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Understanding the higher-order interactions within network data is a key objective of network science. Surveys of metadata triangles (or patterned 3-cycles in metadata-enriched graphs) are often of interest in this pursuit. In this work, we…
Background:Typically, proteins perform key biological functions by interacting with each other. As a consequence, predicting which protein pairs interact is a fundamental problem. Experimental methods are slow, expensive, and may be error…
We develop a robust coarse-grained model for single and double stranded DNA by representing each nucleotide by three interaction sites (TIS) located at the centers of mass of sugar, phosphate, and base. The resulting TIS model includes…
Evaluating cellular systems, from 5G New Radio (NR) and 5G-Advanced to 6G, is challenging because the performance emerges from the tight coupling of propagation, beam management, scheduling, and higher-layer interactions. System-level…
Protein-DNA interactions are crucial for all biological processes. One of the most important fundamental aspects of these interactions is the process of protein searching and recognizing specific binding sites on DNA. A large number of…
Single-cell RNA sequencing (scRNA-seq) technology enables systematic delineation of cellular states and interactions, providing crucial insights into cellular heterogeneity. Building on this potential, numerous computational methods have…
We have extended the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) to support directional bonds and dynamic bonding. The framework supports stochastic formation of new bonds, breakage of existing bonds, and conversion…
Non-coding RNA sequences play a great role in controlling a number of cellular functions, thus raising the need to understand their complex conformational dynamics in quantitative detail. In this perspective, we first show that single…
Estimating the 3D structure of the drivable surface and surrounding environment is a crucial task for assisted and autonomous driving. It is commonly solved either by using 3D sensors such as LiDAR or directly predicting the depth of points…
Deciphering complex gene-gene interactions remains challenging in transcriptomics as traditional methods often miss higher-order and nonlinear dependencies. This study introduces a quantum-inspired framework leveraging tensor networks (TNs)…
In recent years, DL has developed rapidly, and personalized services are exploring using DL algorithms to improve the performance of the recommendation system. For personalized services, a successful recommendation consists of two parts:…
We present BioLangFusion, a simple approach for integrating pre-trained DNA, mRNA, and protein language models into unified molecular representations. Motivated by the central dogma of molecular biology (information flow from gene to…
Recognition and binding of specific sites on DNA by proteins is central for many cellular functions such as transcription, replication, and recombination. In the process of recognition, a protein rapidly searches for its specific site on a…
In this paper, we study network representation learning for tripartite heterogeneous networks which learns node representation features for networks with three types of node entities. We argue that tripartite networks are common in real…
Synthesis and efficient implementation mRNA strands has been shown to have wide utility, especially recently in the development of COVID vaccines. However, the intrinsic chemical stability of mRNA poses a challenge due to the presence of…
The perception system for autonomous driving generally requires to handle multiple diverse sub-tasks. However, current algorithms typically tackle individual sub-tasks separately, which leads to low efficiency when aiming at obtaining…
Single-stranded libraries generated from ancient DNA extracts have specific sequencing requirements. The short library molecules typically associated with ancient DNA templates are expected to behave differently during the annealing to the…
Three-Dimensional (3D) chromatin interactions, such as enhancer-promoter interactions (EPIs), loops, Topologically Associating Domains (TADs), and A/B compartments play critical roles in a wide range of cellular processes by regulating gene…
Entity matching is a fundamental task in data cleaning and data integration. With the rapid adoption of large language models (LLMs), recent studies have explored zero-shot and few-shot prompting to improve entity matching accuracy.…
RNAnet provides a bridge between two widely used Human gene databases. Ensembl describes DNA sequences and transcripts but not experimental gene expression. Whilst NCBI's GEO contains actual expression levels from Human samples. RNAnet…