Similar image search for histopathology: SMILY.

The increasing availability of large institutional and public histopathology image datasets is enabling the searching of these datasets for diagnosis, research, and education. Although these datasets typically have associated metadata such as diagnosis or clinical notes, even carefully curated datasets rarely contain annotations of the location of regions of interest on each image. As pathology images are extremely large (up to 100,000 pixels in each dimension), further laborious visual search of each image may be needed to find the feature of interest. In this paper, we introduce a deep-learning-based reverse image search tool for histopathology images: Similar Medical Images Like Yours (SMILY). We assessed SMILY's ability to retrieve search results in two ways: using pathologist-provided annotations, and via prospective studies where pathologists evaluated the quality of SMILY search results. As a negative control in the second evaluation, pathologists were blinded to whether search results were retrieved by SMILY or randomly. In both types of assessments, SMILY was able to retrieve search results with similar histologic features, organ site, and prostate cancer Gleason grade compared with the original query. SMILY may be a useful general-purpose tool in the pathologist's arsenal, to improve the efficiency of searching large archives of histopathology images, without the need to develop and implement specific tools for each application.

Visualizing Dataflow Graphs of Deep Learning Models in TensorFlow.

We present a design study of the TensorFlow Graph Visualizer, part of the TensorFlow machine intelligence platform. This tool helps users understand complex machine learning architectures by visualizing their underlying dataflow graphs. The tool works by applying a series of graph transformations that enable standard layout techniques to produce a legible interactive diagram. To declutter the graph, we decouple non-critical nodes from the layout. To provide an overview, we build a clustered graph using the hierarchical structure annotated in the source code. To support exploration of nested structure on demand, we perform edge bundling to enable stable and responsive cluster expansion. Finally, we detect and highlight repeated structures to emphasize a model's modular composition. To demonstrate the utility of the visualizer, we describe example usage scenarios and report user feedback. Overall, users find the visualizer useful for understanding, debugging, and sharing the structures of their models.

Beyond network structure: How heterogeneous susceptibility modulates the spread of epidemics.

The compartmental models used to study epidemic spreading often assume the same susceptibility for all individuals, and are therefore, agnostic about the effects that differences in susceptibility can have on epidemic spreading. Here we show that-for the SIS model-differential susceptibility can make networks more vulnerable to the spread of diseases when the correlation between a node's degree and susceptibility are positive, and less vulnerable when this correlation is negative. Moreover, we show that networks become more likely to contain a pocket of infection when individuals are more likely to connect with others that have similar susceptibility (the network is segregated). These results show that the failure to include differential susceptibility to epidemic models can lead to a systematic over/under estimation of fundamental epidemic parameters when the structure of the networks is not independent from the susceptibility of the nodes or when there are correlations between the susceptibility of connected individuals.

Influence of the network topology on epidemic spreading.

The influence of the network's structure on the dynamics of spreading processes has been extensively studied in the last decade. Important results that partially answer this question show a weak connection between the macroscopic behavior of these processes and specific structural properties in the network, such as the largest eigenvalue of a topology related matrix. However, little is known about the direct influence of the network topology on the microscopic level, such as the influence of the (neighboring) network on the probability of a particular node's infection. To answer this question, we derive both an upper and a lower bound for the probability that a particular node is infective in a susceptible-infective-susceptible model for two cases of spreading processes: reactive and contact processes. The bounds are derived by considering the n-hop neighborhood of the node; the bounds are tighter as one uses a larger n-hop neighborhood to calculate them. Consequently, using local information for different neighborhood sizes, we assess the extent to which the topology influences the spreading process, thus providing also a strong macroscopic connection between the former and the latter. Our findings are complemented by numerical results for a real-world email network. A very good estimate for the infection density ρ is obtained using only two-hop neighborhoods, which account for 0.4% of the entire network topology on average.

Analytically solvable processes on networks.

We introduce a broad class of analytically solvable processes on networks. In the special case, they reduce to random walk and consensus process, the two most basic processes on networks. Our class differs from previous models of interactions (such as the stochastic Ising model, cellular automata, infinite particle systems, and the voter model) in several ways, the two most important being (i) the model is analytically solvable even when the dynamical equation for each node may be different and the network may have an arbitrary finite graph and influence structure and (ii) when local dynamics is described by the same evolution equation, the model is decomposable, with the equilibrium behavior of the system expressed as an explicit function of network topology and node dynamics.

Identifying communities by influence dynamics in social networks.

Communities are not static; they evolve, split and merge, appear and disappear, i.e., they are the product of dynamical processes that govern the evolution of a network. A good algorithm for community detection should not only quantify the topology of the network but incorporate the dynamical processes that take place on the network. We present an algorithm for community detection that combines network structure with processes that support the creation and/or evolution of communities. The algorithm does not embrace the universal approach but instead tries to focus on social networks and model dynamic social interactions that occur on those networks. It identifies leaders and communities that form around those leaders. It naturally supports overlapping communities by associating each node with a membership vector that describes the node's involvement in each community. This way, in addition to the overlapping communities, we can identify nodes that are good followers of their leader and also nodes with no clear community involvement that serve as proxies between several communities and that are equally as important. We run the algorithm for several real social networks which we believe represent a good fraction of the wide body of social networks and discuss the results, including other possible applications.