The applicability of recurrent neural networks for biological sequence analysis

Selection of machine learning techniques requires a certain sensitivity to the requirements of the problem. In particular, the problem can be made more tractable by deliberately using algorithms that are biased toward solutions of the requisite kind. In this paper, we argue that recurrent neural networks have a natural bias toward a problem domain of which biological sequence analysis tasks are a subset. We use experiments with synthetic data to illustrate this bias. We then demonstrate that this bias can be exploitable using a data set of protein sequences containing several classes of subcellular localization targeting peptides. The results show that, compared with feed forward, recurrent neural networks will generally perform better on sequence analysis tasks. Furthermore, as the patterns within the sequence become more ambiguous, the choice of specific recurrent architecture becomes more critical.

A New Approach for Eliminating the Spurious States in Recurrent Neural Networks

As is well known, the Convergence Theorem for the Recurrent Neural Networks, is based in Lyapunov ́s second method, which states that associated to any one given net state, there always exist a real number, in other words an element of the one dimensional Euclidean Space R, in such a way that when the state of the net changes then its associated real number decreases. In this paper we will introduce the two dimensional Euclidean space R2, as the space associated to the net, and we will define a pair of real numbers ( x, y ) , associated to any one given state of the net. We will prove that when the net change its state, then the product x ⋅ y will decrease. All the states whose projection over the energy field are placed on the same hyperbolic surface, will be considered as points with the same energy level. On the other hand we will prove that if the states are classified attended to their distances to the zero vector, only one pattern in each one of the different classes may be at the same energy level. The retrieving procedure is analyzed trough the projection of the states on that plane. The geometrical properties of the synaptic matrix W may be used for classifying the n-dimensional state- vector space in n classes. A pattern to be recognized is seen as a point belonging to one of these classes, and depending on the class the pattern to be retrieved belongs, different weight parameters are used. The capacity of the net is improved and the spurious states are reduced. In order to clarify and corroborate the theoretical results, together with the formal theory, an application is presented.

On Recurrent and Deep Neural Networks

L'apprentissage profond est un domaine de recherche en forte croissance en apprentissage automatique qui est parvenu à des résultats impressionnants dans différentes tâches allant de la classification d'images à la parole, en passant par la modélisation du langage. Les réseaux de neurones récurrents, une sous-classe d'architecture profonde, s'avèrent particulièrement prometteurs. Les réseaux récurrents peuvent capter la structure temporelle dans les données. Ils ont potentiellement la capacité d'apprendre des corrélations entre des événements éloignés dans le temps et d'emmagasiner indéfiniment des informations dans leur mémoire interne. Dans ce travail, nous tentons d'abord de comprendre pourquoi la profondeur est utile. Similairement à d'autres travaux de la littérature, nos résultats démontrent que les modèles profonds peuvent être plus efficaces pour représenter certaines familles de fonctions comparativement aux modèles peu profonds. Contrairement à ces travaux, nous effectuons notre analyse théorique sur des réseaux profonds acycliques munis de fonctions d'activation linéaires par parties, puisque ce type de modèle est actuellement l'état de l'art dans différentes tâches de classification. La deuxième partie de cette thèse porte sur le processus d'apprentissage. Nous analysons quelques techniques d'optimisation proposées récemment, telles l'optimisation Hessian free, la descente de gradient naturel et la descente des sous-espaces de Krylov. Nous proposons le cadre théorique des méthodes à région de confiance généralisées et nous montrons que plusieurs de ces algorithmes développés récemment peuvent être vus dans cette perspective. Nous argumentons que certains membres de cette famille d'approches peuvent être mieux adaptés que d'autres à l'optimisation non convexe. La dernière partie de ce document se concentre sur les réseaux de neurones récurrents. Nous étudions d'abord le concept de mémoire et tentons de répondre aux questions suivantes: Les réseaux récurrents peuvent-ils démontrer une mémoire sans limite? Ce comportement peut-il être appris? Nous montrons que cela est possible si des indices sont fournis durant l'apprentissage. Ensuite, nous explorons deux problèmes spécifiques à l'entraînement des réseaux récurrents, à savoir la dissipation et l'explosion du gradient. Notre analyse se termine par une solution au problème d'explosion du gradient qui implique de borner la norme du gradient. Nous proposons également un terme de régularisation conçu spécifiquement pour réduire le problème de dissipation du gradient. Sur un ensemble de données synthétique, nous montrons empiriquement que ces mécanismes peuvent permettre aux réseaux récurrents d'apprendre de façon autonome à mémoriser des informations pour une période de temps indéfinie. Finalement, nous explorons la notion de profondeur dans les réseaux de neurones récurrents. Comparativement aux réseaux acycliques, la définition de profondeur dans les réseaux récurrents est souvent ambiguë. Nous proposons différentes façons d'ajouter de la profondeur dans les réseaux récurrents et nous évaluons empiriquement ces propositions.

