Network Alignment: Theory, Algorithms, and Applications
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Local and global inference methods have been developed to infer structural contacts from multiple sequence alignments of homologous proteins. They rely on correlations in amino acid usage at contacting sites. Because homologous proteins share a common ance ...
Artificial Neural Networks (ANN) are habitually trained via the back-propagation (BP) algorithm. This approach has been extremely successful: Current models like GPT-3 have O(10 11 ) parameters, are trained on O(10 11 ) words and produce awe-inspiring resu ...
Last-mile delivery in the logistics chain contributes to congestion in urban networks due to frequent stops. Crowd-shipping is a sustainable and low-cost alternative to traditional delivery but relies heavily on the availability of occasional couriers. In ...
In the beginning was the metabolism. The biochemical processes that make life possible transformed the soup of chemicals into the life on Earth we know today. Since then, living organisms have evolved, and life on Earth has become more complex. Living orga ...
EPFL2023
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Self-supervised neural language models with attention have recently been applied to biological sequence data, advancing structure, function and mutational effect prediction. Some protein language models, including MSA Transformer and AlphaFold's EvoFormer, ...
NATURE PORTFOLIO2022
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Network alignment is the task of identifying topologically and semantically similar nodes across (two) different networks. It plays an important role in various applications ranging from social network analysis to bioinformatic network interactions. Howeve ...
IEEE COMPUTER SOC2023
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This work addresses the problem of learning the topology of a network from the signals emitted by the network nodes. These signals are generated over time through a linear diffusion process, where neighboring nodes exchange messages according to the underl ...
Despite the structural and functional information contained in the statistical coupling between pairs of residues in a protein, coevolution associated with function is often obscured by artifactual signals such as genetic drift, which shapes a protein's ph ...
Internet ranking algorithms play a crucial role in information technologies and numerical analysis due to their efficiency in high dimensions and wide range of possible applications, including scientometrics and systemic risk in finance (SinkRank, DebtRank ...
Understanding epidemic propagation in large networks is an important but challenging task, especially since we usually lack information, and the information that we have is often counter-intuitive. An illustrative example is the dependence of the final siz ...
