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Hidden Markov Models in Molecular Biology: New Algorithms and Applications
Baldi, Pierre, Chauvin, Yves, Hunkapiller, Tim, McClure, Marcella A.
Hidden Markov Models (HMMs) can be applied to several important problemsin molecular biology. We introduce a new convergent learning algorithm for HMMs that, unlike the classical Baum-Welch algorithm is smooth and can be applied online or in batch mode, with or without the usual Viterbi most likely path approximation. Left-right HMMs with insertion and deletion states are then trained to represent several protein families including immunoglobulins and kinases. In all cases, the models derived capture all the important statistical properties of the families and can be used efficiently in a number of important tasks such as multiple alignment, motif detection, andclassification.
Synchronization and Grammatical Inference in an Oscillating Elman Net
Baird, Bill, Troyer, Todd, Eeckman, Frank
We have designed an architecture to span the gap between biophysics andcognitive science to address and explore issues of how a discrete symbol processing system can arise from the continuum, and how complex dynamics like oscillation and synchronization can then be employed in its operation and affect its learning. We show how a discrete-time recurrent "Elman" network architecture can be constructed from recurrently connected oscillatory associative memory modules described by continuous nonlinear ordinary differential equations.The modules can learn connection weights between themselves which will cause the system to evolve under a clocked "machine cycle" by a sequence of transitions of attractors within the modules, much as a digital computer evolves by transitions ofits binary flip-flop attractors. The architecture thus employs theprinciple of "computing with attractors" used by macroscopic systemsfor reliable computation in the presence of noise. We have specifically constructed a system which functions as a finite state automaton that recognizes or generates the infinite set of six symbol strings that are defined by a Reber grammar. It is a symbol processing system, but with analog input and oscillatory subsymbolic representations.The time steps (machine cycles) of the system are implemented by rhythmic variation (clocking) of a bifurcation parameter.This holds input and "context" modules clamped at their attractors while'hidden and output modules change state, then clamps hidden and output states while context modules are released to load those states as the new context for the next cycle of input. Superior noise immunity has been demonstrated for systems with dynamic attractors over systems with static attractors, and synchronization ("binding") between coupled oscillatory attractors in different modules has been shown to be important for effecting reliable transitions.
Forecasting Demand for Electric Power
Our efforts proceed in the context of a problem suggested by the operational needs of a particular electric utility to make daily forecasts of short-term load or demand. Forecasts are made at midday (1 p.m.) on a weekday t ( Monday - Thursday), for the next evening peak e(t) (occuring usually about 8 p.m. in the winter), the daily minimum d(t
Adaptive Stimulus Representations: A Computational Theory of Hippocampal-Region Function
Gluck, Mark A., Myers, Catherine E.
We present a theory of cortico-hippocampal interaction in discrimination learning. The hippocampal region is presumed to form new stimulus representations which facilitate learning by enhancing the discriminability of predictive stimuli and compressing stimulus-stimulus redundancies. The cortical and cerebellar regions, which are the sites of long-term memory.
Improving Performance in Neural Networks Using a Boosting Algorithm
Drucker, Harris, Schapire, Robert, Simard, Patrice
A boosting algorithm converts a learning machine with error rate less than 50% to one with an arbitrarily low error rate. However, the algorithm discussed here depends on having a large supply of independent training samples. We show how to circumvent this problem and generate an ensemble of learning machines whose performance in optical character recognition problems is dramatically improved over that of a single network. We report the effect of boosting on four databases (all handwritten) consisting of 12,000 digits from segmented ZIP codes from the United State Postal Service (USPS) and the following from the National Institute of Standards and Testing (NIST): 220,000 digits, 45,000 upper case alphas, and 45,000 lower case alphas. We use two performance measures: the raw error rate (no rejects) and the reject rate required to achieve a 1% error rate on the patterns not rejected.
Remote Sensing Image Analysis via a Texture Classification Neural Network
Greenspan, Hayit K., Goodman, Rodney
In this work we apply a texture classification network to remote sensing image analysis.The goal is to extract the characteristics of the area depicted in the input image, thus achieving a segmented map of the region. We have recently proposed a combined neural network and rule-based framework for texture recognition. The framework uses unsupervised and supervised learning, and provides probability estimates for the output classes. We describe the texture classification network and extend it to demonstrate its application to the Landsat and Aerial image analysis domain. 1 INTRODUCTION In this work we apply a texture classification network to remote sensing image analysis. The goal is to segment the input image into homogeneous textured regions and identify each region as one of a prelearned library of textures, e.g.
Analog VLSI Implementation of Multi-dimensional Gradient Descent
Kirk, David B., Kerns, Douglas, Fleischer, Kurt, Barr, Alan H.
The implementation uses noise injection and multiplicative correlation to estimate derivatives, as in [Anderson, Kerns 92]. One intended application of this technique is setting circuit parameters on-chip automatically, rather than manually [Kirk 91]. Gradient descent optimization may be used to adjust synapse weights for a backpropagation or other on-chip learning implementation. The approach combines the features of continuous multidimensional gradient descent and the potential for an annealing style of optimization. We present data measured from our analog VLSI implementation. 1 Introduction This work is similar to [Anderson, Kerns 92], but represents two advances. First, we describe the extension of the technique to multiple dimensions. Second, we demonstrate animplementation of the multidimensional technique in analog VLSI, and provide results measured from the chip. Unlike previous work using noise sources in adaptive systems, we use the noise as a means of estimating the gradient of a function f(y), rather than performing an annealing process [Alspector 88]. We also estimate gr-;:dients continuously in position and time, in contrast to [Umminger 89] and [J abri 91], which utilize discrete position gradient estimates.
A Parallel Gradient Descent Method for Learning in Analog VLSI Neural Networks
Alspector, J., Meir, R., Yuhas, B., Jayakumar, A., Lippe, D.
Typical methods for gradient descent in neural network learning involve calculation of derivatives based on a detailed knowledge of the network model. This requires extensive, time consuming calculations for each pattern presentationand high precision that makes it difficult to implement in VLSI. We present here a perturbation technique that measures, not calculates, the gradient. Since the technique uses the actual network as a measuring device, errors in modeling neuron activation and synaptic weights do not cause errors in gradient descent. The method is parallel in nature and easy to implement in VLSI.