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Papers are ordered (more or less) from the newest to the oldest, using the conference year when both conference and journal versions are listed. See also my ORCID account, arXiv search, Google Scholar account, or dblp search.

Research Papers

  • Pareto optimization of masked superstrings improves compression of pan-genome k-mer sets
    with Ján Plachý, Ondřej Sladký, and Karel Břinda.
    Preprint at bioRxiv. Presented at RECOMB-SEQ 2026 by Ján Plachý.
    To appear in Journal of Computational Biology
  • Breaking 2-Cores for Invertible Bloom Lookup Tables by Structure Prediction
    with Vojtěch Gaďurek.
    In SEA 2026. doi:10.4230/LIPIcs.SEA.2026.19
  • SplineSketch: Even More Accurate Quantiles with Error Guarantees
    with Aleksander Łukasiewicz and Jakub Tětek.
    In SIGMOD 2026. doi:10.1145/3769827. Preprint at arXiv.
  • Streaming Diameter of High-Dimensional Points
    with Magnús M. Halldórsson and Nicolaos Matsakis.
    In ESA 2025 (track S). doi:10.4230/LIPIcs.ESA.2025.58. Preprint at arXiv.
  • FroM Superstring to Indexing: a space-efficient index for unconstrained k-mer sets using the Masked Burrows-Wheeler Transform (MBWT)
    with Ondřej Sladký and Karel Břinda.
    A preliminary version presented at Sequences 2024 by O. Sladký. Bioinformatics Advances, doi:10.1093/bioadv/vbaf290. Preprint at bioRxiv.
  • Towards Efficient k-Mer Set Operations via Function-Assigned Masked Superstrings
    with Ondřej Sladký and Karel Břinda.
    In PSC 2025 (proceedings link). Preprint at bioRxiv. A preliminary version presented at Sequences 2024 by O. Sladký.
  • Fully Scalable MPC Algorithms for Clustering in High Dimension
    with Artur Czumaj, Guichen Gao, Shaofeng H.-C. Jiang, and Robert Krauthgamer.
    In ICALP 2024. doi:10.4230/LIPIcs.ICALP.2024.50. ArXiv preprint.
  • Masked superstrings as a unified framework for textual k-mer set representations
    with Ondřej Sladký and Karel Břinda.
    Preprint at bioRxiv. Presented at RECOMB-SEQ 2023 by O. Sladký. Currently under major update (stay tuned!)
  • Approximation Guarantees for Shortest Superstrings: Simpler and Better
    with Matthias Englert and Nicolaos Matsakis.
    In ISAAC 2023. doi:10.4230/LIPIcs.ISAAC.2023.29. Preprint. (Journal version: incorporated into the SICOMP paper below.)
  • Streaming Facility Location in High Dimension via Geometric Hashing
    with Artur Czumaj, Shaofeng H.-C. Jiang, Robert Krauthgamer, and Mingwei Yang.
    In FOCS 2022, p. 450-461, IEEE. doi:10.1109/FOCS54457.2022.00050. ArXiv preprint (updated with new results since FOCS). Slides for FOCS.
  • Improved Approximation Guarantees for Shortest Superstrings using Cycle Classification by Overlap to Length Ratios
    with Matthias Englert and Nicolaos Matsakis.
    In STOC 2022, p. 317-330, ACM, 2022. doi:10.1145/3519935.3520001. ArXiv preprint.
    Journal version: To appear in SICOMP (incorporates improvements of parts of the analysis from the ISAAC'23 paper above)
  • Streaming Algorithms for Geometric Steiner Forest
    with Artur Czumaj, Shaofeng H.-C. Jiang, and Robert Krauthgamer.
    In ICALP 2022, p. 47:1--47:20. LIPIcs link. ArXiv preprint.
    Journal version: ACM Transactions on Algorithms doi:10.1145/3663666.
  • Improved Analysis of Online Balanced Clustering
    with Marcin Bienkowski, Martin Böhm, Martin Koutecký, Thomas Rothvoß, and Jiří Sgall.
    In WAOA 2021, LNCS 12982, p. 224-233, Springer, 2022.
    doi:10.1007/978-3-030-92702-8_14. ArXiv preprint.
  • Theory meets Practice at the Median: a worst case comparison of relative error quantile algorithms
    with Graham Cormode, Abhinav Mishra, and Joseph Ross.
    In KDD 2021 (Applied Data Science Track), p. 2722–2731. doi:10.1145/3447548.3467152. ArXiv preprint. Video (by Joe).
  • Breaking the Barrier of 2 for the Competitiveness of Longest Queue Drop
    with Antonios Antoniadis, Matthias Englert, and Nicolaos Matsakis.
    In ICALP 2021. LIPIcs link. ArXiv preprint. Video for ICALP (25 min).
    Journal version: ACM Transactions on Algorithms doi:10.1145/3676887.
  • Relative Error Streaming Quantiles
    with Graham Cormode, Zohar Karnin, Edo Liberty, and Justin Thaler.
    In PODS 2021, p. 96-108. doi:10.1145/3452021.3458323.
    Best Paper (proof) Invited to JACM
    2022 ACM SIGMOD Research Highlight Award
    ArXiv preprint.
    Proof-of-concept Python code. Much better implementation in Java, C++, and Python in Apache DataSketches library.
    Video for PODS 2021. Video for WOLA 2020 (longer). WOLA slides.
    Extended abstract (8 pages) in SIGMOD Record and a nice 1-page technical perspective by Rasmus Pagh.
    Journal version: Journal of the ACM doi:10.1145/3617891.
  • A Tight Lower Bound for Comparison-Based Quantile Summaries
    with Graham Cormode.
    In PODS 2020, p. 81-93, ACM, 2020, doi:10.1145/3375395.3387650. ArXiv preprint. BCTCS slides. Video record from PODS (starts at 29:00). View/hide summary.

