35 Search Results for "Davis, Ben"

Document
DOI: 10.4230/LIPIcs.SoCG.2026.78
Mapping Chemical Space: Topological Data Analysis of Chemical Latent Space with Mapper

Authors: Dhruv Meduri, Chuan-Shen Hu, Cong Shen, Kelin Xia, and Bei Wang

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

Abstract
The vast chemical space, encompassing virtually innumerable molecules and materials, presents both immense opportunities and significant challenges. The design and discovery of novel drugs and functional materials may be viewed as a search within this space; however, the sheer scale of potential candidates renders exhaustive exploration infeasible. To address this, we introduce Chemical Mapper, a framework that integrates topological data analysis with deep learning to enable the visual exploration and analysis of chemical latent spaces. At its core, Chemical Mapper employs mapper, a widely used tool in topological data analysis, to investigate the organizational principles of chemical latent spaces defined by molecular representations learned by geometric deep learning models. In doing so, Chemical Mapper not only highlights groups of molecular representations but also uncovers the relationships among them through linkages and branching structures. Our results show that Chemical Mapper reveals intrinsic patterns associated with molecular scaffolds, functional groups, and chemical properties, as well as the structural and functional evolutions of the molecules.
Cite as

Dhruv Meduri, Chuan-Shen Hu, Cong Shen, Kelin Xia, and Bei Wang. Mapping Chemical Space: Topological Data Analysis of Chemical Latent Space with Mapper. In 42nd International Symposium on Computational Geometry (SoCG 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 367, pp. 78:1-78:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{meduri_et_al:LIPIcs.SoCG.2026.78,
  author =	{Meduri, Dhruv and Hu, Chuan-Shen and Shen, Cong and Xia, Kelin and Wang, Bei},
  title =	{{Mapping Chemical Space: Topological Data Analysis of Chemical Latent Space with Mapper}},
  booktitle =	{42nd International Symposium on Computational Geometry (SoCG 2026)},
  pages =	{78:1--78:20},
  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.2026.78},
  URN =		{urn:nbn:de:0030-drops-258854},
  doi =		{10.4230/LIPIcs.SoCG.2026.78},
  annote =	{Keywords: Practice of computational topology, topological data analysis, applications in chemistry, mapper algorithm, high-dimensional data analysis, chemical spaces, geometric deep learning, latent space geometry}
}
Document
DOI: 10.4230/OASIcs.NINeS.2026.13
In-Kernel Aggregation and Broadcast Acceleration for Distributed Communication

Authors: Jianchang Su, Yifan Zhang, and Wei Zhang

Published in: OASIcs, Volume 139, 1st New Ideas in Networked Systems (NINeS 2026)

Abstract
Broadcasting and aggregation dominate the communication overhead in distributed systems, from machine learning training to data analytics. Current acceleration approaches require specialized hardware (RDMA) or dedicated resources (DPDK), limiting their deployment in commodity clouds. However, we present a counter-intuitive alternative: rather than bypassing the kernel, we move operations into it using eBPF. While this imposes severe constraints including no floating-point, limited memory, and stateless execution, we show these restrictions paradoxically drive innovative protocol designs that yield unexpected benefits. We introduce AggBox, which implements broadcast and aggregation operations entirely within eBPF’s constrained environment. Our key innovations include stateless group acknowledgments for reliability, edge quantization for floating-point aggregation using only integer arithmetic, and tail-call chains that create virtual memory beyond eBPF’s 512-byte stack limit. These designs emerge from and exploit the constraints rather than fighting them. AggBox achieves remarkable performance on commodity hardware: 84.5% reduction in broadcast latency, 43× speedup for MapReduce workloads, and 56.1% faster ML gradient aggregation, all without specialized NICs or dedicated cores. Beyond performance, our work demonstrates that constrained environments can drive fundamental innovation in protocol design, offering insights for future resource-limited and verified systems.
Cite as

Jianchang Su, Yifan Zhang, and Wei Zhang. In-Kernel Aggregation and Broadcast Acceleration for Distributed Communication. In 1st New Ideas in Networked Systems (NINeS 2026). Open Access Series in Informatics (OASIcs), Volume 139, pp. 13:1-13:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{su_et_al:OASIcs.NINeS.2026.13,
  author =	{Su, Jianchang and Zhang, Yifan and Zhang, Wei},
  title =	{{In-Kernel Aggregation and Broadcast Acceleration for Distributed Communication}},
  booktitle =	{1st New Ideas in Networked Systems (NINeS 2026)},
  pages =	{13:1--13:23},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-414-7},
  ISSN =	{2190-6807},
  year =	{2026},
  volume =	{139},
  editor =	{Argyraki, Katerina and Panda, Aurojit},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.NINeS.2026.13},
  URN =		{urn:nbn:de:0030-drops-255981},
  doi =		{10.4230/OASIcs.NINeS.2026.13},
  annote =	{Keywords: eBPF, distributed communication, broadcast, aggregation, in-kernel processing, XDP}
}
Document
DOI: 10.4230/OASIcs.NINeS.2026.18
TURBO: Utility-Aware Bandwidth Allocation for Cloud-Augmented Autonomous Control

