Related papers: Some Remarks on Input Choices for Biochemical Syst…

Systems biology models are useful models of complex biological systems that may require a large amount of experimental data to fit each model's parameters or to approximate a likelihood function. These models range from a few to thousands…

Examining individual components of cellular systems has been successful in uncovering molecular reactions and interactions. However, the challenge lies in integrating these components into a comprehensive system-scale map. This difficulty…

We consider the basic features of complex dynamic and control systems, including systems having hierarchical structure. Special attention is paid to the problems of design and synthesis of complex systems and control models, and to the…

Excellent computer simulations are done for a purpose. The most valid purposes are to explore uncharted territory, to resolve a well-posed scientific or technical question, or to make a design choice. Stand-alone modeling can serve the…

This paper is devoted to the extraction of entities and semantic relations between them from scientific texts, where we consider scientific terms as entities. In this paper, we present a dataset that includes annotations for two tasks and…

This paper introduces 'just enough' principles and 'systems engineering' approach to the practice of ontology development to provide a minimal yet complete, lightweight, agile and integrated development process, supportive of stakeholder…

This paper outlines a general formal framework for reasoning systems, intended to support future analysis of inference architectures across domains. We model reasoning systems as structured tuples comprising phenomena, explanation space,…

The article suggests a description of a system of tables with a set of special lists absorbing a semantics of data and reflects a fullness of data. It shows how their parallel processing can be constructed based on the descriptions. The…

Complex systems have interested researchers across a broad range of fields for many years and as computing has become more accesible and feasible, it is now possible to simulate aspects of these systems. A major point of research is how…

Throughout the evolution of biological species on Earth, cells and organs have developed many complex structures and processes to ensure their interactions with individual chemical molecules (small and macromolecular) and nanoscale objects…

Algorithmic systems make decisions that have a great impact in our lives. As our dependency on them is growing so does the need for transparency and holding them accountable. This paper presents a model for evaluating how transparent these…

This is a short introduction to quantum computers, quantum algorithms and quantum error correcting codes. Familiarity with the principles of quantum theory is assumed. Emphasis is put on a concise presentation of the principles avoiding…

Computational techniques are required for narrowing down the vast space of possibilities to plausible prebiotic scenarios, since precise information on the molecular composition, the dominant reaction chemistry, and the conditions for that…

Confounder selection is perhaps the most important step in the design of observational studies. A number of criteria, often with different objectives and approaches, have been proposed, and their validity and practical value have been…

Educators and policy-makers have advocated for reform of undergraduate biology education, calling for greater integration of mathematics and physics in the biology curriculum. While these calls reflect the increasingly interdisciplinary…

This short paper introduces a model for the specification and verification of real-time system design: timed state transition diagrams.

Robotic cell injection is used for automatically delivering substances into a cell and is an integral component of drug development, genetic engineering and many other areas of cell biology. Traditionally, the correctness of functionality…

Biological systems are characterized by the ubiquitous roles of weak, that is, non-covalent molecular interactions, small, often very small, numbers of specific molecules per cell, and Brownian motion. These combine to produce stochastic…

Biomarker discovery for clinical purposes is one of the major areas in which proteomics is used. However, despite considerable effort, the successes have been relatively scarce. In this perspective paper, we try to highlight and analyze the…

The notion of preferences plays an important role in many disciplines including service robotics which is concerned with scenarios in which robots interact with humans. These interactions can be favored by robots taking human preferences…