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Synthetic genetic circuits are implemented in living cells for their operation. During gene expression, proteins are produced from the respective genes, by formation of complexes through the process of transcription and translation. In…
The functioning of a living cell is largely determined by the structure of its regulatory network, comprising non-linear interactions between regulatory genes. An important factor for the stability and evolvability of such regulatory…
Generative Flow Networks (GFlowNets or GFNs) are probabilistic models predicated on Markov flows, and they employ specific amortization algorithms to learn stochastic policies that generate compositional substances including biomolecules,…
Motifs are the fundamental components of complex systems. The topological structure of networks representing complex systems and the frequency and distribution of motifs in these networks are intertwined. The complexities associated with…
At the heart of neural network force fields (NNFFs) is the architecture of neural networks, where the capacity to model complex interactions is typically enhanced through widening or deepening multilayer perceptrons (MLPs) or by increasing…
We study a class of growth algorithms for directed graphs that are candidate models for the evolution of genetic regulatory networks. The algorithms involve partial duplication of nodes and their links, together with innovation of new…
The identification of transcription factor binding sites (TFBSs) on genomic DNA is of crucial importance for understanding and predicting regulatory elements in gene networks. TFBS motifs are commonly described by Position Weight Matrices…
The genomic reality is a highly complex and dynamic system. The recent development of high-throughput technologies has enabled researchers to measure the abundance of many genes (in the order of thousands) simultaneously. The challenge is…
Inferring functional relationships within complex networks from static snapshots of a subset of variables is a ubiquitous problem in science. For example, a key challenge of systems biology is to translate cellular heterogeneity data…
We show the formal equivalence of linearised self-attention mechanisms and fast weight controllers from the early '90s, where a ``slow" neural net learns by gradient descent to program the ``fast weights" of another net through sequences of…
Behavioral changes in animals and humans, as a consequence of an error or a verbal instruction, can be extremely rapid. Improvement in behavioral performances are usually associated in machine learning and reinforcement learning to synaptic…
Gene regulatory networks, i.e. DNA segments in a cell which interact with each other indirectly through their RNA and protein products, lie at the heart of many important intracellular signal transduction processes. In this paper we analyse…
Network motifs are the building blocks of complex networks and are significantly involved in the network dynamics such as information processing and local operations in the brain, biological marks for drug targets, identifying and…
Gene regulatory networks (GRNs) represent the causal relationships between transcription factors (TFs) and target genes in single-cell RNA sequencing (scRNA-seq) data. Understanding these networks is crucial for uncovering disease…
Gene regulatory networks typically have low in-degrees, whereby any given gene is regulated by few of the genes in the network. What mechanisms might be responsible for these low in-degrees? Starting with an accepted framework of the…
Boolean threshold networks have recently been proposed as useful tools to model the dynamics of genetic regulatory networks, and have been successfully applied to describe the cell cycles of \textit{S. cerevisiae} and \textit{S. pombe}.…
A proof is presented that gene regulatory networks (GRNs) based solely on transcription factors cannot control the development of complex multicellular life. GRNs alone cannot explain the evolution of multicellular life in the Cambrian…
When studying a complex system it is often useful to think of the system as a network of interacting units. One can then ask if some properties of the entire network are already explained by a small part of the network - a network motif. A…
Numerous transcription factors self-assemble into different order oligomeric species in a way that is actively regulated by the cell. Until now, no general functional role has been identified for this widespread process. Here we capture the…
Transformers are ubiquitous in wide tasks. Interpreting their internals is a pivotal goal. Nevertheless, their particular components, feed-forward (FF) blocks, have typically been less analyzed despite their substantial parameter amounts.…