Pan-cancer classifications of tumor histological images using deep learning

Histopathological images are essential for the diagnosis of cancer type and selection of optimal treatment. However, the current clinical process of manual inspection of images is time consuming and prone to intra- and inter-observer variability. Here we show that key aspects of cancer image analysis can be performed by deep convolutional neural networks (CNNs) across a wide spectrum of cancer types. In particular, we implement CNN architectures based on Google Inception v3 transfer learning to analyze 27815 H&E slides from 23 cohorts in The Cancer Genome Atlas in studies of tumor/normal status, cancer subtype, and mutation status. For 19 solid cancer types we are able to classify tumor/normal status of whole slide images with extremely high AUCs (0.995±0.008). We are also able to classify cancer subtypes within 10 tissue types with AUC values well above random expectations (micro-average 0.87±0.1). We then perform a cross-classification analysis of tumor/normal status across tumor types. We find that classifiers trained on one type are often effective in distinguishing tumor from normal in other cancer types, with the relationships among classifiers matching known cancer tissue relationships. For the more challenging problem of mutational status, we are able to classify TP53 mutations in three cancer types with AUCs from 0.65-0.80 using a fully-trained CNN, and with similar cross-classification accuracy across tissues. These studies demonstrate the power of CNNs for not only classifying histopathological images in diverse cancer types, but also for revealing shared biology between tumors. We have made software available at: https://github.com/javadnoorb/HistCNNFirst author draf

Efficient Decentralized Visual Place Recognition From Full-Image Descriptors

In this paper, we discuss the adaptation of our decentralized place recognition method described in [1] to full image descriptors. As we had shown, the key to making a scalable decentralized visual place recognition lies in exploting deterministic key assignment in a distributed key-value map. Through this, it is possible to reduce bandwidth by up to a factor of n, the robot count, by casting visual place recognition to a key-value lookup problem. In [1], we exploited this for the bag-of-words method [3], [4]. Our method of casting bag-of-words, however, results in a complex decentralized system, which has inherently worse recall than its centralized counterpart. In this paper, we instead start from the recent full-image description method NetVLAD [5]. As we show, casting this to a key-value lookup problem can be achieved with k-means clustering, and results in a much simpler system than [1]. The resulting system still has some flaws, albeit of a completely different nature: it suffers when the environment seen during deployment lies in a different distribution in feature space than the environment seen during training.Comment: 3 pages, 4 figures. This is a self-published paper that accompanies our original work [1] as well as the ICRA 2017 Workshop on Multi-robot Perception-Driven Control and Planning [2

On the representativeness of convolutional neural networks layers

Convolutional Neural Networks (CNN) are the most popular of deep network models due to their applicability and success in image processing. Although plenty of effort has been made in designing and training better discriminative CNNs, little is yet known about the internal features these models learn. Questions like, what specific knowledge is coded within CNN layers, and how can it be used for other purposes besides discrimination, remain to be answered. To advance in the resolution of these questions, in this work we extract features from CNN layers, building vector representations from CNN activations. The resultant vector embedding is used to represent first images and then known image classes. On those representations we perform an unsupervised clustering process, with the goal of studying the hidden semantics captured in the embedding space. Several abstract entities untaught to the network emerge in this process, effectively defining a taxonomy of knowledge as perceived by the CNN. We evaluate and interpret these sets using WordNet, while studying the different behaviours exhibited by the layers of a CNN model according to their depth. Our results indicate that, while top (i.e., deeper) layers provide the most representative space, low layers also define descriptive dimensions.This work was partially supported by the IBM/BSC Technology Center for Supercomputing (Joint Study Agreement, No. W156463), by the Spanish Government through Programa Severo Ochoa (SEV-2015-0493), by the Spanish Ministry of Science and Technology through TIN2015-65316-P project and by the Generalitat de Catalunya (contracts 2014-SGR-1051).Peer ReviewedPostprint (author's final draft

Effectiveness of landmark analysis for establishing locality in p2p networks

Locality to other nodes on a peer-to-peer overlay network can be established by means of a set of landmarks shared among the participating nodes. Each node independently collects a set of latency measures to landmark nodes, which are used as a multi-dimensional feature vector. Each peer node uses the feature vector to generate a unique scalar index which is correlated to its topological locality. A popular dimensionality reduction technique is the space filling Hilbert’s curve, as it possesses good locality preserving properties. However, there exists little comparison between Hilbert’s curve and other techniques for dimensionality reduction. This work carries out a quantitative analysis of their properties. Linear and non-linear techniques for scaling the landmark vectors to a single dimension are investigated. Hilbert’s curve, Sammon’s mapping and Principal Component Analysis have been used to generate a 1d space with locality preserving properties. This work provides empirical evidence to support the use of Hilbert’s curve in the context of locality preservation when generating peer identifiers by means of landmark vector analysis. A comparative analysis is carried out with an artificial 2d network model and with a realistic network topology model with a typical power-law distribution of node connectivity in the Internet. Nearest neighbour analysis confirms Hilbert’s curve to be very effective in both artificial and realistic network topologies. Nevertheless, the results in the realistic network model show that there is scope for improvements and better techniques to preserve locality information are required

A class of structured P2P systems supporting browsing

Browsing is a way of finding documents in a large amount of data which is complementary to querying and which is particularly suitable for multimedia documents. Locating particular documents in a very large collection of multimedia documents such as the ones available in peer to peer networks is a difficult task. However, current peer to peer systems do not allow to do this by browsing. In this report, we show how one can build a peer to peer system supporting a kind of browsing. In our proposal, one must extend an existing distributed hash table system with a few features : handling partial hash-keys and providing appropriate routing mechanisms for these hash-keys. We give such an algorithm for the particular case of the Tapestry distributed hash table. This is a work in progress as no proper validation has been done yet.Comment: 14 page

Forman-Ricci flow for change detection in large dynamic data sets

We present a viable solution to the challenging question of change detection in complex networks inferred from large dynamic data sets. Building on Forman's discretization of the classical notion of Ricci curvature, we introduce a novel geometric method to characterize different types of real-world networks with an emphasis on peer-to-peer networks. Furthermore we adapt the classical Ricci flow that already proved to be a powerful tool in image processing and graphics, to the case of undirected and weighted networks. The application of the proposed method on peer-to-peer networks yields insights into topological properties and the structure of their underlying data.Comment: Conference paper, accepted at ICICS 2016. (Updated version

Aesthetic preference for art emerges from a weighted integration over hierarchically structured visual features in the brain

It is an open question whether preferences for visual art can be lawfully predicted from the basic constituent elements of a visual image. Moreover, little is known about how such preferences are actually constructed in the brain. Here we developed and tested a computational framework to gain an understanding of how the human brain constructs aesthetic value. We show that it is possible to explain human preferences for a piece of art based on an analysis of features present in the image. This was achieved by analyzing the visual properties of drawings and photographs by multiple means, ranging from image statistics extracted by computer vision tools, subjective human ratings about attributes, to a deep convolutional neural network. Crucially, it is possible to predict subjective value ratings not only within but also across individuals, speaking to the possibility that much of the variance in human visual preference is shared across individuals. Neuroimaging data revealed that preference computations occur in the brain by means of a graded hierarchical representation of lower and higher level features in the visual system. These features are in turn integrated to compute an overall subjective preference in the parietal and prefrontal cortex. Our findings suggest that rather than being idiosyncratic, human preferences for art can be explained at least in part as a product of a systematic neural integration over underlying visual features of an image. This work not only advances our understanding of the brain-wide computations underlying value construction but also brings new mechanistic insights to the study of visual aesthetics and art appreciation