    We prove a tight lower bound for the space used by a deterministic comparison-based quantile summary, which keeps track of all quantiles in a data stream (where items are linearly ordered), up to a small error. The lower bound matches the worst-case performance of the Greenwald-Khanna algorithm, up to a constant factor, and holds even for finding an approximate median in a data stream in the comparison-based model, where an algorithm only compares items and is otherwise completely oblivious of the universe of items.

  • New Results on Multi-Level Aggregation
    with Marcin Bienkowski, Martin Böhm, Jaroslaw Byrka, Marek Chrobak, Christoph Dürr, Lukáš Folwarczný, Łukasz Jeż, Jiří Sgall, Nguyen Kim Thang.
    Theoretical Computer Science, vol. 861, p. 133-143, 2021.
    DOI: 10.1016/j.tcs.2021.02.016 View/hide summary.

    In Online Multi-Level Aggregation (which is a generalization of TCP Acknowledgment and Joint Replenishment Problem) requests are arriving to nodes of an edge-weighted rooted tree and an online algorithm has to serve them by sending a rooted subtree, paying the cost of this subtree. The objective is to minimize the total cost of all subtrees sent plus the total waiting cost of requests. In this paper we study several special variants of the problem, namely, (1) we provide an optimal algorithm for the Single-Phase variant, which was used to contruct lower bounds, (2) we study MLAP on paths, where we prove that 4 is the optimal competitive ratio for the deadline variant. Additionally, we provide results on the offline version. All results are covered in the arXiv preprint of the conference version.

  • Streaming Algorithms for Bin Packing and Vector Scheduling
    with Graham Cormode.
    In WAOA 2019, LNCS 11926, p. 72-88, Springer, 2020. ArXiv preprint. View/hide summary. WAOA slides.

    We design a 1-pass deterministic streaming algorithms for bin packing and vector scheduling. For bin packing, our streaming approximation scheme uses quantile summaries and interestingly, the connection between streaming bin packing and quantile summaries goes also in the other direction. That is, given a streaming algorithm for bin packing, we can estimate the rank of an item in the stream in the same space, which basically suffices to construct a quantile summary. For vector scheduling in dimension d on m machines, we provide 2-approximation using poly(d,m) memory.


