Artificial Neural Networks (ANN) have gained significant popularity thanks to their ability to learn using the well-known backpropagation algorithm. Conversely, Spiking Neural Networks (SNNs), despite having broader capabilities than ANNs, have always posed challenges in the training phase. This paper shows a new method to perform supervised learning on SNNs, using Spike Timing Dependent Plasticity (STDP) and homeostasis, aiming at training the network to identify spatial patterns. Spatial patterns refer to spike patterns without a time component, where all spike events occur simultaneously. The method is tested using the SpiNNaker digital architecture. A SNN is trained to recognise one or multiple patterns and performance metrics are extracted to measure the performance of the network. Some considerations are drawn from the results showing that, in the case of a single trained pattern, the network behaves as the ideal detector, with 100% accuracy in detecting the trained pattern. However, as the number of trained patterns on a single network increases, the accuracy of identification is linked to the similarities between these patterns. This method of training an SNN to detect spatial patterns may be applied to pattern recognition in static images or traffic analysis in computer networks, where each network packet represents a spatial pattern. It will be stipulated that the homeostatic factor may enable the network to detect patterns with some degree of similarity, rather than only perfectly matching patterns. The principles outlined in this article serve as the fundamental building blocks for more complex systems that utilise both spatial and temporal patterns by converting specific features of input signals into spikes. One example of such a system is a computer network packet classifier, tasked with real-time identification of packet streams based on features within the packet content.

Following the initial implementation of a full-scale spiking neural network (SNN) of the cortical microcircuit on NEST, the work was replicated to simulate on SpiNNaker, the Juelich CPU cluster, and the Sussex GPU cluster, in order to compare the performances on the different platforms. All of these researches use the Leaky Integrate and Fire (LIF) model as the basic unit of spiking neurons. In comparison, Izhikevich's spiking neuron models (IZK) can mimic a larger variety of known cortical neuronal dynamics. In spite of this versatility, the IZK neuron is easy to implement and computes fast. In this work, we implement the above-mentioned cortical microcircuit at a reduced-scale and using IZK neurons on SpiNNaker. This is aligned with our ongoing research on a reduced-scale thalamocortical circuit of vision with changing IZK neuron dynamics on SpiNNaker. We validate our SNN with the LIF-based full-scale cortical microcircuit by providing Poisson noise inputs, and measuring objectively the outputs in terms of spike rate, irregularity and synchrony. Our reduced-scale SNN shows similar dynamics to the full-scale SNN and operates within the Asynchronous Irregular regime defined by set bounds on the three quantitative attributes. Next, we test our SNN with inputs from a Dynamic Vision Sensor- (DVS-)based electronic retina (e-retina) that converted a simple periodic environmental input to spike trains. With current parameter settings, the model output identifies the low-frequency, but not the high frequency periodic inputs.

We present here a learning system using the iCub humanoid robot and the SpiNNaker neuromorphic chip to solve the real-world task of object-specific attention. Integrating spiking neural networks with robots introduces considerable complexity for questionable benefit if the objective is simply task performance. But, we suggest, in a cognitive robotics context, where the goal is understanding how to compute, such an approach may yield useful insights to neural architecture as well as learned behavior, especially if dedicated neural hardware is available. Recent advances in cognitive robotics and neuromorphic processing now make such systems possible. Using a scalable, structured, modular approach, we build a spiking neural network where the effects and impact of learning can be predicted and tested, and the network can be scaled or extended to new tasks automatically. We introduce several enhancements to a basic network and show how they can be used to direct performance toward behaviorally relevant goals. Results show that using a simple classical spike-timing-dependent plasticity (STDP) rule on selected connections, we can get the robot (and network) to progress from poor task-specific performance to good performance. Behaviorally relevant STDP appears to contribute strongly to positive learning: "do this" but less to negative learning: "don't do that." In addition, we observe that the effect of structural enhancements tends to be cumulative. The overall system suggests that it is by being able to exploit combinations of effects, rather than any one effect or property in isolation, that spiking networks can achieve compelling, task-relevant behavior.

BACKGROUND: Since their introduction in 2009, the BioNLP Shared Task events have been instrumental in advancing the development of methods and resources for the automatic extraction of information from the biomedical literature. In this paper, we present the Cancer Genetics (CG) and Pathway Curation (PC) tasks, two event extraction tasks introduced in the BioNLP Shared Task 2013. The CG task focuses on cancer, emphasizing the extraction of physiological and pathological processes at various levels of biological organization, and the PC task targets reactions relevant to the development of biomolecular pathway models, defining its extraction targets on the basis of established pathway representations and ontologies. RESULTS: Six groups participated in the CG task and two groups in the PC task, together applying a wide range of extraction approaches including both established state-of-the-art systems and newly introduced extraction methods. The best-performing systems achieved F-scores of 55% on the CG task and 53% on the PC task, demonstrating a level of performance comparable to the best results achieved in similar previously proposed tasks. CONCLUSIONS: The results indicate that existing event extraction technology can generalize to meet the novel challenges represented by the CG and PC task settings, suggesting that extraction methods are capable of supporting the construction of knowledge bases on the molecular mechanisms of cancer and the curation of biomolecular pathway models. The CG and PC tasks continue as open challenges for all interested parties, with data, tools and resources available from the shared task homepage.

MOTIVATION: To create, verify and maintain pathway models, curators must discover and assess knowledge distributed over the vast body of biological literature. Methods supporting these tasks must understand both the pathway model representations and the natural language in the literature. These methods should identify and order documents by relevance to any given pathway reaction. No existing system has addressed all aspects of this challenge. METHOD: We present novel methods for associating pathway model reactions with relevant publications. Our approach extracts the reactions directly from the models and then turns them into queries for three text mining-based MEDLINE literature search systems. These queries are executed, and the resulting documents are combined and ranked according to their relevance to the reactions of interest. We manually annotate document-reaction pairs with the relevance of the document to the reaction and use this annotation to study several ranking methods, using various heuristic and machine-learning approaches. RESULTS: Our evaluation shows that the annotated document-reaction pairs can be used to create a rule-based document ranking system, and that machine learning can be used to rank documents by their relevance to pathway reactions. We find that a Support Vector Machine-based system outperforms several baselines and matches the performance of the rule-based system. The success of the query extraction and ranking methods are used to update our existing pathway search system, PathText. AVAILABILITY: An online demonstration of PathText 2 and the annotated corpus are available for research purposes at http://www.nactem.ac.uk/pathtext2/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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