31 Search Results for "Qi, Qi"


Document
Balancing Minimum Free Energy and Codon Adaptation Index for Pareto Optimal RNA Design

Authors: Xinyu Gu, Yuanyuan Qi, and Mohammed El-Kebir

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


Abstract
The problem of designing an RNA sequence v that encodes for a given target protein w plays an important role in messenger RNA (mRNA) vaccine design. Due to codon degeneracy, there exist exponentially many RNA sequences for a single target protein. These candidate RNA sequences may adopt different secondary structure conformations with varying minimum free energy (MFE), affecting their thermodynamic stability and consequently mRNA half-life. In addition, species-specific codon usage bias, as measured by the codon adaptation index (CAI), also plays an essential role in translation efficiency. While previous works have focused on optimizing either MFE or CAI, more recent works have shown the merits of optimizing both objectives. Importantly, there is a trade-off between MFE and CAI, i.e. optimizing one objective is at the expense of the other. Here, we formulate the Pareto Optimal RNA Design problem, seeking the set of Pareto optimal solutions for which no other solution exists that is better in terms of both MFE and CAI. We introduce DERNA (DEsign RNA), which uses the weighted sum method to enumerate the Pareto front by optimizing convex combinations of both objectives. DERNA uses dynamic programming to solve each convex combination in O(|w|³) time and O(|w|²) space. Compared to a previous approach that only optimizes MFE, we show on a benchmark dataset that DERNA obtains solutions with identical MFE but superior CAI. Additionally, we show that DERNA matches the performance in terms of solution quality of LinearDesign, a recent approach that similarly seeks to balance MFE and CAI. Finally, we demonstrate our method’s potential for mRNA vaccine design using SARS-CoV-2 spike as the target protein.

Cite as

Xinyu Gu, Yuanyuan Qi, and Mohammed El-Kebir. Balancing Minimum Free Energy and Codon Adaptation Index for Pareto Optimal RNA Design. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 21:1-21:20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)


Copy BibTex To Clipboard

@InProceedings{gu_et_al:LIPIcs.WABI.2023.21,
  author =	{Gu, Xinyu and Qi, Yuanyuan and El-Kebir, Mohammed},
  title =	{{Balancing Minimum Free Energy and Codon Adaptation Index for Pareto Optimal RNA Design}},
  booktitle =	{23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
  pages =	{21:1--21:20},
  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.2023.21},
  URN =		{urn:nbn:de:0030-drops-186479},
  doi =		{10.4230/LIPIcs.WABI.2023.21},
  annote =	{Keywords: Multi-objective optimization, dynamic programming, RNA sequence design, reverse translation, mRNA vaccine design}
}
Document
Online Mergers and Applications to Registration-Based Encryption and Accumulators

Authors: Mohammad Mahmoody and Wei Qi

Published in: LIPIcs, Volume 267, 4th Conference on Information-Theoretic Cryptography (ITC 2023)


Abstract
In this work we study a new information theoretic problem, called online merging, that has direct applications for constructing public-state accumulators and registration-based encryption schemes. An {online merger} receives the sequence of sets {1}, {2}, … in an online way, and right after receiving {i}, it can re-partition the elements 1,…,i into T₁,…,T_{m_i} by merging some of these sets. The goal of the merger is to balance the trade-off between the maximum number of sets wid = max_{i ∈ [n]} m_i that co-exist at any moment, called the width of the scheme, with its depth dep = max_{i ∈ [n]} d_i, where d_i is the number of times that the sets that contain i get merged. An online merger can be used to maintain a set of Merkle trees that occasionally get merged. An online merger can be directly used to obtain public-state accumulators (using collision-resistant hashing) and registration-based encryptions (relying on more assumptions). Doing so, the width of an online merger translates into the size of the public-parameter of the constructed scheme, and the depth of the online algorithm corresponds to the number of times that parties need to update their "witness" (for accumulators) or their decryption key (for RBE). In this work, we construct online mergers with poly(log n) width and O(log n / log log n) depth, which can be shown to be optimal for all schemes with poly(log n) width. More generally, we show how to achieve optimal depth for a given fixed width and to achieve a 2-approximate optimal width for a given depth d that can possibly grow as a function of n (e.g., d = 2 or d = log n / log log n). As applications, we obtain accumulators with O(log n / log log n) number of updates for parties' witnesses (which can be shown to be optimal for accumulator digests of length poly(log n)) as well as registration based encryptions that again have an optimal O(log n / log log n) number of decryption updates, resolving the open question of Mahmoody, Rahimi, Qi [TCC'22] who proved that Ω(log n / log log n) number of decryption updates are necessary for any RBE (with public parameter of length poly(log n)). More generally, for any given number of decryption updates d = d(n) (under believable computational assumptions) our online merger implies RBE schemes with public parameters of length that is optimal, up to a constant factor that depends on the security parameter. For example, for any constant number of updates d, we get RBE schemes with public parameters of length O(n^{1/(d+1)}).

