8 Search Results for "Shi, Xiaofei"

Document
DOI: 10.4230/LIPIcs.SWAT.2026.17
Incremental Strongly Connected Components with Predictions

Authors: Ronald Deng, Samuel McCauley, Aidin Niaparast, Helia Niaparast, Bennett Ptak, Shirel Quintanilla, Shikha Singh, and Nathan Vosburg

Published in: LIPIcs, Volume 370, 20th Scandinavian Symposium on Algorithm Theory (SWAT 2026)

Abstract
Algorithms with predictions is a growing area that aims to leverage machine-learned predictions to design faster beyond-worst-case algorithms. In this paper, we use this framework to design a learned data structure for the incremental strongly connected components (SCC) problem. In this problem, the n vertices of a graph are known a priori and the m directed edges arrive over time. The goal is to efficiently maintain the strongly connected components of the graph after each insert. Our algorithm receives a possibly erroneous prediction of the edge sequence and uses it to precompute partial solutions to support fast inserts. We show that our algorithm achieves nearly optimal bounds with good predictions and its performance smoothly degrades with the prediction error. We also implement our data structure and perform experiments on real datasets. Our empirical results show that the theory is predictive of practical runtime improvements.
Cite as

Ronald Deng, Samuel McCauley, Aidin Niaparast, Helia Niaparast, Bennett Ptak, Shirel Quintanilla, Shikha Singh, and Nathan Vosburg. Incremental Strongly Connected Components with Predictions. In 20th Scandinavian Symposium on Algorithm Theory (SWAT 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 370, pp. 17:1-17:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{deng_et_al:LIPIcs.SWAT.2026.17,
  author =	{Deng, Ronald and McCauley, Samuel and Niaparast, Aidin and Niaparast, Helia and Ptak, Bennett and Quintanilla, Shirel and Singh, Shikha and Vosburg, Nathan},
  title =	{{Incremental Strongly Connected Components with Predictions}},
  booktitle =	{20th Scandinavian Symposium on Algorithm Theory (SWAT 2026)},
  pages =	{17:1--17:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-421-5},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{370},
  editor =	{Fraigniaud, Pierre},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SWAT.2026.17},
  URN =		{urn:nbn:de:0030-drops-260530},
  doi =		{10.4230/LIPIcs.SWAT.2026.17},
  annote =	{Keywords: algorithms with predictions, learning augmented algorithms, incremental graph algorithms, strongly connected components, data structures}
}
Document
DOI: 10.4230/LIPIcs.SoCG.2026.48
FPT Approximations for Capacitated Sum of Radii and Diameters

Authors: Arnold Filtser and Ameet Gadekar

Published in: LIPIcs, Volume 367, 42nd International Symposium on Computational Geometry (SoCG 2026)

Abstract
The Capacitated Sum of Radii problem involves partitioning a set of points P, where each point p ∈ P has capacity U_p, into k clusters that minimize the sum of cluster radii, such that the number of points in the cluster centered at point p is at most U_p. We begin by showing that the problem is APX-hard, and that under gap-ETH there is no parameterized approximation scheme (FPT-AS). We then construct a ≈5.83-approximation algorithm in FPT time (improving a previous ≈7.61 approximation in FPT time). Our results also hold when the objective is a general monotone symmetric norm of radii. We also improve the approximation factors for the uniform capacity case, and for the closely related problem of Capacitated Sum of Diameters.
Cite as