Authors: Peter Schafhalter, Alexander Krentsel, Hongbo Wei, Joseph E. Gonzalez, Sylvia Ratnasamy, Scott Shenker, and Ion Stoica

Published in: OASIcs, Volume 139, 1st New Ideas in Networked Systems (NINeS 2026)

Abstract
Autonomous driving system progress has been driven by improvements in machine learning (ML) models, whose computational demands now exceed what edge devices alone can provide. The cloud offers abundant compute, but the network has long been treated as an unreliable bottleneck rather than a co-equal part of the autonomous vehicle control loop. We argue that this separation is no longer tenable: safety-critical autonomy requires co-design of control, models, and network resource allocation itself. We introduce TURBO, a cloud-augmented control framework that addresses this challenge, formulating bandwidth allocation and control pipeline configuration across both the car and cloud as a joint optimization problem. TURBO maximizes benefit to the car while guaranteeing safety in the face of highly variable network conditions. We implement TURBO and evaluate it in both simulation and real-world deployment, showing it can improve average accuracy by up to 15.6%pt over existing on-vehicle-only pipelines. Our code is made available at www.github.com/NetSys/turbo.
Cite as

Peter Schafhalter, Alexander Krentsel, Hongbo Wei, Joseph E. Gonzalez, Sylvia Ratnasamy, Scott Shenker, and Ion Stoica. TURBO: Utility-Aware Bandwidth Allocation for Cloud-Augmented Autonomous Control. In 1st New Ideas in Networked Systems (NINeS 2026). Open Access Series in Informatics (OASIcs), Volume 139, pp. 18:1-18:34, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{schafhalter_et_al:OASIcs.NINeS.2026.18,
  author =	{Schafhalter, Peter and Krentsel, Alexander and Wei, Hongbo and Gonzalez, Joseph E. and Ratnasamy, Sylvia and Shenker, Scott and Stoica, Ion},
  title =	{{TURBO: Utility-Aware Bandwidth Allocation for Cloud-Augmented Autonomous Control}},
  booktitle =	{1st New Ideas in Networked Systems (NINeS 2026)},
  pages =	{18:1--18:34},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-414-7},
  ISSN =	{2190-6807},
  year =	{2026},
  volume =	{139},
  editor =	{Argyraki, Katerina and Panda, Aurojit},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.NINeS.2026.18},
  URN =		{urn:nbn:de:0030-drops-256039},
  doi =		{10.4230/OASIcs.NINeS.2026.18},
  annote =	{Keywords: autonomous vehicles, bandwidth allocation, cloud computing, edge computing, machine learning}
}
Document
DOI: 10.4230/LIPIcs.CSL.2026.7
Bridging Weighted First Order Model Counting and Graph Polynomials

Authors: Qipeng Kuang, Ondřej Kuželka, Yuanhong Wang, and Yuyi Wang

Published in: LIPIcs, Volume 363, 34th EACSL Annual Conference on Computer Science Logic (CSL 2026)

Abstract
The Weighted First-Order Model Counting Problem (WFOMC) asks to compute the weighted sum of models of a given first-order logic sentence over a given domain. It can be solved in time polynomial in the domain size for sentences from the two-variable fragment with counting quantifiers, known as C^2. This polynomial-time complexity is known to be retained when extending C^2 by one of the following axioms: linear order axiom, tree axiom, forest axiom, directed acyclic graph axiom or connectedness axiom. An interesting question remains as to which other axioms can be added to the first-order sentences in this way. We provide a new perspective on this problem by associating WFOMC with graph polynomials. Using WFOMC, we define Weak Connectedness Polynomial and Strong Connectedness Polynomials for first-order logic sentences. It turns out that these polynomials have the following interesting properties. First, they can be computed in polynomial time in the domain size for sentences from C^2. Second, we can use them to solve WFOMC with all of the existing axioms known to be tractable as well as with new ones such as bipartiteness, strong connectedness, having k connected components, etc. Third, the well-known Tutte polynomial can be recovered as a special case of the Weak Connectedness Polynomial, and the Strict and Non-Strict Directed Chromatic Polynomials can be recovered from the Strong Connectedness Polynomials.
Cite as

