Multi-scale strain-stiffening of semiflexible bundle networks

Bundles of polymer filaments are responsible for the rich and unique mechanical behaviors of many biomaterials, including cells and extracellular matrices. In fibrin biopolymers, whose nonlinear elastic properties are crucial for normal blood clotting, protofibrils self-assemble and bundle to form networks of semiflexible fibers. Here we show that the extraordinary strain-stiffening response of fibrin networks is a direct reflection of the hierarchical architecture of the fibrin fibers. We measure the rheology of networks of unbundled protofibrils and find excellent agreement with an affine model of extensible wormlike polymers. By direct comparison with these data, we show that physiological fibrin networks composed of thick fibers can be modeled as networks of tight protofibril bundles. We demonstrate that the tightness of coupling between protofibrils in the fibers can be tuned by the degree of enzymatic intermolecular crosslinking by the coagulation Factor XIII. Furthermore, at high stress, the protofibrils contribute independently to the network elasticity, which may reflect a decoupling of the tight bundle structure. The hierarchical architecture of fibrin fibers can thus account for the nonlinearity and enormous elastic resilience characteristic of blood clots.Comment: 27 pages including 8 figures and Supplementary Dat

Quantification and Comparison of Degree Distributions in Complex Networks

The degree distribution is an important characteristic of complex networks. In many applications, quantification of degree distribution in the form of a fixed-length feature vector is a necessary step. On the other hand, we often need to compare the degree distribution of two given networks and extract the amount of similarity between the two distributions. In this paper, we propose a novel method for quantification of the degree distributions in complex networks. Based on this quantification method,a new distance function is also proposed for degree distributions, which captures the differences in the overall structure of the two given distributions. The proposed method is able to effectively compare networks even with different scales, and outperforms the state of the art methods considerably, with respect to the accuracy of the distance function

Community Detection via Maximization of Modularity and Its Variants

In this paper, we first discuss the definition of modularity (Q) used as a metric for community quality and then we review the modularity maximization approaches which were used for community detection in the last decade. Then, we discuss two opposite yet coexisting problems of modularity optimization: in some cases, it tends to favor small communities over large ones while in others, large communities over small ones (so called the resolution limit problem). Next, we overview several community quality metrics proposed to solve the resolution limit problem and discuss Modularity Density (Qds) which simultaneously avoids the two problems of modularity. Finally, we introduce two novel fine-tuned community detection algorithms that iteratively attempt to improve the community quality measurements by splitting and merging the given network community structure. The first of them, referred to as Fine-tuned Q, is based on modularity (Q) while the second one is based on Modularity Density (Qds) and denoted as Fine-tuned Qds. Then, we compare the greedy algorithm of modularity maximization (denoted as Greedy Q), Fine-tuned Q, and Fine-tuned Qds on four real networks, and also on the classical clique network and the LFR benchmark networks, each of which is instantiated by a wide range of parameters. The results indicate that Fine-tuned Qds is the most effective among the three algorithms discussed. Moreover, we show that Fine-tuned Qds can be applied to the communities detected by other algorithms to significantly improve their results

Data-Driven Sparse Structure Selection for Deep Neural Networks

Deep convolutional neural networks have liberated its extraordinary power on various tasks. However, it is still very challenging to deploy state-of-the-art models into real-world applications due to their high computational complexity. How can we design a compact and effective network without massive experiments and expert knowledge? In this paper, we propose a simple and effective framework to learn and prune deep models in an end-to-end manner. In our framework, a new type of parameter -- scaling factor is first introduced to scale the outputs of specific structures, such as neurons, groups or residual blocks. Then we add sparsity regularizations on these factors, and solve this optimization problem by a modified stochastic Accelerated Proximal Gradient (APG) method. By forcing some of the factors to zero, we can safely remove the corresponding structures, thus prune the unimportant parts of a CNN. Comparing with other structure selection methods that may need thousands of trials or iterative fine-tuning, our method is trained fully end-to-end in one training pass without bells and whistles. We evaluate our method, Sparse Structure Selection with several state-of-the-art CNNs, and demonstrate very promising results with adaptive depth and width selection.Comment: ECCV Camera ready versio

Metrics for Graph Comparison: A Practitioner's Guide

Comparison of graph structure is a ubiquitous task in data analysis and machine learning, with diverse applications in fields such as neuroscience, cyber security, social network analysis, and bioinformatics, among others. Discovery and comparison of structures such as modular communities, rich clubs, hubs, and trees in data in these fields yields insight into the generative mechanisms and functional properties of the graph. Often, two graphs are compared via a pairwise distance measure, with a small distance indicating structural similarity and vice versa. Common choices include spectral distances (also known as $\lambda$ distances) and distances based on node affinities. However, there has of yet been no comparative study of the efficacy of these distance measures in discerning between common graph topologies and different structural scales. In this work, we compare commonly used graph metrics and distance measures, and demonstrate their ability to discern between common topological features found in both random graph models and empirical datasets. We put forward a multi-scale picture of graph structure, in which the effect of global and local structure upon the distance measures is considered. We make recommendations on the applicability of different distance measures to empirical graph data problem based on this multi-scale view. Finally, we introduce the Python library NetComp which implements the graph distances used in this work

The envirome and the connectome: exploring the structural noise in the human brain associated with socioeconomic deprivation

Complex cognitive functions are widely recognized to be the result of a number of brain regions working together as large-scale networks. Recently, complex network analysis has been used to characterize various structural properties of the large scale network organization of the brain. For example, the human brain has been found to have a modular architecture i.e. regions within the network form communities (modules) with more connections between regions within the community compared to regions outside it. The aim of this study was to examine the modular and overlapping modular architecture of the brain networks using complex network analysis. We also examined the association between neighborhood level deprivation and brain network structure – modularity and grey nodes. We compared network structure derived from anatomical MRI scans of 42 middle-aged neurologically healthy men from the least (LD) and the most deprived (MD) neighborhoods of Glasgow with their corresponding random networks. Cortical morphological covariance networks were constructed from the cortical thickness derived from the MRI scans of the brain. For a given modularity threshold, networks derived from the MD group showed similar number of modules compared to their corresponding random networks, while networks derived from the LD group had more modules compared to their corresponding random networks. The MD group also had fewer grey nodes – a measure of overlapping modular structure. These results suggest that apparent structural difference in brain networks may be driven by differences in cortical thicknesses between groups. This demonstrates a structural organization that is consistent with a system that is less robust and less efficient in information processing. These findings provide some evidence of the relationship between socioeconomic deprivation and brain network topology

A Novel BiLevel Paradigm for Image-to-Image Translation

Image-to-image (I2I) translation is a pixel-level mapping that requires a large number of paired training data and often suffers from the problems of high diversity and strong category bias in image scenes. In order to tackle these problems, we propose a novel BiLevel (BiL) learning paradigm that alternates the learning of two models, respectively at an instance-specific (IS) and a general-purpose (GP) level. In each scene, the IS model learns to maintain the specific scene attributes. It is initialized by the GP model that learns from all the scenes to obtain the generalizable translation knowledge. This GP initialization gives the IS model an efficient starting point, thus enabling its fast adaptation to the new scene with scarce training data. We conduct extensive I2I translation experiments on human face and street view datasets. Quantitative results validate that our approach can significantly boost the performance of classical I2I translation models, such as PG2 and Pix2Pix. Our visualization results show both higher image quality and more appropriate instance-specific details, e.g., the translated image of a person looks more like that person in terms of identity