相关论文: Artificial life properties of directed interaction…

Models of biochemical networks are usually presented as connected graphs where vertices indicate proteins and edges are drawn to indicate activation or inhibition relationships. These diagrams are useful for drawing qualitative conclusions…

In a recent paper it was shown that, for chemical reaction networks possessing a subtle structural property called concordance, dynamical behavior of a very circumscribed (and largely stable) kind is enforced, so long as the kinetics lies…

Chemical algorithms are statistical algorithms described and represented as chemical reaction networks. They are particularly attractive for traffic shaping and general control of network dynamics; they are analytically tractable, they…

Metabolic networks perform some of the most fundamental functions in living cells, including energy transduction and building block biosynthesis. While these are the best characterized networks in living systems, understanding their…

An explanatory model for the emergence of evolvable units must display emerging structures that (1) preserve themselves in time (2) self-reproduce and (3) tolerate a certain amount of variation when reproducing. To tackle this challenge,…

Complex systems of intracellular biochemical reactions have a central role in regulating cell identities and functions. Biochemical reaction systems are typically studied using the language and tools of graph theory. However, graph…

In living systems, we often see the emergence of the ingredients necessary for computation -- the capacity for information transmission, storage, and modification -- begging the question of how we may exploit or imitate such biological…

One approach to studying the system-wide organization of biochemistry is to use statistical graph theory. Even in such a heavily simplified method, which disregards most of the dynamic aspects of biochemistry, one is faced with fundamental…

Consider two sets of entities and their members' mutual affinity values, say drug-target affinities (DTA). Drugs and targets are said to interact in their effects on DTAs if drug's effect on it depends on the target. Presence of interaction…

Bidirected graphs are a common generalisation of directed graphs where arcs can also be incoming to both their incident nodes, or outgoing from both their incident nodes. Such arcs allow a walk to change direction. Some algorithms can…

Non-reciprocal interactions play a crucial role in many social and biological complex systems. While directionality has been thoroughly accounted for in networks with pairwise interactions, its effects in systems with higher-order…

Functioning and interaction of distributed devices and concurrent algorithms are analyzed in the context of the theory of algorithms. Our main concern here is how and under what conditions algorithmic interactive devices can be more…

To what extent do the characteristic features of a chemical reaction network reflect its purpose and function? In general, one argues that correlations between specific features and specific functions are key to understanding a complex…

Metabolic networks are probably among the most challenging and important biological networks. Their study provides insight into how biological pathways work and how robust a specific organism is against an environment or therapy. Here we…

The graphical notion of effective resistance has found wide-ranging applications in many areas of pure mathematics, applied mathematics and control theory. By the nature of its construction, effective resistance can only be computed in…

DCOP algorithms usually rely on interaction graphs to operate. In open and dynamic environments, such methods need to address how this interaction graph is generated and maintained among agents. Existing methods require reconstructing the…

What is the prospect of developing artificial general intelligence (AGI)? I investigate this question by systematically comparing living and algorithmic systems, with a special focus on the notion of "agency." There are three fundamental…

Chemical reaction networks can be automatically generated from graph grammar descriptions, where rewrite rules model reaction patterns. Because a molecule graph is connected and reactions in general involve multiple molecules, the rewriting…

Predicting the ground-state 3D molecular conformations from 2D molecular graphs is critical in computational chemistry due to its profound impact on molecular properties. Deep learning (DL) approaches have recently emerged as promising…

We introduce MetaChem, a language for representing and implementing Artificial Chemistries. We motivate the need for modularisation and standardisation in representation of artificial chemistries. We describe a mathematical formalism for…