Related papers: Reverse-Robust Computation with Chemical Reaction …
Chemical reaction networks (CRNs) exhibit complex dynamics governed by their underlying network structure. In this paper, we propose a novel approach to study the dynamics of CRNs by representing them on species graphs (S-graphs). By…
A fundamental property of DNA is that the reverse complement (RC) of a sequence often carries identical biological meaning. However, state-of-the-art DNA language models frequently fail to capture this symmetry, producing inconsistent…
Convolutional neural networks (CNNs) are widely used for image recognition and text analysis, and have been suggested for application on one-dimensional data as a way to reduce the need for pre-processing steps. Pre-processing is an…
A family of results, referred to as inheritance results, tell us which enlargements of a chemical reaction network (CRN) preserve its capacity for nontrivial behaviours such as multistationarity and oscillation. In this paper, the following…
We investigate the dynamics of chemical reaction networks (CRNs) with the goal of deriving an upper bound on their reaction rates. This task is challenging due to the nonlinear nature and discrete structure inherent in CRNs. To address…
In a reversible language, any forward computation can be undone by a finite sequence of backward steps. Reversible computing has been studied in the context of different programming languages and formalisms, where it has been used for…
Substring kernels are classical tools for representing biological sequences or text. However, when large amounts of annotated data are available, models that allow end-to-end training such as neural networks are often preferred. Links…
Both natural and synthetic chemical systems not only exhibit a range of non-trivial dynamics, but also transition between qualitatively different dynamical behaviours as environmental parameters change. Such transitions are called…
Reversibility, weak reversibility and deficiency, detailed and complex balancing are generally not "encoded" in the kinetic differential equations but they are realization properties that may imply local or even global asymptotic stability…
We present a uniform method for translating an arbitrary nondeterministic finite automaton (NFA) into a deterministic mass action input/output chemical reaction network (I/O CRN) that simulates it. The I/O CRN receives its input as a…
We prove that if a given reaction network $\mathcal{N}$ has a weakly reversible deficiency zero realization for all choice of rate constants, then there exists a $\textit{unique}$ weakly reversible deficiency zero network $\mathcal{N}'$…
Molecular computation in chemical reaction networks (CRNs) now constitutes a foundational framework for designing programmable biological systems. However, prevailing design methodologies primarily treat parallelism of chemical reactions as…
Neural networks have in recent years shown promise for helping software engineers write programs and even formally verify them. While semantic information plays a crucial part in these processes, it remains unclear to what degree popular…
We show that standard ResNet architectures can be made invertible, allowing the same model to be used for classification, density estimation, and generation. Typically, enforcing invertibility requires partitioning dimensions or restricting…
Convolutional Neural Networks (CNN) have recently seen tremendous success in various computer vision tasks. However, their application to problems with high dimensional input and output, such as high-resolution image and video segmentation…
Recurrent neural networks are a powerful tool for modeling sequential data, but the dependence of each timestep's computation on the previous timestep's output limits parallelism and makes RNNs unwieldy for very long sequences. We introduce…
We present recurrent transformer networks (RTNs) for obtaining dense correspondences between semantically similar images. Our networks accomplish this through an iterative process of estimating spatial transformations between the input…
Molecule representation learning (MRL) methods aim to embed molecules into a real vector space. However, existing SMILES-based (Simplified Molecular-Input Line-Entry System) or GNN-based (Graph Neural Networks) MRL methods either take…
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…
In this paper, it is presented a methodology for implementing arbitrarily constructed time-homogenous Markov chains with biochemical systems. Not only discrete but also continuous-time Markov chains are allowed to be computed. By employing…