    Journal version: Theory of Computing Systems, vol. 65, p. 916-942, 2021.
    DOI: 10.1007/s00224-020-10011-y
  • A φ-Competitive Algorithm for Scheduling Packets with Deadlines
    with Marek Chrobak, Łukasz Jeż, Jiří Sgall.
    In SODA 2019, p. 123-142, Society for Industrial and Applied Mathematics, 2019. doi:10.1137/1.9781611975482.9
    ArXiv preprint. Slides for DIMAP seminar (longer). SODA slides (shorter). View/hide summary.

    We designed a φ-competitive deterministic algorithm for bounded-delay packet scheduling. In this problem, packets arrive online into a buffer, each with a deadline, a weight, and of length 1. The goal is to schedule a packet in each time slot to maximize the total weight of scheduled packets. Our algorithm is based on the plan which is the maximum-weight subset of pending packets that can be scheduled starting from the current slot.


    Journal version: SICOMP, vol. 51(5), p. 1626–1691, 2022.
    DOI: 10.1137/21M1469753.
  • Parameterized Approximation Schemes for Steiner Trees with Small Number of Steiner Vertices
    with Pavel Dvořák, Andreas Emil Feldmann, Dušan Knop, Tomáš Masařík, and Tomáš Toufar.
    In STACS 2018, LIPIcs, p. 26:1--26:15, Schloss Dagstuhl, 2018. LIPIcs link. ArXiv preprint. View/hide summary.

    Given an edge-weighted undirected graph the Steiner Tree problem asks to compute a minimum weight tree that spans all the terminals. This problem is APX-hard and W[1]-hard when parameterized by the number of Steiner vertices (non-terminals) in an optimal solution (it is FPT w.r.t. parametrization by the number of terminals). We overcame both these lower bounds by combining the paradigms of approximation and parametrization. More precisely, we desinged an efficient parameterized approximation scheme, i.e., a (1+epsilon)-approximation in time f(epsilon, p)*poly(n) where p is the parameter. Our algorithm works also for a more general problem, namely Steiner Forest with a low number of components in an optimal solution, and can be seen as a preprocessing algorithm that iteratively decreses the number of terminals by contracting stars with a good ratio. As a consequence we also obtain a lossy kernel (i.e., a kernel preserving solutions only approximately). We also have some results for the directed version of the problem.


    Journal version: SIAM J. Discrete Math., vol. 35(1), p. 546–574, 2021.
    doi:10.1137/18M1209489.
  • On Packet Scheduling with Adversarial Jamming and Speedup
    with Martin Böhm, Łukasz Jeż, Jiří Sgall.
    In WAOA 2017, LNCS 10787, p. 190-206, Springer, 2018. ArXiv preprint. WAOA slides. View/hide summary.

    We study online scheduling of packets over a channel prone to adversarial jamming errors which interrupt the current transmission (the transmitted packet needs to be resend completely). The distinguishing feature is that packets have small (constant) sizes and the number of sizes is also small. We designed a universal algorithm which works well for any sizes and any speedup (which is a resource augmentation), together with a universal framework how to analyze it locally, which however does not give tight results in all settings. Our main and probably the most interesting result is that our algorithm needs speed 4 to be 1-competitive which is shown by a more sophisticated non-local analysis. We complemented it by a nice lower bound of 2.618 (the golden ratio + 1) on the speedup of any deterministic 1-competitive algorithm.


    Journal version: Annals of Operations Research, vol. 298, p. 7–42, 2021.
    doi:10.1007/s10479-019-03153-x.
  • Logarithmic price of buffer downscaling on line metrics
    with Marcin Bienkowski, Martin Bohm, Łukasz Jeż, Paweł Laskoś-Grabowski, Jan Marcinkowski, Jiří Sgall, Aleksandra Spyra.
    Theoretical Computer Science, vol. 707, p. 89-93, Elsevier, 2018, doi:10.1016/j.tcs.2017.10.008. ArXiv preprint. View/hide summary.

    We consider the reordering buffer problem on a line consisting of n equidistant points. We show that, for any constant delta, an (offline) algorithm that has a buffer (1-delta) k performs worse by a factor of Omega(log n) than an offline algorithm with buffer k. In particular, this demonstrates that the O(log n)-competitive online algorithm MovingPartition by Gamzu and Segev (ACM Trans. on Algorithms, 6(1), 2009) is essentially optimal against any offline algorithm with a slightly larger buffer.