Cite as

Mohammad Mahmoody and Wei Qi. Online Mergers and Applications to Registration-Based Encryption and Accumulators. In 4th Conference on Information-Theoretic Cryptography (ITC 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 267, pp. 15:1-15:23, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)


Copy BibTex To Clipboard

@InProceedings{mahmoody_et_al:LIPIcs.ITC.2023.15,
  author =	{Mahmoody, Mohammad and Qi, Wei},
  title =	{{Online Mergers and Applications to Registration-Based Encryption and Accumulators}},
  booktitle =	{4th Conference on Information-Theoretic Cryptography (ITC 2023)},
  pages =	{15:1--15:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-271-6},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{267},
  editor =	{Chung, Kai-Min},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITC.2023.15},
  URN =		{urn:nbn:de:0030-drops-183432},
  doi =		{10.4230/LIPIcs.ITC.2023.15},
  annote =	{Keywords: Registration-based encryption, Accumulators, Merkle Trees}
}
Document
Track A: Algorithms, Complexity and Games
New Partitioning Techniques and Faster Algorithms for Approximate Interval Scheduling

Authors: Spencer Compton, Slobodan Mitrović, and Ronitt Rubinfeld

Published in: LIPIcs, Volume 261, 50th International Colloquium on Automata, Languages, and Programming (ICALP 2023)


Abstract
Interval scheduling is a basic problem in the theory of algorithms and a classical task in combinatorial optimization. We develop a set of techniques for partitioning and grouping jobs based on their starting and ending times, that enable us to view an instance of interval scheduling on many jobs as a union of multiple interval scheduling instances, each containing only a few jobs. Instantiating these techniques in dynamic and local settings of computation leads to several new results. For (1+ε)-approximation of job scheduling of n jobs on a single machine, we develop a fully dynamic algorithm with O((log n)/ε) update and O(log n) query worst-case time. Further, we design a local computation algorithm that uses only O((log N)/ε) queries when all jobs are length at least 1 and have starting/ending times within [0,N]. Our techniques are also applicable in a setting where jobs have rewards/weights. For this case we design a fully dynamic deterministic algorithm whose worst-case update and query time are poly(log n,1/ε). Equivalently, this is the first algorithm that maintains a (1+ε)-approximation of the maximum independent set of a collection of weighted intervals in poly(log n,1/ε) time updates/queries. This is an exponential improvement in 1/ε over the running time of a randomized algorithm of Henzinger, Neumann, and Wiese [SoCG, 2020], while also removing all dependence on the values of the jobs' starting/ending times and rewards, as well as removing the need for any randomness. We also extend our approaches for interval scheduling on a single machine to examine the setting with M machines.

Cite as

Spencer Compton, Slobodan Mitrović, and Ronitt Rubinfeld. New Partitioning Techniques and Faster Algorithms for Approximate Interval Scheduling. In 50th International Colloquium on Automata, Languages, and Programming (ICALP 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 261, pp. 45:1-45:16, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)


Copy BibTex To Clipboard

@InProceedings{compton_et_al:LIPIcs.ICALP.2023.45,
  author =	{Compton, Spencer and Mitrovi\'{c}, Slobodan and Rubinfeld, Ronitt},
  title =	{{New Partitioning Techniques and Faster Algorithms for Approximate Interval Scheduling}},
  booktitle =	{50th International Colloquium on Automata, Languages, and Programming (ICALP 2023)},
  pages =	{45:1--45:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-278-5},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{261},
  editor =	{Etessami, Kousha and Feige, Uriel and Puppis, Gabriele},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2023.45},
  URN =		{urn:nbn:de:0030-drops-180978},
  doi =		{10.4230/LIPIcs.ICALP.2023.45},
  annote =	{Keywords: interval scheduling, dynamic algorithms, local computation algorithms}
}
Document
Track A: Algorithms, Complexity and Games
Parallel Self-Testing of EPR Pairs Under Computational Assumptions

