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A Novel Approach to Prediction of the 3-Dimensional Structures of Protein Backbones by Neural Networks

Neural Information Processing Systems

One current aim of molecular biology is determination of the (3D) tertiary structures ofproteins in their folded native state from their sequences of amino acid 523 524 Fredholm, Bohr, Bohr, Brunak, Cotterill, Lautrup, and Thtersen residues. Since Kendrew & Perutz solved the first protein structures, myoglobin and hemoglobin, and explained from the discovered structures how these proteins perform their function, it has been widely recognized that protein function is intimately linkedwith protein structure[l]. Within the last two decades X-ray crystallographers have solved the 3-dimensional (3D) structures of a steadily increasing number of proteins in the crystalline state, and recently 2D-NMR spectroscopy has emerged as an alternative method for small proteins in solution. Today approximately three hundred 3D structures have been solved by these methods, although only about half of them can be considered as truly different, and only around a hundred of them are solved at high resolution (that is, less than 2A). The number of protein sequences known today is well over 20,000, and this number seems to be growing at least one order of magnitude faster than the number of known 3D protein structures. Obviously, it is of great importance to develop tools that can predict structural aspects of proteins on the basis of knowledge acquired from known 3D structures.



On the Circuit Complexity of Neural Networks

Neural Information Processing Systems

Viewing n-variable boolean functions as vectors in'R'2", we invoke tools from linear algebra and linear programming to derive new results on the realizability of boolean functions using threshold gat.es. Using this approach, one can obtain: (1) upper-bounds on the number of spurious memories in HopfielJ networks, and on the number of functions implementable by a depth-d threshold circuit; (2) a lower bound on the number of ort.hogonal input.



An Attractor Neural Network Model of Recall and Recognition

Neural Information Processing Systems

This work presents an Attractor Neural Network (ANN) model of Recall andRecognition. It is shown that an ANN model can qualitatively account for a wide range of experimental psychological data pertaining to the these two main aspects of memory access. Certain psychological phenomena are accounted for, including the effects of list-length, wordfrequency, presentationtime, context shift, and aging. Thereafter, the probabilities of successful Recall and Recognition are estimated, in order to possibly enable further quantitative examination of the model. 1 Motivation The goal of this paper is to demonstrate that a Hopfield-based [Hop82] ANN model can qualitatively account for a wide range of experimental psychological data pertaining tothe two main aspects of memory access, Recall and Recognition. Recall is defined as the ability to retrieve an item from a list of items (words) originally presented during a previous learning phase, given an appropriate cue (cued RecalQ, or spontaneously (free RecalQ. Recognition is defined as the ability to successfully acknowledge that a certain item has or has not appeared in the tutorial list learned before. The main prospects of ANN modeling is that some parameter values, that in former, 'classical' models of memory retrieval (see e.g.


ART2/BP architecture for adaptive estimation of dynamic processes

Neural Information Processing Systems

The goal has been to construct a supervised artificial neural network that learns incrementally an unknown mapping. As a result a network consisting ofa combination of ART2 and backpropagation is proposed and is called an "ART2/BP" network. The ART2 network is used to build and focus a supervised backpropagation network. The ART2/BP network has the advantage of being able to dynamically expand itself in response to input patterns containing new information. Simulation results show that the ART2/BP network outperforms a classical maximum likelihood method for the estimation of a discrete dynamic and nonlinear transfer function.


Exploiting Syllable Structure in a Connectionist Phonology Model

Neural Information Processing Systems

In a previous paper (Touretzky & Wheeler, 1990a) we showed how adding a clustering operation to a connectionist phonology model produced a parallel processing accountof certain "iterative" phenomena. In this paper we show how the addition of a second structuring primitive, syllabification, greatly increases the power of the model. We present examples from a non-Indo-European language that appear to require rule ordering to at least a depth of four. By adding syllabification circuitryto structure the model's perception of the input string, we are able to handle these examples with only two derivational steps. We conclude that in phonology, derivation can be largely replaced by structuring.


Speech Recognition Using Connectionist Approaches

Neural Information Processing Systems

This paper is a summary of SPRINT project aims and results. The project focus on the use of neuro-computing techniques to tackle various problems that remain unsolved in speech recognition. First results concern the use of feedforward netsfor phonetic units classification, isolated word recognition, and speaker adaptation.


Connectionist Implementation of a Theory of Generalization

Neural Information Processing Systems

Empirically, generalization between a training and a test stimulus falls off in close approximation to an exponential decay function of distance between the two stimuli in the "stimulus space" obtained by multidimensional scaling. Mathematically, thisresult is derivable from the assumption that an individual takes the training stimulus to belong to a "consequential" region that includes that stimulus but is otherwise of unknown location, size, and shape in the stimulus space (Shepard, 1987). As the individual gains additional information about the consequential region-by finding other stimuli to be consequential or nOl-the theory predicts the shape of the generalization function to change toward the function relating actual probability of the consequence to location in the stimulus space. This paper describes a natural connectionist implementation of the theory, and illustrates how implications of the theory for generalization, discrimination, and classification learning can be explored by connectionist simulation. 1 THE THEORY OF GENERALIZATION Because we never confront exactly the same situation twice, anything we have learned in any previous situation can guide us in deciding which action to take in the present situation only to the extent that the similarity between the two situations is sufficient to justify generalization of our previous learning to the present situation. Accordingly, principles of generalization must be foundational for any theory of behavior. In Shepard (1987) nonarbitrary principles of generalization were sought that would be optimum in any world in which an object, however distinct from other objects, is generally a member of some class or natural kind sharing some dispositional property of potential consequence for the individual. A newly encountered plant or animal might be edible or 665 666 Shepard and Kannappan poisonous.