BACKGROUND: Prediction of transmembrane (TM) helices by statistical methods suffers from lack of sufficient training data. Current best methods use hundreds or even thousands of free parameters in their models which are tuned to fit the little data available for training. Further, they are often restricted to the generally accepted topology "cytoplasmic-transmembrane-extracellular" and cannot adapt to membrane proteins that do not conform to this topology. Recent crystal structures of channel proteins have revealed novel architectures showing that the above topology may not be as universal as previously believed. Thus, there is a need for methods that can better predict TM helices even in novel topologies and families. RESULTS: Here, we describe a new method "TMpro" to predict TM helices with high accuracy. To avoid overfitting to existing topologies, we have collapsed cytoplasmic and extracellular labels to a single state, non-TM. TMpro is a binary classifier which predicts TM or non-TM using multiple amino acid properties (charge, polarity, aromaticity, size and electronic properties) as features. The features are extracted from sequence information by applying the framework used for latent semantic analysis of text documents and are input to neural networks that learn the distinction between TM and non-TM segments. The model uses only 25 free parameters. In benchmark analysis TMpro achieves 95% segment F-score corresponding to 50% reduction in error rate compared to the best methods not requiring an evolutionary profile of a protein to be known. Performance is also improved when applied to more recent and larger high resolution datasets PDBTM and MPtopo. TMpro predictions in membrane proteins with unusual or disputed TM structure (K+ channel, aquaporin and HIV envelope glycoprotein) are discussed. CONCLUSION: TMpro uses very few free parameters in modeling TM segments as opposed to the very large number of free parameters used in state-of-the-art membrane prediction methods, yet achieves very high segment accuracies. This is highly advantageous considering that high resolution transmembrane information is available only for very few proteins. The greatest impact of TMpro is therefore expected in the prediction of TM segments in proteins with novel topologies. Further, the paper introduces a novel method of extracting features from protein sequence, namely that of latent semantic analysis model. The success of this approach in the current context suggests that it can find potential applications in other sequence-based analysis problems. AVAILABILITY: http://linzer.blm.cs.cmu.edu/tmpro/ and http://flan.blm.cs.cmu.edu/tmpro/

In this paper, we tackle the problem of pronunciation inference and out-of-vocabulary (OOV) enrollment in automatic speech recognition (ASR) applications. We combine linguistic and acoustic information of the OOV word using its spelling and a single instance of its utterance to derive an appropriate phonetic baseform. The novelty of the approach is in its employment of an orthography-driven n-best hypothesis and rescoring strategy of the pronunciation alternatives. We make use of decision trees and heuristic tree search to construct and score the n-best hypotheses space. We use acoustic alignment likelihood and phone transition cost to leverage the empirical evidence and phonotactic priors to rescore the hypotheses and refine the baseforms.

article Share on Three open problems in AI Author: Raj Reddy Carnegie Mellon University Carnegie Mellon UniversityView Profile Authors Info & Claims Journal of the ACMVolume 50Issue 1January 2003 pp 83–86https://doi.org/10.1145/602382.602407Published:01 January 2003Publication History 34citation2,438DownloadsMetricsTotal Citations34Total Downloads2,438Last 12 Months108Last 6 weeks16 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my Alerts New Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access

Presents an approach to free-form object modeling from multiple range images. In most conventional approaches, successive views are registered sequentially. In contrast to the sequential approaches, we propose an integral approach which reconstructs statistically optimal object models by simultaneously aggregating all data from multiple views into a weighted least-squares (WLS) formulation. The integral approach has two components. First, a global resampling algorithm constructs partial representations of the object from individual views, so that correspondence can be established among different views. Second, a weighted least-squares algorithm integrates resampled partial representations of multiple views, using the techniques of principal component analysis with missing data (PCAMD). Experiments show that our approach is robust against noise and mismatch.

Presents a new approach to free-formed object modeling from multiple range images. In most conventional approaches, successive views are registered sequentially. In contrast to the sequential approaches, we propose an integral approach which reconstructs statistically optimal object models by simultaneously aggregating all data from multiple views into a weighted least-squares (WLS) formulation. The integral approach has two components. First, a global resampling algorithm constructs partial representations of the object from individual views so that correspondences can be established among different views. The global resampling algorithm is based on the spherical attribute image (SAI) previously introduced in the context of object representation and recognition. Second, a weighted least-squares algorithm integrates resampled partial representations of multiple views, using the technique of principal component analysis with missing data (PCAMD). Experiments using real range images show that our approach is robust against noise and mismatches, and generates accurate object models.>