Authors: Honghao Fu, Daochen Wang, and Qi Zhao

Published in: LIPIcs, Volume 261, 50th International Colloquium on Automata, Languages, and Programming (ICALP 2023)


Abstract
Self-testing is a fundamental feature of quantum mechanics that allows a classical verifier to force untrusted quantum devices to prepare certain states and perform certain measurements on them. The standard approach assumes at least two spatially separated devices. Recently, Metger and Vidick [Metger and Vidick, 2021] showed that a single EPR pair of a single quantum device can be self-tested under computational assumptions. In this work, we generalize their results to give the first parallel self-test of N EPR pairs and measurements on them in the single-device setting under the same computational assumptions. We show that our protocol can be passed with probability negligibly close to 1 by an honest quantum device using poly(N) resources. Moreover, we show that any quantum device that fails our protocol with probability at most ε must be poly(N,ε)-close to being honest in the appropriate sense. In particular, our protocol can test any distribution over tensor products of computational or Hadamard basis measurements, making it suitable for applications such as device-independent quantum key distribution [Metger et al., 2021] under computational assumptions. Moreover, a simplified version of our protocol is the first that can efficiently certify an arbitrary number of qubits of a single cloud quantum computer using only classical communication.

Cite as

Honghao Fu, Daochen Wang, and Qi Zhao. Parallel Self-Testing of EPR Pairs Under Computational Assumptions. In 50th International Colloquium on Automata, Languages, and Programming (ICALP 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 261, pp. 64:1-64:19, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)


Copy BibTex To Clipboard

@InProceedings{fu_et_al:LIPIcs.ICALP.2023.64,
  author =	{Fu, Honghao and Wang, Daochen and Zhao, Qi},
  title =	{{Parallel Self-Testing of EPR Pairs Under Computational Assumptions}},
  booktitle =	{50th International Colloquium on Automata, Languages, and Programming (ICALP 2023)},
  pages =	{64:1--64:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-278-5},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{261},
  editor =	{Etessami, Kousha and Feige, Uriel and Puppis, Gabriele},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2023.64},
  URN =		{urn:nbn:de:0030-drops-181160},
  doi =		{10.4230/LIPIcs.ICALP.2023.64},
  annote =	{Keywords: Quantum complexity theory, self-testing, LWE}
}
Document
New Approximation Algorithms for Touring Regions

Authors: Benjamin Qi and Richard Qi

Published in: LIPIcs, Volume 258, 39th International Symposium on Computational Geometry (SoCG 2023)


Abstract
We analyze the touring regions problem: find a (1+ε)-approximate Euclidean shortest path in d-dimensional space that starts at a given starting point, ends at a given ending point, and visits given regions R₁, R₂, R₃, … , R_n in that order. Our main result is an O (n/√ε log{1/ε} + 1/ε)-time algorithm for touring disjoint disks. We also give an O(min(n/ε, n²/√ε))-time algorithm for touring disjoint two-dimensional convex fat bodies. Both of these results naturally generalize to larger dimensions; we obtain O(n/{ε^{d-1}} log²1/ε + 1/ε^{2d-2}) and O(n/ε^{2d-2})-time algorithms for touring disjoint d-dimensional balls and convex fat bodies, respectively.

Cite as

Benjamin Qi and Richard Qi. New Approximation Algorithms for Touring Regions. In 39th International Symposium on Computational Geometry (SoCG 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 258, pp. 54:1-54:16, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)


Copy BibTex To Clipboard

@InProceedings{qi_et_al:LIPIcs.SoCG.2023.54,
  author =	{Qi, Benjamin and Qi, Richard},
  title =	{{New Approximation Algorithms for Touring Regions}},
  booktitle =	{39th International Symposium on Computational Geometry (SoCG 2023)},
  pages =	{54:1--54:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-273-0},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{258},
  editor =	{Chambers, Erin W. and Gudmundsson, Joachim},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2023.54},
  URN =		{urn:nbn:de:0030-drops-179047},
  doi =		{10.4230/LIPIcs.SoCG.2023.54},
  annote =	{Keywords: shortest paths, convex bodies, fat objects, disks}
}
Document
On Maximizing Sums of Non-Monotone Submodular and Linear Functions

