Related papers: Formal Analysis of the Biological Circuits using H…
To better understand the structure and function of complex systems, researchers often represent direct interactions between components in complex systems with networks, assuming that indirect influence between distant components can be…
Cooperation enables teams to solve complex problems that one individual alone cannot address. In science, collaborative teams have become the predominant way through which progress is achieved. These scientific collaborations arise though…
Mathematical methods provide useful framework for the analysis and design of complex systems. In newer contexts such as biology, however, there is a need to both adapt existing methods as well as to develop new ones. Using a combination of…
The ability to learn and respond to recurrent events depends on the capacity to remember transient biological signals received in the past. Moreover, it may be desirable to remember or ignore these transient signals conditioned upon other…
Computation models such as circuits describe sequences of computation steps that are carried out one after the other. In other words, algorithm design is traditionally subject to the restriction imposed by a fixed causal order. We address a…
Quantum computing will change the way we tackle certain problems. It promises to dramatically speed-up many chemical, financial, and machine-learning applications. However, to capitalize on those promises, complex design flows composed of…
We present an approach for representing abstract argumentation frameworks based on an encoding into classical higher-order logic. This provides a uniform framework for computer-assisted assessment of abstract argumentation frameworks using…
A general theoretical framework is put forth to organize and understand various observed phenomena and mathematical relationships in the field of molecular biology. By modeling each cell in eukaryotic organisms as a processor having a…
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…
Large computer-understandable proofs consist of millions of intermediate logical steps. The vast majority of such steps originate from manually selected and manually guided heuristics applied to intermediate goals. So far, machine learning…
Increasingly used high throughput experimental techniques, like DNA or protein microarrays give as a result groups of interesting, e.g. differentially regulated genes which require further biological interpretation. With the systematic…
Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…
Biological systems are often modeled as a system of ordinary differential equations (ODEs) with time-invariant parameters. However, cell signaling events or pharmacological interventions may alter the cellular state and induce multi-mode…
The functionality of catalysts, enzymes, and supramolecular assemblies emerges not from individual molecules alone, but from the subtle interplay between multiple components arranged in complex systems. Designing such systems is a grand…
Molecular circuits capable of autonomous learning could unlock novel applications in fields such as bioengineering and synthetic biology. To this end, existing chemical implementations of neural computing have mainly relied on emulating…
We present an approach of using AI to model and simulate biology and life. Why is it important? Because at the core of medicine, pharmacy, public health, longevity, agriculture and food security, environmental protection, and clean energy,…
Logical frameworks provide natural and direct ways of specifying and reasoning within deductive systems. The logical framework LF and subsequent developments focus on finitary proof systems, making the formalization of circular proof…
Reactive synthesis, the problem of automatically constructing a hardware circuit from a logical specification, is a long-standing challenge in formal verification. It is elusive for two reasons: It is algorithmically hard, and writing…
Understanding how biochemical systems settle into stable states, such as how protein concentrations reach equilibrium, is central to explaining cellular behavior and designing synthetic biological circuits. However, existing analytical…
Models of transcriptional regulation that assume equilibrium binding of transcription factors have been very successful at predicting gene expression from sequence in bacteria. However, analogous equilibrium models do not perform as well in…