Arnold Filtser and Ameet Gadekar. FPT Approximations for Capacitated Sum of Radii and Diameters. In 42nd International Symposium on Computational Geometry (SoCG 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 367, pp. 48:1-48:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{filtser_et_al:LIPIcs.SoCG.2026.48,
  author =	{Filtser, Arnold and Gadekar, Ameet},
  title =	{{FPT Approximations for Capacitated Sum of Radii and Diameters}},
  booktitle =	{42nd International Symposium on Computational Geometry (SoCG 2026)},
  pages =	{48:1--48:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-418-5},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{367},
  editor =	{Ahn, Hee-Kap and Hoffmann, Michael and Nayyeri, Amir},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2026.48},
  URN =		{urn:nbn:de:0030-drops-258545},
  doi =		{10.4230/LIPIcs.SoCG.2026.48},
  annote =	{Keywords: clustering, sum of radii, sum of diameter, capacitated clustering, fpt}
}
Document
DOI: 10.4230/LIPIcs.ISAAC.2025.18
An Optimal Algorithm for the Stacker Crane Problem on Fixed Topologies

Authors: Yike Chen, Ke Shi, and Chao Xu

Published in: LIPIcs, Volume 359, 36th International Symposium on Algorithms and Computation (ISAAC 2025)

Abstract
The Stacker Crane Problem (SCP) is a variant of the Traveling Salesman Problem. In SCP, pairs of pickup and delivery points are designated on a graph, and a crane must visit these points to move objects from each pickup location to its respective delivery point. The goal is to minimize the total distance traveled. SCP is known to be NP-hard, even on trees. The only positive results, in terms of polynomial-time solvability, apply to graphs that are topologically equivalent to a path or a cycle. We propose an algorithm that is optimal for each fixed topology, running in near-linear time. This is achieved by demonstrating that the problem is fixed-parameter tractable (FPT) when parameterized by both the cycle rank and the number of branch vertices.
Cite as

Yike Chen, Ke Shi, and Chao Xu. An Optimal Algorithm for the Stacker Crane Problem on Fixed Topologies. In 36th International Symposium on Algorithms and Computation (ISAAC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 359, pp. 18:1-18:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{chen_et_al:LIPIcs.ISAAC.2025.18,
  author =	{Chen, Yike and Shi, Ke and Xu, Chao},
  title =	{{An Optimal Algorithm for the Stacker Crane Problem on Fixed Topologies}},
  booktitle =	{36th International Symposium on Algorithms and Computation (ISAAC 2025)},
  pages =	{18:1--18:12},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-408-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{359},
  editor =	{Chen, Ho-Lin and Hon, Wing-Kai and Tsai, Meng-Tsung},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2025.18},
  URN =		{urn:nbn:de:0030-drops-249269},
  doi =		{10.4230/LIPIcs.ISAAC.2025.18},
  annote =	{Keywords: Stacker Crane Problem, Fixed-Parameter Tractable, Min-Cost Circulation}
}
Document
APPROX
DOI: 10.4230/LIPIcs.APPROX/RANDOM.2025.8
Multipass Linear Sketches for Geometric LP-Type Problems

Authors: N. Efe Çekirge, William Gay, and David P. Woodruff

Published in: LIPIcs, Volume 353, Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025)

Abstract
LP-type problems such as the Minimum Enclosing Ball (MEB), Linear Support Vector Machine (SVM), Linear Programming (LP), and Semidefinite Programming (SDP) are fundamental combinatorial optimization problems, with many important applications in machine learning applications such as classification, bioinformatics, and noisy learning. We study LP-type problems in several streaming and distributed big data models, giving ε-approximation linear sketching algorithms with a focus on the high accuracy regime with low dimensionality d, that is, when d < (1/ε)^0.999. Our main result is an O(ds) pass algorithm with O(s(√d/ε)^{3d/s}) ⋅ poly(d, log (1/ε)) space complexity in words, for any parameter s ∈ [1, d log (1/ε)], to solve ε-approximate LP-type problems of O(d) combinatorial and VC dimension. Notably, by taking s = d log (1/ε), we achieve space complexity polynomial in d and polylogarithmic in 1/ε, presenting exponential improvements in 1/ε over current algorithms. We complement our results by showing lower bounds of (1/ε)^Ω(d) for any 1-pass algorithm solving the (1 + ε)-approximation MEB and linear SVM problems, further motivating our multi-pass approach.
Cite as