An Efficient Parameterization of Dynamic Neural Networks for Nonlinear System Identification

Dynamic neural networks (DNNs), which are also known as recurrent neural networks, are often used for nonlinear system identification. The main contribution of this letter is the introduction of an efficient parameterization of a class of DNNs. Having to adjust less parameters simplifies the training problem and leads to more parsimonious models. The parameterization is based on approximation theory dealing with the ability of a class of DNNs to approximate finite trajectories of nonautonomous systems. The use of the proposed parameterization is illustrated through a numerical example, using data from a nonlinear model of a magnetic levitation system.

Recurrent neural network for induction motor speed estimation in industry applications

Many electronic drivers for the induction motor control are based on sensorless technologies. The proposal of this work Is to present an alternative approach of speed estimation, from transient to steady state, using artificial neural networks. The inputs of the network are the RMS voltage, current and speed estimated of the induction motor feedback to the input with a delay of n samples. Simulation results are also presented to validate the proposed approach. © 2006 IEEE.

Estimation of electrical machine speed using sensorless technology and neural networks

The use of sensorless technologies is an increasing tendency on industrial drivers for electrical machines. The estimation of electrical and mechanical parameters involved with the electrical machine control is used very frequently in order to avoid measurement of all variables related to this process. The cost reduction may also be considered in industrial drivers, besides the increasing robustness of the system, as an advantage of the use of sensorless technologies. This work proposes the use of a recurrent artificial neural network to estimate the speed of induction motor for sensorless control schemes using one single current sensor. Simulation and experimental results are presented to validate the proposed approach. ©2008 IEEE.

Adverse drug reaction classification with deep neural networks

We study the problem of detecting sentences describing adverse drug reactions (ADRs) and frame the problem as binary classification. We investigate different neural network (NN) architectures for ADR classification. In particular, we propose two new neural network models, Convolutional Recurrent Neural Network (CRNN) by concatenating convolutional neural networks with recurrent neural networks, and Convolutional Neural Network with Attention (CNNA) by adding attention weights into convolutional neural networks. We evaluate various NN architectures on a Twitter dataset containing informal language and an Adverse Drug Effects (ADE) dataset constructed by sampling from MEDLINE case reports. Experimental results show that all the NN architectures outperform the traditional maximum entropy classifiers trained from n-grams with different weighting strategies considerably on both datasets. On the Twitter dataset, all the NN architectures perform similarly. But on the ADE dataset, CNN performs better than other more complex CNN variants. Nevertheless, CNNA allows the visualisation of attention weights of words when making classification decisions and hence is more appropriate for the extraction of word subsequences describing ADRs.

Using Recurrent Networks for Dimensionality Reduction

This report explores how recurrent neural networks can be exploited for learning high-dimensional mappings. Since recurrent networks are as powerful as Turing machines, an interesting question is how recurrent networks can be used to simplify the problem of learning from examples. The main problem with learning high-dimensional functions is the curse of dimensionality which roughly states that the number of examples needed to learn a function increases exponentially with input dimension. This thesis proposes a way of avoiding this problem by using a recurrent network to decompose a high-dimensional function into many lower dimensional functions connected in a feedback loop.

Exact Solution of the Nonlinear Dynamics of Recurrent Neural Mechanisms for Direction Selectivity

Different theoretical models have tried to investigate the feasibility of recurrent neural mechanisms for achieving direction selectivity in the visual cortex. The mathematical analysis of such models has been restricted so far to the case of purely linear networks. We present an exact analytical solution of the nonlinear dynamics of a class of direction selective recurrent neural models with threshold nonlinearity. Our mathematical analysis shows that such networks have form-stable stimulus-locked traveling pulse solutions that are appropriate for modeling the responses of direction selective cortical neurons. Our analysis shows also that the stability of such solutions can break down giving raise to a different class of solutions ("lurching activity waves") that are characterized by a specific spatio-temporal periodicity. These solutions cannot arise in models for direction selectivity with purely linear spatio-temporal filtering.

Inverse model control using recurrent networks

This paper illustrates how internal model control of nonlinear processes can be achieved by recurrent neural networks, e.g. fully connected Hopfield networks. It is shown that using results developed by Kambhampati et al. (1995), that once a recurrent network model of a nonlinear system has been produced, a controller can be produced which consists of the network comprising the inverse of the model and a filter. Thus, the network providing control for the nonlinear system does not require any training after it has been trained to model the nonlinear system. Stability and other issues of importance for nonlinear control systems are also discussed.

Identification of nonlinear systems with a dynamic recurrent neural network

Two approaches are presented to calculate the weights for a Dynamic Recurrent Neural Network (DRNN) in order to identify the input-output dynamics of a class of nonlinear systems. The number of states of the identified network is constrained to be the same as the number of states of the plant.

Relative order defines a topology for recurrent networks

This paper uses techniques from control theory in the analysis of trained recurrent neural networks. Differential geometry is used as a framework, which allows the concept of relative order to be applied to neural networks. Any system possessing finite relative order has a left-inverse. Any recurrent network with finite relative order also has an inverse, which is shown to be a recurrent network.