Qipeng Kuang, Ondřej Kuželka, Yuanhong Wang, and Yuyi Wang. Bridging Weighted First Order Model Counting and Graph Polynomials. In 34th EACSL Annual Conference on Computer Science Logic (CSL 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 363, pp. 7:1-7:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{kuang_et_al:LIPIcs.CSL.2026.7,
  author =	{Kuang, Qipeng and Ku\v{z}elka, Ond\v{r}ej and Wang, Yuanhong and Wang, Yuyi},
  title =	{{Bridging Weighted First Order Model Counting and Graph Polynomials}},
  booktitle =	{34th EACSL Annual Conference on Computer Science Logic (CSL 2026)},
  pages =	{7:1--7:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-411-6},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{363},
  editor =	{Guerrini, Stefano and K\"{o}nig, Barbara},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CSL.2026.7},
  URN =		{urn:nbn:de:0030-drops-254316},
  doi =		{10.4230/LIPIcs.CSL.2026.7},
  annote =	{Keywords: Weighted First-Order Model Counting, Axiom, Enumerative Combinatorics, Tutte Polynomial}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2026.60
Total Search Problems in ZPP

Authors: Noah Fleming, Stefan Grosser, Siddhartha Jain, Jiawei Li, Hanlin Ren, Morgan Shirley, and Weiqiang Yuan

Published in: LIPIcs, Volume 362, 17th Innovations in Theoretical Computer Science Conference (ITCS 2026)

Abstract
We initiate a systematic study of TFZPP, the class of total NP search problems solvable by polynomial time randomized algorithms. TFZPP contains a variety of important search problems such as Bertrand-Chebyshev (finding a prime between N and 2N), refuter problems for many circuit lower bounds, and Lossy-Code. The Lossy-Code problem has found prominence due to its fundamental connections to derandomization, catalytic computing, and the metamathematics of complexity theory, among other areas. While TFZPP collapses to FP under standard derandomization assumptions in the white-box setting, we are able to separate TFZPP from the major TFNP subclasses in the black-box setting. In fact, we are able to separate it from every uniform TFNP class assuming that NP is not in quasi-polynomial time. To do so, we extend the connection between proof complexity and black-box TFNP to randomized proof systems and randomized reductions. Next, we turn to developing a taxonomy of TFZPP problems. We highlight a problem called Nephew, originating from an infinity axiom in set theory. We show that Nephew is in PWPP∩ TFZPP and conjecture that it is not reducible to Lossy-Code. Intriguingly, except for some artificial examples, most other black-box TFZPP problems that we are aware of reduce to Lossy-Code: - We define a problem called Empty-Child capturing finding a leaf in a rooted (binary) tree, and show that this problem is equivalent to Lossy-Code. We also show that a variant of Empty-Child with "heights" is complete for the intersection of SOPL and Lossy-Code. - We strengthen Lossy-Code with several combinatorial inequalities such as the AM-GM inequality. Somewhat surprisingly, we show the resulting new problems are still reducible to Lossy-Code. A technical highlight of this result is that they are proved by formalizations in bounded arithmetic, specifically in Jeřábek’s theory APC₁ (JSL 2007). - Finally, we show that the Dense-Linear-Ordering problem reduces to Lossy-Code.
Cite as

Noah Fleming, Stefan Grosser, Siddhartha Jain, Jiawei Li, Hanlin Ren, Morgan Shirley, and Weiqiang Yuan. Total Search Problems in ZPP. In 17th Innovations in Theoretical Computer Science Conference (ITCS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 362, pp. 60:1-60:26, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{fleming_et_al:LIPIcs.ITCS.2026.60,
  author =	{Fleming, Noah and Grosser, Stefan and Jain, Siddhartha and Li, Jiawei and Ren, Hanlin and Shirley, Morgan and Yuan, Weiqiang},
  title =	{{Total Search Problems in ZPP}},
  booktitle =	{17th Innovations in Theoretical Computer Science Conference (ITCS 2026)},
  pages =	{60:1--60:26},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-410-9},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{362},
  editor =	{Saraf, Shubhangi},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2026.60},
  URN =		{urn:nbn:de:0030-drops-253473},
  doi =		{10.4230/LIPIcs.ITCS.2026.60},
  annote =	{Keywords: TFNP, lossy code, randomized proof systems, query complexity}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2026.61
Random Unitaries in Constant (Quantum) Time