Authors: Benjamin Qi

Published in: LIPIcs, Volume 248, 33rd International Symposium on Algorithms and Computation (ISAAC 2022)


Abstract
We study the problem of Regularized Unconstrained Submodular Maximization (RegularizedUSM) as defined by [Bodek and Feldman '22]. In this problem, we are given query access to a non-negative submodular function f: 2^N → ℝ_{≥ 0} and a linear function 𝓁: 2^N → ℝ over the same ground set N, and the objective is to output a set T ⊆ N approximately maximizing the sum f(T)+𝓁(T). Specifically, an algorithm is said to provide an (α,β)-approximation for RegularizedUSM if it outputs a set T such that E[f(T)+𝓁(T)] ≥ max_{S ⊆ N}[α ⋅ f(S)+β⋅ 𝓁(S)]. We also study the setting where S and T are constrained to be independent in a given matroid, which we refer to as Regularized Constrained Submodular Maximization (RegularizedCSM). The special case of RegularizedCSM with monotone f has been extensively studied [Sviridenko et al. '17, Feldman '18, Harshaw et al. '19]. On the other hand, we are aware of only one prior work that studies RegularizedCSM with non-monotone f [Lu et al. '21], and that work constrains 𝓁 to be non-positive. In this work, we provide improved (α,β)-approximation algorithms for both {RegularizedUSM} and {RegularizedCSM} with non-monotone f. In particular, we are the first to provide nontrivial (α,β)-approximations for RegularizedCSM where the sign of 𝓁 is unconstrained, and the α we obtain for RegularizedUSM improves over [Bodek and Feldman '22] for all β ∈ (0,1). In addition to approximation algorithms, we provide improved inapproximability results for all of the aforementioned cases. In particular, we show that the α our algorithm obtains for {RegularizedCSM} with unconstrained 𝓁 is essentially tight for β ≥ e/(e+1). Using similar ideas, we are also able to show 0.478-inapproximability for maximizing a submodular function where S and T are subject to a cardinality constraint, improving a 0.491-inapproximability result due to [Oveis Gharan and Vondrak '10].

Cite as

Benjamin Qi. On Maximizing Sums of Non-Monotone Submodular and Linear Functions. In 33rd International Symposium on Algorithms and Computation (ISAAC 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 248, pp. 41:1-41:16, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2022)


Copy BibTex To Clipboard

@InProceedings{qi:LIPIcs.ISAAC.2022.41,
  author =	{Qi, Benjamin},
  title =	{{On Maximizing Sums of Non-Monotone Submodular and Linear Functions}},
  booktitle =	{33rd International Symposium on Algorithms and Computation (ISAAC 2022)},
  pages =	{41:1--41:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-258-7},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{248},
  editor =	{Bae, Sang Won and Park, Heejin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2022.41},
  URN =		{urn:nbn:de:0030-drops-173263},
  doi =		{10.4230/LIPIcs.ISAAC.2022.41},
  annote =	{Keywords: submodular maximization, regularization, continuous greedy, inapproximability}
}
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)


Copy BibTex To Clipboard

@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}},
  journal =	{Leibniz Transactions on Embedded Systems},
  pages =	{03:1--03:30},
  ISSN =	{2199-2002},
  year =	{2022},
  volume =	{8},
  number =	{1},
  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
Short Paper
Representing Computational Relations in Knowledge Graphs Using Functional Languages (Short Paper)

Authors: Yanmin Qi, Heshan Du, Amin Farjudian, and Yunqiang Zhu

Published in: LIPIcs, Volume 240, 15th International Conference on Spatial Information Theory (COSIT 2022)


Abstract
Knowledge representation is the cornerstone of constructing a GKG. The existing representations of spatial and computational relations in GKGs, however, are inadequate. In this paper, we use DE-9IM to represent spatial topological relations. To represent computational relations, we use typed lambda calculus via its implementation in the functional language Haskell, in which functions are first-class primitives. We exemplify our ideas through some basic examples in Haskell.