N. Efe Çekirge, William Gay, and David P. Woodruff. Multipass Linear Sketches for Geometric LP-Type Problems. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 353, pp. 8:1-8:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{cekirge_et_al:LIPIcs.APPROX/RANDOM.2025.8,
  author =	{\c{C}ekirge, N. Efe and Gay, William and Woodruff, David P.},
  title =	{{Multipass Linear Sketches for Geometric LP-Type Problems}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025)},
  pages =	{8:1--8:25},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-397-3},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{353},
  editor =	{Ene, Alina and Chattopadhyay, Eshan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.APPROX/RANDOM.2025.8},
  URN =		{urn:nbn:de:0030-drops-243741},
  doi =		{10.4230/LIPIcs.APPROX/RANDOM.2025.8},
  annote =	{Keywords: Streaming, sketching, LP-type problems}
}
Document
DOI: 10.4230/LIPIcs.WABI.2025.14
Human Readable Compression of GFA Paths Using Grammar-Based Code

Authors: Peter Heringer and Daniel Doerr

Published in: LIPIcs, Volume 344, 25th International Conference on Algorithms for Bioinformatics (WABI 2025)

Abstract
Pangenome graphs offer a compact and comprehensive representation of genomic diversity, improving tasks such as variant calling, genotyping, and other downstream analyses. Although the underlying graph structures scale sublinearly with the number of haplotypes, the widely used GFA file format suffers from rapidly growing file sizes due to the explicit and repetitive encoding of haplotype paths. In this work, we introduce an extension to the GFA format that enables efficient grammar-based compression of haplotype paths while retaining human readability. In addition, grammar-based encoding provides an efficient in-memory data structure that does not require decompression, but conversely improves the runtime of many computational tasks that involve haplotype comparisons. We present sqz, a method that makes use of the proposed format extension to encode haplotype paths using byte pair encoding, a grammar-based compression scheme. We evaluate sqz on recent human pangenome graphs from Heumos et al. and the Human Pangenome Reference Consortium (HPRC), comparing it to existing compressors bgzip, gbz, and sequitur. sqz scales sublinearly with the number of haplotypes in a pangenome graph and consistently achieves higher compression ratios than sequitur and up to 5 times better compression than bgzip in HPRC graphs and up to 10 times in the graph from Heumos et al.. When combined with bgzip, sqz matches or excels the compression ratio of gbz across all our datasets. These results demonstrate the potential of our proposed extension of the GFA format in reducing haplotype path redundancy and improving storage efficiency for pangenome graphs.
Cite as

Peter Heringer and Daniel Doerr. Human Readable Compression of GFA Paths Using Grammar-Based Code. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 14:1-14:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{heringer_et_al:LIPIcs.WABI.2025.14,
  author =	{Heringer, Peter and Doerr, Daniel},
  title =	{{Human Readable Compression of GFA Paths Using Grammar-Based Code}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{14:1--14:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-386-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{344},
  editor =	{Brejov\'{a}, Bro\v{n}a and Patro, Rob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2025.14},
  URN =		{urn:nbn:de:0030-drops-239395},
  doi =		{10.4230/LIPIcs.WABI.2025.14},
  annote =	{Keywords: pangenomics, pangenome graphs, compression, grammar-based code, byte pair encoding}
}
Document
Survey
DOI: 10.4230/TGDK.3.1.3
Uncertainty Management in the Construction of Knowledge Graphs: A Survey

Authors: Lucas Jarnac, Yoan Chabot, and Miguel Couceiro

Published in: TGDK, Volume 3, Issue 1 (2025). Transactions on Graph Data and Knowledge, Volume 3, Issue 1