Authors: Ben Foxman, Natalie Parham, Francisca Vasconcelos, and Henry Yuen

Published in: LIPIcs, Volume 362, 17th Innovations in Theoretical Computer Science Conference (ITCS 2026)

Abstract
Random unitaries are a central object of study in quantum information, with applications to quantum computation, quantum many-body physics, and quantum cryptography. Recent work has constructed unitary designs and pseudorandom unitaries (PRUs) using Θ(log log n)-depth unitary circuits with two-qubit gates. In this work, we show that unitary designs and PRUs can be efficiently constructed in several well-studied models of constant-time quantum computation (i.e., the time complexity on the quantum computer is independent of the system size). These models are constant-depth circuits augmented with certain nonlocal operations, such as (a) many-qubit TOFFOLI gates, (b) many-qubit FANOUT gates, or (c) mid-circuit measurements with classical feedforward control. Recent advances in quantum computing hardware suggest experimental feasibility of these models in the near future. Our results demonstrate that unitary designs and PRUs can be constructed in much weaker circuit models than previously thought. Furthermore, our construction of PRUs in constant-depth with many-qubit TOFFOLI gates shows that, under cryptographic assumptions, there is no polynomial-time learning algorithm for the circuit class QAC⁰. Finally, our results suggest a new approach towards proving that PARITY is not computable in QAC⁰, a long-standing question in quantum complexity theory.
Cite as

Ben Foxman, Natalie Parham, Francisca Vasconcelos, and Henry Yuen. Random Unitaries in Constant (Quantum) Time. In 17th Innovations in Theoretical Computer Science Conference (ITCS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 362, pp. 61:1-61:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{foxman_et_al:LIPIcs.ITCS.2026.61,
  author =	{Foxman, Ben and Parham, Natalie and Vasconcelos, Francisca and Yuen, Henry},
  title =	{{Random Unitaries in Constant (Quantum) Time}},
  booktitle =	{17th Innovations in Theoretical Computer Science Conference (ITCS 2026)},
  pages =	{61:1--61:25},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-410-9},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{362},
  editor =	{Saraf, Shubhangi},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2026.61},
  URN =		{urn:nbn:de:0030-drops-253481},
  doi =		{10.4230/LIPIcs.ITCS.2026.61},
  annote =	{Keywords: Quantum Information, Pseudorandomness, Circuit Complexity}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2026.8
Intersection Theorems: A Potential Approach to Proof Complexity Lower Bounds

Authors: Yaroslav Alekseev and Nikita Gaevoy

Published in: LIPIcs, Volume 362, 17th Innovations in Theoretical Computer Science Conference (ITCS 2026)

Abstract
Recently, Göös et al. [Göös et al., 2024] showed that Res ⋏ uSA = RevRes in the following sense: if a formula φ has refutations of size at most s and width/degree at most w in both Res and uSA, then there is a refutation for φ of size at most poly(s ⋅ 2^w) in RevRes. Their proof relies on the TFNP characterization of the aforementioned proof systems. In our work, we give a direct and simplified proof of this result, simultaneously achieving better bounds: we show that if for a formula φ there are refutations of size at most s in both Res and uSA, then there is a refutation of φ of size at most poly(s) in RevRes. This potentially allows us to "lift" size lower bounds from RevRes to Res for the formulas for which there are upper bounds in uSA. This kind of lifting was not possible before because of the exponential blow-up in size from the width. Similarly, we improve the bounds in another intersection theorem from [Göös et al., 2024] by giving a direct proof of Res ⋏ uNS = RevResT. Finally, we generalize those intersection theorems to some proof systems for which we currently do not have a TFNP characterization. For example, we show that Res(⊕) ⋏ u-wRes(⊕) = RevRes(⊕), which effectively allows us to reduce the problem of proving Pigeonhole Principle lower bounds in Res(⊕) to proving Pigeonhole Principle lower bounds in RevRes(⊕), a potentially weaker proof system.
Cite as

Yaroslav Alekseev and Nikita Gaevoy. Intersection Theorems: A Potential Approach to Proof Complexity Lower Bounds. In 17th Innovations in Theoretical Computer Science Conference (ITCS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 362, pp. 8:1-8:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{alekseev_et_al:LIPIcs.ITCS.2026.8,
  author =	{Alekseev, Yaroslav and Gaevoy, Nikita},
  title =	{{Intersection Theorems: A Potential Approach to Proof Complexity Lower Bounds}},
  booktitle =	{17th Innovations in Theoretical Computer Science Conference (ITCS 2026)},
  pages =	{8:1--8:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-410-9},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{362},
  editor =	{Saraf, Shubhangi},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2026.8},
  URN =		{urn:nbn:de:0030-drops-252953},
  doi =		{10.4230/LIPIcs.ITCS.2026.8},
  annote =	{Keywords: proof complexity, intersection theorems}
}
Document
Brief Announcement
DOI: 10.4230/LIPIcs.DISC.2025.59
Brief Announcement: Carry the Tail in Consensus Protocols

