Related papers: DNA-based chemical compiler
We give the easily recognizable name "cinnamon" and "cinnamon programming" to a new computation model intended to form a theoretical foundation for Control Network Programming (CNP). CNP has established itself as a programming paradigm…
Industrial cyber-physical systems generate vast amounts of semi-structured time-series data that require careful preprocessing before they can be effectively used for machine learning applications such as fault detection and identification.…
DNA constructs and their annotated sequence maps have been rapidly accumulating with the advancement of DNA cloning, synthesis, and assembly methods. Such a resource has the potential to be optimally utilized in an autonomous DNA building…
The computer programs most users interact with daily are driven by a graphical user interface (GUI). However, many scientific applications are used with a command line interface (CLI) for the ease of development and increased flexibility…
This paper envisions an end-to-end program generation scenario using recurrent neural networks (RNNs): Users can express their intention in natural language; an RNN then automatically generates corresponding code in a…
The ability to reason beyond established knowledge allows Organic Chemists to solve synthetic problems and to invent novel transformations. Here, we propose a model which mimics chemical reasoning and formalises reaction prediction as…
PLUMED-GUI is an interactive environment to develop and test complex PLUMED scripts within the Visual Molecular Dynamics (VMD) environment. Computational biophysicists can take advantage of both PLUMED's rich syntax to define collective…
In this paper, we introduce chemical functions, a unified framework that models chemical systems as noisy challenge--response primitives, and formalize the associated chemical function infrastructure. Building on the theory of physical…
Chemputation is the process of programming chemical robots to do experiments using a universal symbolic language, but the literature can be error prone and hard to read due to ambiguities. Large Language Models (LLMs) have demonstrated…
Specialized computational chemistry packages have permanently reshaped the landscape of chemical and materials science by providing tools to support and guide experimental efforts and for the prediction of atomistic and electronic…
We study the composability of discrete chemical reaction networks (CRNs) that stably compute (i.e., with probability 0 of error) integer-valued functions $f:\mathbb{N}^d\to\mathbb{N}$. We consider output-oblivious CRNs in which the output…
Self assembly is a process by which supramolecular species form spontaneously from their components. This process is ubiquitous throughout the life chemistry and is central to biological information processing. It has been predicted that in…
"Code Generation for Generally Mapped Finite Elements" includes performance results for the finite element methods discussed in that manuscript. The authors provided a Zenodo archive with the Firedrake components and dependencies used, as…
Printing custom DNA sequences is essential to scientific and biomedical research, but the technology can be used to manufacture plagues as well as cures. Just as ink printers recognize and reject attempts to counterfeit money, DNA…
Reverse engineering of binary executables is a critical problem in the computer security domain. On the one hand, malicious parties may recover interpretable source codes from the software products to gain commercial advantages. On the…
We demonstrate that a small transformer can learn to execute programs in MicroPy, a simplified yet computationally universal programming language. Given procedure definitions together with an expression to evaluate, the transformer predicts…
This paper presents SimulatorCoder, an agent powered by large language models (LLMs), designed to generate and optimize deep neural network (DNN) accelerator simulators based on natural language descriptions. By integrating domain-specific…
The exploration of novel chemical spaces is one of the most important tasks of cheminformatics when supporting the drug discovery process. Properly designed and trained deep neural networks can provide a viable alternative to brute-force de…
Self-assembly is a phenomenon observed in nature at all scales where autonomous entities build complex structures, without external influences nor centralised master plan. Modelling such entities and programming correct interactions among…
Any file is fundamentally a binary data stream. A practical solution was achieved to interpret binary data stream. A new scripting language named Data Format Scripting Language (DFSL) was developed to describe the physical layout of the…