抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

The modern science of networks has brought significant advances to our understanding of complex systems. One of the most relevant features of graphs representing real systems is community structure, or clustering, i. e. the organization of vertices in clusters, with many edges joining vertices of the same cluster and comparatively few edges joining vertices of different clusters. Such clusters, or communities, can be considered as fairly independent compartments of a graph, playing a similar role like, e. g., the tissues or the organs in the human body. Detecting communities is of great importance in sociology, biology and computer science, disciplines where systems are often represented as graphs. This problem is very hard and not yet satisfactorily solved, despite the huge effort of a large interdisciplinary community of scientists working on it over the past few years. We will attempt a thorough exposition of the topic, from the definition of the main elements of the problem, to the presentation of most methods developed, with a special focus on techniques designed by statistical physicists, from the discussion of crucial issues like the significance of clustering and how methods should be tested and compared against each other, to the description of applications to real networks.

/pdf/community-detection-in-graphs-34rogm3r6p.pdf

Community detection in graphs

BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

We consider the problem of detecting communities or modules in networks, groups of vertices with a higher-than-average density of edges connecting them. Previous work indicates that a robust approach to this problem is the maximization of the benefit function known as ``modularity'' over possible divisions of a network. Here we show that this maximization process can be written in terms of the eigenspectrum of a matrix we call the modularity matrix, which plays a role in community detection similar to that played by the graph Laplacian in graph partitioning calculations. This result leads us to a number of possible algorithms for detecting community structure, as well as several other results, including a spectral measure of bipartite structure in networks and a centrality measure that identifies vertices that occupy central positions within the communities to which they belong. The algorithms and measures proposed are illustrated with applications to a variety of real-world complex networks.

/pdf/finding-community-structure-in-networks-using-the-4em5so8glh.pdf

Finding community structure in networks using the eigenvectors of matrices

In the last two decades, Computer Aided Detection (CAD) systems were developed to help radiologists analyse screening mammograms, however benefits of current CAD technologies appear to be contradictory, therefore they should be improved to be ultimately considered useful. Since 2012, deep convolutional neural networks (CNN) have been a tremendous success in image recognition, reaching human performance. These methods have greatly surpassed the traditional approaches, which are similar to currently used CAD solutions. Deep CNN-s have the potential to revolutionize medical image analysis. We propose a CAD system based on one of the most successful object detection frameworks, Faster R-CNN. The system detects and classifies malignant or benign lesions on a mammogram without any human intervention. The proposed method sets the state of the art classification performance on the public INbreast database, AUC = 0.95. The approach described here has achieved 2nd place in the Digital Mammography DREAM Challenge with AUC = 0.85. When used as a detector, the system reaches high sensitivity with very few false positive marks per image on the INbreast dataset. Source code, the trained model and an OsiriX plugin are published online at https://github.com/riblidezso/frcnn_cad .

/pdf/detecting-and-classifying-lesions-in-mammograms-with-deep-41p9rqz0mh.pdf

Detecting and classifying lesions in mammograms with Deep Learning

In the last two decades Computer Aided Diagnostics (CAD) systems were developed to help radiologists analyze screening mammograms. The benefits of current CAD technologies appear to be contradictory and they should be improved to be ultimately considered useful. Since 2012 deep convolutional neural networks (CNN) have been a tremendous success in image recognition, reaching human performance. These methods have greatly surpassed the traditional approaches, which are similar to currently used CAD solutions. Deep CNN-s have the potential to revolutionize medical image analysis. We propose a CAD system based on one of the most successful object detection frameworks, Faster R-CNN. The system detects and classifies malignant or benign lesions on a mammogram without any human intervention. The proposed method sets the state of the art classification performance on the public INbreast database, AUC = 0.95 . The approach described here has achieved the 2nd place in the Digital Mammography DREAM Challenge with AUC = 0.85 . When used as a detector, the system reaches high sensitivity with very few false positive marks per image on the INbreast dataset. Source code, the trained model and an OsiriX plugin are availaible online at this https URL .

A search technique locating network modules, i.e. internally densely connected groups of nodes in directed networks is introduced by extending the clique percolation method originally proposed for undirected networks. After giving a suitable definition for directed modules we investigate their percolation transition in the Erdős–Renyi graph both analytically and numerically. We also analyse four real-world directed networks, including Google's own web-pages, an email network, a word association graph and the transcriptional regulatory network of the yeast Saccharomyces cerevisiae. The obtained directed modules are validated by additional information available for the nodes. We find that directed modules of real-world graphs inherently overlap and the investigated networks can be classified into two major groups in terms of the overlaps between the modules. Accordingly, in the word-association network and Google's web-pages, overlaps are likely to contain in-hubs, whereas the modules in the email and transcriptional regulatory network tend to overlap via out-hubs.

https://iopscience.iop.org/article/10.1088/1367-2630/9/6/186/pdf

Directed network modules

The graph of communities is a network emerging above the level of individual nodes in the hierarchical organisation of a complex system. In this graph the nodes correspond to communities (highly interconnected subgraphs, also called modules or clusters), and the links refer to members shared by two communities. Our analysis indicates that the development of this modular structure is driven by preferential attachment, in complete analogy with the growth of the underlying network of nodes. We study how the links between communities are born in a growing co-authorship network, and introduce a simple model for the dynamics of overlapping communities.

https://cfinder.org/wiki/papers/Pollner_EurophysLett_06_Preferential_attachment_of_communities.pdf

Preferential attachment of communities: The same principle, but a higher level

We investigate the fundamental statistical features of tagged (or annotated) networks having a rich variety of attributes associated with their nodes. Tags (attributes, annotations, properties, features, etc) provide essential information about the entity represented by a given node, thus, taking them into account represents a significant step towards a more complete description of the structure of large complex systems. Our main goal here is to uncover the relations between the statistical properties of the node tags and those of the graph topology. In order to better characterize the networks with tagged nodes, we introduce a number of new notions, including tag-assortativity (relating link probability to node similarity), and new quantities, such as node uniqueness (measuring how rarely the tags of a node occur in the network) and tag-assortativity exponent. We apply our approach to three large networks representing very different domains of complex systems. A number of the tag related quantities display analogous behaviour (e.g. the networks we studied are tag-assortative, indicating possible universal aspects of tags versus topology), while some other features, such as the distribution of the node uniqueness, show variability from network to network allowing for pin-pointing large scale specific features of real-world complex networks. We also find that for each network the topology and the tag distribution are scale invariant, and this self-similar property of the networks can be well characterized by the tag-assortativity exponent, which is specific to each system.

/pdf/fundamental-statistical-features-and-self-similar-properties-2ld0x0znkn.pdf

Péter Pollner

Papers

Detecting and classifying lesions in mammograms with Deep Learning

Detecting and classifying lesions in mammograms with Deep Learning

Directed network modules

Preferential attachment of communities: The same principle, but a higher level

Fundamental statistical features and self-similar properties of tagged networks