  • Online Chromatic Number is PSPACE-Complete
    with Martin Böhm.
    In IWOCA 2016, LNCS 9843, p. 16-28, Springer, 2016.
    Best Student Paper ArXiv preprint. HALG 2017 poster. View/hide summary.

    We proved PSPACE-hardness of online coloring in which vertices of a known graph G arrives online and Painter colors them immediately without knowing to which induced subgraph of G the colored vertices correspond. Previously, PSPACE-hardness was known only in the variant in which some part of the graph is precolored (which makes the hardness proof substantially easier).


    Journal version: Theory of Computing Systems, vol. 62(6), p. 1366–1391, Springer, 2018. doi:10.1007/s00224-017-9797-2.
  • Online Packet Scheduling with Bounded Delay and Lookahead
    with Martin Böhm, Marek Chrobak, Łukasz Jeż, Fei Li, Jiří Sgall.
    In ISAAC 2016, LIPIcs, p. 21:1--21:13, Schloss Dagstuhl, 2016. LIPIcs link, ArXiv preprint. MAPSP slides. View/hide summary.

    In Online Packet Scheduling problem, packets arrive online into a buffer, each with a deadline, a weight, and of length 1. The goal is to schedule a packet in each time slot to maximize the total weight of scheduled packets. There is a lower bound of phi (the golden ratio, approx. 1.618) on the competitive ratio of deterministic algorithms and it is an important open problem to find a matching algorithm, or to improve the lower bound. In this paper we show a phi-competitive algorithm for a restricted class of instances, called 4-bounded instances, in which a packet arriving at time t has deadline at most t+4. Moreover, we introduced a model with a resource augmentation, namely with lookahead which allows the algorithm to look a little bit into the future. We obtained a nearly tight results for the 2-bounded case with 1-lookahead.


    Journal version: Theoretical Computer Science, vol. 776, p. 95-113, 2019.
    doi:10.1016/j.tcs.2019.01.013. Journal version PDF.
  • Online Algorithms for Multi-Level Aggregation.
    with Marcin Bienkowski, Martin Böhm, Jaroslaw Byrka, Marek Chrobak, Christoph Dürr, Lukáš Folwarczný, Łukasz Jeż, Jiří Sgall, Nguyen Kim Thang.
    In ESA 2016, Leibniz International Proceedings in Informatics (LIPIcs), p. 12:1-12:17, Schloss Dagstuhl, 2016. LIPIcs link, ArXiv preprint. View/hide summary.

    In Online Multi-Level Aggregation (which is a generalization of TCP Acknowledgment and Joint Replenishment Problem) requests are arriving to nodes of an edge-weighted rooted tree and an online algorithm has to serve them by sending a rooted subtree, paying the cost of this subtree. The objective is to minimize the total cost of all subtrees sent plus the total waiting cost of requests. Among other results we designed the first O(1)-competitive algorithm for trees of bounded height, although with exponential dependence on the height.


    Journal version: Operations Research, vol. 68(1), p. 214-232, 2020.
    doi:10.1287/opre.2019.1847.
  • Better algorithms for online bin stretching
    with Martin Böhm, Jiří Sgall, Rob van Stee.
    In WAOA 2014, LNCS 8952, p. 236-247, Springer, 2015. ArXiv preprint. View/hide summary.

    We study a variant of online bin packing with guarantees. There are m bins and we know that the optimum solution packs all items into these bins when they have capacity 1. The goal of the algorithm is to pack the same items into m bins with capacity R > 1, for as small R as possible. (This is equivalent to online makespan minimization scheduling with known optimum.) Our main result is an algorithm which has R = 1.5 and we also have a better algorithm for 3 bins. The main open problem is to improve upon the simple lower bound of 4/3, which holds for m >= 2 bins.


