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Whereas chord transcription has received considerable attention during the past couple of decades, far less work has been devoted to transcribing and encoding the rhythmic patterns that occur in a song. The topic is especially relevant for…
Ontology Matching (OM) is a cornerstone task of semantic interoperability, yet existing systems often rely on handcrafted rules or specialized models with limited adaptability. We present KROMA, a novel OM framework that harnesses Large…
Genome analysis fundamentally starts with a process known as read mapping, where sequenced fragments of an organism's genome are compared against a reference genome. Read mapping is currently a major bottleneck in the entire genome analysis…
Large-scale proteomic analysis is emerging as a powerful technique in biology and relies heavily on data acquired by state-of-the-art mass spectrometers. As with any other field in Systems Biology, computational tools are required to deal…
Receiver operating characteristic (ROC) analysis is one of the most popular approaches for evaluating and comparing the accuracy of medical diagnostic tests. Although various methodologies have been developed for estimating ROC curves and…
Questions of understanding and quantifying the representation and amount of information in organisms have become a central part of biological research, as they potentially hold the key to fundamental advances. In this paper, we demonstrate…
This work presents a statistically principled method for estimating the required number of instances in the experimental comparison of multiple algorithms on a given problem class of interest. This approach generalises earlier results by…
Microscopy images contain rich information about how cells respond to perturbations, making them essential to applications like drug screening. To quantify images, researchers often use representation extraction methods, and recent years…
Recently, haplo-identical transplantation with multiple HLA mismatches has become a viable option for system cell transplants. Haplotype sharing detection requires imputation of donor and recipient. We show that even in high-resolution…
A major challenge for cancer pathologists is to determine whether a new tumor in a patient with cancer is a metastasis or an independent occurrence of the disease. In recent years numerous studies have evaluated pairs of tumor specimens to…
Computer simulations are an important tool for studying the mechanics of biological evolution. In particular, in silico work with agent-based models provides an opportunity to collect high-quality records of ancestry relationships among…
A vital and rapidly growing application, remote sensing offers vast yet sparsely labeled, spatially aligned multimodal data; this makes self-supervised learning algorithms invaluable. We present CROMA: a framework that combines contrastive…
This paper presents and compares alternative transfer learning methods that can increase the power of conditional testing via knockoffs by leveraging prior information in external data sets collected from different populations or measuring…
Although the applications of Non-Homogeneous Poisson Processes to model and study the threshold overshoots of interest in different time series of measurements have proven to provide good results, they needed to be complemented with an…
Motivation: Alternative splicing is an important mechanism in which the regions of pre-mRNAs are differentially joined in order to form different transcript isoforms. Alternative splicing is involved in the regulation of normal…
The advent of high-throughput sequencing technologies has revolutionized genome analysis by enabling the rapid and cost-effective sequencing of large genomes. Despite these advancements, the increasing complexity and volume of genomic data…
DNA pattern matching is essential for many widely used bioinformatics applications. Disease diagnosis is one of these applications, since analyzing changes in DNA sequences can increase our understanding of possible genetic diseases. The…
Alignments provide sophisticated diagnostics that pinpoint deviations in a trace with respect to a process model and their severity. However, approaches based on trace alignments use crisp process models as reference and recent…
Spectral-spatial processing has been increasingly explored in remote sensing hyperspectral image classification. While extensive studies have focused on developing methods to improve the classification accuracy, experimental setting and…
High-throughput screening using cell images is an efficient method for screening new candidates for pharmaceutical drugs. To complete the screening process, it is essential to have an efficient process for analyzing cell images. This paper…