Related papers: Haplotype Inference on Pedigrees with Recombinatio…
We propose a Preconditioned Locally Harmonic Residual (PLHR) method for computing several interior eigenpairs of a generalized Hermitian eigenvalue problem, without traditional spectral transformations, matrix factorizations, or inversions.…
Fully homomorphic encryption (FHE) enables a simple, attractive framework for secure search. Compared to other secure search systems, no costly setup procedure is necessary; it is sufficient for the client merely to upload the encrypted…
Compositional generalization-the ability to interpret novel combinations of familiar components-remains a persistent challenge for neural networks. Behavioral evaluations reveal \emph{when} models fail but offer limited insight into…
Clustering genotypes based upon their phenotypic characteristics is used to obtain diverse sets of parents that are useful in their breeding programs. The Hierarchical Clustering (HC) algorithm is the current standard in clustering of…
Multi-hop question answering (MHQA) involves reasoning across multiple documents to answer complex questions. Dense retrievers typically outperform sparse methods like BM25 by leveraging semantic embeddings; however, they require labeled…
We present a novel method for exact hierarchical sparse polynomial regression. Our regressor is that degree $r$ polynomial which depends on at most $k$ inputs, counting at most $\ell$ monomial terms, which minimizes the sum of the squares…
Background: Haplotypes, the ordered lists of single nucleotide variations that distinguish chromosomal sequences from their homologous pairs, may reveal an individual's susceptibility to hereditary and complex diseases and affect how our…
We propose a simple modification to the iterative hard thresholding (IHT) algorithm, which recovers asymptotically sparser solutions as a function of the condition number. When aiming to minimize a convex function $f(x)$ with condition…
Limited capacity of fronthaul links in a cell-free massive multiple-input multiple-output (MIMO) system can cause quantization errors at a central processing unit (CPU) during data transmission, complicating the centralized rate…
The haplotype resolution from xor-genotype data has been recently formulated as a new model for genetic studies. The xor-genotype data is a cheaply obtainable type of data distinguishing heterozygous from homozygous sites without…
Error mitigation techniques, while instrumental in extending the capabilities of near-term quantum computers, often suffer from exponential resource scaling with noise levels. To address this limitation, we introduce a novel approach,…
Constrained sampling and counting are two fundamental problems in artificial intelligence with a diverse range of applications, spanning probabilistic reasoning and planning to constrained-random verification. While the theory of these…
Combinatorial reconfiguration is a growing research field studying problems on the transformability between a pair of solutions of a search problem. We consider the approximability of optimization variants of reconfiguration problems; e.g.,…
This paper proposes an audio fingerprinting model with holographic reduced representation (HRR). The proposed method reduces the number of stored fingerprints, whereas conventional neural audio fingerprinting requires many fingerprints for…
A basic problem in metagenomics is to assign a sequenced read to the correct species in the reference collection. In typical applications in genomic epidemiology and viral metagenomics the reference collection consists of set of species…
The job sequencing and tool switching problem (SSP) has been extensively studied in the field of operations research, due to its practical relevance and methodological interest. Given a machine that can load a limited amount of tools…
This paper focuses on solving large-scale, ill-conditioned, and overdetermined sparse least squares problems that arise from numerical partial differential equations (PDEs), mainly from the random feature method. To address these…
Pairwise alignment of DNA sequencing data is a ubiquitous task in bioinformatics and typically represents a heavy computational burden. State-of-the-art approaches to speed up this task use hashing to identify short segments (k-mers) that…
A quadratic assignment problem (QAP) is a combinatorial optimization problem that belongs to the class of NP-hard ones. So, it is difficult to solve in the polynomial time even for small instances. Research on the QAP has thus focused on…
Routine single-sample haplotype-resolved assembly remains an unresolved problem. Here we describe a new algorithm that combines PacBio HiFi reads and Hi-C chromatin interaction data to produce a haplotype-resolved assembly without the…