Cutting out the middleman: measuring nuclear area in histopathology slides without segmentation

The size of nuclei in histological preparations from excised breast tumors is predictive of patient outcome (large nuclei indicate poor outcome). Pathologists take into account nuclear size when performing breast cancer grading. In addition, the mean nuclear area (MNA) has been shown to have independent prognostic value. The straightforward approach to measuring nuclear size is by performing nuclei segmentation. We hypothesize that given an image of a tumor region with known nuclei locations, the area of the individual nuclei and region statistics such as the MNA can be reliably computed directly from the image data by employing a machine learning model, without the intermediate step of nuclei segmentation. Towards this goal, we train a deep convolutional neural network model that is applied locally at each nucleus location, and can reliably measure the area of the individual nuclei and the MNA. Furthermore, we show how such an approach can be extended to perform combined nuclei detection and measurement, which is reminiscent of granulometry.Comment: Conditionally accepted for MICCAI 201

A security analysis of automated Chinese turing tests

Text-based Captchas have been widely used to deter misuse of services on the Internet. However, many designs have been broken. It is intellectually interesting and practically relevant to look for alternative designs, which are currently a topic of active research. We motivate the study of Chinese Captchas as an interesting alternative design - counterintuitively, it is possible to design Chinese Captchas that are universally usable, even to those who have never studied Chinese language. More importantly, we ask a fundamental question: is the segmentation-resistance principle established for Roman-character based Captchas applicable to Chinese based designs? With deep learning techniques, we offer the first evidence that computers do recognize individual Chinese characters well, regardless of distortion levels. This suggests that many real-world Chinese schemes are insecure, in contrast to common beliefs. Our result offers an essential guideline to the design of secure Chinese Captchas, and it is also applicable to Captchas using other large-alphabet languages such as Japanese

Deep Big Simple Neural Nets Excel on Handwritten Digit Recognition

Good old on-line back-propagation for plain multi-layer perceptrons yields a very low 0.35% error rate on the famous MNIST handwritten digits benchmark. All we need to achieve this best result so far are many hidden layers, many neurons per layer, numerous deformed training images, and graphics cards to greatly speed up learning.Comment: 14 pages, 2 figures, 4 listing

Gender Detection on Social Networks using Ensemble Deep Learning

Analyzing the ever-increasing volume of posts on social media sites such as Facebook and Twitter requires improved information processing methods for profiling authorship. Document classification is central to this task, but the performance of traditional supervised classifiers has degraded as the volume of social media has increased. This paper addresses this problem in the context of gender detection through ensemble classification that employs multi-model deep learning architectures to generate specialized understanding from different feature spaces

Echo State Property of Deep Reservoir Computing Networks

In the last years, the Reservoir Computing (RC) framework has emerged as a state of-the-art approach for efficient learning in temporal domains. Recently, within the RC context, deep Echo State Network (ESN) models have been proposed. Being composed of a stack of multiple non-linear reservoir layers, deep ESNs potentially allow to exploit the advantages of a hierarchical temporal feature representation at different levels of abstraction, at the same time preserving the training efficiency typical of the RC methodology. In this paper, we generalize to the case of deep architectures the fundamental RC conditions related to the Echo State Property (ESP), based on the study of stability and contractivity of the resulting dynamical system. Besides providing a necessary condition and a sufficient condition for the ESP of layered RC networks, the results of our analysis provide also insights on the nature of the state dynamics in hierarchically organized recurrent models. In particular, we find out that by adding layers to a deep reservoir architecture, the regime of network’s dynamics can only be driven towards (equally or) less stable behaviors. Moreover, our investigation shows the intrinsic ability of temporal dynamics differentiation at the different levels in a deep recurrent architecture, with higher layers in the stack characterized by less contractive dynamics. Such theoretical insights are further supported by experimental results that show the effect of layering in terms of a progressively increased short-term memory capacity of the recurrent models

Crowdsourcing the creation of image segmentation algorithms for connectomics

To stimulate progress in automating the reconstruction of neural circuits, we organized the first international challenge on 2D segmentation of electron microscopic (EM) images of the brain. Participants submitted boundary maps predicted for a test set of images, and were scored based on their agreement with a consensus of human expert annotations. The winning team had no prior experience with EM images, and employed a convolutional network. This “deep learning” approach has since become accepted as a standard for segmentation of EM images. The challenge has continued to accept submissions, and the best so far has resulted from cooperation between two teams. The challenge has probably saturated, as algorithms cannot progress beyond limits set by ambiguities inherent in 2D scoring and the size of the test dataset. Retrospective evaluation of the challenge scoring system reveals that it was not sufficiently robust to variations in the widths of neurite borders. We propose a solution to this problem, which should be useful for a future 3D segmentation challenge

Human Centric Facial Expression Recognition

Facial expression recognition (FER) is an area of active research, both in computer science and in behavioural science. Across these domains there is evidence to suggest that humans and machines find it easier to recognise certain emotions, for example happiness, in comparison to others. Recent behavioural studies have explored human perceptions of emotion further, by evaluating the relative contribution of features in the face when evaluating human sensitivity to emotion. It has been identified that certain facial regions have more salient features for certain expressions of emotion, especially when emotions are subtle in nature. For example, it is easier to detect fearful expressions when the eyes are expressive. Using this observation as a starting point for analysis, we similarly examine the effectiveness with which knowledge of facial feature saliency may be integrated into current approaches to automated FER. Specifically, we compare and evaluate the accuracy of ‘full-face’ versus upper and lower facial area convolutional neural network (CNN) modelling for emotion recognition in static images, and propose a human centric CNN hierarchy which uses regional image inputs to leverage current understanding of how humans recognise emotions across the face. Evaluations using the CK+ dataset demonstrate that our hierarchy can enhance classification accuracy in comparison to individual CNN architectures, achieving overall true positive classification in 93.3% of cases

Limited Generalization Capabilities of Autoencoders with Logistic Regression on Training Sets of Small Sizes

Part 6: Classification Pattern RecognitionInternational audienceDeep learning is promising approach to extract useful nonlinear representations of data. However, it is usually applied with large training sets, which are not always available in practical tasks. In this paper, we consider stacked autoencoders with logistic regression as the classification layer and study their usefulness for the task of image categorization depending on the size of training sets. Hand-crafted image descriptors are proposed and used for training autoencoders in addition to pixel-level features. New multi-column architecture for autoencoders is also proposed. Conducted experiments showed that useful nonlinear features can be learnt by (stacked) autoencoders only using large training sets, but they can yield positive results due to redundancy reduction also on small training sets. Practically useful results (9.1% error rate for 6 classes) were achieved only using hand-crafted features on the training set containing 4800 images

Haruspex: A Neural Network for the Automatic Identification of Oligonucleotides and Protein Secondary Structure in Cryo‐Electron Microscopy Maps

In recent years, three‐dimensional density maps reconstructed from single particle images obtained by electron cryo‐microscopy (cryo‐EM) have reached unprecedented resolution. However, map interpretation can be challenging, in particular if the constituting structures require de‐novo model building or are very mobile. Herein, we demonstrate the potential of convolutional neural networks for the annotation of cryo‐EM maps: our network Haruspex has been trained on a carefully curated set of 293 experimentally derived reconstruction maps to automatically annotate RNA/DNA as well as protein secondary structure elements. It can be straightforwardly applied to newly reconstructed maps in order to support domain placement or as a starting point for main‐chain placement. Due to its high recall and precision rates of 95.1 % and 80.3 %, respectively, on an independent test set of 122 maps, it can also be used for validation during model building. The trained network will be available as part of the CCP‐EM suite