Search · four archives
Search · four archives
20 papers · ranked by Valyu relevance
Tim Vieira, Ryan Cotterell, Jason Eisner
Much algorithmic research in NLP aims to efficiently manipulate rich formal structures. An algorithm designer typically seeks to provide guarantees about their proposed algorithm—for example, that its running time or space complexity is upper-bounded as a certain function of its input size. They may also wish to…
Ohad Kammar, Jack Liell-Cock, Sam Lindley, Cristina Matache + 1 more
Our programs are built from the key primitives 'fork' and 'wait'. 'Fork' creates a child thread and passes its name (thread ID) to the parent thread. 'Wait' allows us to wait for given child threads to finish. We provide a parameterized algebraic theory built from fork and wait, together with basic atomic actions and…
Chengyuan Peng, John Stachurski, Jingni Yang
We study abstract dynamic programs on partially ordered spaces, pairing the order-theoretic approach to dynamic programming with topological and metric foundations. We show that readily verifiable forms of topological stability, such as global stability and contractivity of the policy operators, deliver the fundamental…
Kangbien Park
Humans have long employed directed evolution (DE) to engineer desired biological traits. In this paper, I introduce an algebraic framework that provides a quantitative representation of the general phenotypic traits of asexual populations, enabling the systematic modeling of DE processes. Within this framework, key…
Arseny Shur, Ido Tziony, Yaron Orenstein
Minimizers are sampling schemes which are ubiquitous in almost any high-throughput sequencing analysis. Assuming a fixed alphabet of size σ, a minimizer is defined by two positive integers k, w and a linear order ρ on k-mers. A sequence is processed by a sliding window algorithm that chooses in each window of length w…
Tobias Gürtler, Benjamin Lucien Kaminski
Probabilistic programming languages (PPLs) are an expressive and intuitive means of representing complex probability distributions. In that realm, languages like Dice target an important class of probabilistic programs: those whose probability distributions are discrete. Discrete distributions are common in many…
Michele Boreale, Luisa Collodi, Alessandro Pompa Di Gregorio
We present an algebraic method for analyzing probabilistic programs with counters and discrete states, Generalized Constant Probability (GCP) programs. We define the operational semantics of GCP in terms of the runs of a type of probabilistic pushdown automata (pPDAs). We characterize the resulting (sub-)probability…
Lin, Yi, Vardi, Moshe Y.
Motivated by functional synthesis in sequential circuit construction and quantified boolean formulas (QBF), boolean synthesis serves as one of the core problems in Formal Methods. Recent advances show that decision diagrams (DD) are particularly competitive in symbolic approaches for boolean synthesis, among which…
Mateusz Gruzewski, Marek Palkowski, Ramon Antonio Rodriges Zalipynis
In this article, we present an efficient and concise OpenMP implementation of the Nussinov RNA folding algorithm, a well-known representative of non-serial polyadic dynamic programming (NPDP). Our goal is to develop an optimized implementation that can serve as a template for related dynamic programming applications.…
Patrick Zhong, Federico Rossi, Dylan A. Shell
An important class of robotic applications involves multiple agents cooperating to provide state observations to plan joint actions. We study planning under uncertainty when more than one participant must proactively plan perception and/or communication acts, and decide whether the cost to obtain a state estimate is…
David P. Morton, Oscar Dowson, Bernardo K. Pagnoncelli
We study a class of multi-stage stochastic programs, which incorporate modeling features from Markov decision processes (MDPs). This class includes structured MDPs with continuous action and state spaces. We extend policy graphs to include decision-dependent uncertainty for one-step transition probabilities as well as…
Sravani Boddepalli, Prathamesh Kothavale
—This paper presents a comparative analysis of discrete and continuous action spaces within the contexts of reservoir management and inventory control problems. We explore the computational trade-offs between discrete action discretizations and continuous action settings, focusing on their effects on time complexity…
Christian Antić
This paper investigates the algebraic structure of Krom logic programs, consisting only of facts and rules with at most one body atom. We show that sequential composition endows the class of Krom programs with a natural monoid structure and that this structure admits rich algebraic extensions to Krom seminearrings…
Zhezhen Yu, Dan Levy
Aligning sequencing reads to short tandem repeats (STRs) is challenging: the number of repeat copies in a read often differs from the reference, and small changes inside and around the repeat can lead to many competing alignments. We introduce NW-flex, a simple extension of classical sequence alignment that addresses…
Marco Polo Castillo-Villalba
The analysis of large gene and metabolic networks is often hindered by unknown biochemical parameters and the nonlinear nature of classical S-system models. To address this, we introduce a framework based on combinatorial toric geometry computed with tools such as Normaliz, SageMath, it is worth mentioning this…
Jing Xie, Qi Duan
Biological pathway analysis often requires identifying interventions that block reachability to an undesirable state, such as a disease-associated module, toxic byproduct, or adverse phenotype, while preserving reachability among essential biological functions. Motivated by this setting, we study the Reachability…
Enrico Seiler, Myrthe Willemsen, Vitor C. Piro, Knut Reinert
A continued decrease in sequencing costs has facilitated the exponential increase in available sequencing data, with public databases like the European Nucleotide Archive (ENA) and Sequence Read Archive (SRA) reaching well in the order of petabases [1, 2]. This has been the incentive to develop more scalable tools for…
Authors not listed
The Hidden Subgroup Problem (HSP) unifies several landmark quantum algorithms, yet systematic exploration of its variants and modern applications has slowed. This paper revives HSP-based algorithm design by examining new group structures with direct relevance to post-quantum cryptography, lattice problems, and…
Jie Gao, Weinan Xie, Haoya Liu, Junda Zhou + 3 more
Multi-AGV (Automated Guided Vehicle) systems operating in complex warehouse environments equipped with movable containers encounter several challenges, including high system no-load rate, low task response efficiency, and imbalanced path utilization. To address these issues, we propose an integrated optimization…
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Atomic electrons exist under the central Coulomb potential of the nucleus, a constraint that mandates their wave functions be described by spherical harmonics. While standard quantum mechanics treats these functions as static geometric solutions, the empirical structure of the periodic table (2, 8, 8, 18, 18, ...)…