Observation-based object modeling often requires integration of shape descriptions from different views. To overcome the problems of errors and their accumulation, we have developed a weighted least-squares (WLS) approach which simultaneously recovers object shape and transformation among different views without recovering interframe motion. We show that object modeling from a range image sequence is a problem of principal component analysis with missing data (PCAMD), which can be generalized as a WLS minimization problem. An efficient algorithm is devised. After we have segmented planar surface regions in each view and tracked them over the image sequence, we construct a normal measurement matrix of surface normals, and a distance measurement matrix of normal distances to the origin for all visible regions over the whole sequence of views, respectively. These two matrices, which have many missing elements due to noise, occlusion, and mismatching, enable us to formulate multiple view merging as a combination of two WLS problems. A two-step algorithm is presented. After surface equations are extracted, spatial connectivity among the surfaces is established to enable the polyhedral object model to be constructed. Experiments using synthetic data and real range images show that our approach is robust against noise and mismatching and generates accurate polyhedral object models.>

Observation-based modeling can reduce the cost and effort of model constructions for tasks such as virtual reality environment. Object modeling from a sequence of range images has been formulated as a problem of principal component analysis with missing data (PCAMD), which can be generalized as a weighted least square (WLS) minimization problem. After all visible regions appeared over the whole sequence are segmented and tracked, a normal measurement matrix of surface normals and a distance measurement matrix of normal distances to the origin are constructed respectively. These two measurement matrices, with possibly many missing elements due to occlusion and mismatching, enable us to formulate multiple view merging as a combination of two WLS problems. The solution to the first WLS problem, which employs the quaternion representation of the rotation matrix, yields surface normals and rotation matrices. Subsequently the normal distances and translation vectors are computed by solving the second WLS problem. Experiments using synthetic data and real range images show that our approach is robust against noise and mismatch because it produces a statistically optimal object model by making use of redundancy from multiple views. A toy house model from a sequence of real range images is presented.>

Virtual reality object modeling from a sequence of range images has been formulated as a problem of principal component analysis with missing data (PCAMD), which can be generalized as a weighted least square (WLS) minimization problem. An efficient algorithm has been devised to solve the problem of PCAMD. After all visible P regions appeared over the whole sequence of F views are segmented and tracked, a 3F/spl times/P normal measurement matrix of surface normals and an F/spl times/P distance measurement matrix of normal distances to the origin are constructed respectively. These two measurement matrices, with possibly many missing elements due to occlusion and mismatching, enable us to formulate multiple view merging as a combination of two WLS problems. By combining information at both the signal level and the algebraic level, a modified Jarvis' march algorithm is proposed to recover the spatial connectivity among all the reconstructed surface patches. Experiments using synthetic data and real range images show that our approach is robust against noise and mismatch. A toy house model from a sequence of real range images is presented.>

A description is given of SPHINX an accurate large-vocabulary speaker-independent continuous speech recognition system. The authors have made several recent enhancements, including generalized triphone models, word duration modeling, function-phrase modeling, between-word coarticulation modeling, and corrective training. On the 997-word resource management task, SPHINX attained a word accuracy of 96% with a grammar (perplexity 60), and 82% without grammar (perplexity 997).>

Vector quantization (VQ) is a technique that reduces the computation amount and memory size drastically. In this paper, speaker adaptation algorithms through VQ are proposed in order to improve speaker-independent recognition. The speaker adaptation algorithms use VQ codebooks of a reference speaker and an input speaker. Speaker adaptation is performed by substituting vectors in the codebook of a reference speaker for vectors of the input speaker's codebook, or vice versa. To confirm the effectiveness of these algorithms, word recognition experiments are carried out using the IBM office correspondence task uttered by 11 speakers. The total number of words is 1174 for each speaker, and the number of different words is 422. The average word recognition rate using different speaker's reference through speaker adaptation is 80.9%, and the rate within the second choice is 92.0%.

A new distance measure based on the derivative of linear prediction (LP) phase spectrum is proposed for comparison of speech spectra. Relationships among several distance measures based on the linear prediction coefficients (LPCs) are discussed. The advantages of the new measure and an efficient method of computing it are also discussed.

This correspondence describes research in the development of symbolic registration techniques directed toward the comparison of pairs of images of the same scene to ultimately generate descriptions of the changes in the scene. Unlike most earlier work in image registration, all the matching and analysis will be performed at a symbolic level rather than a signal level. We have applied this registration procedure on several different types of scenes and the system appears to work well both on pairs of images which may be analyzed in part by signal based systems and those which cannot be so analyzed.

This paper considers various factors affecting system em organization for speech understanding research. The structure of the Hearsay system based on a set of cooperating, independent processes using the hypothesize-and-test paradigm is presented. Design considerations for the effective use of multiprocessor and network achitectures in speech understanding systems ems are presented: control of processes, interprocess communication and data sharing, resource allocation, and debugging are discussed.1

This paper describes the structure and operation of the Hearsay-I1speech understanding system by the use of a specific example illustrating the various stages of recognition. The system consists of a set of cooperating independent processes, each representing a source of knowledge. The knowledge is used either to predict what may appear in a given context or to verify hypotheses resulting from a prediction. The structure of the system is illustrated by considering its operation in a particular task situation: Voice-Chess. The representation and use of various sources of knowledge are outlined. Preliminary results of the reduction in search resulting from the use of various sources of knowledge are given.