Threshold model of cascades in temporal networks

Threshold models try to explain the consequences of social influence like the spread of fads and opinions. Along with models of epidemics, they constitute a major theoretical framework of social spreading processes. In threshold models on static networks, an individual changes her state if a certain fraction of her neighbors has done the same. When there are strong correlations in the temporal aspects of contact patterns, it is useful to represent the system as a temporal network. In such a system, not only contacts but also the time of the contacts are represented explicitly. There is a consensus that bursty temporal patterns slow down disease spreading. However, as we will see, this is not a universal truth for threshold models. In this work, we propose an extension of Watts' classic threshold model to temporal networks. We do this by assuming that an agent is influenced by contacts which lie a certain time into the past. I.e., the individuals are affected by contacts within a time window. In addition to thresholds as the fraction of contacts, we also investigate the number of contacts within the time window as a basis for influence. To elucidate the model's behavior, we run the model on real and randomized empirical contact datasets.Comment: 7 pages, 5 figures, 2 table

Neural network setups for a precise detection of the many-body localization transition: finite-size scaling and limitations

Determining phase diagrams and phase transitions semi-automatically using machine learning has received a lot of attention recently, with results in good agreement with more conventional approaches in most cases. When it comes to more quantitative predictions, such as the identification of universality class or precise determination of critical points, the task is more challenging. As an exacting test-bed, we study the Heisenberg spin-1/2 chain in a random external field that is known to display a transition from a many-body localized to a thermalizing regime, which nature is not entirely characterized. We introduce different neural network structures and dataset setups to achieve a finite-size scaling analysis with the least possible physical bias (no assumed knowledge on the phase transition and directly inputing wave-function coefficients), using state-of-the-art input data simulating chains of sizes up to L=24. In particular, we use domain adversarial techniques to ensure that the network learns scale-invariant features. We find a variability of the output results with respect to network and training parameters, resulting in relatively large uncertainties on final estimates of critical point and correlation length exponent which tend to be larger than the values obtained from conventional approaches. We put the emphasis on interpretability throughout the paper and discuss what the network appears to learn for the various used architectures. Our findings show that a it quantitative analysis of phase transitions of unknown nature remains a difficult task with neural networks when using the minimally engineered physical input.Comment: v2: published versio

Fair Evaluation of Global Network Aligners

Biological network alignment identifies topologically and functionally conserved regions between networks of different species. It encompasses two algorithmic steps: node cost function (NCF), which measures similarities between nodes in different networks, and alignment strategy (AS), which uses these similarities to rapidly identify high-scoring alignments. Different methods use both different NCFs and different ASs. Thus, it is unclear whether the superiority of a method comes from its NCF, its AS, or both. We already showed on MI-GRAAL and IsoRankN that combining NCF of one method and AS of another method can lead to a new superior method. Here, we evaluate MI-GRAAL against newer GHOST to potentially further improve alignment quality. Also, we approach several important questions that have not been asked systematically thus far. First, we ask how much of the node similarity information in NCF should come from sequence data compared to topology data. Existing methods determine this more-less arbitrarily, which could affect the resulting alignment(s). Second, when topology is used in NCF, we ask how large the size of the neighborhoods of the compared nodes should be. Existing methods assume that larger neighborhood sizes are better. We find that MI-GRAAL's NCF is superior to GHOST's NCF, while the performance of the methods' ASs is data-dependent. Thus, the combination of MI-GRAAL's NCF and GHOST's AS could be a new superior method for certain data. Also, which amount of sequence information is used within NCF does not affect alignment quality, while the inclusion of topological information is crucial. Finally, larger neighborhood sizes are preferred, but often, it is the second largest size that is superior, and using this size would decrease computational complexity. Together, our results give several general recommendations for a fair evaluation of network alignment methods.Comment: 19 pages. 10 figures. Presented at the 2014 ISMB Conference, July 13-15, Boston, M