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In principle, the generalized master equation can be used to efficiently compute the macroscopic first passage time (FPT) distribution of a complex stochastic system from short-term microscopic simulation data. However, computing its…
Biological structure and function depend on complex regulatory interactions between many genes. A wealth of gene expression data is available from high-throughput genome-wide measurement technologies, but effective gene regulatory network…
Software Testing is a process to identify the quality and reliability of software, which can be achieved through the help of proper test data. However, doing this manually is a difficult task due to the presence of number of predicate nodes…
Multi-goal path finding (MGPF) aims to find a closed and collision-free path to visit a sequence of goals orderly. As a physical travelling salesman problem, an undirected complete graph with accurate weights is crucial for determining the…
We consider a model of mRNA production governed by the dynamics of a gene that exists in three possible states -- inactive, poised and active. The transitions between the adjacent states are controlled by stochastic processes characterized…
We consider the problem of approximating the moment generating function (MGF) of a truncated random variable in terms of the MGF of the underlying (i.e., untruncated) random variable. The purpose of approximating the MGF is to enable the…
Accurate identification of protein-nucleotide binding sites is fundamental to deciphering molecular mechanisms and accelerating drug discovery. However, current computational methods often struggle with suboptimal performance due to…
In this paper, we combine ideas from two different scientific traditions: 1) graph transformation systems (GTSs) stemming from the theory of formal languages and concurrency, and 2) mean field approximations (MFAs), a collection of…
Magnetic resonance fingerprinting (MRF) can successfully recover quantitative multi-parametric maps of human tissue in a very short acquisition time. Due to their pseudo-random nature, the large spatial undersampling artifacts can be…
Many fundamental cellular processes involve small numbers of molecules. When numbers are small, fluctuations dominate, and stochastic models, which account for these fluctuations, are required. In this chapter, we describe minimal…
The inference of gene regulatory networks (GRNs) is a foundational stride towards deciphering the fundamentals of complex biological systems. Inferring a possible regulatory link between two genes can be formulated as a link prediction…
Simulating the mechanical response of advanced materials can be done more accurately using concurrent multiscale models than with single-scale simulations. However, the computational costs stand in the way of the practical application of…
Generating graph-structured data requires learning the underlying distribution of graphs. Yet, this is a challenging problem, and the previous graph generative methods either fail to capture the permutation-invariance property of graphs or…
We propose a new score-based model with one-step sampling. Previously, score-based models were burdened with heavy computations due to iterative sampling. For substituting the iterative process, we train a standalone generator to compress…
Gene expression in individual cells is highly variable and sporadic, often resulting in the synthesis of mRNAs and proteins in bursts. Bursting in gene expression is known to impact cell-fate in diverse systems ranging from latency in HIV-1…
Quantitative modeling of post-transcriptional regulation process is a challenging problem in systems biology. A mechanical model of the regulatory process needs to be able to describe the available spatio-temporal protein concentration and…
Graph Generation is a recently introduced enhanced Column Generation algorithm for solving expanded Linear Programming relaxations of mixed integer linear programs without weakening the expanded relaxations which characterize these methods.…
Proteins are polymerized by cyclic machines called ribosome which use their messenger RNA (mRNA) track also as the corresponding template and the process is called translation. We explore, in depth and detail, the stochastic nature of the…
The dynamics of short-lived mRNA results in bursts of protein production in gene regulatory networks. We investigate the propagation of bursting noise between different levels of mathematical modelling, and demonstrate that conventional…
Semi-autogenous grinding (SAG) mills play a pivotal role in the grinding circuit of mineral processing plants. Accurate prediction of SAG mill throughput as a crucial performance metric is of utmost importance. The potential of applying…