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The $k$-means algorithm is arguably the most popular nonparametric clustering method but cannot generally be applied to datasets with incomplete records. The usual practice then is to either impute missing values under an assumed…
Genomic selection (GS), as a critical crop breeding strategy, plays a key role in enhancing food production and addressing the global hunger crisis. The predominant approaches in GS currently revolve around employing statistical methods for…
Catastrophic forgetting remains a key challenge in Continual Learning (CL). In replay-based CL with severe memory constraints, performance critically depends on the sample selection strategy for the replay buffer. Most existing approaches…
Programs based on hash tables and Burrows-Wheeler are very fast for mapping short reads to genomes but have low accuracy in the presence of mismatches and gaps. Such reads can be aligned accurately with the Smith-Waterman algorithm but it…
Background: Advances in high throughput sequencing technologies provide a huge number of genomes to be analyzed. Thus, computational methods play a crucial role in analyzing and extracting knowledge from the data generated. Investigating…
k-Nearest Neighbors is one of the most fundamental but effective classification models. In this paper, we propose two families of models built on a sequence to sequence model and a memory network model to mimic the k-Nearest Neighbors…
The kernel $k$-means is an effective method for data clustering which extends the commonly-used $k$-means algorithm to work on a similarity matrix over complex data structures. The kernel $k$-means algorithm is however computationally very…
Kernel $k$-means clustering can correctly identify and extract a far more varied collection of cluster structures than the linear $k$-means clustering algorithm. However, kernel $k$-means clustering is computationally expensive when the…
The $k$-center problem is a fundamental optimization problem with numerous applications in machine learning, data analysis, data mining, and communication networks. The $k$-center problem has been extensively studied in the classical…
MR Fingerprinting is a novel quantitative MR technique that could simultaneously provide multiple tissue property maps. When optimizing MRF scans, modeling undersampling errors and field imperfections in cost functions will make the…
Nanopore sequencing is a widely-used high-throughput genome sequencing technology that can sequence long fragments of a genome into raw electrical signals at low cost. Nanopore sequencing requires two computationally-costly processing steps…
Frequent pattern mining is a flagship problem in data mining. In its most basic form, it asks for the set of substrings of a given string $S$ of length $n$ that occur at least $\tau$ times in $S$, for some integer $\tau\in[1,n]$. We…
Genome-to-genome comparisons require designating anchor points, which are given by Maximum Exact Matches (MEMs) between their sequences. For large genomes this is a challenging problem and the performance of existing solutions, even in…
Next-generation sequencing (NGS) is a pivotal technique in genome sequencing due to its high throughput, rapid results, cost-effectiveness, and enhanced accuracy. Its significance extends across various domains, playing a crucial role in…
Cardiac magnetic resonance imaging (CMR) is vital for diagnosing heart diseases, but long scan time remains a major drawback. To address this, accelerated imaging techniques have been introduced by undersampling k-space, which reduces the…
Magnetic resonance imaging (MRI) is one of the most commonly applied tests in neurology and neurosurgery. However, the utility of MRI is largely limited by its long acquisition time, which might induce many problems including patient…
The k-means algorithm can simplify large-scale spatial vectors, such as 2D geo-locations and 3D point clouds, to support fast analytics and learning. However, when processing large-scale datasets, existing k-means algorithms have been…
Markov chain Monte Carlo (MCMC) is a widely used sampling method in modern artificial intelligence and probabilistic computing systems. It involves repetitive random number generations and thus often dominates the latency of probabilistic…
Multi-vector retrieval (MVR) models, exemplified by ColBERT, have established new benchmarks in retrieval accuracy by preserving fine-grained token-level interactions. However, this granularity imposes prohibitive storage and retrieval…
Identification of cancer driver genes is fundamental for the development of targeted therapeutic interventions. The integration of mutational profiles with protein-protein interaction (PPI) networks offers a promising avenue for their…