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The alignment of protein-protein interaction (PPI) networks has many applications, such as the detection of conserved biological network motifs, the prediction of protein interactions, and the reconstruction of phylogenetic trees [1, 2, 3].…
Background: In the Nearest-Neighbor Thermodynamic Model, a standard approach for RNA secondary structure prediction, the energy of the multiloops is modeled using a linear entropic penalty governed by three branching parameters. Although…
MicroRNAs (miRNAs) are small RNA molecules composed of 19-22 nt, which play important regulatory roles in post-transcriptional gene regulation by inhibiting the translation of the mRNA into proteins or otherwise cleaving the target mRNA.…
Approximate nearest neighbor search is fundamental in information retrieval. Previous partition-based methods enhance search efficiency by probing partial partitions, yet they face two common issues. In the query phase, a common strategy is…
Spatially Fractionated Radiation Therapy (SFRT) produces highly heterogeneous dose distributions, for which conventional metrics such as peak, valley, or average dose can yield ambiguous or inconsistent estimates of therapeutic window…
Existing RNN-based approaches for action recognition from depth sequences require either skeleton joints or hand-crafted depth features as inputs. An end-to-end manner, mapping from raw depth maps to action classes, is non-trivial to design…
Real-world tabular databases routinely combine continuous measurements and categorical records, yet missing entries are pervasive and can distort downstream analysis. We propose Statistical-Neural Interaction (SNI), an interpretable…
PPI network alignment aims to find topological and functional similarities between networks of different species. Several alignment approaches have been proposed. Each of these approaches relies on a different alignment method and uses…
Functional protein-protein interactions are crucial in most cellular processes. They enable multi-protein complexes to assemble and to remain stable, and they allow signal transduction in various pathways. Functional interactions between…
HiRE-RNA is a simplified, coarse-grained RNA model for the prediction of equilibrium configurations, dynamics and thermodynamics. Using a reduced set of particles and detailed interactions accounting for base-pairing and stacking we show…
Identifying protein-protein interactions (PPI) is crucial for gaining in-depth insights into numerous biological processes within cells and holds significant guiding value in areas such as drug development and disease treatment. Currently,…
The relationship between RNA structure and function has recently attracted interest within the deep learning community, a trend expected to intensify as nucleic acid structure models advance. Despite this momentum, the lack of standardized,…
MicroRNA (miRNA) are small non-coding RNAs that regulates the gene expression at the post-transcriptional level. Determining whether a sequence segment is miRNA is experimentally challenging. Also, experimental results are sensitive to the…
In post-transcriptional regulation, an mRNA molecule is bound by many proteins and/or miRNAs to modulate its function. To enable combinatorial gene regulation, these binding partners of an RNA must communicate with each other, exhibiting…
Small interfering RNA (siRNA) is a short double-stranded RNA molecule (about 21-23 nucleotides) with the potential to cure diseases by silencing the function of target genes. Due to its well-understood mechanism, many siRNA-based drugs have…
Because protein-protein interactions (PPIs) are crucial to understand living systems, harvesting these data is essential to probe disease development and discern gene/protein functions and biological processes. Some curated datasets contain…
Since microRNAs (miRNAs) play a crucial role in post-transcriptional gene regulation, miRNA identification is one of the most essential problems in computational biology. miRNAs are usually short in length ranging between 20 and 23 base…
The intricate network of interactions observed in RNA three-dimensional structures is often described in terms of a multitude of geometrical properties, including helical parameters, base pairing/stacking, hydrogen bonding and backbone…
While numerous studies have been conducted in the literature exploring different types of machine learning approaches for search ranking, most of them are focused on specific pre-defined problems but only a few of them have studied the…
Interaction between proteins is a fundamental mechanism that underlies virtually all biological processes. Many important interactions are conserved across a large variety of species. The need to maintain interaction leads to a high degree…