Authors: Suyash Gupta, Dakai Kang, Dahlia Malkhi, and Mohammad Sadoghi

Published in: LIPIcs, Volume 356, 39th International Symposium on Distributed Computing (DISC 2025)

Abstract
We present Carry-the-Tail, the first deterministic atomic broadcast protocol in partial synchrony that, after GST, simultaneously guarantees two desirable properties: (i) a constant fraction of commits are proposed by non-faulty leaders against tail-forking attacks, and (ii) optimal, worst-case quadratic communication under a cascade of faulty leaders. The solution also guarantees linear amortized communication, i.e., the steady-state is linear. Combining these two desirable properties was not simultaneously achieved previously: on one hand, prior atomic broadcast solutions achieve per-view linear word communication complexity. However, they face a significant degradation in throughput under tail-forking attack. On the other hand, existing solutions to tail-forking attacks require either quadratic communication steps or computationally-prohibitive SNARK generation. The key technical contribution is Carry, a practical drop-in mechanism for streamlined protocols in the HotStuff family. Carry guarantees good performance against tail-forking and removes most leader-induced stalls, while retaining linear traffic and protocol simplicity. Carry-the-Tail implements the Carry mechanism on HotStuff-2.
Cite as

Suyash Gupta, Dakai Kang, Dahlia Malkhi, and Mohammad Sadoghi. Brief Announcement: Carry the Tail in Consensus Protocols. In 39th International Symposium on Distributed Computing (DISC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 356, pp. 59:1-59:7, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{gupta_et_al:LIPIcs.DISC.2025.59,
  author =	{Gupta, Suyash and Kang, Dakai and Malkhi, Dahlia and Sadoghi, Mohammad},
  title =	{{Brief Announcement: Carry the Tail in Consensus Protocols}},
  booktitle =	{39th International Symposium on Distributed Computing (DISC 2025)},
  pages =	{59:1--59:7},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-402-4},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{356},
  editor =	{Kowalski, Dariusz R.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DISC.2025.59},
  URN =		{urn:nbn:de:0030-drops-248759},
  doi =		{10.4230/LIPIcs.DISC.2025.59},
  annote =	{Keywords: Consensus, Blockchain, BFT}
}
Document
Short Paper
DOI: 10.4230/LIPIcs.TIME.2025.19
Temporal Association Rules from Motifs (Short Paper)

Authors: Mauro Milella, Giovanni Pagliarini, Guido Sciavicco, and Ionel Eduard Stan

Published in: LIPIcs, Volume 355, 32nd International Symposium on Temporal Representation and Reasoning (TIME 2025)

Abstract
A motif is defined as a frequently occurring pattern within a (multivariate) time series. In recent years, various techniques have been developed to mine time series data. However, only a few studies have explored the idea of using motif discovery in temporal association rule mining. Interval-based temporal association rules have been recently defined and studied, along with the temporal version of the known frequent patterns, and therefore, association rule extraction algorithms (such as APRIORI and FP-Growth). In this work, we define a vocabulary of propositional letters wrapping motifs, and show how to extract temporal association rules starting from such a vocabulary. We apply our methodology to time series datasets in the fields of hand signs execution and gait recognition, and we discuss how they capture curious insights within data, keeping a high level of interpretability.
Cite as

Mauro Milella, Giovanni Pagliarini, Guido Sciavicco, and Ionel Eduard Stan. Temporal Association Rules from Motifs (Short Paper). In 32nd International Symposium on Temporal Representation and Reasoning (TIME 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 355, pp. 19:1-19:7, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{milella_et_al:LIPIcs.TIME.2025.19,
  author =	{Milella, Mauro and Pagliarini, Giovanni and Sciavicco, Guido and Stan, Ionel Eduard},
  title =	{{Temporal Association Rules from Motifs}},
  booktitle =	{32nd International Symposium on Temporal Representation and Reasoning (TIME 2025)},
  pages =	{19:1--19:7},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-401-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{355},
  editor =	{Vidal, Thierry and Wa{\l}\k{e}ga, Przemys{\l}aw Andrzej},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.TIME.2025.19},
  URN =		{urn:nbn:de:0030-drops-244653},
  doi =		{10.4230/LIPIcs.TIME.2025.19},
  annote =	{Keywords: Motifs, Interval Temporal Logic, Association Rules}
}
Document
DOI: 10.4230/LIPIcs.ESA.2025.103
On the Satisfiability of Random 3-SAT Formulas with k-Wise Independent Clauses

