21 papers · ranked by Valyu relevance
Vincent P. Ferrera, Samuel Lippl, Kenneth Kay, Fabian Munoz + 3 more
Transitive inference (TI) is the ability to reason about transitive relationships in an ordered set of items (e.g., if A>B and B>C, then A>C). TI is widely held to depend on a linear representation of the serial (rank) order of those items. By what computational mechanism is such an ordering constructed during…
Dhruv Sarkar, Nishant Pandey, Sayak Ray Chowdhury
Nash regret has recently emerged as a principled fairness-aware performance metric for stochastic multi-armed bandits, motivated by the Nash Social Welfare objective. Although this notion has been extended to linear bandits, existing results suffer from suboptimality in ambient dimension d, stemming from proof…
Amir Hossein Salehi Shayegan
Time-fractional diffusion equations have emerged as powerful models for describing anomalous transport phenomena in physics, biology and engineering. To address the computational challenges arising from their non-local operators, we employ the WEB-spline finite element method, which provides a flexible and accurate…
Hongbin Lv, Meixiang Chen, Wen Li
The R-linear convergence of the NQZ algorithm for computing the H-spectral radius of a class of weakly irreducible nonnegative tensors is established by utilizing the directed graphs of tensors. Meanwhile, an upper bound for the root convergence factor R is derived and a general condition ensuring the linear…
Leonard Bohnenkämper, Luca Parmigiani, Cedric Chauve, Jens Stoye
Genomic rearrangements are major drivers of evolution and genetic disease. However, studying rearrangements requires segmenting the genomes of interest into conserved regions, called synteny blocks, that highlight structural differences between genomes. Synteny blocks are typically defined from annotated genes or…
Theodoros Anagnostopoulos, Evanthia Zervoudi, Christos Anagnostopoulos, Apostolos Christopoulos + 1 more
Linear regression analysis focuses on predicting a numeric regressand value based on certain regressor values. In this context, k-Nearest Neighbors (k-NN) is a common non-parametric regression algorithm, which achieves efficient performance when compared with other algorithms in literature. In this research effort an…
Daniel Gibor
In this paper, we present a randomized polynomial-time simplex algorithm with higher probability and tighter bounds for linear programming by applying improved quasi-convex properties, a logarithmic rounding on a given polytope and its logarithmic perturbation. We base our work on the first randomized polynomial-time…
Yang, Yaguang
This paper presents a Matlab implementation of an arc-search infeasible interior point algorithm for linear programming (LP), which has a proven polynomial bound of $\mathcal{O}(\sqrt{n}L)$, the best among all interior-point algorithms for LP. Software architecture and major functions are discussed. Its ease of use is…
Justin Dallant
Given an $n\times n$ matrix $A$, a saddlepoint of $A$ is an entry that is the maximum in its row and the minimum in its column. It is a strict saddlepoint if no other entry in its row or column has the same value. Finding a non-strict saddlepoint requires $Θ(n^2)$ matrix queries in the worst case. In contrast, a strict…
Yury Zabegaev, Inga Berre, Eirik Keilegavlen
Modeling multiphysics processes in porous media requires preconditioned iterative linear solvers to enable efficient simulations at industry-relevant scales. These solvers are typically composed of sub-algorithms that target individual physical processes. Various options are available for each algorithm, with the…
Ahsan Sanaullah, Nathaniel K. Brown, Pramesh Shakya, Arun Deegutla + 4 more
Lossless full text indexes are utilized in a myriad of applications in bioinformatics. The continuously decreasing cost of generating biological data has resulted in the need to build full text indexes on biological datasets of increasing size. Many compressed full text indexes have been developed to address this…
Georgios Vretinaris
We introduce a low-rank algorithm inspired by the Basis-Update and Galerkin (BUG) integrator to efficiently approximate solutions to Sylvester-type equations. The algorithm can exploit both the low-rank structure of the solution as well as any sparsity present to reduce computational complexity. Even when a standard…
Xinyu Gu, Stefan Ivanovic, Daniel W. Feng, Mohammed El-Kebir
Summarizing a collection P of related RNA secondary structures is a key challenge in applications like evolutionary analysis, alternative fold studies and mRNA vaccine design. This requires both clustering the input structures into similar groups and identifying the core structural motifs on which they agree or differ.…
Jianting Pan, Ming Yan
This paper develops an efficient algorithm for computing the Euclidean projection onto the top-k-sum constraint, a key operation in financial risk management and matrix optimization problems. Existing projection methods rely on sorting and therefore incur an initial O(n log n) complexity, which limits their scalability…
Mahmudur Rahman Hera, David Koslicki, Conrado Martínez
With the surge in sequencing data generated from an ever-expanding range of biological studies, designing scalable computational techniques has become essential. One effective strategy to enable large-scale computation is to split long DNA or protein sequences into k-mers, and summarize large k-mer sets into compact…
Sepideh Aghamolaei, Kevin Buchin, Timothy M. Chan, Jacobus Conradi + 4 more
Computing the convex hull of a planar $n$-point set $P$ is one of the most fundamental problems in computational geometry. It has an $Ω(n \log n)$ lower bound in the algebraic computation tree model, and many convex hull algorithms match this bound. Classical results show that, under special input assumptions, sub-$O(n…
Authors not listed
Terminally labeled DNA oligonucleotides have wide applications in modern biology and biotechnological applications. It has been observed that the fluorescent intensity of light released from these fluorescent labels is heavily influenced by the terminal sequence of nucleotides. Recent studies have assayed and published…
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…
Lotte Blank, Anne Drieme, Sariel Har-Peled, Marena Richter
We give linear-time, and thus optimal, $(1+\varepsilon)$-approximation algorithms for numerous variants of the Frechet distance between $c$-packed curves (where $c \in O(1)$), removing an additional log factor that was present in previous algorithms. The key to our new algorithms is a linear-size approximation of the…
Authors not listed
Monoterpene synthases (mTSs) are a large family of enzymes, which have promising industrial applications, yet remain difficult to engineer due to complex and poorly understood sequence-function relationships. Here, we present a structure-based machine learning (ML) framework that accurately predicts whether a mTS…
Authors not listed
Accurate prediction of reaction barriers and transition states is central to understanding electrolyte degradation pathways in battery systems, yet existing approaches face significant computational trade-offs. Classical quantum-chemistry methods like density functional theory (DFT) scale favorably but often miss…