Cite as

Yanmin Qi, Heshan Du, Amin Farjudian, and Yunqiang Zhu. Representing Computational Relations in Knowledge Graphs Using Functional Languages (Short Paper). In 15th International Conference on Spatial Information Theory (COSIT 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 240, pp. 29:1-29:7, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2022)


Copy BibTex To Clipboard

@InProceedings{qi_et_al:LIPIcs.COSIT.2022.29,
  author =	{Qi, Yanmin and Du, Heshan and Farjudian, Amin and Zhu, Yunqiang},
  title =	{{Representing Computational Relations in Knowledge Graphs Using Functional Languages}},
  booktitle =	{15th International Conference on Spatial Information Theory (COSIT 2022)},
  pages =	{29:1--29:7},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-257-0},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{240},
  editor =	{Ishikawa, Toru and Fabrikant, Sara Irina and Winter, Stephan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.COSIT.2022.29},
  URN =		{urn:nbn:de:0030-drops-169147},
  doi =		{10.4230/LIPIcs.COSIT.2022.29},
  annote =	{Keywords: spatial relation, computational relation, functional programming, Haskell, geo-knowledge graph}
}
Document
Fully Dynamic Four-Vertex Subgraph Counting

Authors: Kathrin Hanauer, Monika Henzinger, and Qi Cheng Hua

Published in: LIPIcs, Volume 221, 1st Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2022)


Abstract
This paper presents a comprehensive study of algorithms for maintaining the number of all connected four-vertex subgraphs in a dynamic graph. Specifically, our algorithms maintain the number of paths of length three in deterministic amortized O(m^{1/2}) update time, and any other connected four-vertex subgraph which is not a clique in deterministic amortized update time O(m^{2/3}). Queries can be answered in constant time. We also study the query times for subgraphs containing an arbitrary edge that is supplied only with the query as well as the case where only subgraphs containing a vertex s that is fixed beforehand are considered. For length-3 paths, paws, 4-cycles, and diamonds our bounds match or are not far from (conditional) lower bounds: Based on the OMv conjecture we show that any dynamic algorithm that detects the existence of paws, diamonds, or 4-cycles or that counts length-3 paths takes update time Ω(m^{1/2-δ}). Additionally, for 4-cliques and all connected induced subgraphs, we show a lower bound of Ω(m^{1-δ}) for any small constant δ > 0 for the amortized update time, assuming the static combinatorial 4-clique conjecture holds. This shows that the O(m) algorithm by Eppstein et al. [David Eppstein et al., 2012] for these subgraphs cannot be improved by a polynomial factor.

Cite as

Kathrin Hanauer, Monika Henzinger, and Qi Cheng Hua. Fully Dynamic Four-Vertex Subgraph Counting. In 1st Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 221, pp. 18:1-18:17, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2022)


Copy BibTex To Clipboard

@InProceedings{hanauer_et_al:LIPIcs.SAND.2022.18,
  author =	{Hanauer, Kathrin and Henzinger, Monika and Hua, Qi Cheng},
  title =	{{Fully Dynamic Four-Vertex Subgraph Counting}},
  booktitle =	{1st Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2022)},
  pages =	{18:1--18:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-224-2},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{221},
  editor =	{Aspnes, James and Michail, Othon},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAND.2022.18},
  URN =		{urn:nbn:de:0030-drops-159608},
  doi =		{10.4230/LIPIcs.SAND.2022.18},
  annote =	{Keywords: Dynamic Graph Algorithms, Subgraph Counting, Motif Search}
}
Document
On Polynomially Many Queries to NP or QMA Oracles