Authors: Ioannis Caragiannis, Nick Gravin, and Zhile Jiang

Published in: LIPIcs, Volume 351, 33rd Annual European Symposium on Algorithms (ESA 2025)

Abstract
The problem of identifying the satisfiability threshold of random 3-SAT formulas has received a lot of attention during the last decades and has inspired the study of other threshold phenomena in random combinatorial structures. The classical assumption in this line of research is that, for a given set of n Boolean variables, each clause is drawn uniformly at random among all sets of three literals from these variables, independently from other clauses. Here, we keep the uniform distribution of each clause, but deviate significantly from the independence assumption and consider richer families of probability distributions. For integer parameters n, m, and k, we denote by ℱ_k(n,m) the family of probability distributions that produce formulas with m clauses, each selected uniformly at random from all sets of three literals from the n variables, so that the clauses are k-wise independent. Our aim is to make general statements about the satisfiability or unsatisfiability of formulas produced by distributions in ℱ_k(n,m) for different values of the parameters n, m, and k. Our technical results are as follows: First, all probability distributions in ℱ₂(n,m) with m ∈ Ω(n³) return unsatisfiable formulas with high probability. This result is tight. We show that there exists a probability distribution 𝒟 ∈ ℱ₃(n,m) with m ∈ O(n³) so that a random formula drawn from 𝒟 is almost always satisfiable. In contrast, for m ∈ Ω(n²), any probability distribution 𝒟 ∈ ℱ₄(n,m) returns an unsatisfiable formula with high probability. This is our most surprising and technically involved result. Finally, for any integer k ≥ 2, any probability distribution 𝒟 ∈ ℱ_k(n,m) with m ∈ O(n^{1-1/k}) returns a satisfiable formula with high probability.
Cite as

Ioannis Caragiannis, Nick Gravin, and Zhile Jiang. On the Satisfiability of Random 3-SAT Formulas with k-Wise Independent Clauses. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 103:1-103:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{caragiannis_et_al:LIPIcs.ESA.2025.103,
  author =	{Caragiannis, Ioannis and Gravin, Nick and Jiang, Zhile},
  title =	{{On the Satisfiability of Random 3-SAT Formulas with k-Wise Independent Clauses}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{103:1--103:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-395-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{351},
  editor =	{Benoit, Anne and Kaplan, Haim and Wild, Sebastian 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.2025.103},
  URN =		{urn:nbn:de:0030-drops-245721},
  doi =		{10.4230/LIPIcs.ESA.2025.103},
  annote =	{Keywords: Random 3-SAT, k-wise independence, Random bipartite graph}
}
Document
DOI: 10.4230/LIPIcs.ESA.2025.106
On Estimating the Quantum 𝓁_α Distance

Authors: Yupan Liu and Qisheng Wang

Published in: LIPIcs, Volume 351, 33rd Annual European Symposium on Algorithms (ESA 2025)

Abstract
We study the computational complexity of estimating the quantum 𝓁_α distance T_α(ρ₀,ρ₁), defined via the Schatten α-norm ‖A‖_α := tr(|A|^α)^{1/α}, given poly(n)-size state-preparation circuits of n-qubit quantum states ρ₀ and ρ₁. This quantity serves as a lower bound on the trace distance for α > 1. For any constant α > 1, we develop an efficient rank-independent quantum estimator for T_α(ρ₀,ρ₁) with time complexity poly(n), achieving an exponential speedup over the prior best results of exp(n) due to Wang, Guan, Liu, Zhang, and Ying (IEEE Trans. Inf. Theory 2024). Our improvement leverages efficiently computable uniform polynomial approximations of signed positive power functions within quantum singular value transformation, thereby eliminating the dependence on the rank of the states. Our quantum algorithm reveals a dichotomy in the computational complexity of the Quantum State Distinguishability Problem with Schatten α-norm (QSD_α), which involves deciding whether T_α(ρ₀,ρ₁) is at least 2/5 or at most 1/5. This dichotomy arises between the cases of constant α > 1 and α = 1: - For any 1+Ω(1) ≤ α ≤ O(1), QSD_α is BQP-complete. - For any 1 ≤ α ≤ 1+1/n, QSD_α is QSZK-complete, implying that no efficient quantum estimator for T_α(ρ₀,ρ₁) exists unless BQP = QSZK. The hardness results follow from reductions based on new rank-dependent inequalities for the quantum 𝓁_α distance with 1 ≤ α ≤ ∞, which are of independent interest.
Cite as

