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The Abstract Syntax Description Language (ASDL) is a language for specifying the tree data structures often found in compiler intermediate representations. The ASDL generator reads an ASDL specification and generates code to construct,…

Most available tools propose simulation frameworks to study models of biological systems, but simulation only explores a few of the most probable behaviours of the system. On the contrary, techniques such as model checking, coming from…

In Compiler Design courses, students learn how a program written in high level programming language and designed for humans understanding is systematically converted into low level assembly language understood by machines, through different…

Generating accurate circuit schematics from high-level natural language descriptions remains a persistent challenge in electronic design automation (EDA), as large language models (LLMs) frequently hallucinate components, violate strict…

High-fidelity circuit execution on noisy intermediate-scale quantum devices is bottlenecked by compilation pipelines that disregard complex, correlated noise. To address this, this methodology article proposes a quantum machine learning…

We present a self-certifying compiler for the COGENT systems language. COGENT is a restricted, polymorphic, higher-order, and purely functional language with linear types and without the need for a trusted runtime or garbage collector. It…

Genetic circuit design is a well-studied problem in synthetic biology. Ever since the first genetic circuits -- the repressilator and the toggle switch -- were designed and implemented, many advances have been made in this area of research.…

We introduce GENomic Encoding REpresentation with Language Model (GENEREL), a framework designed to bridge genetic and biomedical knowledge bases. What sets GENEREL apart is its ability to fine-tune language models to infuse biological…

Splicing systems are generative mechanisms introduced by Tom Head in 1987 to model the biological process of DNA recombination. The computational engine of a splicing system is the "splicing operation", a cut-and-paste binary string…

We report on a one-semester compiler construction course based on the idea of implementing a small self-contained compiler for a small model language from scratch, not using other compiler construction frameworks. The course is built around…

The generation of high-fidelity synthetic data is a cornerstone of modern machine learning, yet Large Language Models (LLMs) frequently suffer from hallucinations, logical inconsistencies, and mode collapse when tasked with structured…

Game Description Language (GDL) provides a standardized way to express diverse games in a machine-readable format, enabling automated game simulation, and evaluation. While previous research has explored game description generation using…

Programmable Logic Controllers (PLC) and its programming standard IEC 61131-3 are widely used in embedded systems for the industrial automation domain. We propose a framework for the formal treatment of PLC based on the IEC 61131-3…

Self-driving labs (SDLs) combine fully automated experiments with artificial intelligence (AI) that decides the next set of experiments. Taken to their ultimate expression, SDLs could usher a new paradigm of scientific research, where the…

Logic synthesis is a crucial phase in the circuit design process, responsible for transforming hardware description language (HDL) designs into optimized netlists. However, traditional logic synthesis methods are computationally intensive,…

We describe software and a language for quasibiological computations. Its theoretical basis is a unified theory of complex (adaptive) systems where all laws are regularities of relations between things or agents, and dynamics is made from…

Geometric Semantic Genetic Programming (GSGP) is a state-of-the-art machine learning method based on evolutionary computation. GSGP performs search operations directly at the level of program semantics, which can be done more efficiently…

Many texts, especially in chemistry and biology, describe complex processes. We focus on texts that describe a chemical reaction process and questions that ask about the process's outcome under different environmental conditions. To answer…

Electronic circuits are useful tools for studying potential dynamical behaviors of synthetic genetic networks. The circuit models are complementary to numerical simulations of the networks, especially providing a framework for verification…

Synthetic Biology is an interdisciplinary field that utilizes well-established engineering principles, ranging from electrical, control and computer systems, for analyzing the biological systems, such as biological circuits, enzymes,…