Authors: Sevag Gharibian and Dorian Rudolph

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


Abstract
We study the complexity of problems solvable in deterministic polynomial time with access to an NP or Quantum Merlin-Arthur (QMA)-oracle, such as P^NP and P^QMA, respectively. The former allows one to classify problems more finely than the Polynomial-Time Hierarchy (PH), whereas the latter characterizes physically motivated problems such as Approximate Simulation (APX-SIM) [Ambainis, CCC 2014]. In this area, a central role has been played by the classes P^NP[log] and P^QMA[log], defined identically to P^NP and P^QMA, except that only logarithmically many oracle queries are allowed. Here, [Gottlob, FOCS 1993] showed that if the adaptive queries made by a P^NP machine have a "query graph" which is a tree, then this computation can be simulated in P^NP[log]. In this work, we first show that for any verification class C ∈ {NP, MA, QCMA, QMA, QMA(2), NEXP, QMA_exp}, any P^C machine with a query graph of "separator number" s can be simulated using deterministic time exp(slog n) and slog n queries to a C-oracle. When s ∈ O(1) (which includes the case of O(1)-treewidth, and thus also of trees), this gives an upper bound of P^C[log], and when s ∈ O(log^k(n)), this yields bound QP^{C[log^{k+1}]} (QP meaning quasi-polynomial time). We next show how to combine Gottlob’s "admissible-weighting function" framework with the "flag-qubit" framework of [Watson, Bausch, Gharibian, 2020], obtaining a unified approach for embedding P^C computations directly into APX-SIM instances in a black-box fashion. Finally, we formalize a simple no-go statement about polynomials (c.f. [Krentel, STOC 1986]): Given a multi-linear polynomial p specified via an arithmetic circuit, if one can "weakly compress" p so that its optimal value requires m bits to represent, then P^NP can be decided with only m queries to an NP-oracle.

Cite as

Sevag Gharibian and Dorian Rudolph. On Polynomially Many Queries to NP or QMA Oracles. In 13th Innovations in Theoretical Computer Science Conference (ITCS 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 215, pp. 75:1-75:27, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2022)


Copy BibTex To Clipboard

@InProceedings{gharibian_et_al:LIPIcs.ITCS.2022.75,
  author =	{Gharibian, Sevag and Rudolph, Dorian},
  title =	{{On Polynomially Many Queries to NP or QMA Oracles}},
  booktitle =	{13th Innovations in Theoretical Computer Science Conference (ITCS 2022)},
  pages =	{75:1--75:27},
  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.2022.75},
  URN =		{urn:nbn:de:0030-drops-156717},
  doi =		{10.4230/LIPIcs.ITCS.2022.75},
  annote =	{Keywords: admissible weighting function, oracle complexity class, quantum complexity theory, Quantum Merlin Arthur (QMA), simulation of local measurement}
}
Document
Dynamic Curves for Decentralized Autonomous Cryptocurrency Exchanges

Authors: Bhaskar Krishnamachari, Qi Feng, and Eugenio Grippo

Published in: OASIcs, Volume 92, 4th International Symposium on Foundations and Applications of Blockchain 2021 (FAB 2021)


Abstract
One of the exciting recent developments in decentralized finance (DeFi) has been the development of decentralized cryptocurrency exchanges that can autonomously handle conversion between different cryptocurrencies. Decentralized exchange protocols such as Uniswap, Curve and other types of Automated Market Makers (AMMs) maintain a liquidity pool (LP) of two or more assets constrained to maintain at all times a mathematical relation to each other, defined by a given function or curve. Examples of such functions are the constant-sum and constant-product AMMs. Existing systems however suffer from several challenges. They require external arbitrageurs to restore the price of tokens in the pool to match the market price. Such activities can potentially drain resources from the liquidity pool. In particular dramatic market price changes can result in low liquidity with respect to one or more of the assets and reduce the total value of the LP. We propose in this work a new approach to constructing the AMM by proposing the idea of dynamic curves. It utilizes input from a market price oracle to modify the mathematical relationship between the assets so that the pool price continuously and automatically adjusts to be identical to the market price. This approach eliminates arbitrage opportunities and, as we show through simulations, maintains liquidity in the LP for all assets and the total value of the LP over a wide range of market prices.

Cite as

Bhaskar Krishnamachari, Qi Feng, and Eugenio Grippo. Dynamic Curves for Decentralized Autonomous Cryptocurrency Exchanges. In 4th International Symposium on Foundations and Applications of Blockchain 2021 (FAB 2021). Open Access Series in Informatics (OASIcs), Volume 92, pp. 5:1-5:14, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2021)


