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The computation of electrical flows is a crucial primitive for many recently proposed optimization algorithms on weighted networks. While typically implemented as a centralized subroutine, the ability to perform this task in a fully…

The nonlinearities found in molecular networks usually prevent mathematical analysis of network behaviour, which has largely been studied by numerical simulation. This can lead to difficult problems of parameter determination. However,…

Cataloging the complex behaviors of dynamical systems can be challenging, even when they are well-described by a simple mechanistic model. If such a system is of limited analytical tractability, brute force simulation is often the only…

The construction of a reaction network containing all relevant intermediates and elementary reactions is necessary for the accurate description of chemical processes. In the case of a complex chemical reaction (involving, for instance, many…

We show that deep learning models, and especially architectures like the Transformer, originally intended for natural language, can be trained on randomly generated datasets to predict to very high accuracy both the qualitative and…

Foundation models have shown great promise in various fields of study. A potential application of such models is in computer network traffic analysis, where these models can grasp the complexities of network traffic dynamics and adapt to…

In power system dynamic simulation, up to 90% of the computational time is devoted to solve the network equations, i.e., a set of linear equations. Traditional approaches are based on sparse LU factorization, which is inherently sequential.…

We investigate conditional adversarial networks as a general-purpose solution to image-to-image translation problems. These networks not only learn the mapping from input image to output image, but also learn a loss function to train this…

Massively Multilingual Transformer based Language Models have been observed to be surprisingly effective on zero-shot transfer across languages, though the performance varies from language to language depending on the pivot language(s) used…

Mathematical and computational modelling of biochemical networks is often done in terms of either the concentrations of molecular species or the fluxes of biochemical reactions. When is mathematical modelling from either perspective…

In this paper, we propose a new method to identify biochemical reaction networks (i.e. both reactions and kinetic parameters) from heterogeneous datasets. Such datasets can contain (a) data from several replicates of an experiment performed…

Using random walk sampling methods for feature learning on networks, we develop a method for generating low-dimensional node embeddings for directed graphs and identifying transition states of stochastic chemical reacting systems. We…

Electric circuits manipulate electric charge and magnetic flux via a small set of discrete components to implement useful functionality over continuous time-varying signals represented by currents and voltages. Much of the same…

We present a methodology that explores how sentence structure is reflected in neural representations of machine translation systems. We demonstrate our model-agnostic approach with the Transformer English-German translation model. We…

With the tremendous increase in the amount of biological literature, developing automated methods for extracting big data from papers, building models and explaining big mechanisms becomes a necessity. We describe here our approach to…

We consider the problem of learning data-driven replicas for stiff systems of ordinary differential equations arising in chemical kinetics that can be evaluated with high computational efficiency. We first focus on training emulators for…

We describe a fully data driven model that learns to perform a retrosynthetic reaction prediction task, which is treated as a sequence-to-sequence mapping problem. The end-to-end trained model has an encoder-decoder architecture that…

Zero-one biochemical reaction networks play key roles in cell signalling such as signalling pathways regulated by protein phosphorylation. Multistability of reaction networks is a crucial dynamics feature enabling decision-making in cells.…

Stochasticity is a key characteristic of intracellular processes such as gene regulation and chemical signalling. Therefore, characterising stochastic effects in biochemical systems is essential to understand the complex dynamics of living…

Chemical reaction network theory is a field of applied mathematics concerned with modeling chemical systems, and can be used in other contexts such as in systems biology to study cellular signaling pathways or epidemiology to study the…