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In certain tasks such as pursuit and evasion, multiple agents need to coordinate their behavior to achieve a common goal. An interesting question is, how can such behavior be best evolved? A powerful approach is to control the agents with neural networks, coevolve them in separate subpopulations, and test them together in the common task. In this paper,(More)
BACKGROUND Protein complexes are important for understanding principles of cellular organization and functions. With the availability of large amounts of high-throughput protein-protein interactions (PPI), many algorithms have been proposed to discover protein complexes from PPI networks. However, existing algorithms generally do not take into consideration(More)
Protein complexes participate in many important cellular functions, so finding the set of existent complexes is essential for understanding the organization and regulation of processes in the cell. With the availability of large amounts of high-throughput protein-protein interaction (PPI) data, many algorithms have been proposed to discover protein(More)
Parallel dynamics of neural networks with separable coupling is given starting from Coolen-Sherrington theory. Away from saturation, it is shown that this parallel retrieve dynamics is equivalent to the sequential dynamics for finite temperature. But the finite-size effects were found to be governed by a homogeneous Markov process, not by a time-dependent(More)
The prediction of small complexes (consisting of two or three distinct proteins) is an important and challenging subtask in protein complex prediction from protein-protein interaction (PPI) networks. The prediction of small complexes is especially susceptible to noise (missing or spurious interactions) in the PPI network, while smaller groups of proteins(More)
Protein interactions and complexes behave in a dynamic fashion, but this dynamism is not captured by interaction screening technologies, and not preserved in protein-protein interaction (PPI) networks. The analysis of static interaction data to derive dynamic protein complexes leads to several challenges, of which we identify three. First, many proteins(More)
Neuroevolution is a promising learning method in tasks with extremely large state and action spaces and hidden states. Recent advances allow neuroevolution to take place in real time, making it possible to e.g. construct video games with adap-tive agents. Often some of the desired behaviors for such agents are known, and it would make sense to prescribe(More)
Complexes of physically interacting proteins constitute fundamental functional units responsible for driving biological processes within cells. A faithful reconstruction of the entire set of complexes is therefore essential to understand the functional organisation of cells. In this review, we discuss the key contributions of computational methods developed(More)
The prediction of protein complexes from high-throughput protein-protein interaction (PPI) data remains an important challenge in bioinformatics. Three groups of complexes have been identified as problematic to discover. First, many complexes are sparsely connected in the PPI network, and do not form dense clusters that can be derived by clustering(More)
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