Yupan Liu and Qisheng Wang. On Estimating the Quantum 𝓁_α Distance. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 106:1-106:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{liu_et_al:LIPIcs.ESA.2025.106,
  author =	{Liu, Yupan and Wang, Qisheng},
  title =	{{On Estimating the Quantum 𝓁\underline\alpha Distance}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{106:1--106:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-395-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{351},
  editor =	{Benoit, Anne and Kaplan, Haim and Wild, Sebastian 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.2025.106},
  URN =		{urn:nbn:de:0030-drops-245758},
  doi =		{10.4230/LIPIcs.ESA.2025.106},
  annote =	{Keywords: quantum algorithms, quantum state testing, trace distance, Schatten norm}
}
Document
RANDOM
DOI: 10.4230/LIPIcs.APPROX/RANDOM.2025.64
Searching for Falsified Clause in Random (log{n})-CNFs Is Hard for Randomized Communication

Authors: Artur Riazanov, Anastasia Sofronova, Dmitry Sokolov, and Weiqiang Yuan

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

Abstract
We show that for a randomly sampled unsatisfiable O(log n)-CNF over n variables the randomized two-party communication cost of finding a clause falsified by the given variable assignment is linear in n.
Cite as

Artur Riazanov, Anastasia Sofronova, Dmitry Sokolov, and Weiqiang Yuan. Searching for Falsified Clause in Random (log{n})-CNFs Is Hard for Randomized Communication. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 353, pp. 64:1-64:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{riazanov_et_al:LIPIcs.APPROX/RANDOM.2025.64,
  author =	{Riazanov, Artur and Sofronova, Anastasia and Sokolov, Dmitry and Yuan, Weiqiang},
  title =	{{Searching for Falsified Clause in Random (log\{n\})-CNFs Is Hard for Randomized Communication}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025)},
  pages =	{64:1--64:17},
  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.2025.64},
  URN =		{urn:nbn:de:0030-drops-244306},
  doi =		{10.4230/LIPIcs.APPROX/RANDOM.2025.64},
  annote =	{Keywords: communication complexity, proof complexity, random CNF}
}
Document
RANDOM
DOI: 10.4230/LIPIcs.APPROX/RANDOM.2025.48
Sharp Thresholds for the Overlap Gap Property: Ising p-Spin Glass and Random k-SAT

Authors: Eren C. Kızıldağ

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

Abstract
The Ising p-spin glass and random k-SAT are two canonical examples of disordered systems that play a central role in understanding the link between geometric features of optimization landscapes and computational tractability. Both models exhibit hard regimes where all known polynomial-time algorithms fail and possess the multi Overlap Gap Property (m-OGP), an intricate geometrical property that rigorously rules out a broad class of algorithms exhibiting input stability. We establish that, in both models, the symmetric m-OGP undergoes a sharp phase transition, and we pinpoint its exact threshold. For the Ising p-spin glass, our results hold for all sufficiently large p; for the random k-SAT, they apply to all k growing mildly with the number of Boolean variables. Notably, our findings yield qualitative insights into the power of OGP-based arguments. A particular consequence for the Ising p-spin glass is that the strength of the m-OGP in establishing algorithmic hardness grows without bound as m increases. These are the first sharp threshold results for the m-OGP. Our analysis hinges on a judicious application of the second moment method, enhanced by concentration. While a direct second moment calculation fails, we overcome this via a refined approach that leverages an argument of Frieze [Frieze, 1990] and exploiting concentration properties of carefully constructed random variables.
Cite as

Eren C. Kızıldağ. Sharp Thresholds for the Overlap Gap Property: Ising p-Spin Glass and Random k-SAT. In Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 353, pp. 48:1-48:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{kizildag:LIPIcs.APPROX/RANDOM.2025.48,
  author =	{K{\i}z{\i}lda\u{g}, Eren C.},
  title =	{{Sharp Thresholds for the Overlap Gap Property: Ising p-Spin Glass and Random k-SAT}},
  booktitle =	{Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques (APPROX/RANDOM 2025)},
  pages =	{48:1--48:16},
  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.2025.48},
  URN =		{urn:nbn:de:0030-drops-244147},
  doi =		{10.4230/LIPIcs.APPROX/RANDOM.2025.48},
  annote =	{Keywords: spin glasses, p-spin model, random constraint satisfaction problems, overlap gap property, phase transitions, computational complexity}
}
Document
DOI: 10.4230/LIPIcs.WABI.2025.11
Mutational Signature Refitting on Sparse Pan-Cancer Data