Abstract
Knowledge Graphs (KGs) are a major asset for companies thanks to their great flexibility in data representation and their numerous applications, e.g., vocabulary sharing, Q&A or recommendation systems. To build a KG, it is a common practice to rely on automatic methods for extracting knowledge from various heterogeneous sources. However, in a noisy and uncertain world, knowledge may not be reliable and conflicts between data sources may occur. Integrating unreliable data would directly impact the use of the KG, therefore such conflicts must be resolved. This could be done manually by selecting the best data to integrate. This first approach is highly accurate, but costly and time-consuming. That is why recent efforts focus on automatic approaches, which represent a challenging task since it requires handling the uncertainty of extracted knowledge throughout its integration into the KG. We survey state-of-the-art approaches in this direction and present constructions of both open and enterprise KGs. We then describe different knowledge extraction methods and discuss downstream tasks after knowledge acquisition, including KG completion using embedding models, knowledge alignment, and knowledge fusion in order to address the problem of knowledge uncertainty in KG construction. We conclude with a discussion on the remaining challenges and perspectives when constructing a KG taking into account uncertainty.
Cite as

Lucas Jarnac, Yoan Chabot, and Miguel Couceiro. Uncertainty Management in the Construction of Knowledge Graphs: A Survey. In Transactions on Graph Data and Knowledge (TGDK), Volume 3, Issue 1, pp. 3:1-3:48, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@Article{jarnac_et_al:TGDK.3.1.3,
  author =	{Jarnac, Lucas and Chabot, Yoan and Couceiro, Miguel},
  title =	{{Uncertainty Management in the Construction of Knowledge Graphs: A Survey}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{3:1--3:48},
  ISSN =	{2942-7517},
  year =	{2025},
  volume =	{3},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.3.1.3},
  URN =		{urn:nbn:de:0030-drops-233733},
  doi =		{10.4230/TGDK.3.1.3},
  annote =	{Keywords: Knowledge reconciliation, Uncertainty, Heterogeneous sources, Knowledge graph construction}
}
Document
DOI: 10.4230/LIPIcs.WABI.2024.22
Anchorage Accurately Assembles Anchor-Flanked Synthetic Long Reads

Authors: Xiaofei Carl Zang, Xiang Li, Kyle Metcalfe, Tuval Ben-Yehezkel, Ryan Kelley, and Mingfu Shao

Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)

Abstract
Modern sequencing technologies allow for the addition of short-sequence tags, known as anchors, to both ends of a captured molecule. Anchors are useful in assembling the full-length sequence of a captured molecule as they can be used to accurately determine the endpoints. One representative of such anchor-enabled technology is LoopSeq Solo, a synthetic long read (SLR) sequencing protocol. LoopSeq Solo also achieves ultra-high sequencing depth and high purity of short reads covering the entire captured molecule. Despite the availability of many assembly methods, constructing full-length sequence from these anchor-enabled, ultra-high coverage sequencing data remains challenging due to the complexity of the underlying assembly graphs and the lack of specific algorithms leveraging anchors. We present Anchorage, a novel assembler that performs anchor-guided assembly for ultra-high-depth sequencing data. Anchorage starts with a kmer-based approach for precise estimation of molecule lengths. It then formulates the assembly problem as finding an optimal path that connects the two nodes determined by anchors in the underlying compact de Bruijn graph. The optimality is defined as maximizing the weight of the smallest node while matching the estimated sequence length. Anchorage uses a modified dynamic programming algorithm to efficiently find the optimal path. Through both simulations and real data, we show that Anchorage outperforms existing assembly methods, particularly in the presence of sequencing artifacts. Anchorage fills the gap in assembling anchor-enabled data. We anticipate its broad use as anchor-enabled sequencing technologies become prevalent. Anchorage is freely available at https://github.com/Shao-Group/anchorage; the scripts and documents that can reproduce all experiments in this manuscript are available at https://github.com/Shao-Group/anchorage-test.
Cite as

