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Deep neural network (DNN) models have recently obtained state-of-the-art prediction accuracy for the transcription factor binding (TFBS) site classification task. However, it remains unclear how these approaches identify meaningful DNA…
Oscillation has an important role in bio-dynamical systems such as circadian rhythms and eukaryotic cell cycle. John Tyson et. al. in Nature Review Mol Cell Biol 2008 examined a limited number of network topologies consisting of three nodes…
Mathematical models of stem cell differentiation are commonly based upon the concept of subsequent cell fate decisions, each controlled by a gene regulatory network. These networks exhibit a multistable behavior and cause the system to…
Morphogenesis is central to biology but remains largely unexplored in chemistry. Reaction-diffusion (RD) mechanisms are, however, essential to understand how shape emerges in the living world. While numerical methods confirm the incredible…
Networks are a fundamental tool for modeling complex systems in a variety of domains including social and communication networks as well as biology and neuroscience. Small subgraph patterns in networks, called network motifs, are crucial to…
Feed-forward layers constitute two-thirds of a transformer model's parameters, yet their role in the network remains under-explored. We show that feed-forward layers in transformer-based language models operate as key-value memories, where…
This paper uses a recently presented abstract, tuneable Boolean regulatory network model extended to consider aspects of mobile DNA, such as transposons. The significant role of mobile DNA in the evolution of natural systems is becoming…
Several important biological processes are initiated by the binding of a protein to a specific site on the DNA. The strategy adopted by a protein, called transcription factor (TF), for searching its specific binding site on the DNA has been…
Much of the complexity observed in gene regulation originates from cooperative protein-DNA binding. While studies of the target search of proteins for their specific binding sites on the DNA have revealed design principles for the…
We develop a theoretical framework on the mechanism of combinatorial binding of transcription factors (TFs) with their specific binding sites on DNA. We consider three possible mechanisms viz. monomer, hetero-oligomer and coordinated…
We investigate the win-lose relations between strategies of iterated prisoner's dilemma games by using a directed network concept to display the replicator dynamics results. In the giant strongly-connected component of the win/lose network,…
Over the past few years, microRNAs (miRNAs) have emerged as a new prominent class of gene regulatory factors that negatively regulate expression of approximately one-third of the genes in animal genomes at post-transcriptional level.…
Network science can offer fundamental insights into the structural and functional properties of complex systems. For example, it is widely known that neuronal circuits tend to organize into basic functional topological modules, called…
Trigger waves are self-regenerating propagating fronts that emerge from the coupling of nonlinear reaction kinetics and diffusion. In cells, trigger waves coordinate large-scale processes such as mitotic entry and stress responses. Although…
The articulation process of dynamical networks is studied with a functional map, a minimal model for the dynamic change of relationships through iteration. The model is a dynamical system of a function $f$, not of variables, having a…
Recent advances in artificial neural networks for machine learning, and language modeling in particular, have established a family of recurrent neural network (RNN) architectures that, unlike conventional RNNs with vector-form hidden…
Fibrous networks are ideal functional materials since they provide mechanical rigidity at low weight. Such structures are omnipresent in natural biomaterials from cells to tissues, as well as in man-made materials from polymeric composites…
Complex biological functions are carried out by the interaction of genes and proteins. Uncovering the gene regulation network behind a function is one of the central themes in biology. Typically, it involves extensive experiments of…
A fundamental task in developmental biology is to identify the mechanisms which drive morphogenesis. In many cases, pattern formation is driven by the positional information determined by both the gradient of maternal factors and hard-wired…
We show that gating mechanisms in recurrent neural networks (RNNs) induce lag-dependent and direction-dependent effective learning rates, even when training uses a fixed, global step size. This behavior arises from a coupling between…