Using Neural Networks for Relation Extraction from Biomedical Literature

Using different sources of information to support automated extracting of relations between biomedical concepts contributes to the development of our understanding of biological systems. The primary comprehensive source of these relations is biomedical literature. Several relation extraction approaches have been proposed to identify relations between concepts in biomedical literature, namely, using neural networks algorithms. The use of multichannel architectures composed of multiple data representations, as in deep neural networks, is leading to state-of-the-art results. The right combination of data representations can eventually lead us to even higher evaluation scores in relation extraction tasks. Thus, biomedical ontologies play a fundamental role by providing semantic and ancestry information about an entity. The incorporation of biomedical ontologies has already been proved to enhance previous state-of-the-art results.Comment: Artificial Neural Networks book (Springer) - Chapter 1

DeepBrain: Functional Representation of Neural In-Situ Hybridization Images for Gene Ontology Classification Using Deep Convolutional Autoencoders

This paper presents a novel deep learning-based method for learning a functional representation of mammalian neural images. The method uses a deep convolutional denoising autoencoder (CDAE) for generating an invariant, compact representation of in situ hybridization (ISH) images. While most existing methods for bio-imaging analysis were not developed to handle images with highly complex anatomical structures, the results presented in this paper show that functional representation extracted by CDAE can help learn features of functional gene ontology categories for their classification in a highly accurate manner. Using this CDAE representation, our method outperforms the previous state-of-the-art classification rate, by improving the average AUC from 0.92 to 0.98, i.e., achieving 75% reduction in error. The method operates on input images that were downsampled significantly with respect to the original ones to make it computationally feasible

Dimensions of Neural-symbolic Integration - A Structured Survey

Research on integrated neural-symbolic systems has made significant progress in the recent past. In particular the understanding of ways to deal with symbolic knowledge within connectionist systems (also called artificial neural networks) has reached a critical mass which enables the community to strive for applicable implementations and use cases. Recent work has covered a great variety of logics used in artificial intelligence and provides a multitude of techniques for dealing with them within the context of artificial neural networks. We present a comprehensive survey of the field of neural-symbolic integration, including a new classification of system according to their architectures and abilities.Comment: 28 page

Bio-inspired speed detection and discrimination

In the field of computer vision, a crucial task is the detection of motion (also called optical flow extraction). This operation allows analysis such as 3D reconstruction, feature tracking, time-to-collision and novelty detection among others. Most of the optical flow extraction techniques work within a finite range of speeds. Usually, the range of detection is extended towards higher speeds by combining some multiscale information in a serial architecture. This serial multi-scale approach suffers from the problem of error propagation related to the number of scales used in the algorithm. On the other hand, biological experiments show that human motion perception seems to follow a parallel multiscale scheme. In this work we present a bio-inspired parallel architecture to perform detection of motion, providing a wide range of operation and avoiding error propagation associated with the serial architecture. To test our algorithm, we perform relative error comparisons between both classical and proposed techniques, showing that the parallel architecture is able to achieve motion detection with results similar to the serial approach

Deep Neural Networks - A Brief History

Introduction to deep neural networks and their history.Comment: 14 pages, 14 figure

A Physiologically Based System Theory of Consciousness

A system which uses large numbers of devices to perform a complex functionality is forced to adopt a simple functional architecture by the needs to construct copies of, repair, and modify the system. A simple functional architecture means that functionality is partitioned into relatively equal sized components on many levels of detail down to device level, a mapping exists between the different levels, and exchange of information between components is minimized. In the instruction architecture functionality is partitioned on every level into instructions, which exchange unambiguous system information and therefore output system commands. The von Neumann architecture is a special case of the instruction architecture in which instructions are coded as unambiguous system information. In the recommendation (or pattern extraction) architecture functionality is partitioned on every level into repetition elements, which can freely exchange ambiguous information and therefore output only system action recommendations which must compete for control of system behavior. Partitioning is optimized to the best tradeoff between even partitioning and minimum cost of distributing data. Natural pressures deriving from the need to construct copies under DNA control, recover from errors, failures and damage, and add new functionality derived from random mutations has resulted in biological brains being constrained to adopt the recommendation architecture. The resultant hierarchy of functional separations can be the basis for understanding psychological phenomena in terms of physiology. A theory of consciousness is described based on the recommendation architecture model for biological brains. Consciousness is defined at a high level in terms of sensory independent image sequences including self images with the role of extending the search of records of individual experience for behavioral guidance in complex social situations. Functional components of this definition of consciousness are developed, and it is demonstrated that these components can be translated through subcomponents to descriptions in terms of known and postulated physiological mechanisms

A Unified Model For Developmental Robotics

We present the architecture and distributed algorithms of an implemented system called NeuSter, that unifies learning, perception and action for autonomous robot control. NeuSter comprises several sub-systems that provide online learning for networks of million neurons on machine clusters. It extracts information from sensors, builds its own representations of the environment in order to learn non-predefined goals