Related papers: Experimental Biological Protocols with Formal Sema…
Quantum protocols such as the BB84 Quantum Key Distribution protocol exchange qubits to achieve information-theoretic security guarantees. Many variants thereof were proposed, some of them being already deployed. Existing security proofs in…
An introductory formal languages course exposes advanced undergraduate and early graduate students to automata theory, grammars, constructive proofs, computability, and decidability. Programming students find these topics to be challenging…
Modeling biological processes is a highly demanding task because not all processes are fully understood. Mathematical models allow us to test hypotheses about possible mechanisms of biological processes. The mathematical mechanisms…
We present a simple and concise semantics for temporal planning. Our semantics are developed and formalised in the logic of the interactive theorem prover Isabelle/HOL. We derive from those semantics a validation algorithm for temporal…
The use of semantic technologies is gaining significant traction in science communication with a wide array of applications in disciplines including the Life Sciences, Computer Science, and the Social Sciences. Languages like RDF, OWL, and…
A vast array of transformative technologies developed over the past decade has enabled measurement and perturbation at ever increasing scale, yet our understanding of many systems remains limited by experimental capacity. Overcoming this…
Natural language semantics has recently sought to combine the complementary strengths of formal and distributional approaches to meaning. More specifically, proposals have been put forward to augment formal semantic machinery with…
Formal verification provides strong guarantees of correctness of software, which are especially important in safety or security critical systems. Hoare logic is a widely used formalism for rigorous verification of software against…
In order to reason about the behaviour of programs described in a programming language, a mathematically rigorous definition of that language is needed. In this paper, we present a machine-checked formalisation of concurrent Core Erlang (a…
The discovery and design of functional molecules remain central challenges across chemistry,biology, and materials science. While recent advances in machine learning have accelerated molecular property prediction and candidate generation,…
Numerical computations have become a pillar of all modern quantitative sciences. Any computation involves modeling--even if often this step is not made explicit--and any model has to neglect details while still being physically accurate.…
In many chemical and biological applications, systems of differential equations containing unknown parameters are used to explain empirical observations and experimental data. The DEs are typically nonlinear and difficult to analyze,…
Formal methods apply algorithms based on mathematical principles to enhance the reliability of systems. It would only be natural to try to progress from verification, model checking or testing a system against its formal specification into…
Synthetic biology is an interdisciplinary field aiming to design biochemical systems with desired behaviors. To this end, molecular controllers have been developed which, when embedded into a pre-existing ambient biochemical network,…
We axiomatize the molecular-biology reasoning style, show compliance of the standard reference: Ptashne, A Genetic Switch, and present proof-theory-induced technologies to help infer phenotypes and to predict life cycles from genotypes. The…
Ordinary differential equation models have become a standard tool for the mechanistic description of biochemical processes. If parameters are inferred from experimental data, such mechanistic models can provide accurate predictions about…
The modelling and analysis of biological systems has deep roots in Mathematics, specifically in the field of ordinary differential equations (ODEs). Alternative approaches based on formal calculi, often derived from process algebras or term…
Rule-based reasoning over natural language input arises in domains where decisions must be auditable and justifiable: clinical protocols specify eligibility criteria in prose, evidence rules define admissibility through textual conditions,…
Semantic parsing is a means of taking natural language and putting it in a form that a computer can understand. There has been a multitude of approaches that take natural language utterances and form them into lambda calculus expressions --…
Experiments require human decisions in the design process, which in turn are reformulated and summarized as inputs into a system (computational or otherwise) to generate the experimental design. I leverage this system to promote a language…