    Journal version (part I): A Two-Phase Algorithm for Bin Stretching with Stretching Factor 1.5
    Journal of Combinatorial Optimization, vol. 34(3), p. 810-828, Springer, 2017.
    doi:10.1007/s10878-017-0114-4. ArXiv preprint. View/hide summary.

    We study a variant of online bin packing with guarantees. There are m bins and we know that the optimum solution packs all items into these bins when they have capacity 1. The goal of the algorithm is to pack the same items into m bins with capacity R > 1, for as small R as possible. (This is equivalent to online makespan minimization scheduling with known optimum.) We designed an algorithm with R = 1.5. The main open problem is to improve upon the simple lower bound of 4/3, which holds for m >= 2 bins.


    Journal version (part II): Online Bin Stretching with Three Bins
    Journal of Scheduling, vol. 20(6), p. 601-621, Springer, 2017, doi:10.1007/s10951-016-0504-y. ArXiv preprint. View/hide summary.

    We study a variant of online bin packing with guarantees. There are m bins and we know that the optimum solution packs all items into these bins when they have capacity 1. The goal of the algorithm is to pack the same items into m bins with capacity R > 1, for as small R as possible. (This is equivalent to online makespan minimization scheduling with known optimum.) We present an algorithm for 3 bins and also improved lower bounds for 3, 4, and 5 bins, using computer program shows a strategy for the adversary in the underlying two-player game. The main open problem is to improve upon the simple lower bound of 4/3, which holds for m >= 2 bins.

  • Online colored bin packing
    with Martin Böhm, Jiří Sgall.
    In WAOA 2014, LNCS 8952, p. 35-46, Springer, 2015. ArXiv preprint. View/hide summary.

    In Colored Bin Packing each item has a color in addition to size and the goal is to pack those items online into bins with capacity 1 such that no two items packed consecutively into a bin have the same color. The problem is interesting even when all sizes are 0 and we found an optimal algorithm for this special case together with a matching lower bound. The analysis of the optimal algorithm is in my opinion the most interesting part of the paper. We designed a (simple) algorithm and a lower bound for the general case, both generalizing previous results for two colors. Moreover, for two colors we give a tight analysis of a class of simple algorithms, called Any Fit algorithms.


    Journal version: Colored Bin Packing: Online Algorithms and Lower Bounds
    with Martin Böhm, György Dósa, Leah Epstein, Jiří Sgall.
    Algorithmica, vol. 80(1), p. 155-184, Springer, 2018.
    doi:10.1007/s00453-016-0248-2. View/hide summary.

    In Colored Bin Packing each item has a color in addition to size and the goal is to pack those items online into bins with capacity 1 such that no two items packed consecutively into a bin have the same color. The problem is interesting even when all sizes are 0 and we found an optimal algorithm for this special case together with a matching lower bound. The analysis of the optimal algorithm is in my opinion the most interesting part of the paper. We designed a (simple) algorithm and a lower bound for the general case, both generalizing previous results for two colors. Moreover, for two colors we give a tight analysis of a class of simple algorithms, called Any Fit algorithms.

  • WALTZ: a strong Tzaar-playing program
    with Tomáš Valla.
    In Computer Games, CCIS 408, p. 81–96, Springer, 2014. View/hide summary.

    We analyzed a recent board game Tzaar (a part of the Gipf project) and implemented an artificial intelligence to play the game. We let it play on Boiteajeux, an online board gaming portal, and it was able to match the level of best players on the portal (in 2013). We also propose an enhancement of Proof-number Search.

ACM Newsletters

  • Relative Error Streaming Quantiles [Extended Abstract]
    with Graham Cormode, Zohar Karnin, Edo Liberty, and Justin Thaler.
    In ACM SIGMOD Record, vol. 51(1), p. 69–76, 2022, PDF.. doi:10.1145/3542700.3542717.
    SIGMOD Record link.
    Nice 1-page technical perspective by Rasmus Pagh.
  • Packet Scheduling: Plans, Monotonicity, and the Golden Ratio
    ACM SIGACT News, vol. 52(2), p. 72–84, 2021.
    DOI: 10.1145/3471469.3471481 Preprint.
    A column summarizing the ideas behind the φ-competitive algorithm for packet scheduling (SODA '19).

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