Related papers: Experimental Biological Protocols with Formal Sema…
The difficulties of automatic extraction of definitions and methods from scientific documents lie in two aspects: (1) the complexity and diversity of natural language texts, which requests an analysis method to support the discovery of…
Interactive proof assistants are computer programs carefully constructed to check a human-designed proof of a mathematical claim with high confidence in the implementation. However, this only validates truth of a formal claim, which may…
Automating experimental protocol design and execution remains as a fundamental bottleneck in realizing self-driving laboratories. We introduce PRISM (Protocol Refinement through Intelligent Simulation Modeling), a framework that automates…
The ability to represent intracellular biochemical dynamics via deterministic and stochastic modelling is one of the crucial components to move biological sciences in the observe-predict-control-design knowledge ladder. Compared to the…
Sampled semantics of timed automata is a finite approximation of their dense time behavior. While the former is closer to the actual software or hardware systems with a fixed granularity of time, the abstract character of the latter makes…
The mathematical formalisms used to model biological systems induce both latent and ambiguous assumptions that can limit or distort their representational capabilities. Developing formalisms that can represent systems more precisely is…
Biochemical reactions involving three or more reactants, called higher-molecular reactions, play an important role in theoretical systems and synthetic biology. In particular, such reactions underpin a variety of important bio-dynamical…
The ever-growing complexity of mathematical proofs makes their manual verification by mathematicians very cognitively demanding. Autoformalization seeks to address this by translating proofs written in natural language into a formal…
A modeling formalism is proposed for the description and study of living and life-like systems. It provides an abstract conceptual model framework for real life and evolution of biological organisms. It is proposed, that this model…
Self-driving laboratories based on large language models promise to transform scientific discovery through general experimental automation. However, realizing this vision on precision platforms remains challenging, requiring deterministic…
Can we objectively distinguish chemical systems that are able to process meaningful information from those that are not suitable for information processing? Here, we present a formal method to assess the semantic capacity of a chemical…
Swarm protocols are a recently introduced formalism for specifying, implementing, and verifying peer-to-peer systems called swarms. A swarm consists of distributed agents called machines that communicate by asynchronous event propagation.…
Human beings possess the most sophisticated computational machinery in the known universe. We can understand language of rich descriptive power, and communicate in the same environment with astonishing clarity. Two of the many contributors…
Program synthesis--the automated generation of executable code from high-level specifications--has been a central goal of computer science for over fifty years. This thesis provides a comparative literature review of the main paradigms that…
Characterizing structural and dynamic properties of proteins and large macromolecular assemblies is crucial to understand the molecular mechanisms underlying biological functions. In the field of Structural Biology, no single method…
Large Language Models perform well at natural language interpretation and reasoning, but their inherent stochasticity limits their adoption in regulated industries like finance and healthcare that operate under strict policies. To address…
Gillespie's direct method for stochastic simulation of chemical kinetics is a staple of computational systems biology research. However, the algorithm requires explicit enumeration of all reactions and all chemical species that may arise in…
Since perception tests are highly time-consuming, there is a need to automate as many operations as possible, such as stimulus generation, procedure control, perception testing, and data analysis. The computer-driven system we are…
As learned control policies become increasingly common in autonomous systems, there is increasing need to ensure that they are interpretable and can be checked by human stakeholders. Formal specifications have been proposed as ways to…
Semantic parsers convert natural language to logical forms, which can be evaluated on knowledge bases (KBs) to produce denotations. Recent semantic parsers have been developed with sequence-to-sequence (seq2seq) pre-trained language models…