Copy BibTex To Clipboard

@InProceedings{krishnamachari_et_al:OASIcs.FAB.2021.5,
  author =	{Krishnamachari, Bhaskar and Feng, Qi and Grippo, Eugenio},
  title =	{{Dynamic Curves for Decentralized Autonomous Cryptocurrency Exchanges}},
  booktitle =	{4th International Symposium on Foundations and Applications of Blockchain 2021 (FAB 2021)},
  pages =	{5:1--5:14},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-196-2},
  ISSN =	{2190-6807},
  year =	{2021},
  volume =	{92},
  editor =	{Gramoli, Vincent and Sadoghi, Mohammad},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.FAB.2021.5},
  URN =		{urn:nbn:de:0030-drops-139911},
  doi =		{10.4230/OASIcs.FAB.2021.5},
  annote =	{Keywords: Decentralized Exchange, Automated Market Maker, Decentralized Finance, Dynamic Curves}
}
Document
Invited Talk
An Incentive Analysis of Some Bitcoin Fee Designs (Invited Talk)

Authors: Andrew Chi chih Yao

Published in: LIPIcs, Volume 168, 47th International Colloquium on Automata, Languages, and Programming (ICALP 2020)


Abstract
In the Bitcoin system, miners are incentivized to join the system and validate transactions through fees paid by the users. A simple "pay your bid" auction has been employed to determine the transaction fees. Recently, Lavi, Sattath and Zohar [Lavi et al., 2019] proposed an alternative fee design, called the monopolistic price (MP) mechanism, aimed at improving the revenue for the miners. Although MP is not strictly incentive compatible (IC), they studied how close to IC the mechanism is for iid distributions, and conjectured that it is nearly IC asymptotically based on extensive simulations and some analysis. In this paper, we prove that the MP mechanism is nearly incentive compatible for any iid distribution as the number of users grows large. This holds true with respect to other attacks such as splitting bids. We also prove a conjecture in [Lavi et al., 2019] that MP dominates the RSOP auction in revenue (originally defined in [Goldberg et al., 2006] for digital goods). These results lend support to MP as a Bitcoin fee design candidate. Additionally, we explore some possible intrinsic correlations between incentive compatibility and revenue in general.

Cite as

Andrew Chi chih Yao. An Incentive Analysis of Some Bitcoin Fee Designs (Invited Talk). In 47th International Colloquium on Automata, Languages, and Programming (ICALP 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 168, pp. 1:1-1:12, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2020)


Copy BibTex To Clipboard

@InProceedings{yao:LIPIcs.ICALP.2020.1,
  author =	{Yao, Andrew Chi chih},
  title =	{{An Incentive Analysis of Some Bitcoin Fee Designs}},
  booktitle =	{47th International Colloquium on Automata, Languages, and Programming (ICALP 2020)},
  pages =	{1:1--1:12},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-138-2},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{168},
  editor =	{Czumaj, Artur and Dawar, Anuj and Merelli, Emanuela},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2020.1},
  URN =		{urn:nbn:de:0030-drops-124087},
  doi =		{10.4230/LIPIcs.ICALP.2020.1},
  annote =	{Keywords: Bitcoin, blockchain, incentive compatibility, maximum revenue, mechanism design}
}
Document
Vertex Downgrading to Minimize Connectivity

Authors: Hassene Aissi, Da Qi Chen, and R. Ravi

Published in: LIPIcs, Volume 162, 17th Scandinavian Symposium and Workshops on Algorithm Theory (SWAT 2020)


Abstract
We consider the problem of interdicting a directed graph by deleting nodes with the goal of minimizing the local edge connectivity of the remaining graph from a given source to a sink. We introduce and study a general downgrading variant of the interdiction problem where the capacity of an arc is a function of the subset of its endpoints that are downgraded, and the goal is to minimize the downgraded capacity of a minimum source-sink cut subject to a node downgrading budget. This models the case when both ends of an arc must be downgraded to remove it, for example. For this generalization, we provide a bicriteria (4,4)-approximation that downgrades nodes with total weight at most 4 times the budget and provides a solution where the downgraded connectivity from the source to the sink is at most 4 times that in an optimal solution. We accomplish this with an LP relaxation and rounding using a ball-growing algorithm based on the LP values. We further generalize the downgrading problem to one where each vertex can be downgraded to one of k levels, and the arc capacities are functions of the pairs of levels to which its ends are downgraded. We generalize our LP rounding to get a (4k,4k)-approximation for this case.

