Systems},
  ISSN =	{2199-2002},
  year =	{2022},
  volume =	{8},
  number =	{1},
  editor =	{Vemparala, Manoj-Rohit and Fasfous, Nael and Frickenstein, Alexander and Valpreda, Emanuele and Camalleri, Manfredi and Zhao, Qi and Unger, Christian and Nagaraja, Naveen-Shankar and Martina, Maurizio and Stechele, Walter},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LITES.8.1.3},
  doi =		{10.4230/LITES.8.1.3},
  annote =	{Keywords: Convolutional Neural Networks, Optimization, Hardware Modeling, Pruning}
}
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
Beating Classical Impossibility of Position Verification

Authors: Jiahui Liu, Qipeng Liu, and Luowen Qian

Published in: LIPIcs, Volume 215, 13th Innovations in Theoretical Computer Science Conference (ITCS 2022)


Abstract
Chandran et al. (SIAM J. Comput. '14) formally introduced the cryptographic task of position verification, where they also showed that it cannot be achieved by classical protocols. In this work, we initiate the study of position verification protocols with classical verifiers. We identify that proofs of quantumness (and thus computational assumptions) are necessary for such position verification protocols. For the other direction, we adapt the proof of quantumness protocol by Brakerski et al. (FOCS '18) to instantiate such a position verification protocol. As a result, we achieve classically verifiable position verification assuming the quantum hardness of Learning with Errors. Along the way, we develop the notion of 1-of-2 non-local soundness for a natural non-local game for 1-of-2 puzzles, first introduced by Radian and Sattath (AFT '19), which can be viewed as a computational unclonability property. We show that 1-of-2 non-local soundness follows from the standard 2-of-2 soundness (and therefore the adaptive hardcore bit property), which could be of independent interest.

Cite as

Jiahui Liu, Qipeng Liu, and Luowen Qian. Beating Classical Impossibility of Position Verification. In 13th Innovations in Theoretical Computer Science Conference (ITCS 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 215, pp. 100:1-100:11, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2022)


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@InProceedings{liu_et_al:LIPIcs.ITCS.2022.100,
  author =	{Liu, Jiahui and Liu, Qipeng and Qian, Luowen},
  title =	{{Beating Classical Impossibility of Position Verification}},
  booktitle =	{13th Innovations in Theoretical Computer Science Conference (ITCS 2022)},
  pages =	{100:1--100:11},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-217-4},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{215},
  editor =	{Braverman, Mark},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2022.100},
  URN =		{urn:nbn:de:0030-drops-156963},
  doi =		{10.4230/LIPIcs.ITCS.2022.100},
  annote =	{Keywords: cryptographic protocol, position verification, quantum cryptography, proof of quantumness, non-locality}
}
Document
Evaluation of Rule-Based Learning and Feature Selection Approaches For Classification

Authors: Fatima Chiroma, Mihaela Cocea, and Han Liu

Published in: OASIcs, Volume 66, 2018 Imperial College Computing Student Workshop (ICCSW 2018)


Abstract
Feature selection is typically employed before or in conjunction with classification algorithms to reduce the feature dimensionality and improve the classification performance, as well as reduce processing time. While particular approaches have been developed for feature selection, such as filter and wrapper approaches, some algorithms perform feature selection through their learning strategy. In this paper, we are investigating the effect of the implicit feature selection of the PRISM algorithm, which is rule-based, when compared with the wrapper feature selection approach employing four popular algorithms: decision trees, naïve bayes, k-nearest neighbors and support vector machine. Moreover, we investigate the performance of the algorithms on target classes, i.e. where the aim is to identify one or more phenomena and distinguish them from their absence (i.e. non-target classes), such as when identifying benign and malign cancer (two target classes) vs. non-cancer (the non-target class).

Cite as

Fatima Chiroma, Mihaela Cocea, and Han Liu. Evaluation of Rule-Based Learning and Feature Selection Approaches For Classification. In 2018 Imperial College Computing Student Workshop (ICCSW 2018). Open Access Series in Informatics (OASIcs), Volume 66, pp. 6:1-6:6, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2019)


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@InProceedings{chiroma_et_al:OASIcs.ICCSW.2018.6,
  author =	{Chiroma, Fatima and Cocea, Mihaela and Liu, Han},
  title =	{{Evaluation of Rule-Based Learning and Feature Selection Approaches For Classification}},
  booktitle =	{2018 Imperial College Computing Student Workshop (ICCSW 2018)},
  pages =	{6:1--6:6},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-097-2},
  ISSN =	{2190-6807},
  year =	{2019},
  volume =	{66},
  editor =	{Pirovano, Edoardo and Graversen, Eva},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.ICCSW.2018.6},
  URN =		{urn:nbn:de:0030-drops-101872},
  doi =		{10.4230/OASIcs.ICCSW.2018.6},
  annote =	{Keywords: Feature Selection, Prism, Rule-based Learning, Wrapper Approach}
}
Document
Utility-Based Scheduling of (m,k)-firm Real-Time Tasks - New Empirical Results

Authors: Florian Kluge

Published in: LITES, Volume 4, Issue 1 (2017). Leibniz Transactions on Embedded Systems, Volume 4, Issue 1


Abstract
The concept of a firm real-time task implies the notion of a firm deadline that should not be missed by the jobs of this task. If a deadline miss occurs, the concerned job yields no value to the system. For some applications domains, this restrictive notion can be relaxed. For example, robust control systems can tolerate that single executions of a control loop miss their deadlines, and still yield an acceptable behaviour. Thus, systems can be developed under more optimistic assumptions, e.g. by allowing overloads. However, care must be taken that deadline misses do not accumulate. This restriction can be expressed by the model of (m,k)-firm real-time tasks that require that from any k consecutive jobs at least m are executed successfully. In this article, we extend our prior work on the MKU scheduling heuristic. MKU uses history-cognisant utility functions as means for making decisions in overload situations. We present new theoretical results on MKU and on other schedulers for (m,k)-firm real-time tasks. Based on extensive simulations, we assess the performance of these schedulers. The results allow us to identify task set characteristics that can be used as guidelines for choosing a scheduler for a concrete use case.

Cite as

Florian Kluge. Utility-Based Scheduling of (m,k)-firm Real-Time Tasks - New Empirical Results. In LITES, Volume 4, Issue 1 (2017). Leibniz Transactions on Embedded Systems, Volume 4, Issue 1, pp. 02:1-02:25, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2017)


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@Article{kluge:LITES-v004-i001-a002,
  author =	{Kluge, Florian},
  title =	{{Utility-Based Scheduling of (m,k)-firm Real-Time Tasks - New Empirical Results}},
  booktitle =	{LITES, Volume 4, Issue 1 (2017)},
  pages =	{02:1--02:25},
  journal =	{Leibniz Transactions on Embedded Systems},
  ISSN =	{2199-2002},
  year =	{2017},
  volume =	{4},
  number =	{1},
  editor =	{Kluge, Florian},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LITES-v004-i001-a002},
  doi =		{10.4230/LITES-v004-i001-a002},
  annote =	{Keywords: Real-time Scheduling, (m, k)-Firm Real-Time Tasks}
}
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