Xiaofei Carl Zang, Xiang Li, Kyle Metcalfe, Tuval Ben-Yehezkel, Ryan Kelley, and Mingfu Shao. Anchorage Accurately Assembles Anchor-Flanked Synthetic Long Reads. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 22:1-22:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{zang_et_al:LIPIcs.WABI.2024.22,
  author =	{Zang, Xiaofei Carl and Li, Xiang and Metcalfe, Kyle and Ben-Yehezkel, Tuval and Kelley, Ryan and Shao, Mingfu},
  title =	{{Anchorage Accurately Assembles Anchor-Flanked Synthetic Long Reads}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{22:1--22:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-340-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{312},
  editor =	{Pissis, Solon P. and Sung, Wing-Kin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.22},
  URN =		{urn:nbn:de:0030-drops-206660},
  doi =		{10.4230/LIPIcs.WABI.2024.22},
  annote =	{Keywords: Genome assembly, de Bruijn graph, synthetic long reads, anchor-guided assembly, LoopSeq}
}
Document
DOI: 10.4230/LIPIcs.ICALP.2018.90
Improved Algorithms for Adaptive Compressed Sensing

Authors: Vasileios Nakos, Xiaofei Shi, David P. Woodruff, and Hongyang Zhang

Published in: LIPIcs, Volume 107, 45th International Colloquium on Automata, Languages, and Programming (ICALP 2018)

Abstract
In the problem of adaptive compressed sensing, one wants to estimate an approximately k-sparse vector x in R^n from m linear measurements A_1 x, A_2 x,..., A_m x, where A_i can be chosen based on the outcomes A_1 x,..., A_{i-1} x of previous measurements. The goal is to output a vector x^ for which |x-x^|_p <=C * min_{k-sparse x'} |x-x'|_q, with probability at least 2/3, where C > 0 is an approximation factor. Indyk, Price and Woodruff (FOCS'11) gave an algorithm for p=q=2 for C = 1+epsilon with O((k/epsilon) loglog (n/k)) measurements and O(log^*(k) loglog (n)) rounds of adaptivity. We first improve their bounds, obtaining a scheme with O(k * loglog (n/k) + (k/epsilon) * loglog(1/epsilon)) measurements and O(log^*(k) loglog (n)) rounds, as well as a scheme with O((k/epsilon) * loglog (n log (n/k))) measurements and an optimal O(loglog (n)) rounds. We then provide novel adaptive compressed sensing schemes with improved bounds for (p,p) for every 0 < p < 2. We show that the improvement from O(k log(n/k)) measurements to O(k log log (n/k)) measurements in the adaptive setting can persist with a better epsilon-dependence for other values of p and q. For example, when (p,q) = (1,1), we obtain O(k/sqrt{epsilon} * log log n log^3 (1/epsilon)) measurements. We obtain nearly matching lower bounds, showing our algorithms are close to optimal. Along the way, we also obtain the first nearly-optimal bounds for (p,p) schemes for every 0 < p < 2 even in the non-adaptive setting.
Cite as

Vasileios Nakos, Xiaofei Shi, David P. Woodruff, and Hongyang Zhang. Improved Algorithms for Adaptive Compressed Sensing. In 45th International Colloquium on Automata, Languages, and Programming (ICALP 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 107, pp. 90:1-90:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{nakos_et_al:LIPIcs.ICALP.2018.90,
  author =	{Nakos, Vasileios and Shi, Xiaofei and Woodruff, David P. and Zhang, Hongyang},
  title =	{{Improved Algorithms for Adaptive Compressed Sensing}},
  booktitle =	{45th International Colloquium on Automata, Languages, and Programming (ICALP 2018)},
  pages =	{90:1--90:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-076-7},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{107},
  editor =	{Chatzigiannakis, Ioannis and Kaklamanis, Christos and Marx, D\'{a}niel and Sannella, Donald},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2018.90},
  URN =		{urn:nbn:de:0030-drops-90945},
  doi =		{10.4230/LIPIcs.ICALP.2018.90},
  annote =	{Keywords: Compressed Sensing, Adaptivity, High-Dimensional Vectors}
}
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