Authors: Gal Gilad, Teresa M. Przytycka, and Roded Sharan

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

Abstract
Mutational processes shape cancer genomes, leaving characteristic marks that are termed signatures. The level of activity of each such process, or its signature exposure, provides important information on the disease, improving patient stratification and the prediction of drug response. Thus, there is growing interest in developing refitting methods that decipher those exposures. Previous work in this domain was unsupervised in nature, employing algebraic decomposition and probabilistic inference methods. Here we provide a supervised approach to the problem of signature refitting and show its superiority over current methods. Our method, SuRe, leverages a neural network model to capture correlations between signature exposures in real data. We show that SuRe outperforms previous methods on sparse mutation data from tumor type specific data sets, as well as pan-cancer data sets, with an increasing advantage as the data become sparser. We further demonstrate its utility in clinical settings.
Cite as

Gal Gilad, Teresa M. Przytycka, and Roded Sharan. Mutational Signature Refitting on Sparse Pan-Cancer Data. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 11:1-11:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{gilad_et_al:LIPIcs.WABI.2025.11,
  author =	{Gilad, Gal and Przytycka, Teresa M. and Sharan, Roded},
  title =	{{Mutational Signature Refitting on Sparse Pan-Cancer Data}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{11:1--11:23},
  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.2025.11},
  URN =		{urn:nbn:de:0030-drops-239374},
  doi =		{10.4230/LIPIcs.WABI.2025.11},
  annote =	{Keywords: mutational signatures, signature refitting, cancer genomics, genomic data analysis, somatic mutations}
}
Document
DOI: 10.4230/LIPIcs.WABI.2025.17
An Efficient Data Structure and Algorithm for Long-Match Query in Run-Length Compressed BWT

Authors: Ahsan Sanaullah, Degui Zhi, and Shaojie Zhang

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

Abstract
String matching problems in bioinformatics are typically for finding exact substring matches between a query and a reference text. Previous formulations often focus on maximum exact matches (MEMs). However, multiple occurrences of substrings of the query in the text that are long enough but not maximal may not be captured by MEMs. Such long matches can be informative, especially when the text is a collection of similar sequences such as genomes. In this paper, we describe a new type of match between a pattern and a text that aren't necessarily maximal in the query, but still contain useful matching information: locally maximal exact matches (LEMs). There are usually a large amount of LEMs, so we only consider those above some length threshold ℒ. These are referred to as long LEMs. The purpose of long LEMs is to capture substring matches between a query and a text that are not necessarily maximal in the pattern but still long enough to be important. Therefore efficient long LEMs finding algorithms are desired for these datasets. However, these datasets are too large to query on traditional string indexes. Fortunately, these datasets are very repetitive. Recently, compressed string indexes that take advantage of the redundancy in the data but retain efficient querying capability have been proposed as a solution. We therefore give an efficient algorithm for computing all the long LEMs of a query and a text in a BWT runs compressed string index. We describe an O(m+occ) expected time algorithm that relies on an O(r) words space string index for outputting all long LEMs of a pattern with respect to a text given the matching statistics of the pattern with respect to the text. Here m is the length of the query, occ is the number of long LEMs outputted, and r is the number of runs in the BWT of the text. The O(r) space string index we describe relies on an adaptation of the move data structure by Nishimoto and Tabei. We are able to support LCP[i] queries in constant time given SA[i]. In other words, we answer PLCP[i] queries in constant time. These PLCP queries enable the efficient long LEM query. Long LEMs may provide useful similarity information between a pattern and a text that MEMs may ignore. This information is particularly useful in pangenome and biobank scale haplotype panel contexts.
Cite as

Ahsan Sanaullah, Degui Zhi, and Shaojie Zhang. An Efficient Data Structure and Algorithm for Long-Match Query in Run-Length Compressed BWT. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 17:1-17:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{sanaullah_et_al:LIPIcs.WABI.2025.17,
  author =	{Sanaullah, Ahsan and Zhi, Degui and Zhang, Shaojie},
  title =	{{An Efficient Data Structure and Algorithm for Long-Match Query in Run-Length Compressed BWT}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{17:1--17:25},
  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.2025.17},
  URN =		{urn:nbn:de:0030-drops-239433},
  doi =		{10.4230/LIPIcs.WABI.2025.17},
  annote =	{Keywords: BWT, LEM, Long LEM, MEM, Run Length Compressed BWT, Move Data Structure, Pangenome}
}
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