Cite as

Hassene Aissi, Da Qi Chen, and R. Ravi. Vertex Downgrading to Minimize Connectivity. In 17th Scandinavian Symposium and Workshops on Algorithm Theory (SWAT 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 162, pp. 5:1-5:15, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2020)


Copy BibTex To Clipboard

@InProceedings{aissi_et_al:LIPIcs.SWAT.2020.5,
  author =	{Aissi, Hassene and Chen, Da Qi and Ravi, R.},
  title =	{{Vertex Downgrading to Minimize Connectivity}},
  booktitle =	{17th Scandinavian Symposium and Workshops on Algorithm Theory (SWAT 2020)},
  pages =	{5:1--5:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-150-4},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{162},
  editor =	{Albers, Susanne},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SWAT.2020.5},
  URN =		{urn:nbn:de:0030-drops-122527},
  doi =		{10.4230/LIPIcs.SWAT.2020.5},
  annote =	{Keywords: Vertex Interdiction, Vertex Downgrading, Network Interdiction, Approximation Algorithm}
}
Document
Proving Tree Algorithms for Succinct Data Structures

Authors: Reynald Affeldt, Jacques Garrigue, Xuanrui Qi, and Kazunari Tanaka

Published in: LIPIcs, Volume 141, 10th International Conference on Interactive Theorem Proving (ITP 2019)


Abstract
Succinct data structures give space-efficient representations of large amounts of data without sacrificing performance. They rely on cleverly designed data representations and algorithms. We present here the formalization in Coq/SSReflect of two different tree-based succinct representations and their accompanying algorithms. One is the Level-Order Unary Degree Sequence, which encodes the structure of a tree in breadth-first order as a sequence of bits, where access operations can be defined in terms of Rank and Select, which work in constant time for static bit sequences. The other represents dynamic bit sequences as binary balanced trees, where Rank and Select present a low logarithmic overhead compared to their static versions, and with efficient insertion and deletion. The two can be stacked to provide a dynamic representation of dictionaries for instance. While both representations are well-known, we believe this to be their first formalization and a needed step towards provably-safe implementations of big data.

Cite as

Reynald Affeldt, Jacques Garrigue, Xuanrui Qi, and Kazunari Tanaka. Proving Tree Algorithms for Succinct Data Structures. In 10th International Conference on Interactive Theorem Proving (ITP 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 141, pp. 5:1-5:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


Copy BibTex To Clipboard

@InProceedings{affeldt_et_al:LIPIcs.ITP.2019.5,
  author =	{Affeldt, Reynald and Garrigue, Jacques and Qi, Xuanrui and Tanaka, Kazunari},
  title =	{{Proving Tree Algorithms for Succinct Data Structures}},
  booktitle =	{10th International Conference on Interactive Theorem Proving (ITP 2019)},
  pages =	{5:1--5:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-122-1},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{141},
  editor =	{Harrison, John and O'Leary, John and Tolmach, Andrew},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITP.2019.5},
  URN =		{urn:nbn:de:0030-drops-110609},
  doi =		{10.4230/LIPIcs.ITP.2019.5},
  annote =	{Keywords: Coq, small-scale reflection, succinct data structures, LOUDS, bit vectors, self balancing trees}
}
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}
}
  • Refine by Author
  • 2 Qi, Benjamin
  • 2 Zhao, Qi
  • 1 Affeldt, Reynald
  • 1 Aissi, Hassene
  • 1 Balaji, Nikhil
  • Show More...

  • Refine by Classification
  • 3 Theory of computation → Approximation algorithms analysis
  • 2 Theory of computation → Data structures design and analysis
  • 2 Theory of computation → Design and analysis of algorithms
  • 1 Applied computing → Bioinformatics
  • 1 Applied computing → Computational biology
  • Show More...

  • Refine by Keyword
  • 2 Scala
  • 1 #P-complete
  • 1 Abstract Peer Types
  • 1 Accumulators
  • 1 Approximate Computing
  • Show More...

  • Refine by Type
  • 31 document

  • Refine by Publication Year
  • 11 2019
  • 5 2015
  • 5 2022
  • 5 2023
  • 2 2020
  • Show More...

Questions / Remarks / Feedback
X

Feedback for Dagstuhl Publishing


Thanks for your feedback!

Feedback submitted

Could not send message

Please try again later or send an E-mail