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Spectral computed tomography (CT) offers the possibility to reconstruct attenuation images at different energy levels, which can be then used for material decomposition. However, traditional methods reconstruct each energy bin individually…
Ontologies are the prime way of organizing data in the Semantic Web. Often, it is necessary to combine several, independently developed ontologies to obtain a knowledge graph fully representing a domain of interest. The complementarity of…
Many diseases are considered to be closely related to the changes in the gut microbial community, including colorectal cancer (CRC), which is one of the most common cancers in the world. The diagnostic classification and etiological…
Genome-scale metabolic models (GEMs) are essential tools for systems biology and rational chassis design, but conventional top-down reconstruction depends heavily on sequence homology and often leaves unknown enzymes and metabolic dark…
Discovering gene-disease associations is crucial for understanding disease mechanisms, yet identifying these associations remains challenging due to the time and cost of biological experiments. Computational methods are increasingly vital…
Computer-Assisted Interventions enable clinicians to perform precise, minimally invasive procedures, often relying on advanced imaging methods. Cone-beam computed tomography (CBCT) can be used to facilitate computer-assisted interventions,…
Metagenome assembly is the process of transforming a set of short, overlapping, and potentially erroneous DNA segments from environmental samples into the accurate representation of the underlying microbiomes's genomes. State-of-the-art…
Coarse-graining (CG) of molecular simulations simplifies the particle representation by grouping selected atoms into pseudo-beads and drastically accelerates simulation. However, such CG procedure induces information losses, which makes…
Reproducibility of research is essential for science. However, in the way modern computational biology research is done, it is easy to lose track of small, but extremely critical, details. Key details, such as the specific version of a…
Molecular conformer generation (MCG) is an important task in cheminformatics and drug discovery. The ability to efficiently generate low-energy 3D structures can avoid expensive quantum mechanical simulations, leading to accelerated virtual…
The 3-dimensional (3D) structure of the genome is of significant importance for many cellular processes. In this paper, we study the problem of reconstructing the 3D structure of chromosomes from Hi-C data of diploid organisms, which poses…
Online learners spend millions of hours per year testing their new skills on assignments with known answers. This paper explores whether framing research questions as assignments with unknown answers helps learners generate novel, useful,…
Natural language is characterized by compositionality: the meaning of a complex expression is constructed from the meanings of its constituent parts. To facilitate the evaluation of the compositional abilities of language processing…
To solve a new task from minimal experience, it is essential to effectively reuse knowledge from previous tasks, a problem known as meta-learning. Compositional solutions, where common elements of computation are flexibly recombined into…
Despite rapid progress in the field, it is still challenging to discover new ways to take advantage of quantum computation: all quantum algorithms need to be designed by hand, and quantum mechanics is notoriously counterintuitive. In this…
During the eukaryotic cell cycle, chromatin undergoes several conformational changes, which are believed to play key roles in gene expression regulation during interphase, and in genome replication and division during mitosis. In this…
Leveraging over 30,000 images each with up to 89 labels collected by Recology---an integrated resource recovery company with both residential and commercial trash, recycling and composting services---the authors develop ContamiNet, a…
De novo whole genome assembly reconstructs genomic sequence from short, overlapping, and potentially erroneous DNA segments and is one of the most important computations in modern genomics. This work presents HipMER, a high-quality…
In a real-world corpus, knowledge frequently recurs across documents but often contains inconsistencies due to ambiguous naming, outdated information, or errors, leading to complex interrelationships between contexts. Previous research has…
International Classification of Diseases (ICD) are the de facto codes used globally for clinical coding. These codes enable healthcare providers to claim reimbursement and facilitate efficient storage and retrieval of diagnostic…